Hemoglobin levels and skeletal muscle: results from the InCHIANTI study.
Anemia is associated with reduced physical performance and muscle strength. The aim of the study was to explore whether anemia and hemoglobin levels are associated with differences in quantitative and qualitative measures of muscle and fat. The study sample consisted of 909 participants 65 years and older enrolled in the "Invecchiare in Chianti" (InCHIANTI) study, a prospective population-based study of older people aimed at identifying risk factors for late-life disability. All the analyses were performed considering continuous hemoglobin levels as well as the dichotomous anemia variable (defined according to World Health Organization criteria as hemoglobin <12 g/dL in women and <13 g/dL in men). A peripheral quantitative computed tomography (pQCT) scan was performed in all participants to evaluate total, muscular, and fat cross-sectional areas of the calf and relative muscle density. Ankle extension strength was measured using a hand-held dynamometer. Linear regression analyses were used to assess the multivariate relationship of pQCT and skeletal muscle strength measures with hemoglobin levels and anemia after adjustment for demographics, chronic conditions, medication use, and other biological variables. Participants were aged 74.8 +/- 6.8 years. In our sample, 94 participants (10.3%) were anemic. Hemoglobin levels were significantly associated with muscle density (beta = 0.225 [SE, standard error 0.098], p=.02), muscle area/total area ratio (beta=0.778 [SE 0.262], p=.003), fat area/total area ratio (beta=-0.869 [SE 0.225]; p<.001). Skeletal muscle strength and muscle density were highly associated with anemia (beta=-3.266 [SE 1.173], p=.005 and beta=-0.816 [SE 0.374], p=.03, respectively). Results did not change when analyses were rerun in a restricted sample of participants not affected by major medical conditions. The present study shows that hemoglobin levels are associated with the parameters of body composition obtained by pQCT, and that decreases in muscular strength measures occur in the presence of anemia.


Evolution of a predictive internal model in an embodied and situated agent.
We show how simulated robots evolved for the ability to display a context-dependent periodic behavior can spontaneously develop an internal model and rely on it to fulfill their task when sensory stimulation is temporarily unavailable. The analysis of some of the best evolved agents indicates that their internal model operates by anticipating sensory stimuli. More precisely, it anticipates functional properties of the next sensory state rather than the exact state that sensors will assume. The characteristics of the states that are anticipated and of the sensorimotor rules that determine how the agents react to the experienced states, however, ensure that they produce very similar behaviour during normal and blind phases in which sensory stimulation is available or is self-generated by the agent, respectively. Agents' internal models also ensure an effective transition during the phases in which agents' internal dynamics is decoupled and re-coupled with the sensorimotor flow. Our results suggest that internal models might have arisen for behavioral reasons and successively exapted for other cognitive functions. Moreover, the obtained results suggest that self-generated internal states should not necessarily match in detail the corresponding sensory states and might rather encode more abstract and motor-oriented information.


Perturbation of the pulmonary surfactant monolayer by single-walled carbon nanotubes: a molecular dynamics study.
Single-walled carbon nanotubes (SWCNTs) are at present synthesized on a large scale with a variety of applications. The increasing likelihood of exposure to SWCNTs, however, puts human health at a high risk. As the front line of the innate host defense system, the pulmonary surfactant monolayer (PSM) at the air-water interface of the lungs interacts with the inhaled SWCNTs, which in turn inevitably perturb the ultrastructure of the PSM and affect its biophysical functions. Here, using molecular dynamics simulations, we demonstrate how the diameter and length of SWCNTs critically regulate their interactions with the PSM. Compared to their diameters, the inhalation toxicity of SWCNTs was found to be largely affected by their lengths. Short SWCNTs with lengths comparable to the monolayer thickness are found to vertically insert into the PSM with no indication of translocation, possibly leading to accumulation of SWCNTs in the PSM with prolonged retention and increased inflammation potentials. The perturbation also comes from the forming water pores across the PSM. Longer SWCNTs are found to horizontally insert into the PSM during inspiration, and they can be wrapped by the PSM during deep expiration via a tube diameter-dependent self-rotation. The potential toxicity of longer SWCNTs comes from severe lipid depletion and the PSM-rigidifying effect. Our findings could help reveal the inhalation toxicity of SWCNTs, and pave the way for the safe use of SWCNTs as vehicles for pulmonary drug delivery.


Needle-based confocal laser endomicroscopy of pancreatic cystic lesions: a prospective multicenter validation study in patients with definite diagnosis.
Needle-based confocal laser endomicroscopy (nCLE) enables observation of the inner wall of pancreatic cystic lesions (PCLs) during an endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA). This study prospectively evaluated the diagnostic performance of nCLE for large, single, noncommunicating PCLs using surgical histopathology or EUS-FNA cytohistopathology as a reference diagnosis. From April 2013 to March 2016, consecutive patients referred for EUS-FNA of indeterminate PCLs without evidence of malignancy or chronic pancreatitis were prospectively enrolled at five centers. EUS-FNA and nCLE were performed and cystic fluid was aspirated for cytohistopathological and carcinoembryonic antigen (CEA) analysis. The diagnostic performance of nCLE was assessed against the reference standard and compared with that of EUS and CEA. This study was registered on ClinicalTrials.gov (NCT01563133). 206 patients underwent nCLE and 78 PCLs (mean size 40 mm, range 20 - 110 mm) had reference diagnoses (53 premalignant and 25 benign PCLs). Post-procedure pancreatitis occurred in 1.3 % of the patients. nCLE was conclusive in 71 of the 78 cases (91 %). The sensitivies and specifities of nCLE for the diagnosis of serous cystadenoma, mucinous PCL, and premalignant PCL were all ≥ 0.95 (with 95 % confidence interval from 0.85 to 1.0). The AUROC was significantly larger for nCLE than for CEA or EUS. nCLE had excellent diagnostic performance that surpassed that of CEA and EUS for the diagnosis of large, single, noncommunicating PCLs. The nCLE procedure should be considered in patients with indeterminate PCLs to ensure a more specific diagnosis.


Effect of needle length when immunizing obese adolescents with hepatitis B vaccine.
Several studies have noted that obese adolescents and adults achieve lower titers of antibody in response to vaccines such as hepatitis B virus (HBV) vaccine. The objective of this study was to determine whether use of a longer (1.5-in) rather than a standard (1-in) needle to penetrate the thicker deltoid fat pad among obese youth would result in higher antibody titers after immunization against HBV. Obese adolescents from a large metropolitan area who had not previously received the HBV vaccine were randomly assigned to be immunized with HBV vaccine by using either a 1-inch or a 1.5-inch needle. Those who were immunized with a 1.5-inch needle achieved significantly higher antibody titers to hepatitis B surface antigen (median titers: 1-inch = 189.8 mIU/mL, 1.5-inch = 345.4 mIU/mL; P = .03). This finding supports the hypothesis that needle length accounts for a significant portion of the discrepancy in immune response to HBV vaccine that is seen among those with obesity.


Bandit-Based Task Assignment for Heterogeneous Crowdsourcing.
We consider a task assignment problem in crowdsourcing, which is aimed at collecting as many reliable labels as possible within a limited budget. A challenge in this scenario is how to cope with the diversity of tasks and the task-dependent reliability of workers; for example, a worker may be good at recognizing the names of sports teams but not be familiar with cosmetics brands. We refer to this practical setting as heterogeneous crowdsourcing. In this letter, we propose a contextual bandit formulation for task assignment in heterogeneous crowdsourcing that is able to deal with the exploration-exploitation trade-off in worker selection. We also theoretically investigate the regret bounds for the proposed method and demonstrate its practical usefulness experimentally.


Time series analysis of the clinical laboratory test result on chemotherapy for gastric cancer.
Time series analysis may be helpful to estimate hematological data on gastric cancer patients who receive S 1, but untreated raw clinical data are not suitable for this approach. Hematological monitoring data interpolated by spline were analyzed by an attractor plot, which is a form of time series analysis. Hematological data of three gastric cancer patients were interpolated by cubic spline. The leave-one-out cross validation method was carried out and an attractor plot was adopted to evaluate red blood count (RBC) data. Well-predicted data, such as RBC, changed slightly; however, data with great deviation, such as the white blood count (WBC), were poorly predicted. The reaction of marrow function to chemotherapy was observable by spline interpolation of RBC data. Furthermore, an attractor plot clarified the tendency of the interpolated hematological monitoring data. It is suggested that spline interpolation is effective as a pretreatment to analyze clinical data from a time series.


Follow-up study of twenty-four families with Li-Fraumeni syndrome.
The Li-Fraumeni cancer family syndrome is manifested by susceptibility to breast cancer, sarcomas, and other neoplasms in children and young adults. The present study utilized clinical follow-up data on 545 members of 24 Li-Fraumeni kindreds living and cancer-free at family ascertainment. Two hypotheses were tested based on a model of autosomal dominant genetic predisposition: (a) that syndrome cancers would continue to occur excessively during follow-up compared to the general population, and (b) that the tumors would occur primarily among those family members likely to carry the gene. Population cancer rates were compared with cancer rates in follow-up of the cohort from ascertainment to 1988. Risk of carrying the gene for the syndrome at the time of ascertainment was calculated for each family member under two models with somewhat different definitions of affection with the syndrome. Cancer occurrence after ascertainment was then analyzed according to the risks. Cancer did continue to occur excessively among the entire cohort during follow-up [relative risk (RR 2.1)]. The excess was greatest below age 20 (RR 21.1), declined with increasing age, and was most pronounced for neoplasms featured in the syndrome (RR 18.2). Among persons less than age 45, at least 87% of cancers occurred in those at higher risk of carrying the gene under both genetic models (RR 22.9 and 21.3). The clinical data, therefore, reliably identify individuals likely to carry a dominantly inherited gene conferring susceptibility to a specific constellation of neoplasms. Recent identification of a germ line mutation in the tumor suppressor gene p53 in persons with the syndrome may, if confirmed, have implications for ultimately defining the component tumors of the syndrome and for the causes and prevention of those tumors arising outside these families.


