[Physical therapy education in Brazil: reflections on the expansion of teaching and training models].
This article on physical therapy education in Brazil focuses on the expansion of teaching, field of activities, and professional profile. The number of PT courses began multiplying rapidly in 1997, but the Sprocess lacked regulation and entailed both privatization of education and a geographic concentration of courses. This increase in both courses and trained physical therapists did not redound in greater access to PT services. The privatist curative-rehabilitation model that has been adopted is not appropriate to the new epidemiological reality or to current healthcare standards. Recent years have seen initiatives to bring change to physical therapy education and build a new professional profile.


The SIB Swiss Institute of Bioinformatics Semantic Web of data.
The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/) is a federation of bioinformatics research and service groups. The international life science community in academia and industry has been accessing the freely available databases provided by SIB since its inception in 1998. In this paper we present the 11 databases which currently offer semantically enriched data in accordance with the FAIR principles (Findable, Accessible, Interoperable, Reusable), as well as the Swiss Personalized Health Network initiative (SPHN) which also employs this enrichment. The semantic enrichment facilitates the manipulation of large data sets from public databases and private data sets. Examples are provided to illustrate that the data from the SIB databases can not only be queried using precise criteria individually, but also across multiple databases, including a variety of non-SIB databases. Data manipulation, be it exploration, extraction, annotation, combination, and publication, is possible using the SPARQL query language. Providing documentation, tutorials and sample queries makes it easier to navigate this web of semantic data. Through this paper, the reader will discover how the existing SIB knowledge graphs can be leveraged to tackle the complex biological or clinical questions that are being addressed today.


Stan and BART for Causal Inference: Estimating Heterogeneous Treatment Effects Using the Power of Stan and the Flexibility of Machine Learning.
A wide range of machine-learning-based approaches have been developed in the past decade, increasing our ability to accurately model nonlinear and nonadditive response surfaces. This has improved performance for inferential tasks such as estimating average treatment effects in situations where standard parametric models may not fit the data well. These methods have also shown promise for the related task of identifying heterogeneous treatment effects. However, the estimation of both overall and heterogeneous treatment effects can be hampered when data are structured within groups if we fail to correctly model the dependence between observations. Most machine learning methods do not readily accommodate such structure. This paper introduces a new algorithm, stan4bart, that combines the flexibility of Bayesian Additive Regression Trees (BART) for fitting nonlinear response surfaces with the computational and statistical efficiencies of using Stan for the parametric components of the model. We demonstrate how stan4bart can be used to estimate average, subgroup, and individual-level treatment effects with stronger performance than other flexible approaches that ignore the multilevel structure of the data as well as multilevel approaches that have strict parametric forms.


Hepatic Artery Anomalies in Pancreaticoduodenectomy: Outcomes from a High-Volume Center.
Hepatic artery anomalies (HAA) may have an impact on surgical and oncological outcomes of patients undergoing pancreaticoduodenectomy (PD). Patients who underwent PD at our institution between July 2015 and January 2020 were retrospectively reviewed and classified into two groups: group 1, with presence of HAA, and group 2, with no HAA. A weighted logistic regression model was employed to assess the association between HAA and postoperative complications, and to assess the association between HAA and R status in patients with pancreatic cancer. 502 patients were considered for analysis, with 75 (15%) of them in group 1. They had either an accessory (n = 28, 40.8%) or replaced (n = 26, 36.6%) right hepatic artery. Most patients underwent surgery for a malignancy (n = 451; 90%); among them, vascular resection was performed in 69 cases (15%). The presence of a HAA was reported at preoperative imaging only in 4 cases (5%) and the aberrant vessel was preserved in 72% of patients. At weighted multivariable logistic regression analysis, HAA were not associated to higher odds of morbidity (odds ratio [OR]: 0.753, 95% confidence interval [CI]: 0.543-1.043) nor to R1 status in case of pancreatic cancer (OR: 1.583, 95% CI: 0.979-2.561). At our institution, the presence of HAA does not have an impact on postoperative outcomes or affects oncological clearance after PD. Hospitals', surgeons', volume and systematic review of preoperative imaging are all factors that help reduce possible adverse events.


Sustained neuronal activity generated by glial plasticity.
Astrocytes release gliotransmitters, notably glutamate, that can affect neuronal and synaptic activity. In particular, astrocytic glutamate release results in the generation of NMDA receptor (NMDA-R)-mediated slow inward currents (SICs) in neurons. However, factors underlying the emergence of SICs and their physiological roles are essentially unknown. Here we show that, in acute slices of rat somatosensory thalamus, stimulation of lemniscal or cortical afferents results in a sustained increase of SICs in thalamocortical (TC) neurons that outlasts the duration of the stimulus by 1 h. This long-term enhancement of astrocytic glutamate release is induced by group I metabotropic glutamate receptors and is dependent on astrocytic intracellular calcium. Neuronal SICs are mediated by extrasynaptic NR2B subunit-containing NMDA-Rs and are capable of eliciting bursts. These are distinct from T-type Ca(2+) channel-dependent bursts of action potentials and are synchronized in neighboring TC neurons. These findings describe a previously unrecognized form of excitatory, nonsynaptic plasticity in the CNS that feeds forward to generate local neuronal firing long after stimulus termination.


Pediatric T-cell acute lymphoblastic leukemia.
The most common pediatric malignancy is acute lymphoblastic leukemia (ALL), of which T-cell ALL (T-ALL) comprises 10-15% of cases. T-ALL arises in the thymus from an immature thymocyte as a consequence of a stepwise accumulation of genetic and epigenetic aberrations. Crucial biological processes, such as differentiation, self-renewal capacity, proliferation, and apoptosis, are targeted and deranged by several types of neoplasia-associated genetic alteration, for example, translocations, deletions, and mutations of genes that code for proteins involved in signaling transduction, epigenetic regulation, and transcription. Epigenetically, T-ALL is characterized by gene expression changes caused by hypermethylation of tumor suppressor genes, histone modifications, and miRNA and lncRNA abnormalities. Although some genetic and gene expression patterns have been associated with certain clinical features, such as immunophenotypic subtype and outcome, none has of yet generally been implemented in clinical routine for treatment decisions. The recent advent of massive parallel sequencing technologies has dramatically increased our knowledge of the genetic blueprint of T-ALL, revealing numerous fusion genes as well as novel gene mutations. The challenges now are to integrate all genetic and epigenetic data into a coherent understanding of the pathogenesis of T-ALL and to translate the wealth of information gained in the last few years into clinical use in the form of improved risk stratification and targeted therapies. Here, we provide an overview of pediatric T-ALL with an emphasis on the acquired genetic alterations that result in this disease. © 2016 Wiley Periodicals, Inc.


Inhibiting the progression of arterial calcification with vitamin K in HemoDialysis patients (iPACK-HD) trial: rationale and study design for a randomized trial of vitamin K in patients with end stage kidney disease.
Cardiovascular disease, which is due in part to progressive vascular calcification, is the leading cause of death among patients with end stage kidney disease (ESKD) on dialysis. A role for vitamin K in the prevention of vascular calcification is plausible based on the presence of vitamin K dependent proteins in vascular tissue, including matrix gla protein (MGP). Evidence from animal models and observational studies support a role for vitamin K in the prevention of vascular calcification. A large-scale study is needed to investigate the effect of vitamin K supplementation on the progression of vascular calcification in patients with ESKD, a group at risk for sub-clinical vitamin K deficiency. We plan a prospective, randomized, double-blind, multicenter controlled trial of incident ESKD patients on hemodialysis in centers within North America. Eligible subjects with a baseline coronary artery calcium score of greater than or equal to 30 Agatston Units, will be randomly assigned to either the treatment group (10 mg of phylloquinone three times per week) or to the control group (placebo administration three times per week). The primary endpoint is the progression of coronary artery calcification defined as a greater than 15% increase in CAC score over baseline after 12 months. Vitamin K supplementation is a simple, safe and cost-effective nutritional strategy that can easily be integrated into patient care. If vitamin K reduces the progression of coronary artery calcification it may lead to decreased morbidity and mortality in men and women with ESKD. NCT 01528800.


Endovascular aortic devices: the Parodi and Palmaz system.
Based on the concept of endoluminal aneurysm exclusion, we began to develop a plan for endovascular treatment for abdominal aortic aneurysm (AAA) in 1976.Two prototypes have been developed and were marked by a high failure rate.' The first was a thin fabric graft mounted on a metallic cage-like structure composed by a self-expandable mesh with a zigzag configuration. The apparatus was compressed inside a tubular sheath, which acted as a vessel introducer and carrier. Experiments in normal canine aor- tas led to the abandonment of this prototype due to an inconsistent deployment of the metallic cage. The radial expansion properties of the cage were difficult to control and predict. Over-expansion resulted in aortic wall injury and subsequent rupture. Controversially, underexpansion led to leakage of blood be- tween the apparatus and the host aorta with subsequent device migrations. The second prototype involved a Dacron graft fitted on a Silastic bag with a cylindrical lumen, which could be distended by injection of silicone into the bag. Unfortunately, this method was associated with prompt graft thrombosis of the aorta in all experimental essays.


Investigating the role of Simpson's paradox in the analysis of top-ranked features in high-dimensional bioinformatics datasets.
An important problem in bioinformatics consists of identifying the most important features (or predictors), among a large number of features in a given classification dataset. This problem is often addressed by using a machine learning-based feature ranking method to identify a small set of top-ranked predictors (i.e. the most relevant features for classification). The large number of studies in this area has, however, an important limitation: they ignore the possibility that the top-ranked predictors occur in an instance of Simpson's paradox, where the positive or negative association between a predictor and a class variable reverses sign upon conditional on each of the values of a third (confounder) variable. In this work, we review and investigate the role of Simpson's paradox in the analysis of top-ranked predictors in high-dimensional bioinformatics datasets, in order to avoid the potential danger of misinterpreting an association between a predictor and the class variable. We perform computational experiments using four well-known feature ranking methods from the machine learning field and five high-dimensional datasets of ageing-related genes, where the predictors are Gene Ontology terms. The results show that occurrences of Simpson's paradox involving top-ranked predictors are much more common for one of the feature ranking methods.


