A mammalian transcription factor-specific peptide repository for targeted proteomics.
Site-specific transcription factors (TFs) play an essential role in mammalian development and function as they are vital for the majority of cellular processes. Despite their biological importance, TF proteomic data is scarce in the literature, likely due to difficulties in detecting peptides as the abundance of TFs in cells tends to be low. In recent years, significant improvements in MS-based technologies in terms of sensitivity and specificity have increased the interest in developing quantitative methodologies specifically targeting relatively lowly abundant proteins such as TFs in mammalian models. Such efforts would be greatly aided by the availability of TF peptide-specific information as such data would not only enable improvements in speed and accuracy of protein identifications, but also ameliorate cross-comparisons of quantitative proteomics data and allow for a more efficient development of targeted proteomics assays. However, to date, no comprehensive TF proteotypic peptide database has been developed. To address this evident lack of TF peptide data in public repositories, we are generating a comprehensive, experimentally derived TF proteotypic peptide spectral library dataset based on in vitro protein expression. Our library currently contains peptide information for 89 TFs and this number is set to increase in the near future. All MS data have been deposited in the ProteomeXchange with identifier PXD001212 (http://proteomecentral.proteomexchange.org/dataset/PXD001212).


Neurobehavioral effects of manganese in workers from a ferroalloy plant after temporary cessation of exposure.
The goal of this study was to assess long-term neurobehavioral effects associated with low airborne concentrations of manganese in a ferroalloy plant. During a period of forced cessation of work (1 to 42 d) neurobehavioral performance on tests of simple reaction time, finger tapping, digit span, additions, symbol digit, and shapes comparison was evaluated for 58 workers exposed from 1 to 28 (mean 13, SD 7) years to manganese. Airborne manganese concentrations in total dust had been reduced in the last 10 years from 70-159 micrograms x m-3 (geometric means in different areas) to 27-270 micrograms x m-3. For each worker, manganese concentrations in blood and urine were measured, and a cumulative exposure index was also calculated. Blood manganese and urinary manganese ranged from 4 to 18 micrograms x 1-1 (0.07 to 0.03 mumol x 1-1) and from 0.7 to 7 micrograms x 1-1 (0.01 to 0.13 mumol x 1-1) respectively. Significant relationships were found between the blood manganese and urinary manganese levels and between these biological measures and the cumulative exposure index. Correlations were also found between the blood manganese level, the urinary manganese level, and the cumulative exposure index and the following tests: finger tapping, symbol digit, digit span, and additions. The correlation coefficients increased as the latency time after the cessation of exposure and work seniority increased. The results support the hypothesis that the neurobehavioral effects observed at exposure levels well below current occupational standards are related to manganese body burden, which is better reflected by the blood manganese level after the cessation of exposure.


A literature review: Graduate nurses' preparedness for recognising and responding to the deteriorating patient.
To explore the research literature that provided data on factors that influence new graduate nurse's preparedness for recognition and response to patient deterioration in the acute care setting. Nurses have a significant role in recognising subtle signs of patient deterioration and responding appropriately to prevent adverse events and improve patient outcomes. This pivotal position has often fallen to the new graduate who must be prepared to make high-consequence decisions in relation to a suspected decline in their patient's condition. An integrative review was undertaken. A comprehensive literature search was conducted using online databases, reference lists of key articles and expert advice. Multiple keyword combinations were used. All relevant studies were subsequently appraised for rigour and quality. Seventeen primary research studies drawn from novice and experienced registered nurse experiences emerged as relevant to the review. Thematic analysis of the studies provided six major themes related to the aim of the review. Emergent themes were as follows: clinical staff support, lack of nurse experience, overwhelming workload, holistic patient assessment, past experiences and lack of available resources. This review highlighted the importance of positive staff support and subsequent confidence building. Graduates then felt able to present effective assessments and less fearful of reprimand when escalating an intervention call. The need for further research to investigate graduate nurses' experiences of recognising and responding to the deteriorating patient emerged. Realistic workloads and access to supportive experienced staff would allow graduates time to focus on grouping clinical information to understand the 'total picture' of the patient. Results indicated undergraduate and hospital in-service education programmes needed to offer the opportunity to practice reasoning. Complex clinical situations involving patient deterioration through simulation and clinical placement opportunities appeared most useful.


The role of alpha-lipoic acid in diabetic polyneuropathy treatment.
Diabetic neuropathy represents late diabetes complications, and diabetes duration and long-term hyperglycemia are the main reasons for polyneuropathy. The goal was to estimate the effects of alpha-lipoic acid on symptoms of diabetic neuropathy after 600 mg i.v. for 3 weeks and 3 months of 300-600 mg of alpha-lipoic acid per os. This study has been designed as a multicentric, in 5-centers in B&H, carried out by 5 physicians with 20 diabetic patients each. Following parameters were monitored in 100 diabetics suffering from Type 1 and Type 2 diabetes, both men and women: diabetes duration, diabetes therapy, duration of polyneuropathy symptoms, height, weight, BMI (body mass index), subjective assessment of patients, objective examinations of physicians and subjective assessment of physicians. 100 diabetics, average age 61,36; oldest 79, youngest 40, suffered from diabetes in average 11,9 years. There were 35 men and 65 women, 16 with Type 1 and 80 with Type 2 diabetes, while 4 patients were not classified. 69 were having insulin therapy and 31 oral hypoglicemics. Shortest diabetic status was less than a year, and longest was 28 years. Average duration of polyneuropathic symptoms was 3,02 years, shortest was less than a year, and the longest was 15 years. Average height was 1,70 m, average weight 76,13 kg, and average BMI 26,51 kg/m2. Significant statistic differences in improvement were recorded (P>0,05) according to Fridman's test for repeated measurements compared to initial findings in assessments: sensory symptoms of polyneuropathy, pain sensations as polyneuropathy symptoms, total score of polyneuropathy symptoms, subjective assessment of patients, subjective findings of physicians, and significant differences were not find (P>0,05) in autonomous and motoric neuropathy. Based on the conducted study, we have concluded that the application of alpha-lipoic acid during 3 months has helped to decrease the symptoms of diabetic neuropathy and in only one case out of 100 included patients there was no subjective improvement after drug application.


Leukaemia inhibitory factor significantly enhances the blastocyst formation rates of human embryos cultured in serum-free medium.
The aim of this study was to investigate the effect of leukaemia inhibitory factor (LIF) on human blastocyst formation rates in vitro. To do this, it was first necessary to devise a complex serum-free medium (CSFM) in which to test its activity. Blastocyst formation rates in CSFM microdrops (18.4%) showed no difference to those obtained previously for embryos cultured in 1 ml T6 medium containing 10% serum (25%). The majority of blastocysts were of optimal blastocyst grade (BG1/BG2) as compared to the poor grade (BG3). The percentage of BG1/BG2 blastocysts was decreased in CSFM microdrops (10.2%) compared to that observed in T6 medium (24.8%). Addition of 1000 IU/ml LIF to CSFM microdrops increased the blastocyst formation rate from 18.4 to 43.6% (P = 0.025) and increased the percentage of BG1/BG2 blastocysts (33%; P = 0.025) to levels comparable with those observed in T6 medium. Thus LIF significantly increased the quality and number of human blastocysts formed in CSFM medium, increasing the potential for blastocyst transfer in human in-vitro fertilization (IVF).