Risk factors for latex sensitization among health care workers.
Health care workers, children with spina bifida and rubber industry workers show higher prevalence of latex sensitization compared to the general population, and they are considered at-risk groups. Our aim was to establish the prevalence of latex allergy among health care workers at the Clínica Universitaria of Navarra and to analyze potential risk factors, including personal and family history of atopy, sex, as well as factors leading to enhanced exposure to latex, such as being a nurse, belonging to surgical departments, having undergone previous surgery and the number of gloves employed per week. Health care workers (n = 1,150) (doctors, nurses, assistant nurses, laboratory technicians and practicing medical and nursing students) were evaluated using a questionnaire and skin prick test (SPT). Serum specific IgE was determined by CAP-FEIA (Pharmacia, Sweden) in those with positive SPT. The participation index was 26.17%: 301 volunteers answered the questionnaire and underwent SPT. Fifteen subjects presented positive SPT to latex. It was found that 5% of the health care workers from the Clínica Universitaria were sensitized to latex allergens. Thirteen were females and two males. Mean age was 38.4 (+/- 7.09) years. Nine were nurses, three assistant nurses, one nursing student and two medical doctors. Eight belonged to medical, five to surgical and two to laboratory departments. There were no significant differences among the subjects in the prevalence of latex sensitization. Fourteen reported symptoms related to latex, mostly pruritus, dryness and/or redness of the hands (n = 12) and rhinitis (n = 6). Only one subject reported no symptoms when using latex products. Eight were atopic; personal history of atopy was the only significant (odds ratio = 5.10, p < 0.01) risk factor for latex sensitization. It was concluded that atopic health care workers show a more increased risk of latex sensitization than those who are nonatopic.


Surgical treatment of the high jugular bulb in patients with Ménière's disease and pulsatile tinnitus.
The aim of this retrospective study was to evaluate the functional results of surgical lowering of the high jugular bulb in the treatment of patients with Ménière's disease and pulsatile tinnitus. Fifteen patients with disabling Ménière's disease associated with pulsatile tinnitus and a high and medial jugular bulb were included in this study. As treatment a complete mastoidectomy was performed, after which the jugular bulb was freed by an infralabyrinthine and subfacial approach. The bulb was then displaced downwards with surgical wax. Functional results of surgery were assessed by a questionnaire according to the 1995 guidelines of the United States American Academy Committee on Hearing and Equilibrium, audiometric and vestibular tests, and by magnetic resonance and computed tomographic imaging with vascular sequences. Surgical treatment was contraindicated in two cases: one had hypoplasia of the contralateral sigmoid sinus and the other a small petrous hemangioma located around the jugular bulb that was discovered peroperatively. Among the 13 patients treated by definitive surgery, attacks of vertigo were reported as disabling in 12 cases preoperatively (92%) versus 1 (8%) after surgical treatment. No significant change in hearing was observed after surgery. Tinnitus had been reported in all patients preoperatively and decreased in intensity in four (31%) and disappeared in three (23%) after surgery.


Development of a luciferase based viral inhibition assay to evaluate vaccine induced CD8 T-cell responses.
Emergence of SIV and HIV specific CD8 T cells has been shown to correlate with control of in vivo replication. Poor correlation between IFN-γ ELISPOT responses and in vivo control of the virus has triggered the development of more relevant assays to assess functional HIV-1 specific CD8 T-cell responses for the evaluation and prioritization of new HIV-1 vaccine candidates. We previously established a viral inhibition assay (VIA) that measures the ability of vaccine-induced CD8 T-cell responses to inhibit viral replication in autologous CD4 T cells. In this assay, viral replication is determined by measuring p24 in the culture supernatant. Here we describe the development of a novel VIA, referred to as IMC LucR VIA that exploits replication-competent HIV-1 infectious molecular clones (IMCs) in which the complete proviral genome is strain-specific and which express the Renilla luciferase (LucR) gene to determine viral growth and inhibition. The introduction of the luciferase readout does provide significant improvement of the read out time. In addition to switching to the LucR read out, changes made to the overall protocol resulted in the miniaturization of the assay from a 48 to a 96-well plate format, which preserved sample and allowed for the introduction of replicates. The overall assay time was reduced from 13 to 8 days. The assay has a high degree of specificity, and the previously observed non-specific background inhibition in cells from HIV-1 negative volunteers has been reduced dramatically. Importantly, we observed an increase in positive responses, indicating an improvement in sensitivity compared to the original VIA. Currently, only a limited number of "whole-genome" IMC-LucR viruses are available and our efforts will focus on expanding the panel to better evaluate anti-viral breadth. Overall, we believe the IMC LucR VIA provides a platform to assess functional CD8 T-cell responses in large-scale clinical trial testing, which will enhance the ability to select the most promising HIV-1 vaccine candidates capable of controlling HIV-1 replication in vivo.


Genetic Influences on Physiological and Subjective Responses to an Aerobic Exercise Session among Sedentary Adults.
Objective. To determine whether genetic variants suggested by the literature to be associated with physiology and fitness phenotypes predicted differential physiological and subjective responses to a bout of aerobic exercise among inactive but otherwise healthy adults. Method. Participants completed a 30-minute submaximal aerobic exercise session. Measures of physiological and subjective responding were taken before, during, and after exercise. 14 single nucleotide polymorphisms (SNPs) that have been previously associated with various exercise phenotypes were tested for associations with physiological and subjective response to exercise phenotypes. Results. We found that two SNPs in the FTO gene (rs8044769 and rs3751812) were related to positive affect change during exercise. Two SNPs in the CREB1 gene (rs2253206 and 2360969) were related to change in temperature during exercise and with maximal oxygen capacity (VO(2) max). The SLIT2 SNP rs1379659 and the FAM5C SNP rs1935881 were associated with norepinephrine change during exercise. Finally, the OPRM1 SNP rs1799971 was related to changes in norepinephrine, lactate, and rate of perceived exertion (RPE) during exercise. Conclusion. Genetic factors influence both physiological and subjective responses to exercise. A better understanding of genetic factors underlying physiological and subjective responses to aerobic exercise has implications for development and potential tailoring of exercise interventions.


Homing and group cohesion in Atlantic cod Gadus morhua revealed by tagging experiments.
Homing behaviour and group cohesion in Atlantic cod Gadus morhua from the northern Gulf of St Lawrence were studied based on tagging-recapture data from two periods, the 1980s and a recent period from 1996 to 2008. Two or more tags from a single tagging experiment were frequently recovered together in subsequent years. The null hypothesis was tested that the frequency of matching tag recoveries occurred by chance only through random mixing of tagged G. morhua before their recapture by the commercial fishery. The alternative hypothesis was that non-random, positive association (group cohesion) existed among tagged individuals that persisted through time and during migrations. Results show that the G. morhua population exhibits a homing behaviour, with temporal stability across seasons and years: 50% of recaptured fish in the recent period were caught <34 km from their mark site, even 3 years after release. In the 1980s, G. morhua were located at <10 km from their release site 1 year after tagging during summer and at <16 km during spring and autumn combined. Despite the increasing distance between the mark and recapture sites over time, the difference was not significant. In addition, occurrences of two or more tagged fish from the same release event that were caught together indicated a non-random association among individual fish for periods of one to several years and through migrations over several hundred kilometres. Hence G. morhua showed group cohesion in addition to site fidelity. These two interacting behaviours may be fundamental for the rebuilding and conservation of depleted fish stocks.


The validity of the M test in a residential forensic facility.
The validity of the M Test as a screening measure for malingering was assessed in a residential forensic treatment center. Clinically, malingering was recognized by the treatment staff as a significant problem among incompetent to proceed (ITP) defendants in this setting. A total of 79 ITP defendants completed the M Test under standard instructions. To assess the predictive validity of the M Test, its sensitivity and specificity were determined using three separate measures of malingering status. Using the original scoring procedure, the results provided estimates of sensitivity of 11, 31, and 29 percent and estimates of specificity of 67, 70, and 69 percent, respectively, for the three malingering status measures. A revised scoring procedure improved the sensitivity estimates to the statistically significant level of 86 percent for the malingering status measure that was defined as feigned or grossly exaggerated psychotic symptoms. The pattern of correlations between the M Test scales and a variety of other clinical measures suggested that, in this forensic treatment setting, the subject's pattern of responses to the M Test was primarily determined by the severity of cognitive impairment of that subject.


Tumor suppressor miR-215 counteracts hypoxia-induced colon cancer stem cell activity.
Cancer stem cells, also known as tumor-initiating cells (TICs), are a population of aggressive and self-renewing cells that are responsible for the initiation and progression of many cancers, including colorectal carcinoma. Intratumoral hypoxia, i.e. reduced oxygen supply following uncontrolled proliferation of cancer cells, is thought to support TIC activity by inducing specific hypoxia-responsive mechanisms that are not yet entirely understood. Using previously established and fully characterized patient-derived TIC cultures, we could observe increased sphere and colony formation under hypoxic conditions. Mechanistically, microRNA (miRNA)-profiling experiments allowed us to identify miR-215 as one of the main hypoxia-induced miRNAs in primary colon TICs. Through stable overexpression of miR-215, followed by a set of functional in vitro and in vivo investigations, miR-215 was pinpointed as a negative feedback regulator, working against the TIC-promoting effects of hypoxia. Furthermore, we could single out LGR5, a bona fide marker of non-neoplastic intestinal stem cells, as a downstream target of hypoxia/miR-215 signaling. The strong tumor- and TIC-suppressor potential of miR-215 and the regulatory role of the hypoxia/miR-215/LGR5 axis may thus represent interesting points of attack for the development of innovative anti-CSC therapy approaches.


Phosphoserine phosphatase deficiency in a patient with Williams syndrome.
Decreased serine levels were found in plasma and cerebrospinal fluid (CSF) of a boy with pre- and postnatal growth retardation, moderate psychomotor retardation, and facial dysmorphism suggestive of Williams syndrome. Fluorescence in situ hybridisation with an elastin gene probe indicated the presence of a submicroscopic 7q11.23 deletion, confirming this diagnosis. Further investigation showed that the phosphoserine phosphatase (EC 184.108.40.206.) activity in lymphoblasts and fibroblasts amounted to about 25% of normal values. Oral serine normalised the plasma and CSF levels of this amino acid and seemed to have some clinical effect. These data suggest that the elastin gene and the phosphoserine phosphatase gene might be closely linked. This seems to be the first report of phosphoserine phosphatase deficiency.