Resting-state regional homogeneity as a biological marker for patients with Internet gaming disorder: A comparison with patients with alcohol use disorder and healthy controls.
Internet gaming disorder (IGD) shares core clinical features with other addictive disorders, such as gambling disorder and substance use disorder. Designation of IGD as a formal disorder requires elucidation of its neurobiological features and comparison of these with those of other addictive disorders. The aims of the present study were to identify the neurobiological features of the resting-state brain of patients with IGD, alcohol use disorder (AUD), and healthy controls, and to examine brain regions related to the clinical characteristics of IGD. Functional magnetic resonance imaging was performed on 16 subjects with IGD, 14 subjects with AUD, and 15 healthy controls during the resting-state. We computed regional homogeneity (ReHo) measures to identify intrinsic local connectivity and to explore associations with clinical status and impulsivity. We found significantly increased ReHo in the posterior cingulate cortex (PCC) of the IGD and AUD groups, and decreased ReHo in the right superior temporal gyrus (STG) of those with IGD, compared with the AUD and HC groups. We also found decreased ReHo in the anterior cingulate cortex of patients with AUD. Scores on Internet addiction severity were positively correlated with ReHo in the medial frontal cortex, precuneus/PCC, and left inferior temporal cortex (ITC) among those with IGD. Furthermore, impulsivity scores were negatively correlated with that in the left ITC in individuals with IGD. Our results provide evidence of distinctive functional changes in the resting-state of patients with IGD and demonstrate that increased ReHo in the PCC may be a common neurobiological feature of IGD and AUD and that reduced ReHo in the STG may be a candidate neurobiological marker for IGD, differentiating individuals with this disorder from those with AUD and healthy controls.


Kirkwood-Buff Integrals Using Molecular Simulation: Estimation of Surface Effects.
Kirkwood-Buff (KB) integrals provide a connection between microscopic properties and thermodynamic properties of multicomponent fluids. The estimation of KB integrals using molecular simulations of finite systems requires accounting for finite size effects. In the small system method, properties of finite subvolumes with different sizes embedded in a larger volume can be used to extrapolate to macroscopic thermodynamic properties. KB integrals computed from small subvolumes scale with the inverse size of the system. This scaling was used to find KB integrals in the thermodynamic limit. To reduce numerical inaccuracies that arise from this extrapolation, alternative approaches were considered in this work. Three methods for computing KB integrals in the thermodynamic limit from information of radial distribution functions (RDFs) of finite systems were compared. These methods allowed for the computation of surface effects. KB integrals and surface terms in the thermodynamic limit were computed for Lennard-Jones (LJ) and Weeks-Chandler-Andersen (WCA) fluids. It was found that all three methods converge to the same value. The main differentiating factor was the speed of convergence with system size L. The method that required the smallest size was the one which exploited the scaling of the finite volume KB integral multiplied by L. The relationship between KB integrals and surface effects was studied for a range of densities.


The management and clinical outcomes of pregnancies in women with urea cycle disorders: A review of the literature and results of an international survey.
An increasing number of women with urea cycle disorders (UCDs) are reaching child-bearing age and becoming pregnant. Improved diagnostics and increased awareness of inherited metabolic diseases has also led to more previously undetected women being diagnosed with a UCD during or shortly after pregnancy. Pregnancy increases the risk of acute metabolic decompensation with hyperammonemia-which can occur in any trimester, and/or the postpartum period, and may lead to encephalopathy, psychosis, coma, and even death, if not diagnosed promptly and treated appropriately. There are also (theoretical) concerns that a maternal UCD, or its treatment, may cause potential risks for the unborn child. Currently evidence on management and outcome of pregnancies in UCDs is limited to case reports and there are no clear guidelines. In order to inform management and investigate outcomes of pregnancies in women with a UCD, we performed a retrospective review of published cases and analyzed data collected from an international online survey. We conclude that, although risk during the intra- and postpartum period exists, multidisciplinary management by an experienced team and a prospective plan usually result in successful pregnancy, labor, delivery, and postpartum period. No deaths were reported in mothers managed accordingly. With the exception of male neonates with Ornithine Transcarbamylase deficiency, the clinical outcome of children born to mothers with UCDs appears positive, although follow-up is limited. The outcome for women presenting with a first acute metabolic decompensation during pregnancy or postpartum is less favorable. Deaths were associated with diagnostic delay/late management of hyperammonemia in previously undiagnosed women.


Tanshinone IIA inhibits human gastric carcinoma AGS cell growth by decreasing BiP, TCTP, Mcl‑1 and Bcl‑xL and increasing Bax and CHOP protein expression.
Tanshinone IIA (Tan-IIA) is extracted from Danshen (Salviae Miltiorrhizae Radix) and is a natural anti-cancer agent, which possesses antitumor activity in a variety of human cancer cells. Tan-IIA can induce apoptosis and inhibit the proliferation of gastric cancer through different molecular mechanisms. However, the efficacy and molecular mechanism of Tan-IIA in gastric cancer have not been well studied. In the present study, the cytotoxicity of Tan-IIA in human gastric cancer AGS cells by 3-(4,5-dimethylthiazol-2-y1)-2,5-diphenyltetrazolium bromide assay was examined. The protein expression levels of B-cell lymphoma-extra large (Bcl-xL), Bcl-2-associated X protein (Bax), myeloid cell leukemia 1 protein (Mcl-1), translationally-controlled tumor protein (TCTP), binding immunoglobulin protein (BiP), calnexin, protein kinase-like endoplasmic reticulum kinase, eIF2α, activating transcription factor 4 (ATF4), inositol-requiring enzyme 1α (IRE1α), ATF6, caspase-12, caspase-9, caspase-3, C/EBP-homologous protein (CHOP) and β-actin in AGS cells were measured by western blot analysis. The results showed that Tan-IIA inhibited AGS cells in a time-and dose-dependent manner. AGS cells treated with Tan-IIA upregulated the protein expression of caspase-12, caspase-9, caspase--3, CHOP and Bax, but downregulated the protein expression of BiP, TCTP, Mcl-1 and Bcl-xL. These findings indicated that Tan-IIA inhibits the growth of human gastric cancer AGS cells. One of the molecular mechanisms may be through decreasing the protein expression of BiP to induce the activation of endoplasmic reticulum stress, followed by increasing the protein expression of caspase-12 to upregulate CHOP expression. The other may be through decreasing the protein expression of Mcl-1, Bcl-xL and TCTP, but increasing Bax, caspase-9 and caspase-3 to induce apoptosis. The chemotherapeutic potential of Tan-IIA for human gastric cancer warrants further study in the future.


Women as consumers of maternity care: measuring "satisfaction" or "dissatisfaction"?
The measurement of "satisfaction" has been intrinsic to the models of evaluation of health care. However, a thoughtful approach to its use has not always been evident in which this concept is understood to represent a complex group of theoretical constructs involving attitudes, expectations, and perceptions that may be both positive and critical. These constructs require investigation and evaluation using recognized and developed methodologies. At the same time the importance of listening to patients and to women and their partners in evaluating and carrying out research on maternity care cannot be underestimated if the instruments used are to have construct and face validity. Qualitative data of this kind have a dual function of contributing to a more complex picture of women's experience and of suggesting that researchers need to explore the issues related to "dissatisfaction" at least as much as those arising from a positive overall view of care.


Worldwide trends in mortality from biliary tract malignancies.
Intrahepatic cholangiocarcinomas are malignant tumors arising from the intrahepatic biliary tract. The pathogenesis of these tumors remains unknown. Although there is a marked global variation in prevalence, some recent studies have suggested an increase in mortality from intrahepatic cholangiocarcinoma in several regions of low endemicity. As the study of mortality trends may yield clues to possible etiological factors, we analyzed worldwide time trends in mortality from biliary tract malignancies. Annual age-standardized rates for individual countries were compiled for deaths from biliary tract malignancies using the WHO database. These data were used to analyze gender and site-specific trends in mortality rates. An increasing trend for mortality from intrahepatic cholangiocarcinoma was noted in most countries. The average estimated annual percentage change (EAPC) in mortality rates for males was 6.9 +/- 1.5, and for females was 5.1 +/- 1.0. Increased mortality rates were observed in all geographic regions. Within Europe, increases were higher in Western Europe than in Central or Northern Europe. In contrast, mortality rates for extrahepatic biliary tract malignancies showed a decreasing trend in most countries, with an overall average EAPC of -0.3 +/- 0.4 for males, but -1.3 +/- 0.4 for females. There has been a marked global increase in mortality from intrahepatic, but not extra-hepatic, biliary tract malignancies.


Predictors of a Good Diuretic Response and Administration Methods for Carperitide in Patients With Acute Heart Failure.
In Japan, carperitide has been recommended for the treatment of pulmonary congestion in patients with acute heart failure. Identifying useful indicators to support the decision to administer carperitide and the optimal timing of administration may lead to better improvement of pulmonary congestion. Therefore, we investigated the factors associated with good diuretic response to carperitide in patients with acute heart failure and the optimal timing of carperitide administration. This retrospective cohort study investigated 293 hospitalized patients who were diagnosed with acute heart failure and treated with carperitide at the Department of Cardiology, Showa University Fujigaoka Hospital. The primary endpoint was the diuretic response to carperitide. Patients with urine output ≥100 mL/h were defined as the good diuretic response group, and those with a urine output <100 mL/h during the first 6 hours of carperitide administration were defined as the poor diuretic response group. Multivariate analysis was used to examine the predictors of good diuretic response. The relationship between the time from intravenous furosemide to carperitide administration and urine output was also investigated. The patients' median age was 77 (range: 28-99) years, and 75.5% had New York Heart Association stage IV acute heart failure. The median urine output within 6 hours of carperitide administration was 104.5 (range: 6.6-1571.3) mL/h, and 118 patients (53.6%) showed a good diuretic response. Significant predictors of good diuretic response were age < 75 years [odds ratio (OR) 4.186; 95% confidence interval (CI), 2.129-8.230; P < 0.001], no prior use of loop diuretics (OR 2.155; 95% CI, 1.104-4.207; P = 0.024), blood urea nitrogen <20 mg/dL (OR 2.637; 95% CI, 1.340-5.190; P = 0.005), and white blood cell count <8.6 × 109/L (OR 3.162; 95% CI, 1.628-6.140; P = 0.001). The median urine output in the group with <2 hours between intravenous furosemide and carperitide administration was significantly higher than that in the group with an interval >6 hours [127.3; interquartile range (IQR), 77.6-216.2 mL/h vs. 66.2; IQR. 51.8-114.8 mL/h; P = 0.012). The 4 predictors (age, no prior use of loop diuretics, blood urea nitrogen, and white blood cell count) of good diuretic response are useful indicators to support decision-making for carperitide administration. Additionally, the administration of carperitide within 2 hours of intravenous furosemide may lead to the improvement of pulmonary congestion.