Prognostic value of direct spread in Dukes' C cases of rectal cancer.
Seventy-six cancers with involved lymph nodes but with limitation of direct spread in continuity to the bowel wall (Astler-Coller C1 cases) were matched with Astler-Coller C2 cases for clinical variables, macroscopic appearance of tumor, grade of differentiation, and number of positive lymph nodes. Despite this stringent matching, spread was shown to be an important prognostic variable in univariate survival analysis. Estimated five-year survival for Astler-Coller C1 cases was just below 80 percent, equivalent to B2 (Dukes' B) cases. When spread was analyzed in the presence of additional prognostic variables (character of invasive margin and lymphocytic infiltration) by multivariate modeling, its independent prognostic status was maintained. Improved survival for C1 cases was not explained by a lower incidence of local pelvic recurrence. Mechanisms to account for the better prognosis are proposed. This study reaffirms the importance of multivariate techniques of analysis in the assessment of prognosis of patients with rectal cancer.


Long-term management of asthma.
Long-term management of asthma includes identification and avoidance of precipitating factors of asthma, pharmacotherapy and home management plan. Common precipitating factors include viral upper respiratory infections, exposure to smoke, dust, cold food and cold air. Avoidance of common precipitating factors has been shown to help in better control of asthma. Pharmacotherapy is the main stay of treatment of asthma. Commonly used drugs for better control of asthma are long and short acting bronchodilators, mast cell stabilizers, inhaled steroids, theophylline and steroid sparing agents. After assessment of severity most appropriate medications are selected. For mild episodic asthma the medications are short acting beta agonists as and when required. For mild persistent asthma: as and when required bronchodilators along with a daily maintenance treatment in form of low dose inhaled steroids or cromolyn or oral theophylline or leukotriene antagonists are required. Moderate persistent asthma should be treated with inhaled steroids along with long acting beta agonists for symptom control. For severe persistent asthma the recommended treatment includes inhaled steroids, long acting beta agonists with or without theophylline. If symptoms are not well controlled, a minimal dose of oral prednisolone preferably on alternate days may be needed in few patients. Patients should be followed up every 8-12 weeks. On each follow up visit patients should be examined by a doctor, compliance to medications should be checked and actual inhalation technique is observed. Depending on the assessment, medications may be decreased or stepped up. For exercise induced bronchoconstriction: cromolyn, short or long acting beta agonists or leukotriene antagonists may be used. In children with seasonal asthma, maintenance treatment according to assessed severity should be started 2 weeks in advance and continued throughout the season. These patients should be reassessed after discontinuing the treatment. Parents should be given a written plan for management of acute exacerbation at home.


Toward refined estimates of ambient PM2.5 exposure: Evaluation of a physical outdoor-to-indoor transport model.
Because people spend the majority of their time indoors, the variable efficiency with which ambient PM2.5 penetrates and persists indoors is a source of error in epidemiologic studies that use PM2.5 concentrations measured at central-site monitors as surrogates for ambient PM2.5 exposure. To reduce this error, practical methods to model indoor concentrations of ambient PM2.5 are needed. Toward this goal, we evaluated and refined an outdoor-to-indoor transport model using measured indoor and outdoor PM2.5 species concentrations and air exchange rates from the Relationships of Indoor, Outdoor, and Personal Air Study. Herein, we present model evaluation results, discuss what data are most critical to prediction of residential exposures at the individual-subject and populations levels, and make recommendations for the application of the model in epidemiologic studies. This paper demonstrates that not accounting for certain human activities (air conditioning and heating use, opening windows) leads to bias in predicted residential PM2.5 exposures at the individual-subject level, but not the population level. The analyses presented also provide quantitative evidence that shifts in the gas-particle partitioning of ambient organics with outdoor-to-indoor transport contribute significantly to variability in indoor ambient organic carbon concentrations and suggest that methods to account for these shifts will further improve the accuracy of outdoor-to-indoor transport models.


Pragmatic Recommendations for the Management of Acute Respiratory Failure and Mechanical Ventilation in Patients with COVID-19 in Low- and Middle-Income Countries.
Management of patients with severe or critical COVID-19 is mainly modeled after care for patients with severe pneumonia or acute respiratory distress syndrome (ARDS) from other causes, and these recommendations are based on evidence that often originates from investigations in resource-rich intensive care units located in high-income countries. Often, it is impractical to apply these recommendations to resource-restricted settings, particularly in low- and middle-income countries (LMICs). We report on a set of pragmatic recommendations for acute respiratory failure and mechanical ventilation management in patients with severe/critical COVID-19 in LMICs. We suggest starting supplementary oxygen when SpO2 is persistently lower than 94%. We recommend supplemental oxygen to keep SpO2 at 88-95% and suggest higher targets in settings where continuous pulse oximetry is not available but intermittent pulse oximetry is. We suggest a trial of awake prone positioning in patients who remain hypoxemic; however, this requires close monitoring, and clear failure and escalation criteria. In places with an adequate number and trained staff, the strategy seems safe. We recommend to intubate based on signs of respiratory distress more than on refractory hypoxemia alone, and we recommend close monitoring for respiratory worsening and early intubation if worsening occurs. We recommend low-tidal volume ventilation combined with FiO2 and positive end-expiratory pressure (PEEP) management based on a high FiO2/low PEEP table. We recommend against using routine recruitment maneuvers, unless as a rescue therapy in refractory hypoxemia, and we recommend using prone positioning for 12-16 hours in case of refractory hypoxemia (PaO2/FiO2 < 150 mmHg, FiO2 ≥ 0.6 and PEEP ≥ 10 cmH2O) in intubated patients as standard in ARDS patients. We also recommend against sharing one ventilator for multiple patients. We recommend daily assessments for readiness for weaning by a low-level pressure support and recommend against using a T-piece trial because of aerosolization risk.