Animal galloping and human hopping: an energetics and biomechanics laboratory exercise.
This laboratory exercise demonstrates fundamental principles of mammalian locomotion. It provides opportunities to interrogate aspects of locomotion from biomechanics to energetics to body size scaling. It has the added benefit of having results with robust signal to noise so that students will have success even if not "meticulous" in attention to detail. First, using respirometry, students measure the energetic cost of hopping at a "preferred" hop frequency. This is followed by hopping at an imposed frequency half of the preferred. By measuring the O2 uptake and work done with each hop, students calculate mechanical efficiency. Lessons learned from this laboratory include 1) that the metabolic cost per hop at half of the preferred frequency is nearly double the cost at the preferred frequency; 2) that when a person is forced to hop at half of their preferred frequency, the mechanical efficiency is nearly that predicted for muscle but is much higher at the preferred frequency; 3) that the preferred hop frequency is strongly body size dependent; and 4) that the hop frequency of a human is nearly identical to the galloping frequency predicted for a quadruped of our size. Together, these exercises demonstrate that humans store and recover elastic recoil potential energy when hopping but that energetic savings are highly frequency dependent. This stride frequency is dependent on body size such that frequency is likely chosen to maximize this function. Finally, by requiring students to make quantitative solutions using appropriate units and dimensions of the physical variables, these exercises sharpen analytic and quantitative skills.


The MacArthur Competence Assessment Tool-Fitness to Plead: a preliminary evaluation of a research instrument for assessing fitness to plead in England and Wales.
This study concerns the preliminary evaluation of an instrument, the MacArthur Competence Assessment Tool-Fitness to Plead (MacCAT-FP), for assessing competence to stand trial, according to the legal requirements in England and Wales. The purposes of the study were to ascertain whether the instrument can be administered practically to groups of prisoners, both those with mental illness and those without; to examine its internal consistency and interrater reliability; to determine whether it can distinguish between fit and unfit individuals, as judged by expert forensic psychiatrists; and to discover whether it is sensitive to changes over time. The instrument was administered to two groups of remanded prisoners: those transferred to psychiatric units for treatment and those without mental illness. In addition to the MacCAT-FP, scales measuring symptom severity and IQ were administered to all participants. Results suggest that the instrument is practical, with good internal consistency and interrater reliability. The correlation of scores with psychiatrists' opinions as to fitness was 0.77. Scores of unfit patients were significantly different from those of fit individuals. The instrument was able to detect significant differences in scores over time. It is suggested that once the instrument has been further validated for research purposes, it may be developed for clinical application.


Clinical utility of a blood-based BRAF(V600E) mutation assay in melanoma.
BRAF inhibitors (BRAFi) have led to clinical benefit in patients with melanoma. The development of a blood-based assay to detect and quantify BRAF levels in these patients has diagnostic, prognostic, and predictive capabilities that could guide treatment decisions. Blood BRAF(V600E) detection and quantification were performed on samples from 128 patients with stage II (19), III (67), and IV (42) melanoma. Tissue BRAF analysis was performed in all patients with stage IV disease and in selected patients with stage II and III disease. Clinical outcomes were correlated to initial BRAF levels as well as BRAF level dynamics. Serial analysis was performed on 17 stage IV melanoma patients treated with BRAFi and compared with tumor measurements by RECIST. The assay was highly sensitive (96%) and specific (95%) in the stage IV setting, using a blood level of 4.8 pg as "positive." BRAF levels typically decreased following BRAFi. A subset of these patients (5) had an increase in BRAF(V600E) values 42 to 112 days before clinical or radiographic disease progression (PD). From 86 patients with resected, stage II or III melanoma, 39 had evidence of disease relapse (45.3%). Furthermore, BRAF mutation in the blood after surgical resection in these patients was not associated with a difference in relapse risk, although tissue BRAF status was only available for a subset of patients. In summary, we have developed a highly sensitive and specific, blood-based assay to detect BRAF(V600) mutation in patients with melanoma.


Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano.
The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.


JTD special edition 'Hot Topics in COPD'-The microbiome in COPD.
The pathogenesis of chronic obstructive pulmonary disease (COPD) and its exacerbations, are intricately linked to colonisation and infection with bacteria and other microbes. Despite their undeniable importance, we have a poor understanding of the complex relationships between COPD phenotypes, physiology, cellular and molecular biology and the roles of colonising microbe or infecting pathogens. The management algorithms for the care of patients with COPD that include microbial influences, have almost exclusively been developed using microbial methods that were entirely dependent on the ability to grow bacteria on suitable media. The shortcomings of this approach are becoming clear now that it is possible to completely and accurately define the microbial ecology of ecosystems using genomic methods, which do not rely on the ability to cultivate the organisms present. Whilst our appreciation of the relationships between some bacterial ecosystems and the organ in which they reside in humans is now relatively advanced, this is not true for lung. This perspective serves to highlight the growing importance of including an accurate description of bacterial ecology in any attempt to decipher the pathobiology of COPD. While this field is in its infancy, there is significant potential to gain new insights which will translate into more rational and effective treatment algorithms for patients with COPD.


First marriages in the United States: data from the 2006-2010 National Survey of Family Growth.
This report shows trends and group differences in current marital status, with a focus on first marriages among women and men aged 15-44 years in the United States. Trends and group differences in the timing and duration of first marriages are also discussed. These data are based on the 2006-2010 National Survey of Family Growth (NSFG). National estimates of probabilities of first marriage by age and probabilities of separation and divorce for women and men's first marriages are presented by a variety of demographic characteristics. Data are compared with similar measures for 1982, 1995, and 2002. The analyses presented in this report are based on a nationally representative sample of 12,279 women and 10,403 men aged 15-44 years in the household population of the United States. The overall response rate for the 2006-2010 NSFG was 77%-78% for women and 75% for men. The percentage of women who were currently cohabiting (living with a man in a sexual relationship) rose from 3.0% in 1982 to 11% in 2006-2010; it was higher in some groups, including Hispanic groups, and the less educated. In 2006-2010, women and men married for the first time at older ages than in previous years. The median age at first marriage was 25.8 for women and 28.3 for men. Premarital cohabitation contributed to the delay in first marriage for both women and men.


Novel orphan nuclear receptors-coregulator interactions controlling anti-cancer drug metabolism.
In recent years, it has become clear that drug metabolizing enzymes and efflux transporters are directly under the control of tissue-specific orphan receptors, mainly pregnenolone x-receptor (PXR), and constitutive androstene receptor (CAR), that coordinately regulate their transcription. The consequences of xenobiotic activation of these receptors leads to unpredictability of drug kinetics and in some cases drug pharmacodynamics. Since receptor specific co-regulators are critically involved in this process, this review serves to highlight important new advances in this area of research. Specifically, this review focuses on co-regulator interactions described for PXR and CAR and some models that provide an explanation for receptor activation and repression. PXR is basally repressed and is activated in a ligand and tissue specific manner through a complex shift in co-repressor (Silencing mediator of retinoid and thyroid receptor (SMRT) and nuclear receptor co-repressor (N-CoR)) and co-activator (Steroid receptor coactivator-1(SRC-1), PPAR and glucocorticoid receptor coactivator-1(PGC-1), Hepatocyte nuclear factor 4 (HNF-4)) interactions favoring activation. Other higher order complexes impinge on this shift and include small heterodimer partner (SHP) mediated inhibition of co-activators and still others involved in histone acetylation/deacetylation (e.g., SWI/SNF, HDACs). Similar interactions have been proposed for CAR and these will be discussed in detail. Finally, this review will focus on the implications of understanding receptor-co-regulator interactions with the eventual aim of assessing polymorphisms in this transcriptional complex as a method to normalize the effects of drug metabolism.


Stimulation of pancreatic acinar cell growth by CCK, epidermal growth factor, and insulin in vitro.
Effects of regulatory molecules on growth of mouse pancreatic acinar cells in culture were examined. The cholecystokinin (CCK) analogue caerulein and cholecystokinin octapeptide (CCK-8) each led to threefold increases in incorporation of [3H]thymidine into DNA. Gastrin, which interacts weakly with the CCK receptor, stimulated DNA synthesis, but only at much higher concentrations. In contrast, other secretagogues that utilize Ca2+ as an intracellular messenger, including carbachol, bombesin, substance P, and the ionophore A23187, did not induce trophic responses. Factors that affect intracellular cAMP concentration, such as secretin, somatostatin, VIP, DBcAMP, and forskolin, did not increase DNA synthesis in cultured pancreatic cells. Insulin and epidermal growth factor induced two- and threefold increases in [3H] thymidine incorporation into DNA, respectively. The effects of insulin were mediated via insulin-like growth factor I receptors. Steroid hormones had little effect on pancreatic acinar cell DNA synthesis. The stimulatory effects of CCK, insulin, and EGF were additive. The combination of caerulein, EGF, and insulin in a hormonally defined medium led to a tenfold increase in the incorporation of [3H]thymidine into DNA. These data indicate that CCK, EGF, and insulin directly increase DNA synthesis in pancreatic acinar cells.