Use of performance standards in behavioral health carve-out contracts among Fortune 500 firms.
To determine the prevalence and nature of performance standards in specialty managed behavioral healthcare contracts among Fortune 500 companies. This was a cross-sectional survey of all companies listed on the Fortune 500 during 1994, 1995, or both. From April 1997 to May 1998 we conducted a mailed survey with phone follow-up. Of the 68% of firms that responded, over one third reported carve-out contracts. The survey focused on whether companies had behavioral health carve-out contracts with specialty vendors and characteristics of these contracts, including the use of performance standards. More than three quarters of the Fortune 500 companies reporting specialty behavioral healthcare contracts used at least one performance standard. Most common were administrative standards (70.2%) and customer service standards (69.4%). About half of the companies used quality standards, whereas only a third used provider-related standards. Most (58.8%) companies using performance standards also specified financial consequences. Larger Fortune 500 firms were significantly more likely to use performance standards. Risk contracts and contracts that included all covered employees were also more likely to include some categories of standards. Administrative and customer service standards may be most common because companies find it easier to specify those standards, especially compared with clinical quality measures. To the extent that employers want to obtain the most value from their behavioral healthcare purchasing, we expect that more will begin to adopt quality standards in their contracts, especially as performance measures become more refined. Reliance on accreditation, however, is an alternative approach for employers.


Far lateral approaches (XLIF) in adult scoliosis.
To review the literature on the use of extreme lateral interbody fusion (XLIF) in adult spinal deformity, to discuss on its limits and advantages and to propose a guide to surgical strategy. Surgical technique XLIF is a minimally invasive surgery (MIS) technique to anteriorly access the spine from midthoracic to L5. Important aspects of the technique are a muscle splitting approach through the psoas, use of advanced neuromonitoring to detect the lumbar plexus within the psoas, bilateral annulus release and large footprint interbody cages, supported by the stronger bone of ring apophyses. Large, laterally inserted cages provide strong correction of coronally asymmetrical disc spaces. Literature review MEDLINE database, the Web using Google Scholar and proceedings of the Society for Lateral Access Surgery meetings were searched for relevant articles on technique, results and complications. XLIF with posterior percutaneous pedicle screw instrumentation provides 40-75 % correction of coronal curves, with modest increase of lordosis. Only anterior XLIF can provide less correction. Self-limited thigh symptoms are frequent after transpsoas access. Permanent neural deficit and visceral complications have also been reported. Combined XLIF-MIS could have a lower complication compared to open circumferential surgery in historical series. XLIF is a promising MIS option for adult deformity. Specific surgical strategies are needed to avoid imbalance and define ideal fusion levels and methods. An XLIF-based MIS strategy with a reduced number of levels of lumbar scoliosis can lead to significant advantages. Evaluation of the incidence, complications, their avoidance and real impact on patients' outcomes is necessary to better understand the advantages of this approach. Studies comparing effectiveness and safety of traditional versus XLIF approaches are needed to assist evidence-based decision making.


Study of correlation between the NAT2 phenotype and genotype status among Greenlandic Inuit.
N-acetyltransferase 2 (NAT2) is the main enzyme metabolizing isoniazid and genotype-based treatment has been studied for years without becoming common practice. To investigate whether genotype-based isoniazid treatment is feasible in Greenland, we sequenced the coding sequence of NAT2 and determined the NAT2 enzyme-activity by caffeine test. No additional genetic variants were identified in the coding sequence of NAT2, so that genotype status in 260 study participants could be assessed by a well-established 7-SNP panel. Studying the enzyme activity by the ratio of the two caffeine metabolites AFMU and 1X in 260 participants showed a high rate of slow phenotypes with intermediate or rapid genotype. These misclassifications were mainly observed in urine samples with pH<3, a deviation from the standard protocol due to the field work character of the study, where immediate pH adjustment to pH=3.5 was not possible. We excluded these samples. For the remaining 143 individuals with pH>3, we observed a moderate level of discrepancies (19 of the 116 individuals with intermediate or rapid genotype status having a slow phenotype). Further investigation showed that drinking coffee and not tea or cola was the most important factor for high levels of both metabolites. The concordance between phenotype and genotype status with regard to slow metabolism supported the recommendation of lower isoniazid doses in individuals with slow genotype status in order to avoid liver injury, a frequent side effect. The phenotypical variation observed for individuals with intermediate or rapid genotype status warrants further research before increased dosing of isoniazid can be recommended.


Changes in iron availability in Arabidopsis are rapidly sensed in the leaf vasculature and impaired sensing leads to opposite transcriptional programs in leaves and roots.
The OLIGOPEPTIDE TRANSPORTER 3 (OPT3) has recently been identified as a component of the systemic network mediating iron (Fe) deficiency responses in Arabidopsis. Reduced expression of OPT3 induces an over accumulation of Fe in roots and leaves, due in part by an elevated expression of the IRON-REGULATED TRANSPORTER 1. Here we show however, that opt3 leaves display a transcriptional program consistent with an Fe overload, suggesting that Fe excess is properly sensed in opt3 leaves and that the OPT3-mediated shoot-to-root signaling is critical to prevent a systemic Fe overload. We also took advantage of the tissue-specific localization of OPT3, together with other Fe-responsive genes, to determine the timing and location of early transcriptional events during Fe limitation and resupply. Our results show that the leaf vasculature responds more rapidly than roots to both Fe deprivation and resupply, suggesting that the leaf vasculature is within the first tissues that sense and respond to changes in Fe availability. Our data highlight the importance of the leaf vasculature in Fe homeostasis by sensing changes in apoplastic levels of Fe coming through the xylem and relaying this information back to roots via the phloem to regulate Fe uptake at the root level.


Cytotoxic T cells in teleost fish.
The presence of antigen-specific cytotoxic T cells has been suggested in a number of in vivo and in vitro studies in fish. Acute allograft rejection with an accelerated response on second-set grafts and the presence of graft-versus-host reaction (GVHR) has been reported in teleost. Alloantigen- and virus-specific cytotoxicity has also been demonstrated in ex vivo studies in ginbuna and rainbow trout. In addition, alloantigen-specific cytotoxic T cell clones have been produced in cultures initiated with peripheral blood leukocytes (PBL) from an alloantigen-immunized channel catfish. Over the last decade several fish genomes have been sequenced and genetic information is rapidly accumulating. Thanks to these genome data bases and EST analysis, mRNA expression of T cell surface marker genes in alloantigen- or virus-specific effector cells has been reported in some fish species, e.g. TCR α or β and CD8α in ginbuna and rainbow trout, and TCR α, β or γ in channel catfish. These findings suggest the presence of CD8(+) cytotoxic T lymphocyte (CTL) in fish similar to those of higher vertebrates. Recently, monoclonal antibodies against CD8α and CD4 antigens have been produced in some fish species. Investigation on the characteristics of CTL and cell-mediated immune mechanisms is now possible at defined T cell subsets, although identification of T cell subset is limited in a few fish species at present. In this review, we describe the recent progress in this field focusing on cells involved in antigen specific cytotoxicity.


Satisfaction With Elimination of all Visitation Restrictions in a Mixed-Profile Intensive Care Unit.
Open and patient-tailored guidelines have been recommended as the preferred visitation model in critical care settings; however, many critical care units continue to restrict visitation. To determine whether a transition from minimally restrictive to unrestricted visitation hours improves satisfaction of patients' family members and whether such a transition affects nurses' satisfaction and nurses' perceptions of satisfaction among patients' families. Using a prospective, observational design in a 24-bed intensive care unit in a tertiary care hospital, validated instruments were used to survey family members visiting patients and all nurses working in the unit before and after a change in the visitation policy. Visitation hour guidelines were changed from closed during nursing hand-off report (3 hours daily) to open at all times, depending on patients' preference and clinical status. One hundred three family members (50 before and 53 after the change in visitation guidelines) and 128 nurses (61 before and 67 after the policy change) were surveyed. Unrestricted visitation hours significantly improved family members' satisfaction with the convenience of visitation hours and waiting room ambiance, and nurses' perceptions of families' satisfaction also improved. Elimination of even minimal restrictions on visitation hours improved family satisfaction and improved nurses' perceptions of family satisfaction with the visitation policy. Nurses' satisfaction did not change. These findings support open and patient-centered visitation guidelines in critical care settings.


Renal epithelial cells produce and spread HIV-1 via T-cell contact.
Increasing evidence supports the role of the kidney as a reservoir for HIV-1. In-vitro co-cultivation of HIV-infected T cells with renal tubule epithelial (RTE) cells results in virus transfer to the latter, whereas cell-free virus infection is inefficient. We further characterized the fate of HIV-1 after it is internalized in renal epithelial cells. Primary or immortalized CD4 cells were infected with a green fluorescent protein (GFP)-expressing replication competent HIV-1. HIV-1 transfer from T cells to RTE cells was carried out in a co-culture system and evaluated by fluorescence-activated cell sorting analysis. HIV-1 integration in renal cells was evaluated by Alu-PCR and the production of infectious particles was assessed by p24-ELISA and TZM-bl assay. HIV-infected renal cells were used as donor cells in a co-culture system to evaluate their ability to transfer the virus back to T cells. Renal cells become productively infected by HIV-1 and multiple copies of HIV-1 can be transferred from infected T cells to renal cells. Two separate cell populations were identified among infected renal cells based on reporter gene GFP expression level (low vs. high), only the high showing sensitivity to azidothymidine and ritonavir. Co-cultivation of HIV-1-infected renal cells with noninfected T cells resulted in HIV-1 transmission to T cells, supporting bidirectional exchange of virus between T cells and kidney-derived cells. Persistent expression and generation of infectious virus in renal cells required HIV integration. These results support the kidney as a potential reservoir where virus is exchanged between interstitial T cells and RTE cells.