Lucanthone and its derivative hycanthone inhibit apurinic endonuclease-1 (APE1) by direct protein binding.
Lucanthone and hycanthone are thioxanthenone DNA intercalators used in the 1980s as antitumor agents. Lucanthone is in Phase I clinical trial, whereas hycanthone was pulled out of Phase II trials. Their potential mechanism of action includes DNA intercalation, inhibition of nucleic acid biosyntheses, and inhibition of enzymes like topoisomerases and the dual function base excision repair enzyme apurinic endonuclease 1 (APE1). Lucanthone inhibits the endonuclease activity of APE1, without affecting its redox activity. Our goal was to decipher the precise mechanism of APE1 inhibition as a prerequisite towards development of improved therapeutics that can counteract higher APE1 activity often seen in tumors. The IC(50) values for inhibition of APE1 incision of depurinated plasmid DNA by lucanthone and hycanthone were 5 µM and 80 nM, respectively. The K(D) values (affinity constants) for APE1, as determined by BIACORE binding studies, were 89 nM for lucanthone/10 nM for hycanthone. APE1 structures reveal a hydrophobic pocket where hydrophobic small molecules like thioxanthenones can bind, and our modeling studies confirmed such docking. Circular dichroism spectra uncovered change in the helical structure of APE1 in the presence of lucanthone/hycanthone, and notably, this effect was decreased (Phe266Ala or Phe266Cys or Trp280Leu) or abolished (Phe266Ala/Trp280Ala) when hydrophobic site mutants were employed. Reduced inhibition by lucanthone of the diminished endonuclease activity of hydrophobic mutant proteins (as compared to wild type APE1) supports that binding of lucanthone to the hydrophobic pocket dictates APE1 inhibition. The DNA binding capacity of APE1 was marginally inhibited by lucanthone, and not at all by hycanthone, supporting our hypothesis that thioxanthenones inhibit APE1, predominantly, by direct interaction. Finally, lucanthone-induced degradation was drastically reduced in the presence of short and long lived free radical scavengers, e.g., TRIS and DMSO, suggesting that the mechanism of APE1 breakdown may involve free radical-induced peptide bond cleavage.


The effect of dexrazoxane on myocardial injury in doxorubicin-treated children with acute lymphoblastic leukemia.
Doxorubicin chemotherapy is very effective in children with acute lymphoblastic leukemia (ALL) but also injures myocardial cells. Dexrazoxane, a free-radical scavenger, may protect the heart from doxorubicin-associated damage. To determine whether dexrazoxane decreases doxorubicin-associated injury of cardiomyocytes, we randomly assigned 101 children with ALL to receive doxorubicin alone (30 mg per square meter of body-surface area every three weeks for 10 doses) and 105 to receive dexrazoxane (300 mg per square meter) followed immediately by doxorubicin. Serial measurements of serum cardiac troponin T were obtained in 76 of 101 patients in the doxorubicin group and 82 of 105 patients in the group given dexrazoxane and doxorubicin. A total of 2377 serum samples (mean, 15.1 samples per patient) were obtained before, during, and after treatment with doxorubicin. Troponin T levels were evaluated in a blinded fashion to determine whether they were elevated (>0.01 ng per milliliter)--the primary end point--or extremely elevated (>0.025 ng per milliliter). Elevations of troponin T occurred in 35 percent of the patients (55 of 158). Patients treated with doxorubicin alone were more likely than those who received dexrazoxane and doxorubicin to have elevated troponin T levels (50 percent vs. 21 percent, P<0.001) and extremely elevated troponin T levels (32 percent vs. 10 percent, P<0.001). The median follow-up was 2.7 years. The rate of event-free survival at 2.5 years was 83 percent in both groups (P=0.87 by the log-rank test). Dexrazoxane prevents or reduces cardiac injury, as reflected by elevations in troponin T, that is associated with the use of doxorubicin for childhood ALL without compromising the antileukemic efficacy of doxorubicin. Longer follow-up will be necessary to determine the influence of dexrazoxane on echocardiographic findings at four years and on event-free survival.


Long-Term Balancing Selection in LAD1 Maintains a Missense Trans-Species Polymorphism in Humans, Chimpanzees, and Bonobos.
Balancing selection maintains advantageous genetic and phenotypic diversity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo-Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees, and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 My of independent evolution. Although the majority of these trSNPs were found in three genes of the major histocompatibility locus cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1. All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic diversity. Here, we focus on the trSNP in LAD1, a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction; the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1.


Deep learning for electroencephalogram (EEG) classification tasks: a review.
Electroencephalography (EEG) analysis has been an important tool in neuroscience with applications in neuroscience, neural engineering (e.g. Brain-computer interfaces, BCI's), and even commercial applications. Many of the analytical tools used in EEG studies have used machine learning to uncover relevant information for neural classification and neuroimaging. Recently, the availability of large EEG data sets and advances in machine learning have both led to the deployment of deep learning architectures, especially in the analysis of EEG signals and in understanding the information it may contain for brain functionality. The robust automatic classification of these signals is an important step towards making the use of EEG more practical in many applications and less reliant on trained professionals. Towards this goal, a systematic review of the literature on deep learning applications to EEG classification was performed to address the following critical questions: (1) Which EEG classification tasks have been explored with deep learning? (2) What input formulations have been used for training the deep networks? (3) Are there specific deep learning network structures suitable for specific types of tasks? A systematic literature review of EEG classification using deep learning was performed on Web of Science and PubMed databases, resulting in 90 identified studies. Those studies were analyzed based on type of task, EEG preprocessing methods, input type, and deep learning architecture. For EEG classification tasks, convolutional neural networks, recurrent neural networks, deep belief networks outperform stacked auto-encoders and multi-layer perceptron neural networks in classification accuracy. The tasks that used deep learning fell into five general groups: emotion recognition, motor imagery, mental workload, seizure detection, event related potential detection, and sleep scoring. For each type of task, we describe the specific input formulation, major characteristics, and end classifier recommendations found through this review. This review summarizes the current practices and performance outcomes in the use of deep learning for EEG classification. Practical suggestions on the selection of many hyperparameters are provided in the hope that they will promote or guide the deployment of deep learning to EEG datasets in future research.


Targeting of bone morphogenetic protein growth factor complexes to fibrillin.
Both latent transforming growth factor-beta (TGF-beta)-binding proteins fibrillins are components of microfibril networks, and both interact with members of the TGF-beta family of growth factors. Interactions between latent TGF-beta-binding protein-1 and TGF-beta and between fibrillin-1 and bone morphogenetic protein-7 (BMP-7) are mediated by the prodomain of growth factor complexes. To extend this information, investigations were performed to test whether stable complexes are formed by additional selected TGF-beta family members. Using velocity sedimentation in sucrose gradients as an assay, complex formation was demonstrated for BMP-7 and growth and differentiation factor-8 (GDF-8), which are known to exist in prodomain/growth factor complexes. Comparison of these results with complex formation by BMP-2, BMP-4 (full-length and shortened propeptides), BMP-10, and GDF-5 allowed us to conclude that all, except for BMP-2 and the short BMP-4 propeptides, formed complexes with their growth factors. Using surface plasmon resonance, binding affinities between fibrillin and all propeptides were determined. Binding studies revealed that the N-terminal end of fibrillin-1 serves as a universal high affinity docking site for the propeptides of BMP-2, -4, -7, and -10 and GDF-5, but not GDF-8, and located the BMP/GDF binding site within the N-terminal domain in fibrillin-1. Rotary shadowing electron microscopy of molecules of BMP-7 complex bound to fibrillin-1 confirmed these findings and also showed that prodomain binding targets the growth factor to fibrillin. Immunolocalization of BMP-4 demonstrated fibrillar staining limited to certain tissues, indicating tissue-specific targeting of BMP-4. These data implicate the fibrillin microfibril network in the extracellular control of BMP signaling and demonstrate differences in how prodomains target their growth factors to the extracellular space.