Women and children living in areas of armed conflict in Africa: a geospatial analysis of mortality and orphanhood.
The population effects of armed conflict on non-combatant vulnerable populations are incompletely understood. We aimed to study the effects of conflict on mortality among women of childbearing age (15-49 years) and on orphanhood among children younger than 15 years in Africa. We tested the extent to which mortality among women aged 15-49 years, and orphanhood among children younger than 15 years, increased in response to nearby armed conflict in Africa. Data on location, timing, and intensity of armed conflicts were obtained from the Uppsala Conflict Data Program, and data on the location, timing, and outcomes of women and children from Demographic and Health Surveys done in 35 African countries from 1990 to 2016. Mortality among women was obtained from sibling survival data. We used cluster-area fixed-effects regression models to compare survival of women during periods of nearby conflict (within 50 km) to survival of women in the same area during times without conflict. We used similar methods to examine the extent to which children living near armed conflicts are at increased risk of becoming orphans. We examined the effects of varying conflict intensity using number of direct battle deaths and duration of consecutive conflict exposure. We analysed data on 1 629 352 women (19 286 387 person-years), of which 103 011 (6·3%) died (534·1 deaths per 100 000 women-years), and 2 354 041 children younger than 15 years, of which 204 276 (8·7%) had lost a parent. On average, conflict within 50 km increased women's mortality by 112 deaths per 100 000 person-years (95% CI 97-128; a 21% increase above baseline), and the probability that a child has lost at least one parent by 6·0% (95% CI 3-8). This effect was driven by high-intensity conflicts: exposure to the highest (tenth) decile conflict in terms of conflict-related deaths increased the probability of female mortality by 202% (187-218) and increased the likelihood of orphanhood by 42% compared with a conflict-free period. Among the conflict-attributed deaths, 10% were due to maternal mortality. African women of childbearing age are at a substantially increased risk of death from nearby high-intensity armed conflicts. Children exposed to conflict are analogously at increased risk of becoming orphans. This work fills gaps in literature on the harmful effects of armed conflict on non-combatants and highlights the need for humanitarian interventions to protect vulnerable populations. Bill & Melinda Gates Foundation to the BRANCH Consortium.


Shp2 controls female body weight and energy balance by integrating leptin and estrogen signals.
In mammals, leptin regulates food intake and energy balance mainly through the activation of LepRb in the hypothalamus, and estrogen has a leptin-like effect in the hypothalamic control of metabolism. However, it remains to be elucidated how estrogen signaling is intertwined with the leptin pathway. We show here that Shp2, a nonreceptor tyrosine phosphatase, acts to integrate leptin and estrogen signals. The expression of a dominant-active mutant (Shp2(D61A)) in forebrain neurons conferred female, but not male, transgenic mice resistance to high-fat diet (HFD)-induced obesity and liver steatosis, accompanied by improved insulin sensitivity and glucose homeostasis. Fed with either HFD or regular chow food, Shp2(D61A) female mice showed dramatically enhanced leptin sensitivity. Microinjection of Shp2(D61A)-expressing adeno-associated virus into mediobasal hypothalamus elicited a similar antiobese effect in female mice. Biochemical analyses showed a physical association of Shp2 with estrogen receptor alpha, which is necessary for the synergistic and persistent activation of Erk by leptin and estrogen. Together, these results elucidate a mechanism for the direct cross talk of leptin and estrogen signaling and offer one explanation for the propensity of postmenopausal women to develop obesity.


Diagnosis, prevention, and management of statin adverse effects and intolerance: Canadian Working Group Consensus update.
The Proceedings of a Canadian Working Group Consensus Conference, first published in 2011, provided a summary of statin-associated adverse effects and intolerance and management suggestions. In this update, new clinical studies identified since then that provide further insight into effects on muscle, cognition, cataracts, diabetes, kidney disease, and cancer are discussed. Of these, the arenas of greatest controversy pertain to purported effects on cognition and the emergence of diabetes during long-term therapy. Regarding cognition, the available evidence is not strongly supportive of a major adverse effect of statins. In contrast, the linkage between statin therapy and incident diabetes is more firm. However, this risk is more strongly associated with traditional risk factors for new-onset diabetes than with statin itself and any possible negative effect of new-onset diabetes during statin treatment is far outweighed by the cardiovascular risk reduction benefits. Additional studies are also discussed, which support the principle that systematic statin rechallenge, and lower or intermittent statin dosing strategies are the main methods for dealing with suspected statin intolerance at this time.


Plasma intact fibroblast growth factor 23 levels in women with bulimia nervosa: A cross-sectional pilot study.
Fibroblast growth factor (FGF) 23, a circulating 26-kDa peptide produced by osteogenic cells, is a novel phosphaturic factor. In our previous study, binge-eating/purging type anorexia nervosa (AN-BP) patients had elevated plasma intact FGF23 (iFGF23) levels, while restricting type (AN-R) patients had plasma iFGF23 levels similar to healthy controls. Although bulimia nervosa (BN) patients as well as some patients with AN-BP regularly engage in binge eating, there have been no studies regarding plasma iFGF23 levels in BN patients. Therefore, this study was performed to determine plasma iFGF23 concentrations in BN patients and healthy controls. The study population consisted of 13 female BN patients and 11 healthy female controls. Blood samples were collected from all subjects after overnight fasting. Plasma iFGF23 was measured using an ELISA kit in a cross-sectional manner. The two-tailed Mann-Whitney U-test was used to assess differences between BN patients and healthy controls. In addition, BN patients were divided into two groups based on questionnaire-reported binge eating frequency immediately prior to participation in this study: high frequency of binge eating (once a week or more; HF group; n = 8) and low frequency of binge eating (less than once a week; LF group; n = 5). Two-tailed Mann-Whitney U-test with Bonferroni's correction was performed after the Kruskal-Wallis test to assess differences between HF group, LF group, and healthy controls. Median (quartiles) plasma iFGF23 levels were greater in BN patients (35.5 [14.8-65.0] pg/ml) than in controls (3.8 [not detected-5.3] pg/ml; p = 0.002). In addition, median (quartiles) plasma iFGF23 levels were greater in the HF group (62.3 [44.4-73.4] pg/ml) than in controls (p < 0.001) and in the LF group (12.9 [not detected-30.3] pg/ml; p = 0.011), while there were no differences between the LF group and controls (p = 0.441). This is the first study to show that BN patients have elevated plasma iFGF23 levels. Moreover, this study showed that BN patients with a high frequency of binge eating have elevated plasma iFGF23 levels, while iFGF23 levels are similar to healthy controls in those with a low frequency of binge eating. Plasma iFGF23 level may be a suitable indicator of binge eating in BN patients.


Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana.
Post-translational modifications of histones play important roles in maintaining normal transcription patterns by directly or indirectly affecting the structural properties of the chromatin. In plants, methylation of histone H3 lysine 4 (H3K4me) is associated with genes and required for normal plant development. We have characterized the genome-wide distribution patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana seedlings using chromatin immunoprecipitation and high-resolution whole-genome tiling microarrays (ChIP-chip). All three types of H3K4me are found to be almost exclusively genic, and two-thirds of Arabidopsis genes contain at least one type of H3K4me. H3K4me2 and H3K4me3 accumulate predominantly in promoters and 5' genic regions, whereas H3K4me1 is distributed within transcribed regions. In addition, H3K4me3-containing genes are highly expressed with low levels of tissue specificity, but H3K4me1 or H3K4me2 may not be directly involved in transcriptional activation. Furthermore, the preferential co-localization of H3K4me3 and H3K27me3 found in mammals does not appear to occur in plants at a genome-wide level, but H3K4me2 and H3K27me3 co-localize at a higher-than-expected frequency. Finally, we found that H3K4me2/3 and DNA methylation appear to be mutually exclusive, but surprisingly, H3K4me1 is highly correlated with CG DNA methylation in the transcribed regions of genes. H3K4me plays widespread roles in regulating gene expression in plants. Although many aspects of the mechanisms and functions of H3K4me appear to be conserved among all three kingdoms, we observed significant differences in the relationship between H3K4me and transcription or other epigenetic pathways in plants and mammals.


Astrocyte-shed extracellular vesicles regulate the peripheral leukocyte response to inflammatory brain lesions.
Brain injury induces a peripheral acute cytokine response that directs the transmigration of leukocytes into the brain. Because this brain-to-peripheral immune communication affects patient recovery, understanding its regulation is important. Using a mouse model of inflammatory brain injury, we set out to find a soluble mediator for this phenomenon. We found that extracellular vesicles (EVs) shed from astrocytes in response to intracerebral injection of interleukin-1β (IL-1β) rapidly entered into peripheral circulation and promoted the transmigration of leukocytes through modulation of the peripheral acute cytokine response. Bioinformatic analysis of the protein and microRNA cargo of EVs identified peroxisome proliferator-activated receptor α (PPARα) as a primary molecular target of astrocyte-shed EVs. We confirmed in mice that astrocytic EVs promoted the transmigration of leukocytes into the brain by inhibiting PPARα, resulting in the increase of nuclear factor κB (NF-κB) activity that triggered the production of cytokines in liver. These findings expand our understanding of the mechanisms regulating communication between the brain and peripheral immune system and identify astrocytic EVs as a molecular regulator of the immunological response to inflammatory brain damage.


State of the science on controversial topics: orthodontic therapy and gingival recession (a report of the Angle Society of Europe 2013 meeting).
Controversy exists in the literature between the role of orthodontic treatment and gingival recession. Whilst movement of teeth outside the alveolar bone has been reported as a risk factor for gingival recession, others have found no such association. The Angle Society of Europe devoted a study day to explore the evidence surrounding these controversies. The aim of the day was for a panel of experts to evaluate the current evidence base in relation to either the beneficial or detrimental effects of orthodontic treatment on the gingival tissue. There remains a relatively weak evidence base for the role of orthodontic treatment and gingival recession and thus a need to undertake a risk assessment and appropriate consent prior to the commencement of treatment. In further prospective, well designed trials are needed.