Iterative hard thresholding in genome-wide association studies: Generalized linear models, prior weights, and double sparsity.
Consecutive testing of single nucleotide polymorphisms (SNPs) is usually employed to identify genetic variants associated with complex traits. Ideally one should model all covariates in unison, but most existing analysis methods for genome-wide association studies (GWAS) perform only univariate regression. We extend and efficiently implement iterative hard thresholding (IHT) for multiple regression, treating all SNPs simultaneously. Our extensions accommodate generalized linear models, prior information on genetic variants, and grouping of variants. In our simulations, IHT recovers up to 30% more true predictors than SNP-by-SNP association testing and exhibits a 2-3 orders of magnitude decrease in false-positive rates compared with lasso regression. We also test IHT on the UK Biobank hypertension phenotypes and the Northern Finland Birth Cohort of 1966 cardiovascular phenotypes. We find that IHT scales to the large datasets of contemporary human genetics and recovers the plausible genetic variants identified by previous studies. Our real data analysis and simulation studies suggest that IHT can (i) recover highly correlated predictors, (ii) avoid over-fitting, (iii) deliver better true-positive and false-positive rates than either marginal testing or lasso regression, (iv) recover unbiased regression coefficients, (v) exploit prior information and group-sparsity, and (vi) be used with biobank-sized datasets. Although these advances are studied for genome-wide association studies inference, our extensions are pertinent to other regression problems with large numbers of predictors.


Preferences for results delivery from exome sequencing/genome sequencing.
The aim of this study was to explore the implications of sequencing information and stated preferences for return of results among research participants. Six focus groups were held with 39 ClinSeq participants. The groups included participants who had received results, those who had not, those affected with cardiovascular disease, and healthy adults. Audio recordings of the sessions were transcribed and coded and analyzed for themes. All participants expressed interest in receiving results that are medically actionable, nonactionable, carrier, and less so variants that cannot be interpreted. Most participants preferred to receive results in person, although several endorsed use of Internet-based resources that they could return to. Participants identified benefits for health management along with satisfying curiosity, making scientific contributions, and partnering in research. Value was seen in gaining control over health risks. Concerns were distress and/or fear that may result. Some participants were opposed to or ambivalent about learning certain types of results, particularly those having to do with diseases that were incurable or that might have implications for the health of their children. There was relative enthusiasm about the value of learning sequencing information, yet it was tempered by concern about negative feeling responses and aversion to learning about incurable conditions.


Placental transfer of long-chain polyunsaturated fatty acids (LC-PUFA).
Considerable evidence exists for marked beneficial effects of omega-3 long-chain polyunsaturated fatty acids (LC-PUFA) during pregnancy. The omega-3 LC-PUFA docosahexaenoic acid (DHA) is incorporated in large amounts in fetal brain and other tissues during the second half of pregnancy, and several studies have provided evidence for a link between early DHA status of the mother and visual and cognitive development of her child after birth. Moreover, the supplementation of omega-3 LC-PUFA during pregnancy increases slightly infant size at birth, and significantly reduces early preterm birth before 34 weeks of gestation by 31%. In our studies using stable isotope methodology in vivo, we demonstrated active and preferential materno-fetal transfer of DHA across the human placenta and found the expression of human placental fatty acid binding and transport proteins. From the correlation of DHA values with placental fatty acid transport protein 4 (FATP 4), we conclude that this protein is of key importance in mediating DHA transport across the human placenta. Given the great importance of placental DHA transport for infant outcome, further studies are needed to fully appreciate the effects and optimal strategies of omega-3 fatty acid interventions in pregnancy, dose response relationships, and the potential differences between subgroups of subjects such as women with gestational diabetes or other gestational pathology. Such studies should contribute to optimize substrate intake during pregnancy and lactation that may improve pregnancy outcome as well as fetal growth and development.


Controlling aminosilane layer thickness to extend the plasma half-life of stealth persistent luminescence nanoparticles in vivo.
Therapeutics and diagnostics both initiated the development and rational design of nanoparticles intended for biomedical applications. Yet, the fate of these nanosystems in vivo is hardly manageable and generally results in their rapid uptake by the mononuclear phagocyte system, i.e. liver and spleen. To overcome this essential limitation, efforts have been made to understand the influence of physico-chemical parameters on the behaviour of nanoparticles in vivo and on their ability to be uptaken by phagocytic cells. Notably, polyethylene glycol grafting and precise control of its density have not only been shown to prevent protein adsorption on the surface of nanoparticles, but also to significantly reduce macrophage uptake in vitro. In this article, we suggest the use of persistent luminescence to study the influence of another parameter, aminosilane layer thickness, on both in vitro protein adsorption and in vivo biodistribution of stealth persistent nanophosphors.


Chronic Exposure to Paraquat Induces Alpha-Synuclein Pathogenic Modifications in Drosophila.
Parkinson's disease (PD) is characterized by the progressive accumulation of neuronal intracellular aggregates largely composed of alpha-Synuclein (αSyn) protein. The process of αSyn aggregation is induced during aging and enhanced by environmental stresses, such as the exposure to pesticides. Paraquat (PQ) is an herbicide which has been widely used in agriculture and associated with PD. PQ is known to cause an increased oxidative stress in exposed individuals but the consequences of such stress on αSyn conformation remains poorly understood. To study αSyn pathogenic modifications in response to PQ, we exposed Drosophila expressing human αSyn to a chronic PQ protocol. We first showed that PQ exposure and αSyn expression synergistically induced fly mortality. The exposure to PQ was also associated with increased levels of total and phosphorylated forms of αSyn in the Drosophila brain. Interestingly, PQ increased the detection of soluble αSyn in highly denaturating buffer but did not increase αSyn resistance to proteinase K digestion. These results suggest that PQ induces the accumulation of toxic soluble and misfolded forms of αSyn but that these toxic forms do not form fibrils or aggregates that are detected by the proteinase K assay. Collectively, our results demonstrate that Drosophila can be used to study the effect of PQ or other environmental neurotoxins on αSyn driven pathology.


Frequent optical imaging during breast cancer neoadjuvant chemotherapy reveals dynamic tumor physiology in an individual patient.
Imaging tumor response to neoadjuvant chemotherapy in vivo offers unique opportunities for patient care and clinical decision-making. Detailed imaging studies may allow oncologists to optimize therapeutic drug type and dose based on individual patient response. Most radiologic methods are used sparingly because of cost; thus, important functional information about tumor response dynamics may be missed. In addition, current clinical standards are based on determining tumor size changes; thus, standard anatomic imaging may be insensitive to early or frequent biochemical responses. Because optical methods provide functional imaging end points, our objective is to develop a low-barrier-to-access bedside approach that can be used for frequent, functional assessment of dynamic tumor physiology in individual patients. Diffuse Optical Spectroscopic Imaging (DOSI) is a noninvasive, bedside functional imaging technique that quantifies the concentration and molecular state of tissue hemoglobin, water, and lipid. Pilot clinical studies have shown that DOSI may be a useful tool for quantifying neoadjuvant chemotherapy response, typically by comparing the degree of change in tumor water and deoxy-hemoglobin concentration before and after therapy. Patient responses at 1 week and mid-therapy have been used to predict clinical outcome. In this report, we assess the potential value of frequent DOSI monitoring by performing measurements on 19 different days in a 51-year-old subject with infiltrating ductal carcinoma (initial tumor size 60 x 27 mm) who received neoadjuvant chemotherapy (anthracyclines and bevacizumab) over an 18-week period. A composite index, the Tissue Optical Index (TOI), showed a significant ( approximately 50%) decrease over the nearly 18 weeks of chemotherapy. Tumor response was sensitive to the type of chemotherapy agent, and functional indices fluctuated in a manner consistent with dynamic tumor physiology. Final pathology revealed 4 mm of residual disease, which was detectible by DOSI at the conclusion of chemotherapy before surgery. This case study suggests that DOSI may be a bedside-capable tool for frequent longitudinal monitoring of therapeutic functional response to neoadjuvant chemotherapy.


A small omnivorous bitterling fish (Acheilognathus macropterus) facilitates dominance of cyanobacteria, rotifers and Limnodrilus in an outdoor mesocosm experiment.
Small omnivorous fish often dominate in subtropical shallow lakes, and they may affect the community structure of aquatic organisms on at least two trophic levels. However, in the study of aquatic food webs in subtropical lakes, most ecologists have focused on the effects of large-sized omnivorous species (e.g. common carp), studies of small-sized species being scarce. We conducted a mesocosm experiment with two treatments (fish presence and absence) to examine the effects of a small-sized omnivore, bitterling (Acheilognathus macropterus), on phytoplankton, zooplankton and benthic macroinvertebrates. Our results showed that bitterling presence significantly increased the chlorophyll a concentration and biomass of phytoplankton, which became dominated by cyanobacteria (mainly Aphanizomenon spp.) that accounted for >99% of both total phytoplankton abundance and biomass. Both the abundance and biomass of zooplankton were also higher in the fish-present treatment, but small rotifers became dominant, and the zooplankton:phytoplankton biomass ratio decreased, indicating less grazing on phytoplankton. Moreover, both the abundance and biomass of benthic macroinvertebrates (tubificids) were higher in the bitterling-present treatment than in the controls, which is opposite to the situation found when omni-benthivorous fish (e.g. crucian carp) dominate. Higher biomass of tubificids may, in turn, result in higher sediment nutrient release. Our study suggests that A. macropterus, and maybe also other bitterling species, can alter both pelagic and benthic assemblages via both top-down and bottom-up control effects and lead to more turbid water in eutrophic lakes. Thus, more attention should be paid to these small omnivorous species in the restoration and management of shallow subtropical lakes.