Public support for alcohol control initiatives across seven countries.
Public support for greater alcohol controls is a key consideration in governments' decisions to introduce new alcohol-related regulations, policies, and programs. The aim of this study was to asses public support for a range of recommended alcohol control initiatives across seven countries with varying sociocultural profiles. Adults (n = 7545; aged 18-91 years) from Australia, Canada, China, India, New Zealand, the United Kingdom, and the United States completed an online survey assessing demographic characteristics, alcohol consumption patterns, and support for 14 alcohol control initiatives. Across the total sample, means for each initiative ranged from 3.49 to 4.09 (on a 5-point agreement scale), indicating generally favourable responses. Stated support levels (i.e., selecting 'Agree' or 'Strongly agree') for specific initiatives in individual countries ranged from 33% to 86%. Across countries, support was higher for initiatives related to product labelling (e.g., clearly visible standard drink quantity information and pregnancy warning labels) and lower for initiatives related to alcohol advertising restrictions (e.g., prohibiting alcohol advertising during televised sporting programs and on road-side billboards). Support levels varied by age, gender, income level, drinking status, and drinking frequency. The high levels of support across countries for many of the assessed initiatives indicate that the public would be receptive to more stringent alcohol control policies, especially in relation to product labelling and the dissemination of public education campaigns. Further advocacy work appears to be required to foster higher levels of support for restricting alcohol companies' marketing activities.


Structure-function relationships associated with extracellular matrix alterations in diabetic glomerulopathy.
Proteinuria and progressive renal insufficiency are the primary manifestations of diabetic nephropathy. Accumulating evidence suggests that these clinical features can be linked, at least in part, to pathologic changes in the glomerular extracellular matrix. Most evidence suggests that glomerular basement membrane thickening and mesangial matrix expansion consist of at least three elements. These are (1) an accumulation of normal extracellular components; (2) an increase in the novel peptide chains of the normal components of Type IV collagen; and (3) an increase in matrix elements not normally expressed in the glomerulus. The pathogenetic features underlying these changes include increased synthesis and decreased degradation of matrix. Abnormal physico-chemical interactions among these matrix elements likely contribute to alterations in three-dimensional structure, leading to proteinuria and loss of glomerular basement membrane filtering surface area. Many of these changes may be explained in whole or in part by direct or secondary effects of hyperglycemia, as well as by hemodynamic changes.


Information and repetition change children's visual strategies when viewing magic tricks with and without gaze cues.
Gaze cues and direct gaze attract visual attention. However, few studies have explored visual cues in children within realistic contexts. The effect of information and repetitive stimulus presentation has not been thoroughly studied with dynamic stimuli. The aim of the present study was to investigate how information affects the visual strategies of children measured by the number of fixations on certain areas of interest and their durations. Furthermore, this study examined the effect of gaze cues and direct gaze. In two consecutive experiments, children's visual strategies when viewing magic tricks were measured by an eye tracker. Gaze cues were only present in Experiment 1.The results showed that repetitive stimulus presentation and information caused children to change their visual strategies when viewing magic tricks with and without gaze cues. However, the effect was larger when the gaze cues were not present. These findings in children were similar to those in adults.


Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland.
The common zoonotic pathogen Campylobacter coli is an important cause of bacterial gastroenteritis worldwide but its evolution is incompletely understood. Using multilocus sequence type (MLST) data of 7 housekeeping genes from a national survey of Campylobacter in Scotland (2005/6), and a combined population genetic-phylogenetics approach, we investigated the evolutionary history of C. coli. Genealogical reconstruction of isolates from clinical infection, farm animals and the environment, revealed a three-clade genetic structure. The majority of farm animal, and all disease causing genotypes belonged to a single clade (clade 1) which had comparatively low synonymous sequence diversity, little deep branching genetic structure, and a higher number of shared alleles providing evidence of recent clonal decent. Calibration of the rate of molecular evolution, based on within-species genetic variation, estimated a more rapid rate of evolution than in traditional estimates. This placed the divergence of the clades at less than 2500 years ago, consistent with the introduction of an agricultural niche having had an effect upon the evolution of the C. coli clades. Attribution of clinical isolate genotypes to source, using an asymmetric island model, confirmed that strains from chicken and ruminants, and not pigs or turkeys, are the principal source of human C. coli infection. Taken together these analyses are consistent with an evolutionary scenario describing the emergence of agriculture-associated C. coli lineage that is an important human pathogen.


Moving Beyond the Limits of Detection: The Past, the Present, and the Future of Diagnostic Imaging in Canine Osteoarthritis.
Osteoarthritis (OA) is the most common orthopedic condition in dogs, characterized as the chronic, painful end-point of a synovial joint with limited therapeutic options other than palliative pain control or surgical salvage. Since the 1970s, radiography has been the standard-of-care for the imaging diagnosis of OA, despite its known limitations. As newer technologies have been developed, the limits of detection have lowered, allowing for the identification of earlier stages of OA. Identification of OA at a stage where it is potentially reversible still remains elusive, however, yet there is hope that newer technologies may be able to close this gap. In this article, we review the changes in the imaging of canine OA over the past 50 years and give a speculative view on future innovations which may provide for earlier identification, with the ultimate goal of repositioning the limit of detection to cross the threshold of this potentially reversible disease.


Collagenase promotes the cellular responses to injury and wound healing in vivo.
This study focuses on the growth-promoting and migration-enhancing role that Clostridial collagenase plays in vitro and in vivo. For in vitro studies, biosynthesized extracellular matrices were treated with purified Clostridial collagenase, nonspecific proteases, or buffer controls. Keratinocytes were subsequently plated upon these matrices in the presence or absence of Clostridial collagenase and/or heparin-binding epidermal-like growth factor, and cell proliferation and migration were quantified. To examine the effects of Clostridial collagenase in vivo, we performed a double-blind study of full-thickness wounds on the backs of Yucatan Micropigs, testing the effects of purified Clostridial collagenase, Regranex (PDGF-BB), and Solosite (carboxymethyl cellulose) on wound healing. Matrix pretreatment with Clostridial collagenase stimulates a 2-fold increase in proliferation and postinjury migration; when Clostridial collagenase and/or heparin-binding epidermal-like growth factor are added to the growth media, there is an additional doubling of growth and migration, yielding approximately 5-fold enhancement of keratinocyte proliferation and migration. Papain-urea treatment under similar conditions results in a 50% decrease in cell number over a 1-week time course. In vivo studies: By all parameters measured, including granulation tissue formation, inflammation, re-epithelization, and time to wound closure, purified Clostridial collagenase was superior (analysis of variance, P > .05) to other treatments tested. On the basis of these findings, we concluded that Clostridial collagenase stimulates keratinocyte cellular responses to injury in vitro and may represent a novel therapeutic approach for promotion of wound healing in vivo.