An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer.
Perhaps the major challenge in developing more effective therapeutic strategies for the treatment of breast cancer patients is confronting the heterogeneity of the disease, recognizing that breast cancer is not one disease but multiple disorders with distinct underlying mechanisms. Gene-expression profiling studies have been used to dissect this complexity, and our previous studies identified a series of intrinsic subtypes of breast cancer that define distinct populations of patients with respect to survival. Additional work has also used signatures of oncogenic pathway deregulation to dissect breast cancer heterogeneity as well as to suggest therapeutic opportunities linked to pathway activation. We used genomic analyses to identify relations between breast cancer subtypes, pathway deregulation, and drug sensitivity. For these studies, we use three independent breast cancer gene-expression data sets to measure an individual tumor phenotype. Correlation between pathway status and subtype are examined and linked to predictions for response to conventional chemotherapies. We reveal patterns of pathway activation characteristic of each molecular breast cancer subtype, including within the more aggressive subtypes in which novel therapeutic opportunities are critically needed. Whereas some oncogenic pathways have high correlations to breast cancer subtype (RAS, CTNNB1, p53, HER1), others have high variability of activity within a specific subtype (MYC, E2F3, SRC), reflecting biology independent of common clinical factors. Additionally, we combined these analyses with predictions of sensitivity to commonly used cytotoxic chemotherapies to provide additional opportunities for therapeutics specific to the intrinsic subtype that might be better aligned with the characteristics of the individual patient. Genomic analyses can be used to dissect the heterogeneity of breast cancer. We use an integrated analysis of breast cancer that combines independent methods of genomic analyses to highlight the complexity of signaling pathways underlying different breast cancer phenotypes and to identify optimal therapeutic opportunities.


Practicality and time complexity of a sparsified RNA folding algorithm.
Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n(3)). Recently, it has been claimed that RNA folding can be achieved in average time O(n(2)) using a sparsification technique. A proof of quadratic time complexity was based on the assumption that computational RNA folding obeys the "polymer-zeta property". Several variants of sparse RNA folding algorithms were later developed. Here, we present our own version, which is readily applicable to existing RNA folding programs, as it is extremely simple and does not require any new data structure. We applied it to the widely used Vienna RNAfold program, to create sibRNAfold, the first public sparsified version of a standard RNA folding program. To gain a better understanding of the time complexity of sparsified RNA folding in general, we carried out a thorough run time analysis with synthetic random sequences, both in the context of energy minimization and base pairing maximization. Contrary to previous claims, the asymptotic time complexity of a sparsified RNA folding algorithm using standard energy parameters remains O(n(3)) under a wide variety of conditions. Consistent with our run-time analysis, we found that RNA folding does not obey the "polymer-zeta property" as claimed previously. Yet, a basic version of a sparsified RNA folding algorithm provides 15- to 50-fold speed gain. Surprisingly, the same sparsification technique has a different effect when applied to base pairing optimization. There, its asymptotic running time complexity appears to be either quadratic or cubic depending on the base composition. The code used in this work is available at: .


Statistical analysis plan for the POLAR-RCT: The Prophylactic hypOthermia trial to Lessen trAumatic bRain injury-Randomised Controlled Trial.
The Prophylactic hypOthermia to Lessen trAumatic bRain injury-Randomised Controlled Trial (POLAR-RCT) will evaluate whether early and sustained prophylactic hypothermia delivered to patients with severe traumatic brain injury improves patient-centred outcomes. The POLAR-RCT is a multicentre, randomised, parallel group, phase III trial of early, prophylactic cooling in critically ill patients with severe traumatic brain injury, conducted in Australia, New Zealand, France, Switzerland, Saudi Arabia and Qatar. A total of 511 patients aged 18-60 years have been enrolled with severe acute traumatic brain injury. The trial intervention of early and sustained prophylactic hypothermia to 33 °C for 72 h will be compared to standard normothermia maintained at a core temperature of 37 °C. The primary outcome is the proportion of favourable neurological outcomes, comprising good recovery or moderate disability, observed at six months following randomisation utilising a midpoint dichotomisation of the Extended Glasgow Outcome Scale (GOSE). Secondary outcomes, also assessed at six months following randomisation, include the probability of an equal or greater GOSE level, mortality, the proportions of patients with haemorrhage or infection, as well as assessment of quality of life and health economic outcomes. The planned sample size will allow 80% power to detect a 30% relative risk increase from 50% to 65% (equivalent to a 15% absolute risk increase) in favourable neurological outcome at a two-sided alpha of 0.05. Consistent with international guidelines, a detailed and prospective analysis plan has been developed for the POLAR-RCT. This plan specifies the statistical models for evaluation of primary and secondary outcomes, as well as defining covariates for adjusted analyses and methods for exploratory analyses. Application of this statistical analysis plan to the forthcoming POLAR-RCT trial will facilitate unbiased analyses of these important clinical data. ClinicalTrials.gov, NCT00987688 (first posted 1 October 2009); Australian New Zealand Clinical Trials Registry, ACTRN12609000764235 . Registered on 3 September 2009.


Precise predictions for V + jets dark matter backgrounds.
High-energy jets recoiling against missing transverse energy (MET) are powerful probes of dark matter at the LHC. Searches based on large MET signatures require a precise control of the Z ( ν ν ¯ ) + jet background in the signal region. This can be achieved by taking accurate data in control regions dominated by Z ( ℓ + ℓ - ) + jet, W ( ℓ ν ) + jet and γ + jet production, and extrapolating to the Z ( ν ν ¯ ) + jet background by means of precise theoretical predictions. In this context, recent advances in perturbative calculations open the door to significant sensitivity improvements in dark matter searches. In this spirit, we present a combination of state-of-the-art calculations for all relevant V + jets processes, including throughout NNLO QCD corrections and NLO electroweak corrections supplemented by Sudakov logarithms at two loops. Predictions at parton level are provided together with detailed recommendations for their usage in experimental analyses based on the reweighting of Monte Carlo samples. Particular attention is devoted to the estimate of theoretical uncertainties in the framework of dark matter searches, where subtle aspects such as correlations across different V + jet processes play a key role. The anticipated theoretical uncertainty in the Z ( ν ν ¯ ) + jet background is at the few percent level up to the TeV range.


Role of the Thrombelastograph as an adjunctive test in thrombophilia screening.
The Thrombelastograph (TEG) provides a global assessment of haemostatic function. We have investigated the potential role of TEG in thrombophilia testing by studying 87 consecutive patients (all with personal or family history of thrombosis). For each patient, routine thrombophilia screening tests and TEG were performed in parallel. In keeping with previous reports, at least one thrombophilic trait was identified in 34% of the patients. Among those patients with previous thrombosis, the yield from screening was higher (54% with prothrombotic trait). Overall, a hypercoaguable TEG was demonstrated in 45% of patients. However, TEG and standard thrombophilia testing did not necessarily identify the same subset of individuals. Of 39 patients with hypercoaguable TEG, only 17 had a demonstrable thrombophilic trait. Conversely, of 30 patients with proven thrombophilia, 17 also had a hypercoaguable TEG. We conclude that TEG cannot be used as a sole initial screening test in patients referred for thrombophilia testing, as it fails to identify 43% of underlying thrombophilic traits. However, TEG may be a useful adjunctive test, particularly in patients in whom the regular thrombophilia screen proves unremarkable. Prospective studies are warranted to determine whether a hypercoaguable TEG can be used to predict a subset of patients at increased risk for recurrent thrombotic events.


Increased microRNA-155 expression in the serum and peripheral monocytes in chronic HCV infection.
Hepatitis C Virus (HCV), a single stranded RNA virus, affects millions of people worldwide and leads to chronic infection characterized by chronic inflammation in the liver and in peripheral immune cells. Chronic liver inflammation leads to progressive liver damage. MicroRNAs (miRNA) regulate inflammation (miR-155, -146a and -125b) as well as hepatocyte function (miR-122). Here we hypothesized that microRNAs are dysregulated in chronic HCV infection. We examined miRNAs in the circulation and in peripheral monocytes of patients with chronic HCV infection to evaluate if specific miRNA expression correlated with HCV infection. We found that monocytes from chronic HCV infected treatment-naïve (cHCV) but not treatment responder patients showed increased expression of miR-155, a positive regulator of TNFα, and had increased TNFα production compared to monocytes of normal controls. After LPS stimulation, miR-155 levels were higher in monocytes from cHCV patients compared to controls. MiR-125b, which has negative regulatory effects on inflammation, was decreased in cHCV monocytes compared to controls. Stimulation of normal monocytes with TLR4 and TLR8 ligands or HCV core, NS3 and NS5 recombinant proteins induced a robust increase in both miR-155 expression and TNFα production identifying potential mechanisms for in vivo induction of miR-155. Furthermore, we found increased serum miR-155 levels in HCV patients compared to controls. Serum miR-125b and miR-146a levels were also increased in HCV patients. Serum levels of miR-122 were elevated in cHCV patients and correlated with increased ALT and AST levels and serum miR-155 levels. In conclusion, our novel data demonstrate that miR-155, a positive regulator of inflammation, is upregulated both in monocytes and in the serum of patients with chronic HCV infection. Our study suggests that HCV core, NS3, and NS5 proteins or TLR4 and TLR8 ligands can mediate increased miR-155 and TNFα production in chronic HCV infection. The positive correlation between serum miR-155 and miR-122 increase in cHCV may be an indicator of inflammation-induced hepatocyte damage.


Ultrasonographic measured optic nerve sheath diameter as an accurate and quick monitor for changes in intracranial pressure.
Ultrasonographic measurement of the optic nerve sheath diameter (ONSD) is known to be an accurate monitor of elevated intracranial pressure (ICP). However, it is yet unknown whether fluctuations in ICP result in direct changes in ONSD. Therefore, the authors researched whether ONSD and ICP simultaneously change during tracheal manipulation in patients in the intensive care unit (ICU) who have suffered a traumatic brain injury (TBI). The authors included 18 ICP-monitored patients who had sustained TBI and were admitted to the ICU. They examined the optic nerve sheath by performing ultrasound before, during, and after tracheal manipulation, which is known to increase ICP. The correlation between ONSD and ICP measurements was determined, and the diagnostic performance of ONSD measurement was tested using receiver operating characteristic curve analysis. In all patients ICP increased above 20 mm Hg during manipulation of the trachea, and this increase was directly associated with a dilation of the ONSD of > 5.0 mm. After tracheal manipulation stopped, ICP as well as ONSD decreased immediately to baseline levels. The correlation between ICP and ONSD was high (R(2) = 0.80); at a cutoff of ≥ 5.0 mm ONSD, a sensitivity of 94%, a specificity of 98%, and an area under the curve of 0.99 (95% CI 0.97-1.00) for detecting elevated ICP were determined. In patients who have sustained a TBI, ultrasonography of the ONSD is an accurate, simple, and rapid measurement for detecting elevated ICP as well as immediate changes in ICP. Therefore, it might be a useful tool to monitor ICP, especially in conditions in which invasive ICP monitoring is not available, such as at trauma scenes.