Quantitative evaluation of the benefit of fiducial image-guidance for prostate cancer intensity modulated radiation therapy using daily dose volume histogram analysis.
To quantitatively evaluate the extent to which fiducial-based image-guidance improves dose coverage of the target volume and sparing of critical organs for prostate cancer patients treated with intensity modulated radiotherapy (IMRT) and determination of planning margins by original approach of detailed daily dose volume histogram (DVH) and patient's position correction analysis. Sixty-two patients divided in two groups (clinical target volume (CTV) → planning target volume (PTV) margin 10 and 7 mm) were treated with IMRT using implanted fiducial markers. Each patient's treatment fraction was recalculated as it would have been treated without fiducial-guided positioning. For both plans (IGRT and non-IGRT), equivalent uniform doses (EUD), maximal and minimal doses for target volumes, normal tissue complication probability (NTCP), maximum and mean doses for organs at risk and the whole DVH differences were assessed. In the group with 10 mm margins, the only significant difference was worse rectal NTCP by 4.5%, but the CTV dose coverage remained at the same level. Recalculated plans with 7 mm margin could not achieve the prescribed target volume coverage, and the EUD decreased by 3.7 and 0.6 Gy for PTV and CTV, respectively. Desired CTV → PTV margin for non-IGRT plans should be no lower than 12 mm to guarantee 95% instances when delivered dose to CTV maintain as planned, for IGRT plans decrease this requirement to 2 mm. Prostate IMRT strategies involving margin reduction below 7 mm require image-guidance to maintain the planned dose coverage. Using fiducial-based image-guidance and large margins seems to be superfluous.


Effects of forest management on vertebrates: synthesizing two decades of data from hardwood forests in Missouri, USA.
Modern forest management seeks to balance multiple social, economic, and ecological goals. Different management approaches create different types of disturbances in a forest ecosystem and thus also differ in their impacts on plants, animals, and insects. Understanding these impacts is important for conservation of forest ecosystem function, but challenging due to the large spatial and temporal scale over which management occurs. Most past research has focused on relatively small areas, short time scales, and/or a small number of species. To address this, we examined the effects of two common silvicultural systems (even and uneven aged) on abundance and richness of three vertebrate taxa (birds, small mammals, and herpetofauna) over a two-decade period in a temperate hardwood forest in Missouri, USA. The two systems removed a similar amount of biomass overall, but differed in the intensity, number, and configuration of harvests applied. We found that vertebrate population responses varied by taxa, occurred at multiple spatial scales, and were concentrated in the period following the first harvest entry. Birds generally had the largest changes in relative abundance, both positive and negative, following management. Small mammals and reptiles had smaller, but generally positive, responses; amphibians were mixed. Bird species tended to respond in the same way to both silvicultural systems, while small mammals and herpetofauna did not respond consistently. Thus, for birds, the total amount of harvest disturbance across the landscape drives population responses, while for others the size and configuration of individual harvests is likely more important. Synthesizing results across the vertebrate community at large spatial and temporal scales allows managers to better understand trade-offs when making decisions that will affect wildlife in contrasting ways.


Potential of preparing cement clinker by adding the fluorine-containing sludge into raw meal.
Fluorine-containing sludge from semiconductor industries were one kind of hazardous wastes, there was hardly effective treatment to realize its safe disposal and utilization. This paper evaluated the potential of preparing cement clinker by adding the sludge into raw meal by a series of experiments. The results revealed 2.0 % addition of the sludge markedly improved the burnability of the produced clinker, and promoted the formation of alite with more amounts and smaller size, but the 5.0 % addition of the sludge resulted in the abundant formation of interstitial phases to inhibit the formation of alite and belite. The better workability was gained with the addition of 2.0 %, and the optimal 28 d compressive strength was 50.76 MPa. The distribution of fluorine was higher in silicate phases, and it was mainly accumulated in the interfaces of silicate phases. Fluorine in the sludge was immobilized by calcium to form the binding forms of calcium fluoride in produced clinker and hydration products. The immobilization ratios of fluorine, copper, zinc and nickel were more than 99.5 %, and the addition of the sludge (≤5.0 %) into raw meal could not induce further environment hazards.


All-trans retinoic acid reduces cancer stem cell-like cell-mediated resistance to gefitinib in NSCLC adenocarcinoma cells.
The enrichment of cancer stem cell-like cells (CSCs) has been considered to be responsible for tumor progression after an initial response to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (EGFR-TKIs) in patients with non-small cell lung adenocarcinoma (NSCLC/ADC). CSCs with ALDH1A1bright /CD44high expression contribute to the TKIs resistance in NSCLC/ADC cells. All-trans retinoic acid (ATRA) has been shown to be a potential targeted therapy against CSCs due to its ability to inhibit ALDH1A1 activity. We therefore investigated whether ATRA could circumvent the resistance to improve the response to gefitinib in NSCLC/ADC cells. Treatment of NSCLC/ADC A549 and H1650 cells with gefitinib enriched the gefitinib surviving cells (GSCs). The expression of ALDH1A1 and CD44 and the IC50 values for gefitinib were determined by flow cytometry (FCM) and crystal violet assay in GSCs and ATRA-treated GSCs, respectively. Using DEAB as the positive control, direct inhibitory effect of ATRA on ALDH1A1 activity was determined by ALDEFLUOR assay, RESULTS: GSCs showed higher expression of ALDH1A1 and CD44 and IC50 values for gefitinib than their respective parental cells, suggesting that gefitinib can lead to propagation of CSC-enriched gefitinib-resistant cells. Treatment with ATRA was found to significantly reduce the increased expression of ALDH1A1 and CD44 and the IC50 values for gefitinib in A549GSC and H1650GSC cells, and ATRA could directly inhibit active ALDH1A1 as compared to DEAB. Our findings suggest that combination treatment with ATRA prevents gefitinib-induced enrichment of ALDH1A1bright/CD44high CSCs and enhances gefitinib-induced growth inhibition of NSCLC/ADC cells.


Photovoltaic materials.
Solid-state photovoltaic cells are feasible devices for converting solar energy directly to electricity. Recent cost reductions have spurred an incipient industry, but further advances in materials science and technology are needed before photovoltaic cells can compete with other sources for the supply of large amounts of energy. In this article energy loss mechanisms in solid-state photovoltaic cells are examined and related to materials properties. Various systems under development are reviewed which illustrate some key concepts, opportunities, and problems of this most promising emerging technology. Areas where contributions from innovative materials research would have a significant effect are also indicated.


Analytical studies on tobacco-specific N-nitrosamines in tobacco and tobacco smoke.
Chemical-analytical studies have led to the identification of approximately 3000 compounds in tobacco and 4000 in tobacco smoke. These include carcinogens in processed tobacco as well as tumor initiators, tumor promoters, cocarcinogens, and organ-specific carcinogens in tobacco smoke. The latter group includes N-nitrosamines, in particular those that derive from nicotine and other tobacco alkaloids, the TSNA. In vitro nitrosation of nicotine yields NNN, NNA, and NNK. Nitrosation of other tobacco alkaloids leads to the formation of NAT, and NAB. Our analytical studies using GC-TEA have led to the identification of seven TSNA in tobacco and tobacco smoke. In addition to NNN, NAT, NAB, and NNK, we also identified NNAL, iso-NNAL, and, most recently, iso-NNAC. Their levels range from 0.01 to 92 ppm in tobacco and from 6 to 530 ng/cigarette in tobacco smoke. The high levels observed in snuff are primarily due to fermentation and aging. Technological methods exist today to reduce the levels of TSNA in both tobacco and cigarette smoke.


Stem cell origins and animal models of hepatocellular carcinoma.
Hepatocellular carcinoma (HCC) is a common malignant tumor that almost always occurs within a preexisting background of chronic liver disease and cirrhosis. Currently, medical therapy is not effective in treating most HCC, and the only hope of cure is either resection or liver transplantation. A small minority of patients is eligible for these therapies, which entail major morbidity at the very least. In spite of immense scientific advances during the past 3 decades, patient survival has improved very little. In order to reduce morbidity and mortality from HCC, improvements in early diagnosis and development of novel local and systemic therapies for advanced disease are essential, in addition to efforts geared towards primary prevention. Studies with experimental animal models that closely mimic human disease are very valuable in understanding physiological, cellular and molecular mechanisms underlying the disease. Furthermore, appropriate animal models have the potential to increase our understanding of the effects of image-guided minimally invasive therapies and thereby help to improve such therapies. In this review, we examine the evidence for stem cell origins of such tumors, critically evaluate existing models and reflect on how to develop new models for minimally invasive, image-guided treatment of HCC.


The regulatory connection between the activity of granule cell NMDA receptors and dendritic differentiation of cerebellar Purkinje cells.
It is known that cerebellar granule cells are powerful inducers for the differentiation of Purkinje cells. However, the detailed mechanism of this regulation has not yet been clarified. Here, using cerebellar neuronal culture, we show that the activation of NMDA receptors expressed by granule cells triggers the signaling pathway for the dendritic differentiation of Purkinje cells. This signal has been shown to promote the granule cell survival through BDNF-mediated TrkB activation, leading to Purkinje cell differentiation by increasing the granule-Purkinje cell interaction. Among the possible signal molecules provided to the dendrites of Purkinje cells from granule cells, nitric oxide was found to have no effect on the dendritic outgrowth and branching, but electrical activity and the subsequent intracellular Ca(2+) increase were thought to play an important role in the branching and thickening of the dendrites, because blockade of both non-NMDA and metabotropic glutamate receptors caused a significant decrease in the number of branch points and the diameter of Purkinje dendrites without apparently affecting the dendrite extension and spine formation. Collectively, these results suggest that Purkinje cell differentiation is regulated by two successive steps. The first step is initiated by the NMDA receptor-mediated signal in granule cells, which acts as a trophic factor for granule cells. The second step involves the activation of granule-Purkinje synapses, providing neurotrophic substances and electrical activity essential for Purkinje cell differentiation.