An integrated health and social care organisation in Sweden: creation and structure of a unique local public health and social care system.
Research and citizens have noted failures in coordinating health and social services and professionals, and the need to address this issue to realize benefits from increasing specialisation. Different methods have been proposed and one has been structural integration of separate services within one organisation. This paper reports an empirical longitudinal study of the development of an integrated health and social care organisation in Sweden combining service provision, purchasing and political governance for a defined population. The study found a combination of influences contributed to the development of this new organisation. The initial structural macro-integration facilitated, but did not of itself result in better clinical care coordination. Other actions were needed to modify the specialised systems and cultures which the organisation inherited. The study design was not able to establish with any degree of certainty whether better patient and cost outcomes resulted, but it did find structural and process changes which make improved outcomes likely. The study concludes that coordinated actions at different levels and of different types were needed to achieve care coordination for patients and that a phased approach was necessary where management capacity and outside expertise are limited.


Identification of quantitative trait loci associated with the susceptibility of mouse spermatozoa to cryopreservation.
Although it is known that the susceptibility of mouse spermatozoa to freezing-thawing varies greatly with genetic background, the underlying mechanisms remain to be elucidated. In this study, to map genetic regions responsible for the susceptibility of spermatozoa to freezing-thawing, we performed in vitro fertilization using spermatozoa from recombinant inbred mice derived from the C57BL/6J and DBA/2J strains, whose spermatozoa showed distinct fertilization abilities after freezing. Genome-wide interval mapping identified two suggestive quantitative trait loci (QTL) associated with fertilization on chromosomes 1 and 11. The strongest QTL on chromosome 11 included 70 genes at 59.237260-61.324742 Mb and another QTL on chromosome 1 included 43 genes at 153.969506-158.217850 Mb. These regions included at least 15 genes involved with testicular expression and possibly with capacitation or sperm motility. Specifically, the Abl2 gene on chromosome 1, which may affect subcellular actin distribution, had polymorphisms between C57BL/6J and DBA/2J that caused at least three amino acid substitutions. A correlation analysis using recombinant inbred strains revealed that the fertilization rate was strongly correlated with the capacitation rate of frozen-thawed spermatozoa after preincubation. This result is consistent with the fact that C57BL/6J frozen-thawed spermatozoa recover their fertilization capacity following treatment with methyl-β-cyclodextrin to enhance sperm capacitation. Thus, our data provide important clues to the molecular mechanisms underlying cryodamage to mouse spermatozoa.


Structural Basis of Telomerase Inhibition by the Highly Specific BIBR1532.
BIBR1532 is a highly specific telomerase inhibitor, although the molecular basis for inhibition is unknown. Here we present the crystal structure of BIBR1532 bound to Tribolium castaneum catalytic subunit of telomerase (tcTERT). BIBR1532 binds to a conserved hydrophobic pocket (FVYL motif) on the outer surface of the thumb domain. The FVYL motif is near TRBD residues that bind the activation domain (CR4/5) of hTER. RNA binding assays show that the human TERT (hTERT) thumb domain binds the P6.1 stem loop of CR4/5 in vitro. hTERT mutations of the FVYL pocket alter wild-type CR4/5 binding and cause telomere attrition in cells. Furthermore, the hTERT FVYL mutations V1025F, N1028H, and V1090M are implicated in dyskeratosis congenita and aplastic anemia, further supporting the biological and clinical relevance of this novel motif. We propose that CR4/5 contacts with the telomerase thumb domain contribute to telomerase ribonucleoprotein assembly and promote enzymatic activity.


Risk factors for typhlitis.
A case-control study was undertaken to identify risk factors for typhlitis in patients with hematological malignancies. A data base file with a total of 410 episodes of fever and neutropenia in patients cared for between May 1987 and 1996 was reviewed. Typhlitis was defined as a symptom complex of fever, intense abdominal pain and tenderness in the presence of neutropenia. Five cases of typhlitis were identified. Three controls for every patient were randomly selected from the same cohort. Diarrhea and jaundice were more frequent in patients than in controls (p=0.03). The presence of mucositis, prolonged duration of profound neutropenia and idarubicin treatment proved to be risk factors for typhlitis.


Exploring differences in Canadian adult men and women with diabetes management: results from the Canadian Community Health Survey.
Over 2 million Canadians are known to have diabetes. In addition to the economic burden placed on the healthcare system, the human cost associated with diabetes poses a heavy burden on those living with diabetes. The literature shows that apparent differences exist in diabetes complications and diabetes management between men and women. How self-care management and utilization of health services differ by sex is not clearly understood.The purpose of this study was to explore sex differences in diabetes self-care and medical management in the Canadian population, using a nationally representative sample. Data collected from the cross-sectional, population-based Canadian Community Health Survey (2007-2008) were used in these analyses. A bootstrap variance estimation method and bootstrap weights provided by Statistics Canada were used to calculate 95% confidence intervals. Bivariate analyses identified variables of interest between females and males that were used in subsequent multivariate analyses. A total of 131,959 respondents were surveyed for the years of 2007 and 2008, inclusive. Fully adjusted multinomial and logistic regression analyses revealed sex differences for those living with diabetes. Compared to men with diabetes, women were more likely to be in the lowest income quintiles than the highest (OR: 1.8, 95% CI: 1.3-2.6) and were more likely not to have a job in the previous week (OR: 1.8, 95% CI: 1.4-2.4). Women were also more likely to avoid foods with fats or high calories (OR: 2.1, 95% CI: 1.4-3.0 and OR: 2.2, 95% CI: 1.6-3.0, respectively), to be concerned about heart disease (OR: 1.6, 95% CI: 1.1-2.2), and to be non-smokers (OR: 2.2, 95% CI: 1.6-3.0). However, despite their increased concern, women checked their blood-glucose less frequently on a daily basis than men (μwomen = 1.7, 95% CI: 1.7-1.8; μmen = 3.1, 95% CI: 2.9-3.2). Women were more likely to have an anxiety disorder (OR: 2.3, 95% CI: 1.7-3.2) and a mood disorder (OR: 2.4, 95% CI: 1.8-3.1), and more likely to be physically inactive (OR: 1.5, 95% CI: 1.2-1.8). Our findings underscore the importance of addressing sex differences which may interfere with diabetes self-care. In women, addressing socioeconomic and psychological barriers, as well as limitations to active living are important; in men, the benefit of more effective nutrition therapy and smoking cessation interventions are suggested. The results for this study highlight the need to further investigate and eliminate disparities between the sexes in order to optimize health outcomes among Canadians with diabetes.