Identifying patients at risk of complete nonresponse in the outpatient treatment of depression.
Although complete nonresponse in depression treatment is considered to be a major problem in clinical practice, research in this area is very limited. The objective of this preliminary study was to determine the frequency and predictors of complete nonresponse in different treatments for depression. Post hoc analysis of the pooled data of 3 consecutive randomized controlled trials of outpatient depression treatment was conducted. The subjects were 313 patients with major depressive disorder and 17-item Hamilton Rating Scale for Depression (HAM-D-17) scores between 14 and 25 who were treated for 6 months with either pharmacotherapy, short-term psychodynamic supportive psychotherapy or combined therapy. Complete nonresponse was defined as a <25% response according to the HAM-D-17. Sociodemographic factors, depression features and adherence were investigated as predictors in a multivariate stepwise logistic regression analysis. Overall, nonresponse occurred in 34% of the patients. In pharmacotherapy this was 46%, in psychotherapy 39% and in combined therapy 28%. The severity of somatic symptoms was associated with nonresponse in both combined therapy and psychotherapy. No predictive factors were found in the case of pharmacotherapy. In psychotherapy, nonresponse was related to age above 40 years, chronic depression and nonadherence by the patient. In the case of combined therapy, younger age, previous use of an antidepressant and having a previous depressive episode were associated with nonresponse. Easily measurable patient characteristics may help to identify patients at risk of complete nonresponse to treatment. It is suggested that predictors may differ across treatment modalities. However, head-to-head comparisons are required before it can be recommended to take this into account when selecting the most appropriate treatment for individual depressed patients.


The melanocortin system regulates body pigmentation and social behaviour in a colour polymorphic cichlid fish.
The melanocortin system is a neuroendocrine system that regulates a range of physiological and behavioural processes. We examined the extent to which the melanocortin system simultaneously regulates colour and behaviour in the cichlid fish Astatotilapia burtoni We found that yellow males are more aggressive than blue males, in line with previous studies. We then found that exogenous α-melanocyte-stimulating hormone (α-MSH) increases yellowness of the body and dispersal of xanthophore pigments in both morphs. However, α-MSH had a morph-specific effect on aggression, with only blue males showing an increase in the rate of aggression. Exogenous agouti signalling peptide (ASIP), a melanocortin antagonist, did not affect coloration but reduced the rate of aggression in both colour morphs. Blue males had higher cortisol levels than yellow males. Neural gene expression of melanocortin receptors (mcr) and ligands was not differentially regulated between colour morphs. In the skin, however, mc1r and pro-opiomelanocortin (pomc) β were upregulated in blue males, while asip 1 was upregulated in yellow males. The effects of α-MSH on behaviour and body coloration, combined with morph-specific regulation of the stress response and the melanocortin system, suggest that the melanocortin system contributes to the polymorphism in behaviour and coloration in A. burtoni.


Abdominoplasty-related nerve injuries: systematic review and treatment options.
Abdominoplasty is a common cosmetic procedure; nerve injury is an underexplored risk of the procedure. The authors review existing literature to examine the incidence and treatment of nerve injuries after abdominoplasty procedures and provide a treatment algorithm based on their results. A search of the literature on MEDLINE, EMBASE, and the Cochrane Database of Systematic Reviews was undertaken. After full-text review, 23 articles met our criteria. Any mentions of nerve injury, including references to a lack of nerve injury, were documented. All data were pooled for analysis. From our combined data, we calculated the risks of postabdominoplasty nerve injury by dividing the total number of nerve injuries by the total number of patients. Pooled data showed that 1.94% of patients sustained specific nerve injury, and 1.02% of patients sustained permanent injury after abdominoplasty. In addition, 7.67% experienced decreased sensation, 1.07% reported chronic pain, and 0.44% reported temporary weakness or paralysis. Nerves directly injured were the lateral femoral cutaneous (1.36% of patients) and iliohypogastric (0.10%) nerves. Nerves injured from surgical positioning were the brachial plexus (0.10%), musculocutaneous (0.10%), radial (0.05%), sciatic (0.19%), and common peroneal (0.05%) nerves. Although our results showed a low incidence of postabdominoplasty nerve injury, the lasting impact on affected patients' quality of life can be significant. Appropriate and timely treatment by a multidisciplinary team is critical to optimize patient outcomes. Better reporting of nerve injuries in future studies of abdominoplasty will provide more accurate information about the incidence and consequences of these injuries. 4.


Renal biopsy in elderly patients: clinicopathological correlation in 117 Korean patients.
In the elderly with renal disease, the clinical presentations are frequently inconsistent with the pathologic findings. We tried to clarify the differences in pathological findings between the young and the elderly, in Korea and in Western countries, and the usefulness of a percutaneous renal biopsy in the elderly with renal disease. We analyzed the clinical presentations and spectrums of renal histopathology by reviewing medical records and renal biopsy reports retrospectively in 117 Korean patients aged 60 years or more with renal disease. 85 patients had primary renal disease. The remaining 32 patients had renal diseases associated with systemic conditions. Out of the 85 patients with primary renal disease, 61 cases presented as idiopathic nephrotic syndrome. Compared with renal biopsy results of younger adult patients (age 15-59, n = 1,908), membranous nephropathy, crescentic glomerulonephritis, membranoproliferative glomerulonephritis, amyloidosis, light chain disease, and thrombotic thrombocytopenic purpura were more prevalent, but IgA nephropathy and lupus nephritis were less common in the elderly patients. In clinical presentation, nephrotic syndrome and rapidly progressive renal failure were more prevalent, but asymptomatic urinary abnormality was less common in elderly patients. The responsiveness to treatment was good in elderly patients with minimal-change lesion (complete remission in all patients) but poor in crescentic glomerulonephritis, IgA nephropathy, and membranoproliferative glomerulonephritis. From the above findings, the clinical presentation, patterns of histopathology and responsiveness to treatment of elderly Korean patients were similar to those of the younger Korean control group and the Western elderly group. Percutaneous renal biopsy is a useful diagnostic aid and can be used as a therapeutic guideline even in elderly patients with renal disease.


Flavor characterization of sugar-added pennywort (Centella asiatica L.) juices treated with ultra-high pressure and thermal processes.
The flavor characteristics of pennywort juices with added sugar treated by ultra-high pressure, pasteurization, and sterilization were investigated using solid phase microextraction combined with gas chromatography-mass spectrometry. It was found that sesquiterpene hydrocarbons comprised the major class of volatile components present and the juices had a characteristic aroma due to the presence of volatiles including beta-caryophyllene and humulene and alpha-copaene. In comparison with heated juices, HPP-treated samples could retain more volatile compounds such as linalool and geraniol similar to those present in fresh juice, whereas some volatiles such as alpha-terpinene and ketone class were apparently formed by thermal treatment. All processing operations produced juice that was not significantly different in the concentration of total volatiles. Practical Application: Pennywort juice is considered a nutraceutical drink for health benefits. Therefore, to preserve all aroma and active components in this juice, a nonthermal process such as ultra-high pressure should be a more appropriate technique for retention of its nutritive values than pasteurization and sterilization.


Loss of Tuberous Sclerosis Complex 2 (TSC2) Is Frequent in Hepatocellular Carcinoma and Predicts Response to mTORC1 Inhibitor Everolimus.
Hepatocellular carcinoma (HCC) is the third leading cause of cancer deaths worldwide and hyperactivation of mTOR signaling plays a pivotal role in HCC tumorigenesis. Tuberous sclerosis complex (TSC), a heterodimer of TSC1 and TSC2, functions as a negative regulator of mTOR signaling. In the current study, we discovered that TSC2 loss-of-function is common in HCC. TSC2 loss was found in 4 of 8 HCC cell lines and 8 of 28 (28.6%) patient-derived HCC xenografts. TSC2 mutations and deletions are likely to be the underlying cause of TSC2 loss in HCC cell lines, xenografts, and primary tumors for most cases. We further demonstrated that TSC2-null HCC cell lines and xenografts had elevated mTOR signaling and, more importantly, were significantly more sensitive to RAD001/everolimus, an mTORC1 inhibitor. These preclinical findings led to the analysis of TSC2 status in HCC samples collected in the EVOLVE-1 clinical trial of everolimus using an optimized immunohistochemistry assay and identified 15 of 139 (10.8%) samples with low to undetectable levels of TSC2. Although the sample size is too small for formal statistical analysis, TSC2-null/low tumor patients who received everolimus tended to have longer overall survival than those who received placebo. Finally, we performed an epidemiology survey of more than 239 Asian HCC tumors and found the frequency of TSC2 loss to be approximately 20% in Asian HBV(+) HCC. Taken together, our data strongly argue that TSC2 loss is a predictive biomarker for the response to everolimus in HCC patients.


Measuring nitrification, denitrification, and related biomarkers in terrestrial geothermal ecosystems.
Research on the nitrogen biogeochemical cycle in terrestrial geothermal ecosystems has recently been energized by the discovery of thermophilic ammonia-oxidizing archaea (AOA). This chapter describes methods that have been used for measuring nitrification and denitrification in hot spring environments, including isotope pool dilution and tracer approaches, and the acetylene block approach. The chapter also summarizes qualitative and quantitative methods for measurement of functional and phylogenetic biomarkers of thermophiles potentially involved in these processes.


Synaptic desensitization of NMDA receptors by calcineurin.
Desensitization is a phenomenon that is common to many ligand-gated ion channels but has been demonstrated only rarely with physiological stimulation. Numerous studies describe desensitization of the N-methyl-D-aspartate (NMDA) subtype of glutamate receptor by exogenous agonists, but whether synaptic stimulation causes desensitization has been unknown. Synaptic stimulation of NMDA receptors on rat hippocampal neurons resulted in desensitization that was prevented by intracellular 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA), adenosine-5'-O-(3-thiotriphosphate) (ATP-gamma-S), or inhibitors of phosphatase 2B (calcineurin), but not by inhibitors of phosphatases 1 and 2A or of tyrosine phosphatases. Synaptic NMDA receptors may fluctuate between phosphorylated and dephosphorylated forms, depending on the rate of synaptic stimulation and the magnitude of the associated influx of calcium through NMDA receptors.