Micronuclei and pesticide exposure.
Micronucleus (MN) is a biomarker widely used in biomonitoring studies carried out to determine the genetic risk associated to pesticide exposure. Many in vitro and in vivo studies, as well as epidemiological approaches, have demonstrated the ability of certain chemical pesticides to produce genetic effects including cancer and other chronic pathologies in humans; thus, biomonitoring studies have been carried out to characterise the genetic risk associated to pesticide exposure. It must be noted that 'pesticide exposure' is a broad term covering complex mixtures of chemicals and many variables that can reduce or potentiate their risk. In addition, there are large differences in pesticides used in the different parts of the world. Although pesticides constitute a wide group of environmental pollutants, the main focus on their risk has been addressed to people using pesticides in their working places, at the chemical industry or in the crop fields. Here, we present a brief review of biomonitoring studies carried out in people occupationally exposed to pesticides and that use MN in lymphocytes or buccal cells as a target to determine the induction of genotoxic damage. Thus, people working in the chemical industry producing pesticides, people spraying pesticides and people dedicated to floriculture or agricultural works in general are the subject of specific sections. MN is a valuable genotoxic end point when clear exposure conditions exist like in pesticide production workers; nevertheless, better study designs are needed to overcome the uncertainty in exposure, genetic susceptibility and statistical power in the studies of sprayers and floriculture or agricultural workers.


What is the role of ovarian ablation in the management of primary and metastatic breast cancer today?
Ovarian ablation has been used for more than a century in the treatment of breast cancer. Methods of irreversible ovarian ablation include surgical oophorectomy and ovarian irradiation. Potentially reversible castration can be accomplished medically using luteinizing hormone releasing hormone (LHRH) analogues. In addition, cytotoxic chemotherapy unpredictably produces amenorrhea and primary ovarian failure in 10%-95% of premenopausal women as a function of patient age, cumulative dose, and the specific agents used. In the metastatic setting, ovarian ablation and tamoxifen monotherapies produce comparable outcomes and may be more effective when used together. While many early adjuvant trials of ovarian ablation were methodologically flawed, a more recent meta-analysis by the Early Breast Cancer Trialists' Collaborative Group of 12 properly designed randomized trials found significantly greater disease-free and overall survival rates for women under the age of 50, regardless of nodal status, receiving ovarian ablation as a single adjuvant therapy. Several important issues regarding the role of ovarian ablation in the treatment of breast cancer remain unresolved. Data suggest that ovarian ablation followed by some years of tamoxifen produces similar results to those seen with adjuvant chemotherapy in women with hormone-receptor positive breast cancer; however, the value of combining these modalities is still unclear. Other areas of ongoing investigation include the appropriate duration of therapy with LHRH analogues in the adjuvant setting, the long-term sequelae of ovarian suppression among young breast cancer survivors, and refinement of the population most likely to benefit from ovarian ablation or suppression.


A facilitative role for corticosterone in the acquisition of a spatial task under moderate stress.
Emotionally charged experiences alter memory storage via the activation of hormonal systems. Previously, we have shown that compared with rats trained for a massed spatial learning task in the water maze in warm water (25 degrees C), animals that were trained in cold water (19 degrees C) performed better and showed higher levels of the stress hormone corticosterone. Here, we examined whether manipulating the levels of corticosterone can determine the strength of spatial information acquisition and retention. Rats were injected with metyrapone (25, 50, and 75 mg/kg, i.p.) or with corticosterone (10 and 25 mg/kg, i.p.) and trained in a massed spatial task in either cold (19 degrees C) or warm (25 degrees C) water. We found that whereas animals injected with vehicle performed well in the spatial task in cold water (moderate stress), rats injected with the intermediate metyrapone dose showed impairment in performance. Moreover, whereas animals injected with vehicle on average did not perform well in warm water (mild stress), rats injected with the lower corticosterone dose showed improvement in performance in warm water. These two mirror experiments of corticosterone blockade and enhancement strongly suggest that corticosterone is instrumental in the acquisition and retention of the spatial learning task.


Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases Bacteroides fragilis Abundance Compared with an Isocaloric Snack in College Freshmen.
Changes in gut microbiota are associated with cardiometabolic disorders and are influenced by diet. Almonds are a rich source of fiber, unsaturated fats, and polyphenols, all nutrients that can favorably alter the gut microbiome. The aim of this study was to examine the effects of 8 wk of almond snacking on the gut (fecal) microbiome diversity and abundance compared with an isocaloric snack of graham crackers in college freshmen. A randomized, controlled, parallel-arm, 8-wk intervention in 73 college freshmen (age: 18-19 y; 41 women and 32 men; BMI: 18-41 kg/m2) with no cardiometabolic disorders was conducted. Participants were randomly allocated to either an almond snack group (56.7 g/d; 364 kcal; n = 38) or graham cracker control group (77.5 g/d; 338 kcal/d; n = 35). Stool samples were collected at baseline and 8 wk after the intervention to assess primary microbiome outcomes, that is, gut microbiome diversity and abundance. Almond snacking resulted in 3% greater quantitative alpha-diversity (Shannon index) and 8% greater qualitative alpha-diversity (Chao1 index) than the cracker group after the intervention (P < 0.05). Moreover, almond snacking for 8 wk decreased the abundance of the pathogenic bacterium Bacteroides fragilis by 48% (overall relative abundance, P < 0.05). Permutational multivariate ANOVA showed significant time effects for the unweighted UniFrac distance and Bray-Curtis beta-diversity methods (P < 0.05; R 2 ≤ 3.1%). The dietary and clinical variables that best correlated with the underlying bacterial community structure at week 8 of the intervention included dietary carbohydrate (percentage energy), dietary fiber (g), and fasting total and HDL cholesterol (model Spearman rho = 0.16; P = 0.01). Almond snacking for 8 wk improved alpha-diversity compared with cracker snacking. Incorporating a morning snack in the dietary regimen of predominantly breakfast-skipping college freshmen improved the diversity and composition of the gut microbiome. This trial was registered at clinicaltrials.gov as NCT03084003.


Detecting proliferation of adult hemocytes in Drosophila by BrdU incorporation.
Drosophila and mammalian hematopoiesis share several similarities that ranges from phases to the battery of transcription factors and signaling molecules that execute this process. These resounding similarities along with the rich genetic tools available in fruitfly makes it a popular invertebrate model to study blood cell development both during normal and aberrant conditions. The larval system is the most extensively studied to date. Several studies have shown that these hemocytes just like mammalian counterpart proliferate and get routinely regenerated upon infection. However, employing the same protocol it was concluded that blood cell proliferation although abundant in larval stages is absent in adult fruitfly. The current protocol describes the strategies that can be employed to document the hemocyte proliferation in adulthood. The fact that a subset of blood cells tucked away in the hematopoietic hub are not locked in senescence, rather they still harbour the proliferative capacity to tide over challenges was successfully demonstrated by this method. Although we have adopted bacterial infection as a bait to evoke this proliferative capacity of the hemocytes, we envision that it can also efficiently characterize the proliferative responses of hemocytes in tumorigenic conditions as well as scenarios of environmental and metabolic stresses during adulthood.


Molecular and biochemical analysis of the enzymes of cysteine biosynthesis in the plant Arabidopsis thaliana.
Among the amino acids produced by plants cysteine plays a special role as a mediator between assimilatory sulfate reduction and provision of reduced sulfur for cell metabolism. Part of this characteristic feature is the presence of cysteine synthesis in plastids, mitochondria and cytosol. Plants are the major source of reduced sulfur for human and animal nutrition. Cysteine biosynthesis deserves special attention, since reduced sulfur is channelled from cysteine into many sulfur-containing compounds in food and feed. Recent investigations are reviewed that focus on structure and regulation of cysteine synthesis in the model plant Arabidopsis thaliana. These data indicate that cysteine synthesis is not just an intermediate reaction step but that it is part of a regulatory network that mediates between inorganic sulfur supply and the demand for reduced sulfur during plant growth and in response to environmental changes.


Effect of repeated public releases on cesarean section rates.
Public release of and feedback (here after public release) on institutional (clinics and hospitals) cesarean section rates has had the effect of reducing cesarean section rates. However, compared to the isolated intervention, there was scant evidence of the effect of repeated public releases (RPR) on cesarean section rates. The objectives of this study were to evaluate the effect of RPR for reducing cesarean section rates. From January 2003 to July 2007, the nationwide monthly institutional cesarean section rates data (1,951,303 deliveries at 1194 institutions) were analyzed. We used autoregressive integrated moving average (ARIMA) time-series intervention models to assess the effect of the RPR on cesarean section rates and ordinal logistic regression model to determine the characteristics of the change in cesarean section rates. Among four RPR, we found that only the first one (August 29, 2005) decreased the cesarean section rate (by 0.81 percent) and continued to have an impact period through the last observation in May 2007. Baseline cesarean section rates (OR, 4.7; 95% CI, 3.1 to 7.1) and annual number of deliveries (OR, 2.8; 95% CI, 1.6 to 4.7) of institutions in the upper third of each category at before first intervention had a significant contribution to the decrease of cesarean section rates. We could not found the evidence that RPR has had the significant effect of reducing cesarean section rates. Institutions with upper baseline cesarean section rates and annual number of deliveries were more responsive to RPR.


Regional cerebral blood flow measured by the gamma camera after direct injection of 133Xe into the distal stump of the occluded middle cerebral artery.
Regional cerebral blood flow (rCBF) was measured after intracarotid injection of 133Xe concurrently with measurements of local cerebral blood flow (LCBF) after injection of 133Xe directly into the distal stump of the occluded middle cerebral artery (MCA) by the use of the gamma camera after producing experimental ischemia in baboons by occluding the MCA. Regional MCA stump pressure (rMCAP) was also measured. Regions of ischemia assessed by intracarotid injection of 133Xe correlated well with the territory of infarct defined by injection of 133Xe into the distal MCA stump. Flow values in ischemic regions obtained by direct injection of 133Xe into the MCA were 15% to 20% lower than those obtained by intracarotid injection of 133Xe. Possible explanations for these differences are discussed. During induced hypertension autoregulation in ischemic areas was abolished and paradoxical responses of LCBF and rMCAP to changes in arterial carbon dioxide tension (PaCO2) were confirmed.