Bioassay-guided fractionation of extracts from Codiaeum variegatum against Entamoeba histolytica discovers compounds that modify expression of ceramide biosynthesis related genes.
Leaves of Codiaeum variegatum ("garden croton") are used against bloody diarrhoea by local populations in Cameroon. This study aims to search for the active components from C. variegatum against Entamoeba histolytica, and thereby initiate the study of their mechanism of action. A bioassay-guided screening of the aqueous extracts from C. variegatum leaves and various fractions was carried out against trophozoites of E. histolytica axenic culture. We found that the anti-amoebic activity of extracts changed with respect to the collection criteria of leaves. Thereby, optimal conditions were defined for leaves' collection to maximise the anti-amoebic activity of the extracts. A fractionation process was performed, and we identified several sub-fractions (or isolated compounds) with significantly higher anti-amoebic activity compared to the unfractionated aqueous extract. Anti-amoebic activity of the most potent fraction was confirmed with the morphological characteristics of induced death in trophozoites, including cell rounding and lysis. Differential gene expression analysis using high-throughput RNA sequencing implies the potential mechanism of its anti-amoebic activity by targeting ceramide, a bioactive lipid involved in disturbance of biochemical processes within the cell membrane including differentiation, proliferation, cell growth arrest and apoptosis. Regulation of ceramide biosynthesis pathway as a target for anti-amoebic compounds is a novel finding which could be an alternative for drug development against E. histolytica.


Indicators of phagocytosis in women with acne during comprehensive treatment that included immunotherapy and probiotics.
Introduction: Acne is one of the most common dermatological diseases. It may have a chronic course, leaving permanent marks, and in last years has been tending to have more and more severe clinical course with widespread skin lesions. According to recent studies, the development of acne is due to the combined effect of endogenous and exogenous factors, among which endocrine diseases (quite a significant aspect), disorders of metabolic processes, reduced systemic immunity and phagocytic ability of mononuclear phagocytes and granulocytes at various stages of phagocytosis of pyogenic cocci, which contributes to more severe clinical course, and frequent relapse of this diseases. It was also proved that the intestinal microbiota plays an important role in the formation of homeostasis and immune response. The aim of the studyis to determine the evolution of phagocytosis indices in patients with acne under differentcomprehensive treatments, using oral antibiotics, immunotherapy, probiotics and low-dose birth control pills. Materials and methods: We observed 93 women with acne aged from 18 to 25 years old. In 19 (20,43 %) patients mild acne was diagnosed, in 41 (44.09%) - moderate acne, in 33 (35.48 %) persons - severe acne, 54 (58,06%) persons suffered from acne up to 1 year, 39 (41,93%) - from 1 to 3 years. To assess the state of phagocytosis in patients with acne vulgaris, we determined phagocytic activity (PA) and phagocytic index (PI) of polymorphonuclear leukocytes, nitro blue tetrazolium recovery test (NBT test spontaneous) and NBT-test pyrogenal stimulated by the recognized methods. Results: Analysis of the studied parameters of phagocytosis at the end of treatment showed a significant increase in patients of the core group who were administered a comprehensive treatment which included oral antibiotic, probiotic, low-dose birth control pills and autohemotherapy, as compared with the patients of other groups under study. Conclusions: Using combined therapy for women with acne occurring against the backdrop of a sluggish process of phagocytosis and concomittant intestinal dysbiosis leads to normalization of the leading indices of phagocytosis (PI, PA, NBT tests both spontaneous and stimulated), and enchances their phagocytic activity both during capture and formation of bactericidal activity and in the final stages of phagocytosis justifying the feasibility of a combined use of antibiotics, probiotic, low-dose birth control pills and autohemotherapy in the treatment of acne.


Biodiesel versus diesel: a pilot study comparing exhaust exposures for employees at a rural municipal facility.
Many organizations interested in renewable, domestic energy have switched from petroleum diesel to biodiesel blends for use in transportation and heavy-duty equipment. Although considerable evidence exists on the negative health effects of petroleum diesel exhaust exposures in occupational settings, there has been little research examining biodiesel exposures. Working collaboratively with a local municipality, concentrations of particulate matter (PM) and other air toxics were measured at a recycling facility in southwestern New Hampshire while heavy equipment operated first on petroleum diesel and then on a B20 blend (20% soy-based biodiesel/80% petroleum diesel). This pilot study used a combination of established industrial hygiene and environmental air monitoring methods to estimate occupational exposure profiles to PM and air toxics from combustion of petroleum diesel and biodiesel. Results indicate that B20 use dramatically reduces work area respirable particle, PM2.5 (PM < or = 2.5 microm in aerodynamic diameter), and formaldehyde levels compared with petroleum diesel. Some volatile organic compound concentrations were higher for petroleum diesel and others were higher for the B20 blend. Overall, this study suggests that biodiesel blends reduce worker exposure to and health risk from petroleum diesel exhaust, but additional exposure research is recommended.


Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast.
Quantification of intracellular metabolite fluxes by 13C-tracer experiments is maturing into a routine higher-throughput analysis. The question now arises as to which mutants should be analyzed. Here we identify key experiments in a systems biology approach with a genome-scale model of Saccharomyces cerevisiae metabolism, thereby reducing the workload for experimental network analyses and functional genomics. Genome-scale 13C flux analysis revealed that about half of the 745 biochemical reactions were active during growth on glucose, but that alternative pathways exist for only 51 gene-encoded reactions with significant flux. These flexible reactions identified in silico are key targets for experimental flux analysis, and we present the first large-scale metabolic flux data for yeast, covering half of these mutants during growth on glucose. The metabolic lesions were often counteracted by flux rerouting, but knockout of cofactor-dependent reactions, as in the adh1, ald6, cox5A, fum1, mdh1, pda1, and zwf1 mutations, caused flux responses in more distant parts of the network. By integrating computational analyses, flux data, and physiological phenotypes of all mutants in active reactions, we quantified the relative importance of 'genetic buffering' through alternative pathways and network redundancy through duplicate genes for genetic robustness of the network. The apparent dispensability of knockout mutants with metabolic function is explained by gene inactivity under a particular condition in about half of the cases. For the remaining 207 viable mutants of active reactions, network redundancy through duplicate genes was the major (75%) and alternative pathways the minor (25%) molecular mechanism of genetic network robustness in S. cerevisiae.


A new mitochondrial DNA deletion associated with diabetic amyotrophy, diabetic myoatrophy and diabetic fatty liver.
Mitochondrial dysfunctions of the muscle in diabetic amyotrophy and of the liver in diabetic fatty liver have been reported. We investigated mitochondrial gene mutations in three cases: (1) a patient with diabetic amyotrophy in the muscles of the lower extremities, and neuropathy; (2) 5 diabetics with myoatrophy, diabetic nephropathy, and chronic renal failure; and (3) an IDDM patient with a diabetic fatty liver. We identified a 5778-bp deletion (8214-13991) in mitochondrial DNA from the muscle and liver biopsy specimens by the primer shift PCR and PCR-direct sequence methods. It is speculated that 5778-bp deletion is due to homogeneous recombination in the 7-bp repeat sequence of TCCTAGA flanking the region deleted in the mitochondrial DNA. Determination of respiratory chain enzyme activities in fresh muscle mitochondria demonstrated the defect in complex I activity. The deletion covers areas coding ND3, ND4, ND4L, and ND5 in complex I. The 5778-bp deletion might cause a defect in mitochondrial oxidative phosphorylation and contribute to the pathogenesis of diabetic amyotrophy, myoatrophy with diabetic nephropathy, and chronic renal failure, as well as diabetic fatty liver in IDDM.