Joining the dots: The links between education and health and implications for indigenous children.
This paper provides a general overview of the literature investigating the nexus between education and health; discussing the relationship between these domains at individual, family and community levels. We then briefly examine the programme and research implications of such a framework for interventions aimed at improving education and health, with specific reference to young Indigenous Australians. We find that while education and health are inextricably linked, throughout the life course and at different levels of influence, there is less empirical work exploring this relationship in an Indigenous context. Given the gravity of literacy and numeracy failure rates in school-based education and its potential impact on Indigenous health, we assert an urgent case for rigorous research into interventions that address the barriers to effectiveness in implementing quality educational experiences and opportunities for Indigenous children.


Comparative infection modeling and control of COVID-19 transmission patterns in China, South Korea, Italy and Iran.
The COVID-19 has become a pandemic. The timing and nature of the COVID-19 pandemic response and control varied among the regions and from one country to the other, and their role in affecting the spread of the disease has been debated. The focus of this work is on the early phase of the disease when control measures can be most effective. We proposed a modified susceptible-exposed-infected-removed model (SEIR) model based on temporal moving windows to quantify COVID-19 transmission patterns and compare the temporal progress of disease spread in six representative regions worldwide: three Chinese regions (Zhejiang, Guangdong and Xinjiang) vs. three countries (South Korea, Italy and Iran). It was found that in the early phase of COVID-19 spread the disease follows a certain empirical law that is common in all regions considered. Simulations of the imposition of strong social distancing measures were used to evaluate the impact that these measures might have had on the duration and severity of COVID-19 outbreaks in the three countries. Measure-dependent transmission rates followed a modified normal distribution (empirical law) in the three Chinese regions. These rates responded quickly to the launch of the 1st-level Response to Major Public Health Emergency in each region, peaking after 1-2 days, reaching their inflection points after 10-19 days, and dropping to zero after 11-18 days since the 1st-level response was launched. By March 29th, the mortality rates were 0.08% (Zhejiang), 0.54% (Guangdong) and 3.95% (Xinjiang). Subsequent modeling simulations were based on the working assumption that similar infection transmission control measures were taken in South Korea as in Zhejiang on February 25th, in Italy as in Guangdong on February 25th, and in Iran as in Xinjiang on March 8th. The results showed that by June 15th the accumulated infection cases could have been reduced by 32.49% (South Korea), 98.16% (Italy) and 85.73% (Iran). The surface air temperature showed stronger association with transmission rate of COVID-19 than surface relative humidity. On the basis of these findings, disease control measures were shown to be particularly effective in flattening and shrinking the COVID-10 case curve, which could effectively reduce the severity of the disease and mitigate medical burden. The proposed empirical law and the SEIR-temporal moving window model can also be used to study infectious disease outbreaks worldwide.


Analysis of terpenes and turpentines using gas chromatography with vacuum ultraviolet detection.
The separation and identification of natural mixtures of terpenes is challenging and laborious. A gas chromatographic method based on vacuum ultraviolet spectroscopic detection, which is characterized by full-scan absorption in the range of 125-240 nm, was developed and applied to analyze terpenes. In this study, the vacuum ultraviolet absorption spectra of 41 different standard terpenes were investigated and compared. The spectra were found to be highly featured and easily differentiated. Several commercial turpentine samples were analyzed and the vacuum ultraviolet detector demonstrated good specificity for qualitative identification of constituent terpenes. A total of 31 terpenes were detected in the four turpentine samples. α-Pinene was the predominant terpene ranging from 744.2 ± 9.7 to 917 ± 21 mg/mL. The other major constituents in the turpentines included β-pinene, δ-3-carene, camphene, and p-isopropyltoluene. Deconvolution of co-eluting signals of terpenes was achieved utilizing the data analysis software. The technique has been demonstrated to be a powerful tool for reliable and accurate qualitative and quantitative analysis of terpenes from complex natural mixtures.


LESSONS LEARNED ANALYZING COMPLICATIONS AFTER LAPAROSCOPIC TOTAL GASTRECTOMY FOR GASTRIC CANCER.
Laparoscopic surgery has been gradually accepted as an option for the surgical treatment ofgastric cancer. There are still points that are controversial or situations that are eventually associated with intra-operative difficulties or postoperative complications. To establish the relationship between the difficulties during the execution of total gastrectomy and the occurrence of eventual postoperative complications. The operative protocols and postoperative evolution of 74 patients operated for gastriccancer, who were subjected to laparoscopic total gastrectomy (inclusion criteria) were reviewed. The intraoperative difficulties recorded in the operative protocol and postoperative complications of a surgical nature wereanalyzed (inclusion criteria). Postoperative medical complications were excluded (exclusion criteria). For the discussion, an extensive bibliographical review was carried out. Intra-operative difficulties or complications reported correspond to 33/74 and of these; 18 events (54.5%) were related to postoperative complications and six were absolutely unexpected. The more frequent were leaks of the anastomosis and leaks of the duodenal stump; however, other rare complications were observed. Seven were managed with conservative measures and 17 (22.9%) required surgical re-exploration, with a postoperative mortality of two patients (2.7%). We have learned that there are infrequent and unexpected complications; the treating team must be mindful of and, in front of suspicion of complications, anappropriate decision must be done which includes early re-exploration. Finally, after the experience reported, some complications should be avoided.


Ocean change within shoreline communities: from biomechanics to behaviour and beyond.
Humans are changing the physical properties of Earth. In marine systems, elevated carbon dioxide concentrations are driving notable shifts in temperature and seawater chemistry. Here, we consider consequences of such perturbations for organism biomechanics and linkages amongst species within communities. In particular, we examine case examples of altered morphologies and material properties, disrupted consumer-prey behaviours, and the potential for modulated positive (i.e. facilitative) interactions amongst taxa, as incurred through increasing ocean acidity and rising temperatures. We focus on intertidal rocky shores of temperate seas as model systems, acknowledging the longstanding role of these communities in deciphering ecological principles. Our survey illustrates the broad capacity for biomechanical and behavioural shifts in organisms to influence the ecology of a transforming world.


High dose methylprednisolone in the immediate management of acute, blunt spinal cord injury: what is the current practice in emergency departments, spinal units, and neurosurgical units in the UK?
The National Acute Spinal Cord Injuries Studies and the Cochrane Review advocate the administration of high dose methylprednisolone following acute traumatic spinal cord injury. However, controversy surrounds its use and approaches between different units are often inconsistent. A questionnaire was sent to all emergency departments receiving major trauma and all specialist neurosurgical and spinal units in the UK to determine the current practice regarding the use of high dose methylprednisolone in the immediate management of acute, blunt spinal cord injuries. Of 250 emergency departments, 187 replied to the questionnaire. Twelve of the 26 departments with a neurosurgical or spinal service on site stated they received consistent advice from specialist teams. Sixty four departments had a written policy regarding the treatment of spinal injuries, which in 51 departments contained advice about the administration of methylprednisolone. Of the 128 departments who gave methylprednisolone, 88 did so only on the advice of a specialist team, with the remaining 40 giving steroids immediately on identification of the injury. Ten out of 11 spinal units replied, of whom only two advised the used of steroids. Of the 34 neurosurgical units approached, seven out of 17 responders had a policy recommending the use of steroids. Of the 10 units who did not consistently recommend the use of steroids, seven had practise that varied between consultants. Currently practice varies in the UK regarding the immediate use of methylprednisolone after spinal injury. Clear guidelines need to be established to achieve a more consistent approach.


Epigenetic Effects of an Adenosine Derivative in a Wistar Rat Model of Liver Cirrhosis.
The pathological characteristic of cirrhosis is scarring which results in a structurally distorted and dysfunctional liver. Previously, we demonstrated that Col1a1 and Pparg genes are deregulated in CCl4 -induced cirrhosis but their normal expression levels are recovered upon treatment with IFC-305, an adenosine derivative. We observed that adenosine was able to modulate S-adenosylmethionine-dependent trans-methylation reactions, and recently, we found that IFC-305 modulates HDAC3 expression. Here, we investigated whether epigenetic mechanisms, involving DNA methylation processes and histone acetylation, could explain the re-establishment of gene expression mediated by IFC-305 in cirrhosis. Therefore, Wistar rats were CCl4 treated and a sub-group received IFC-305 to reverse fibrosis. Global changes in DNA methylation, 5-hydroxymethylation, and histone H4 acetylation were observed after treatment with IFC-305. In particular, during cirrhosis, the Pparg gene promoter is depleted of histone H4 acetylation, whereas IFC-305 administration restores normal histone acetylation levels which correlates with an increase of Pparg transcript and protein levels. In contrast, the promoter of Col1a1 gene is hypomethylated during cirrhosis but gains DNA methylation upon treatment with IFC-305 which correlates with a reduction of Col1a1 transcript and protein levels. Our results suggest a model in which cirrhosis results in a general loss of permissive chromatin histone marks which triggers the repression of the Pparg gene and the upregulation of the Col1a1 gene. Treatment with IFC-305 restores epigenetic modifications globally and specifically at the promoters of Pparg and Col1a1 genes. These results reveal one of the mechanisms of action of IFC-305 and suggest a possible therapeutic function in cirrhosis. J. Cell. Biochem. 119: 401-413, 2018. © 2017 Wiley Periodicals, Inc.


Visual loss caused by pseudotumor cerebri in an infant on peritoneal dialysis.
Infants with chronic renal insufficiency have multiple risk factors for developing pseudotumor cerebri (PTC) and are at particular risk for being diagnosed with PTC late, because of their inability to express symptoms. We describe a 13-month-old infant dependent on peritoneal dialysis, without evidence of central nervous system infection or inflammation, who developed acute vision loss secondary to PTC. Signs of PTC in infants include torticollis, inattentiveness, inability to track, facial paresis, or new-onset strabismus. Physicians responsible for the care of children with renal failure should be aware of the potential for PTC, as the diagnosis should be made as early as possible to prevent permanent visual loss.