Profiling and targeting of cellular mitochondrial bioenergetics: inhibition of human gastric cancer cell growth by carnosine.
L-Carnosine (β-alanyl-L-histidine) is a naturally occurring dipeptide distributed in various organs of mammalians. We previously showed that carnosine inhibited proliferation of human gastric cancer cells through targeting both mitochondrial bioenergetics and glycolysis pathway. But the mechanism underlying carnosine action on mitochondrial bioenergetics of tumor cells remains unclear. In the current study we investigated the effect of carnosine on the growth of human gastric cancer SGC-7901 cells in vitro and in vivo. We firstly showed that hydrolysis of carnosine was not a prerequisite for its anti-gastric cancer effect. Treatment of SGC-7901 cells with carnosine (20 mmol/L) significantly decreased the activities of mitochondrial respiratory chain complexes I-IV and mitochondrial ATP production, and downregulated 13 proteins involved in mitochondrial bioenergetics. Furthermore, carnosine treatment significantly suppressed the phosphorylation of Akt, while inhibition of Akt activation with GSK690693 significantly reduced the localization of prohibitin-1 (PHB-1) in the mitochondria of SGC-7901 and BGC-823 cells. In addition, we showed that silencing of PHB-1 gene with shRNA markedly reduced the mitochondrial PHB-1 in SGC-7901 cells, and significantly decreased the colony formation capacity and growth rate of the cells. In SGC-7901 cell xenograft nude mice, administration of carnosine (250 mg kg/d, ip, for 3 weeks) significantly inhibited the tumor growth and decreased the expression of mitochondrial PHB-1 in tumor tissue. Taken together, these results suggest that carnosine may act on multiple mitochondrial proteins to down-regulate mitochondrial bioenergetics and then to inhibit the growth and proliferation of SGC-7901 and BGC-823 cells.


Service use patterns of youth with, and at high risk for, HIV: a care typology.
This paper uses confirmatory structural equation models to develop and test a theoretical model for understanding the service utilization history of 4679 youth who received services from 10 national HIV/AIDS demonstration models of youth-appropriate and youth-attractive services funded by the Special Projects of National Significance (SPNS) Program, HIV/AIDS Bureau, Health Resources and Services Administration. Although the projects differ from one another in the areas of emphasis in their service models, each is targeted to youth at high risk for HIV, or those youth who have already contracted HIV. Collectively, the projects represent a comprehensive adolescent HIV service model. This paper examines the characteristics of the services provided to young people ranging from outreach to intensive participation in medical treatment. Major typologies of service utilization are derived empirically through exploratory factor and cluster analysis methods. Confirmatory structural equation modeling methods are used to refine the exploratory results using a derivation and replication strategy and methods of statistical estimation appropriate for non-normally distributed service utilization indicators. The model hypothesizes that youth enter the service system through a general construct of connectedness to a comprehensive service model and through service-specific methods, primarily of outreach or emergency services. Estimates are made of the degree to which a comprehensive service model drives the services as opposed to specific service entry points.


[Comparisons among measurement tools in traumatic brain injury outcomes].
Traumatic brain injury (TBI) is considered the most important cause of disability among young people and the most common neurological cause of morbidity. Consequently, there is increasing interest in scales to monitor recovery in TBI. Among these scales, two have been widely adopted: the Glasgow Outcome Scale (GOS) and the Disability Rating Scale (DRS). The purpose of this paper is to compare the results found in DRS and in the original and extended GOS. Sixty-three closed-head injury victims, aged between 12 and 65, on an outpatient follow-up program at a trauma center in the city of São Paulo, with 6 months to 3 years post-TBI, had their characteristics and outcomes assessed. When comparing the results obtained by the scales, it was concluded that although the three of them were strongly correlated, extended GOS showed to be more sensitive in detecting changes in victims with better post-traumatic conditions.


Cnm of Streptococcus mutans is important for cell surface structure and membrane permeability.
Streptococcus mutans, a Gram-positive facultative anaerobic bacterium, is a major pathogen of dental caries. The protein Cnm of S. mutans is involved in collagen binding, but its other biological functions are unknown. In this study, a Cnm-deficient isogenic mutant and a complementation strain were generated from a Cnm-positive S. mutans strain to help determine the properties of Cnm. Initially, comparison of the cell surface structure was performed by electron microscopy, which demonstrated that Cnm appears to be localized on the cell surface and associated with a protruding cell surface structure. Deep RNA sequencing of the strains revealed that the defect in Cnm caused upregulated expression of many genes related to ABC transporters and cell-surface proteins, while a few genes were downregulated. The amount of biofilm formed by the Cnm-defective strain increased compared with the parental and complemented strains, but the biofilm structure was thinner because of elevated expression of genes encoding glucan synthesis enzymes, leading to increased production of extracellular polysaccharides. Particular antibiotics, including bacitracin and chloramphenicol, had a lower minimum inhibitory concentration for the Cnm-defective strain than particular antibiotics, including bacitracin and chloramphenicol, compared with the parental and complemented strains. Our results suggest that S. mutans Cnm is located on the cell surface, gives rise to the observed protruding cell surface, and is associated with several biological properties related to membrane permeability.


Tooth structure and fracture strength of cavities.
This study evaluated, in vitro, the loss of tooth substance after cavity preparation for direct and indirect restorations and its relationship with fracture strength of the prepared teeth. Sixty sound human maxillary first premolars were assigned to 6 groups (n=10). MOD direct composite cavities (Groups I, II and III) and indirect inlay cavities (Groups IV, V and VI) were prepared maintaining standardized dimensions: 2-mm deep pulpal floors, 1.5-mm wide gingival walls and 2-mm high axial walls. Buccolingual width of the occlusal box was established at 1/4 (Groups I and IV), 1/3 (Groups II and V) or 1/2 (Groups III and VI) of the intercuspal distance. Teeth were weighed (digital balance accurate to 0.001 g) before and after preparation to record tooth substance mass lost during cavity preparation. The prepared teeth were submitted to occlusal loading to determine their fracture strength using a universal testing machine at a crosshead speed of 0.5 mm/min. Data were analyzed by two-way ANOVA and Tukey test (alpha= 0.05). 1/4-inlay cavities had higher percent mean mass loss (9.71%) than composite resin cavities with the same width (7.07%). 1/3-inlay preparations also produced higher percent mean mass loss (13.91%) than composite resin preparations with the same width (10.02%). 1/2-inlay cavities had 21.34% of mass loss versus 16.19% for the 1/2-composite resin cavities. Fracture strength means (in kgf) were: GI = 187.65; GII = 143.62; GIII = 74.10; GIV = 164.22; GV = 101.92; GVI = 50.35. Statistically significant difference (p<0.05) were observed between Groups I and IV, II and V, III and VI. Higher tooth structure loss and lower fracture strength were recorded after preparation of inlay cavities, regardless of the width of the occlusal box, compared to the direct composite resin cavities.


Metastatic model of HPV+ oropharyngeal squamous cell carcinoma demonstrates heterogeneity in tumor metastasis.
Human papillomavirus induced (HPV+) cancer incidence is rapidly rising, comprising 60-80% of oropharyngeal squamous cell carcinomas (OPSCCs); while rare, recurrent/metastatic disease accounts for nearly all related deaths. An in vivo pre-clinical model for these invasive cancers is necessary for testing new therapies. We characterize an immune competent recurrent/metastatic HPV+ murine model of OPSSC which consists of four lung metastatic (MLM) cell lines isolated from an animal with HPV+ OPSCC that failed cisplatin/radiation treatment. These individual metastatic clonal cell lines were tested to verify their origin (parental transgene expression and define their physiological properties: proliferation, metastatic potential, heterogeneity and sensitivity/resistance to cisplatin and radiation. All MLMs retain expression of parental HPV16 E6 and E7 and degrade P53 yet are heterogeneous from one another and from the parental cell line as defined by Illumina expression microarray. Consistent with this, reverse phase protein array defines differences in protein expression/activation between MLMs as well as the parental line. While in vitro growth rates of MLMs are slower than the parental line, in vivo growth of MLM clones is greatly enhanced. Moreover, in vivo resistance to standard therapies is dramatically increased in 3 of the 4 MLMs. Lymphatic and/or lung metastasis occurs 100% of the time in one MLM line. This recurrent/metastatic model of HPV+ OPSCC retains the characteristics evident in refractory human disease (heterogeneity, resistance to therapy, metastasis in lymph nodes/lungs) thus serving as an ideal translational system to test novel therapeutics. Moreover, this system may provide insights into the molecular mechanisms of metastasis.


The Morphometrical and Histopathological Changes which were Observed after Topical Ozone Therapy on an Exophytic Fibrous Gingival Lesion: A Case Report.
We are presenting 2 cases where ozone therapy was used in the form of ozonated oil on an exophytic fibrous gingival lesion. A 42-years female patient was selected, who presented with a mild to moderately painful, exophytic, fibrous lesion on the upper anterior gingiva. This gingival lesion was treated with 2ml of ozonated oil, thrice daily for one week. After the ozone therapy, the postoperative outcomes were measured and analyzed. Finally, the lesion was subjected to an excisional biopsy and a histopathological evaluation. After the ozone therapy, the patient revealed that there was less pain. On examination of the lesion, an improvement was observed in the clinical sign of the inflammation and also a reduction in the surface ulceration. During the final biopsy, less bleeding was observed. The morphometrical analysis showed a reduction in the size of the lesion. The histopathological analysis showed a reduction in the collagen fibres and in the inflammatory cells in the connective tissue stroma. Topical ozone therapy provides potential benefits for the treatment of exophytic gingival lesions. The observed benefits in present case report needs to be verified in future with well-controlled clinical trials.