erg, a human ets-related gene on chromosome 21: alternative splicing, polyadenylation, and translation.
The avian acute leukemia virus E26 induces a mixed erythroid-myeloid leukemia in chickens and carries two distinct oncogenes, v-myb and v-ets. Recently, a novel gene named erg, closely related to the v-ets oncogene, was identified in human COLO 320 cells and the nucleotide sequence of its approximately 5.0-kilobase transcript, erg 1 was determined. In the present study, the nucleotide sequence of the alternatively spliced transcript, erg 2, was found to differ from erg 1 by a splicing event that causes a coding frameshift near the amino terminus, resulting in an additional 99-amino acid insertion at the amino-terminus. Expression of complementary DNAs for the two transcripts in vitro resulted in synthesis of polypeptides of approximately 41 and 52 kilodaltons, suggesting the use of alternative translation initiation codons in the case of erg proteins. The erg gene was localized by somatic cell genetic analysis to human chromosome 21. It is proposed that alternative sites of splicing and polyadenylation, together with alternative sites of translation initiation, allow the synthesis of two related polypeptides from a single erg gene transcriptional unit.


High-resolution melting-curve analysis of ligation-mediated real-time PCR for rapid evaluation of an epidemiological outbreak of extended-spectrum-beta-lactamase-producing Escherichia coli.
Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated Escherichia coli isolates (n = 15) and control isolates (n = 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (n = 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing E. coli strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE.


Hippocampal remapping is constrained by sparseness rather than capacity.
Grid cells in the medial entorhinal cortex encode space with firing fields that are arranged on the nodes of spatial hexagonal lattices. Potential candidates to read out the space information of this grid code and to combine it with other sensory cues are hippocampal place cells. In this paper, we investigate a population of grid cells providing feed-forward input to place cells. The capacity of the underlying synaptic transformation is determined by both spatial acuity and the number of different spatial environments that can be represented. The codes for different environments arise from phase shifts of the periodical entorhinal cortex patterns that induce a global remapping of hippocampal place fields, i.e., a new random assignment of place fields for each environment. If only a single environment is encoded, the grid code can be read out at high acuity with only few place cells. A surplus in place cells can be used to store a space code for more environments via remapping. The number of stored environments can be increased even more efficiently by stronger recurrent inhibition and by partitioning the place cell population such that learning affects only a small fraction of them in each environment. We find that the spatial decoding acuity is much more resilient to multiple remappings than the sparseness of the place code. Since the hippocampal place code is sparse, we thus conclude that the projection from grid cells to the place cells is not using its full capacity to transfer space information. Both populations may encode different aspects of space.


Muscarinic-receptor stimulation enhances polyphosphoinositide breakdown in guinea-pig ileum smooth muscle.
Muscarinic-receptor stimulation by 0.1 mM-carbachol in longitudinal muscle of the guinea-pig ileum increases the incorporation of [3H]inositol into inositol-containing phospholipid. This effect was blocked by 16 microM-atropine. After 60 min incubation, carbachol increased the accumulation of total inositol phosphates 20-fold in the presence of 10 mM-Li+. Less than 20% of the total inositol phosphate corresponded to inositol 1-phosphate by ion-exchange chromatography, whereas of the remainder about two-thirds corresponded to inositol bisphosphate and one third to inositol trisphosphate. It is concluded that stimulation of muscarinic receptors in guinea-pig ileum enhances breakdown of polyphosphoinositides, suggesting that this may be a primary event associated with Ca2+ mobilization in the guinea-pig ileum.


Long-term controlled normoglycemia in diabetic non-human primates after transplantation with hCD46 transgenic porcine islets.
Xenotransplantation of porcine islets into diabetic non-human primates is characterized by (i) an initial massive graft loss possibly due to the instant blood-mediated inflammatory reaction and (ii) the requirement of intensive, clinically unfriendly immunosuppressive therapy. We investigated whether the transgenic expression of a human complement-regulatory protein (hCD46) on porcine islets would improve the outcome of islet xenotransplantation in streptozotocin-induced diabetic Cynomolgus monkeys. Immunosuppression consisted of thymoglobulin, anti-CD154 mAb for costimulation blockade, and mycophenolate mofetil. Following the transplantation of islets from wild-type pigs (n = 2) or from 1,3-galactosyltransferase gene-knockout pigs (n = 2), islets survived for a maximum of only 46 days, as evidenced by return to hyperglycemia and the need for exogenous insulin therapy. The transplantation of islets from hCD46 pigs resulted in graft survival and insulin-independent normoglycemia in four of five monkeys for the 3 months follow-up of the experiment. One normalized recipient, selected at random, was followed for >12 months. Inhibition of complement activation by the expression of hCD46 on the pig islets did not substantially reduce the initial loss of islet mass, rather was effective in limiting antibody-mediated rejection. This resulted in a reduced need for immunosuppression to preserve a sufficient islet mass to maintain normoglycemia long-term.


Human and chicken TLR pathways: manual curation and computer-based orthology analysis.
The innate immune responses mediated by Toll-like receptors (TLR) provide an evolutionarily well-conserved first line of defense against microbial pathogens. In the Reactome Knowledgebase we previously integrated annotations of human TLR molecular functions with those of over 4000 other human proteins involved in processes such as adaptive immunity, DNA replication, signaling, and intermediary metabolism, and have linked these annotations to external resources, including PubMed, UniProt, EntrezGene, Ensembl, and the Gene Ontology to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. We have now used a combination of manual expert curation and computer-based orthology analysis to generate a set of annotations for TLR molecular function in the chicken (Gallus gallus). Mammalian and avian lineages diverged approximately 300 million years ago, and the avian TLR repertoire consists of both orthologs and distinct new genes. The work described here centers on the molecular biology of TLR3, the host receptor that mediates responses to viral and other doubled-stranded polynucleotides, as a paradigm for our approach to integrated manual and computationally based annotation and data analysis. It tests the quality of computationally generated annotations projected from human onto other species and supports a systems biology approach to analysis of virus-activated signaling pathways and identification of clinically useful antiviral measures.


Perspectives From COPD Subjects on Portable Long-Term Oxygen Therapy Devices.
Oxygen therapy for patients with COPD and severe hypoxemia requires the use of oxygen delivery devices that allow mobility as needed. However, the characteristics of some devices may limit the freedom of individuals to be as physically active as they desire. Limited mobility may negatively affect the perceived quality of life of individuals with COPD. The aim of this study was to understand perceived limitations that patients with COPD experience in using long-term oxygen therapy (LTOT) devices. We performed a qualitative analysis of 311 responses to an open-ended question from a previously deployed electronic survey designed to investigate how LTOT devices affect oxygen-dependent patients with COPD. Our thematic analysis was facilitated by NVivo, a qualitative data analysis software package. This involved identifying patterns and themes within the robust, text-rich data from the open-ended survey question regarding the survey subjects' experiences with their LTOT devices. Cluster analysis was also performed to highlight relationships between various concepts. Themes generated revealed that subjects experienced decreased mobility, which resulted in feelings of decreased autonomy and isolation. We also found that subjects perceived a decrease in quality of life due to their described experience of portable oxygen cylinders being heavy and cumbersome. Subjects described feelings of fear and anxiety due to insufficient support for breathing provided by pulse-dose portable oxygen concentrators, as well as portable oxygen cylinders that run out before they are able to complete errands and other activities of daily living. Some subjects also reported that they willingly pay for liquid oxygen systems out-of-pocket because of the mobility it affords, which in their perception improves their quality of life. Oxygen-dependent individuals with COPD may be at risk of adverse outcomes associated with decreased mobility encouraged by unsatisfactory physical and technical characteristics of portable oxygen cylinders and concentrators.