The in vitro antifungal activity of sudanese medicinal plants against Madurella mycetomatis, the eumycetoma major causative agent.
Eumycetoma is a debilitating chronic inflammatory fungal infection that exists worldwide but it is endemic in many tropical and subtropical regions. The major causative organism is the fungus Madurella mycetomatis. The current treatment of eumycetoma is suboptimal and characterized by low cure rate and high recurrence rates. Hence, an alternative therapy is needed to address this. Here we determined the antifungal activity of seven Sudanese medicinal plant species against Madurella mycetomatis. Of these, only three species; Boswellia papyrifera, Acacia nubica and Nigella sativa, showed some antifungal activity against M. mycetomatis and were further studied. Crude methanol, hexane and defatted methanol extracts of these species were tested for their antifungal activity. B. papyrifera had the highest antifungal activity (MIC50 of 1 ug/ml) and it was further fractionated. The crude methanol and the soluble ethyl acetate fractions of B. papyrifera showed some antifungal activity. The Gas-Liquid-Chromatography hybrid Mass-Spectrophotometer analysis of these two fractions showed the existence of beta-amyrin, beta-amyrone, beta-Sitosterol and stigmatriene. Stigmatriene had the best antifungal activity, compared to other three phytoconstituents, with an MIC-50 of 32 μg/ml. Although the antifungal activity of the identified phytoconstituents was only limited, the antifungal activity of the complete extracts is more promising, indicating synergism. Furthermore these plant extracts are also known to have anti-inflammatory activity and can stimulate wound-healing; characteristics which might also be of great value in the development of novel therapeutic drugs for this chronic inflammatory disease. Therefore further exploration of these plant species in the treatment of mycetoma is encouraging.


Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array.
Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology since they may contribute to the etiology of cancer, provide selective drug targets, or serve as a marker set for cancer diagnosis. While conventional identification of splice variants generally targets individual genes, we present here a new exon-centric array (GeneChip Human Exon 1.0 ST) that allows genome-wide identification of differential splice variation, and concurrently provides a flexible and inclusive analysis of gene expression. We analyzed 20 paired tumor-normal colon cancer samples using a microarray designed to detect over one million putative exons that can be virtually assembled into potential gene-level transcripts according to various levels of prior supporting evidence. Analysis of high confidence (empirically supported) transcripts identified 160 differentially expressed genes, with 42 genes occupying a network impacting cell proliferation and another twenty nine genes with unknown functions. A more speculative analysis, including transcripts based solely on computational prediction, produced another 160 differentially expressed genes, three-fourths of which have no previous annotation. We also present a comparison of gene signal estimations from the Exon 1.0 ST and the U133 Plus 2.0 arrays. Novel splicing events were predicted by experimental algorithms that compare the relative contribution of each exon to the cognate transcript intensity in each tissue. The resulting candidate splice variants were validated with RT-PCR. We found nine genes that were differentially spliced between colon tumors and normal colon tissues, several of which have not been previously implicated in cancer. Top scoring candidates from our analysis were also found to substantially overlap with EST-based bioinformatic predictions of alternative splicing in cancer. Differential expression of high confidence transcripts correlated extremely well with known cancer genes and pathways, suggesting that the more speculative transcripts, largely based solely on computational prediction and mostly with no previous annotation, might be novel targets in colon cancer. Five of the identified splicing events affect mediators of cytoskeletal organization (ACTN1, VCL, CALD1, CTTN, TPM1), two affect extracellular matrix proteins (FN1, COL6A3) and another participates in integrin signaling (SLC3A2). Altogether they form a pattern of colon-cancer specific alterations that may particularly impact cell motility.


Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.
Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA), Atypical, and leukocytes). Computer-assisted semen analysis (CASA) was also performed. Results showed that the most abundant genera among all samples were Lactobacillus (19.9%), Pseudomonas (9.85%), Prevotella (8.51%) and Gardnerella (4.21%). The proportion of Lactobacillus and Gardnerella was significantly higher in the normal samples, while that of Prevotella was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups: Lactobacillus, Pseudomonas, and Prevotella predominant group. Remarkably, most normal samples (80.6%) were clustered in Lactobacillus predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health. Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas. In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.


Children's nutrient intake at preschool and at home.
A preschool-based dietary survey, using 7-d records, was carried out in a suburb of Stockholm. The aim was to assess the intake of food and the quality of the diet of preschool children aged 3-5 y at preschool and at home, and to compare the dietary intake with the Swedish dietary recommendations for preschool children. The respective mean intakes of protein, fat, carbohydrates and sucrose, expressed as a percentage of total energy intake were 14, 38, 50 and 9 at preschool, and at home 14, 36, 52 and 12 on weekdays, 14, 34, 55 and 16 on weekend days. The mean intakes of seven vitamins and minerals were low only for selenium as compared with the recommended level. No differences were found in nutrient density between diet at preschool and diet at home, with the exception of dietary fibre (higher at preschool). On weekdays there was a significantly higher nutrient density for calcium, zinc, selenium, vitamin A, riboflavin, vitamin C and dietary fibre compared with weekend days. The average intakes of energy and nutrients per meal at preschool compared with the recommended levels for children aged 4-6 y were low for all meals (breakfast, lunch and afternoon snack). This, however, was compensated for by home meals.


Hospital nursing and 30-day readmissions among Medicare patients with heart failure, acute myocardial infarction, and pneumonia.
Provisions of the Affordable Care Act that increase hospitals' financial accountability for preventable readmissions have heightened interest in identifying system-level interventions to reduce readmissions. To determine the relationship between hospital nursing; that is, nurse work environment, nurse staffing levels, and nurse education, and 30-day readmissions among Medicare patients with heart failure, acute myocardial infarction, and pneumonia. Analysis of linked data from California, New Jersey, and Pennsylvania that included information on the organization of hospital nursing (ie, work environment, patient-to-nurse ratios, and proportion of nurses holding a BSN degree) from a survey of nurses, as well as patient discharge data, and American Hospital Association Annual Survey data. Robust logistic regression was used to estimate the relationship between nursing factors and 30-day readmission. Nearly 1 quarter of heart failure index admissions [23.3% (n=39,954)], 19.1% (n=12,131) of myocardial infarction admissions, and 17.8% (n=25,169) of pneumonia admissions were readmitted within 30 days. Each additional patient per nurse in the average nurse's workload was associated with a 7% higher odds of readmission for heart failure [odds ratio (OR)=1.07; confidence interval CI, 1.05-1.09], 6% for pneumonia patients (OR=1.06; CI, 1.03-1.09), and 9% for myocardial infarction patients (OR=1.09; CI, 1.05-1.13). Care in a hospital with a good versus poor work environment was associated with odds of readmission that were 7% lower for heart failure (OR=0.93; CI, 0.89-0.97), 6% lower for myocardial infarction (OR=0.94; CI, 0.88-0.98), and 10% lower for pneumonia (OR=0.90; CI, 0.85-0.96) patients. Improving nurses' work environments and staffing may be effective interventions for preventing readmissions.


Sequence analysis of the 5' non coding region of Turkish HCV isolates: implications for PCR diagnosis.
Hepatitis C virus (HCV) is a positive-strand RNA virus related to pestiviruses and flaviviruses. The 5' noncoding region (NCR) of the virus genome consists of 324-341 nucleotides and is generally highly conserved among different HCV isolates which has made this region the choice for primer selection in amplification of HCV sequences by polymerase chain reaction (PCR). In this study, we report the partial nucleotide sequences of the 5'-NCR from type 1a (n = 4), type 1b (n = 6) and type 4 (n = 1) Turkish HCV isolates. Sequence information was obtained by direct sequencing of RT-PCR product using biotinylated primers and single strands were sequenced using T7 DNA polymerase after binding to streptavidin coated magnetic beads. In comparison to prototype type 1a consensus sequence, all type 1b sequences had A-G substitution at position - 99. Nucleotid changes from the prototype 1a sequence were found in 12 of the 174 nucleotide positions. The most variable domain spans 51 nucleotides (positions - 167 to - 117) where nine polymorphic sites were identified. Although the nucleotide sequence of the 5'-noncoding region is highly conserved there are type-specific polymorphic sites within this region that has to be taken into consideration in the design of oligonucleotide primers for reliable amplification of sequences from different HCV genotypes.


Beet Stalks and Leaves (Beta vulgaris L.) Protect Against High-Fat Diet-Induced Oxidative Damage in the Liver in Mice.
Some flavonoids identified in beet stalks can help the antioxidant endogenous defenses during a chronic inflammation process. The current study investigates the effect of polyphenols present in beet stalks and leaves on liver oxidative damage in mice fed a high-fat diet (HF). The control (CT) or HF diet groups were supplemented with dehydrated beet stalks and leaves (SL) or beet stalk and leaf ethanolic extract (EX). In terms of Vitexin-rhaminoside equivalents (VRE), EX groups received ~5.91 mg of VRE·100 g−1 diet, while the SL groups received ~3.07 mg VRE·100 g−1 diet. After 8 weeks, we evaluated fasting blood glucose; cholesterol, hepatic Malondialdehyde (MDA) levels and hepatic Glutathione (GSH), Glutathione peroxidase (GPx), Glutathione reductase (GR) and Superoxide dismutase (SOD) activity. Dehydrated beet stalks and leaves (HFSL) attenuated the deleterious effects of a HF diet on lipid metabolism, reduced fasting blood glucose levels, ameliorated cholesterol levels and reduced GPx and GR activities (p < 0.05) compared to the HF group. However; the addition of ethanolic extract from beet stalks and leaves was unable (p > 0.05) to prevent the liver damage caused by HF diet in mice. The presence of flavonoids, such as Vitexin derivatives in beet stalks and leaves can help the liver damage induced by HF diet.