Central lymph nodes in frozen sections can effectively guide extended lymph node resection for papillary thyroid carcinoma.
The scope of lateral neck lymph node dissection (LND) in papillary thyroid carcinoma (PTC) remains controversial. Our research aimed to explore the value of central lymph node metastasis (CLNM) in frozen sections for predicting neck lateral lymph node metastasis (NLLNM) and to guide clinical surgeons in performing surgical lymph node dissection. A total of 275 patients with PTC with suspected 'Cervical lymph node metastasis (LNM, including CLNM and NLLNM)' underwent unilateral or bilateral thyroidectomy and an intraoperative frozen diagnosis of central lymph nodes (LNs), as well as central and neck lateral LND. Validity indices and consistency of central LNs in frozen sections were calculated. In total, 216 patients then met the inclusion criteria and were enrolled in the follow-up study. The clinical and pathological data of the patients were retrospectively analyzed. The relationship between the number, metastatic diameter, and the ratio of CLNM to NLLNM was investigated. CLNM in frozen and paraffin-embedded sections was associated with NLLNM. Univariate and multivariate analyses revealed the following risk factors for NLLNM metastasis: maximum diameter, total number, and ratio of metastatic LNs. A significant result was obtained when a cut-off value of 2.050 mm for the maximum metastatic diameter, 5.5 in the total number, and 0.5342 for the CLNM ratio level was used. Interaction term analyses showed that the association between the number of CLNM and NLLNM differed according to maximum diameter. Central LNs in frozen sections accurately predicted NLLNM. In patients with PTC with >5 CLNMs, ≥2 and ≤5 CLNMs and maximum metastatic diameter > 2 mm, neck lateral LND should be considered. Our findings will facilitate the identification of patients who are likely to benefit from extended lateral neck LND.


Health problems of victims before and after disaster: a longitudinal study in general practice.
We aimed to quantify the health problems and to assess the possible risk factors for developing health problems in persons affected by the explosion of a firework depot at Enschede, The Netherlands, on May 13, 2000. The explosion considerably damaged buildings in the local neighbourhood and caused 22 immediate deaths and injuries in over 1000 people. A longitudinal study of (89% of all) victims (n = 9329) and controls (n = 7392) with pre-disaster baseline morbidity for 16 months and post-disaster data for 2.5 years was conducted using the electronic medical records of general practitioners. Symptoms and diagnoses were recorded using the International Classification of Primary Care (ICPC). Prevalence rates for clusters of symptoms were compared between victim and control groups pre- and post-disaster. Risk factors for developing health problems were examined in hierarchical linear models. Two and a half years post-disaster, the prevalence of psychological problems in victims who had to relocate was about double and in the non-relocated victims one-third more than controls. Victims with pre-disaster psychological problems were at a greater risk for post-disaster psychological problems. Relocated victims showed an excess of medically unexplained physical symptoms (MUPS) especially in a period of increased media attention. Both groups of victims showed some increase of gastrointestinal (GI) morbidity 2.5 years post-disaster compared with their pre-disaster rate, and compared with the control group. Two and a half years post-disaster an excess of psychological problems, MUPS, and gastrointestinal morbidity was observed. Pre-disaster psychological problems and inevitable relocation were predictors of more post-disaster psychological problems.


The impact of including passive benefits in cost-effectiveness analysis: the case of automated external defibrillators on commercial aircraft.
Traditional cost-utility analysis assumes that all benefits from health-related interventions are captured by the quality-adjusted life-years (QALYs) gained by the few individuals whose outcome is improved by the intervention. However, it is possible that many individuals who do not directly benefit from an intervention receive utility, and therefore QALYs, because of the passive benefit (aka sense of security) provided by the existence of the intervention. The objective of this study was to evaluate the impact that varying quantities of passive benefit have on the cost-effectiveness of airline defibrillator programs. A decision analytic model with Markov processes was constructed to evaluate the cost-effectiveness of defibrillator deployment on domestic commercial passenger aircraft over 1 year. Airline passengers were assigned small incremental utility gains (.001-.01) during an estimated 3-hour flight to evaluate the impact of passive benefit on overall cost-effectiveness. In the base case analysis with no allowance for passive benefit, the cost-effectiveness of airline automated external defibrillator deployment was US dollars 34000 per QALY gained. If 1% of all passengers received utility gain of.01, the cost-effectiveness declined to US dollars 30000. Cost-effectiveness was enhanced when the quantity of passive benefit was raised or the percentage of individuals receiving passive benefit increased. Automated external defibrillator deployment on passenger aircraft is likely to be cost-effective. If a small percentage of airline passengers receive incremental utility gains from passive benefit of automated external defibrillator availability, the impact on overall cost-effectiveness may be substantial. Further research should attempt to clarify the magnitude and percentage of patients who receive passive benefit.


Analysis of cellular DNA content using flow cytometry in skin squamous cell carcinoma and its relationship to clinical behaviors.
Our report includes a technique using the flow cytometer to analyze the cellular DNA content of paraffin-embedded histological material from tumors. This technique allows for the retrospective study of tumors from patients whose clinical outcome is already known. We have applied this process to study skin squamous cell carcinomas (SCCs). We reviewed and studied 34 patients positive for SCCs, With or without lymph node or distant metastasis. All received radical treatment from December 1982 to December 1988. The DNA distribution pattern of SCCs in relation to the clinical stage and the histological grade was evaluated. Our findings indicated that patients with diploid tumors had a better prognosis than those with aneuploid tumors. The DNA distribution pattern correlates well with the clinical stage and is a better determinant than histological grading or clinical behaviors.


Protein phosphatase 6 promotes transforming growth factor-β signaling in mouse embryonic fibroblasts.
Transforming growth factor-beta (TGF-β) is a multifunctional cytokine that controls various cellular processes. Protein phosphatase 6 (PP6) is an evolutionarily conserved serine/threonine protein phosphatase with diverse functions in cell signaling. However, it hasn't been linked to TGF-β signaling. We found that TGF-β treatment increased PP6 protein levels via transcriptional and post-translational regulation. Loss of the Ppp6c gene suppressed TGF-β-induced canonical Smad3 phosphorylation and its transcriptional activity. PP6 knockout also inhibited non-canonical p38 mitogen-activated protein kinase (MAPK) pathway. Moreover, PP6 depletion suppressed cell migration induced by TGF-β. These findings uncovered the role of PP6 as a positive regulator for TGF-β signaling.


Mutational analysis of the equine infectious anemia virus Tat-responsive element.
A hairpinlike structure is predicted to exist at the 5' end of equine infectious anemia virus (EIAV) RNA which is similar in many ways to the human immunodeficiency type 1 (HIV-1) Tat-responsive element (TAR). In EIAV, this structure has a shorter stem than in HIV-1 and lacks the uridine bulge. Primer extension analysis of EIAV RNA was used to identify the transcriptional start site in the viral long terminal repeat. Premature termination of primer elongation at the predicted double-stranded RNA region was frequently observed and suggests that the inferred hairpin structure exists under these conditions. We have functionally characterized EIAV TAR by site-directed mutagenesis and transient gene expression analysis. It is demonstrated here that the secondary structure of this element is essential for Tat action. Mutations that disrupted base pairing abolished TAR function, and compensatory mutations that restored the stem structure resulted in Tat activation. The TAR loop appears to be closed by two U.G base pairs that are likely to provide a unique structural motif recognized by the Tat protein. With one exception, substitutions of nucleotides within the EIAV loop sequence decreased TAR function. All nucleotide substitutions of the cytidine at position +14 increased EIAV Tat responsiveness; however, its deletion abolished trans activation. Our results lead us to propose that the EIAV and HIV-1 Tat systems employ closely related cis- and trans-acting components that probably act by the same mechanism.


HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly.
De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges and potential solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline for rebuilding both haploid sub-assemblies from the polymorphic diploid genome assembly. It is designed to work on pre-existing diploid assemblies, which are typically created by using de novo assemblers. HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-closing method for haploid sub-assemblies. Using HM2, we demonstrate that two haploid sub-assemblies reconstructed from a real, highly-polymorphic diploid assembly show greatly improved continuity. Source code, executables and the testing dataset are freely available at https://github.com/mapleforest/HaploMerger2/releases/. email@example.com. Supplementary data are available at Bioinformatics online.


Genome‑wide DNA hypomethylation drives a more invasive pancreatic cancer phenotype and has predictive occult distant metastasis and prognosis potential.
Genome‑wide DNA hypomethylation is the most common molecular feature in human cancers associated with chromosomal instability (CIN), which is involved in the mechanisms that regulate pancreatic cancer (PC) metastasis. It was investigated whether genome‑wide DNA hypomethylation affects the phenotype in PC via CIN in vitro, and its significance on the biological behavior of PC was verified. The relative demethylation level (RDL) of long interspersed nucleotide element‑1 (LINE‑1) in human PC cell lines was used to characterize DNA hypomethylation using methylation‑specific quantitative (q)PCR. CIN was estimated by changes in chromosomal copy number using comparative genomic hybridization analysis. Abnormal segregation of chromosomes was assessed by immunocytochemistry, and the DNA damage response was evaluated using the number of anti‑γH2AX positive cells. Invasion ability was assessed using a Matrigel invasion assay. Clinical specimens from 49 patients with PC who underwent curative surgery were evaluated for a correlation of DNA hypomethylation with clinical outcome. Successful induction of genome‑wide DNA hypomethylation in PC cells led to copy number changes in specific chromosomal regions. The number of cells with abnormal segregation of chromosomes significantly increased with the number of anti‑γH2AX positive cells. The invasive potential of these cells also significantly increased. The occurrence of occult distant metastasis in the clinical specimens and receiver operating characteristic analysis clearly identified those who were and were not likely to have occult distant metastasis, with high LINE‑1 RDL significantly correlated with the presence of occult distant metastasis (P=0.035) and poor prognosis (P=0.048). The significance of genome‑wide DNA hypomethylation on the biological behavior of PC, which promotes a more invasive phenotype via CIN in vitro and predicts the susceptibility to occult distant metastasis and poor prognosis in patients with PC was revealed.


The expression and function of Sgt1 protein in eukaryotic cells.
The Sgt1 protein was discovered in yeast but later it was found in other eucaryotic organisms, including plants and mammals. It was suggested that the Sgt1 protein plays a role in the CBF3 kinetochore and the SCF ubiquitin ligase complexes. Since the distribution, properties and functions of the mammalian Sgt1 have not been extensively studied, we examined the expression of Sgt1 protein in the rat tissues and here we report the preliminary results. Using northern and western blots we found that the Sgt1 protein is expressed in various tissues and that brain, skeletal muscles and spleen contain high levels of this protein and its mRNA. Then, by western blot, we checked the localization of Sgt1 in some areas of the rat brain such as cortex, cerebellum and hippocampus and we found that cerebellum and cortex contain highest amounts of this protein. Using immunohistochemistry we found that the Sgt1 protein is present in both neurons and glial cells.