Fabrication of poly-crystalline Si-based Mie resonators via amorphous Si on SiO2 dewetting.
We report the fabrication of Si-based dielectric Mie resonators via a low cost process based on solid-state dewetting of ultra-thin amorphous Si on SiO2. We investigate the dewetting dynamics of a few nanometer sized layers annealed at high temperature to form submicrometric Si-particles. Morphological and structural characterization reveal the polycrystalline nature of the semiconductor matrix as well as rather irregular morphologies of the dewetted islands. Optical dark field imaging and spectroscopy measurements of the single islands reveal pronounced resonant scattering at visible frequencies. The linewidth of the low-order modes can be ∼20 nm in full width at half maximum, leading to a quality factor Q exceeding 25. These values reach the state-of-the-art ones obtained for monocrystalline Mie resonators. The simplicity of the dewetting process and its cost-effectiveness opens the route to exploiting it over large scales for applications in silicon-based photonics.


Localization and imaging of radiolabeled monoclonal antibodies against colorectal carcinoma in tumor-bearing nude mice.
Four monoclonal antibodies (MoAbs) (35, 115, 17-1A, and B72.3) directed towards human carcinoma surface antigens have been studied in athymic nude mice with LS174T, CO112, or SW948 colon carcinoma xenografts or negative control melanoma (MEL-1), lymphoma (Namalwa), and breast (MCF-7) carcinoma xenografts to evaluate the effects of antigenic heterogeneity and time after administration on localization and imaging. 125I-labeled 115 showed the highest uptake of any antibody in LS174T tumors. MoAbs 35 and B72.3 showed similar but lower levels of uptake in LS174T and CO112 tumors, but B72.3 concentrated less in SW948 tumors. 17-1A showed the highest degree of accumulation in SW948 tumor xenografts. No specific uptake of the four anti-carcinoma MoAbs was observed in MEL-1, Namalwa, or MCF-7 xenografts. The specificity of the in vivo tumor localization of the four anti-carcinoma MoAbs was confirmed by the low degree of accumulation of a control MoAb against influenza virus in LS174T tumors. Imaging studies with 131I-labeled colorectal cancer MoAbs showed specific uptake and retention in LS174T tumors, with progressive clearance from the whole body. The colorectal cancer MoAbs were compared for immunohistochemical binding against biopsies from patients with colorectal cancer and adjacent normal colonic tissue. Most colorectal cancer specimens showed moderate to strong staining with the four MoAbs. The percentage of positive cells varied within and between tumors demonstrating antigenic heterogeneity. Absent to slight focal staining was seen with normal colon tissue. B72.3 showed the highest degree of staining specificity. This study indicates a difference in the immunohistochemical binding of a panel of MoAbs against biopsies of colon adenocarcinoma and a dependence of in vivo localization on the human colon cancer cell line used as target. This has important implications for future clinical diagnostic and therapeutic studies.


Well-being in mothers of children with congenital heart defects: a 3-year follow-up.
This prospective case-cohort study compared subjective well-being (SWB) among mothers whose children had various degrees of congenital heart defects (CHD) with mothers of children without CHD (controls). Nationwide CHD registry data were linked to data collected from the Norwegian Mother and Child Cohort Study at gestational week 30, 6 months, and 36 months postpartum. A total of 175 mothers of children with mild, moderate, and severe CHD were identified in a cohort of 44,144 mothers. The SWB index was operationalized by means of three subscales: a cognitive aspect, positive affect, and negative affect. Mothers of children with severe CHD reported significantly lower SWB than the controls at 6 months postpartum (p = .003), with further decrease in SWB at 36 months postpartum (p = .001). SWB levels in the mild and moderate CHD group did not deviate significantly from controls. The findings suggest a pattern in which all stressors concerning the severely ill child lead to significant deterioration of maternal well-being. Having a child with mild or moderate CHD, which is a less severe and shorter-term stressor, did not reduce mothers' well-being.


Use of a community trail among new and habitual exercisers: a preliminary assessment.
We evaluated physical activity patterns and trail use among new and habitually active exercisers using onsite trail interviews. Using a cross-sectional study design, 414 adults who accessed two new trails that bisect a rural community of 26,809 residents were interviewed during the first summer of the trails' official operation (2001). The trails comprise 12 miles of level and paved surface and run parallel to adjacent water sheds, businesses, and neighborhoods. Recent trail activity patterns were obtained, including the following: frequency of use, mode of activity, duration, distance traveled on trail, access points, time of day used, use of exercise companions, and distance traveled to get to trail. Perceived enablers and barriers related to trail use were also obtained. Data were compared between newly adopted exercisers (new exercisers) and individuals active prior to development of the trails (habitually active exercisers). Twenty-three percent of the trail users were new exercisers. New exercisers were more dependent on the trails as a primary outlet for physical activity than were habitually active exercisers (P < .001). New exercisers traveled shorter distances to access the trails and rated convenience as a primary reason for using them. Both safety and terrain issues emerged as enablers for trail use, and unsafe conditions emerged as a concern among new exercisers. A community trail may be an important vehicle for promoting physically active lifestyles. However, new exercisers must overcome issues of proximal and safe access from residential areas in addition to other safety concerns to achieve regular physical activity.


Immunological mechanisms of the antitumor effects of supplemental oxygenation.
Antitumor T cells either avoid or are inhibited in hypoxic and extracellular adenosine-rich tumor microenvironments (TMEs) by A2A adenosine receptors. This may limit further advances in cancer immunotherapy. There is a need for readily available and safe treatments that weaken the hypoxia-A2-adenosinergic immunosuppression in the TME. Recently, we reported that respiratory hyperoxia decreases intratumoral hypoxia and concentrations of extracellular adenosine. We show that it also reverses the hypoxia-adenosinergic immunosuppression in the TME. This, in turn, stimulates (i) enhanced intratumoral infiltration and reduced inhibition of endogenously developed or adoptively transfered tumor-reactive CD8 T cells, (ii) increased proinflammatory cytokines and decreased immunosuppressive molecules, such as transforming growth factor-β (TGF-β), (iii) weakened immunosuppression by regulatory T cells, and (iv) improved lung tumor regression and long-term survival in mice. Respiratory hyperoxia also promoted the regression of spontaneous metastasis from orthotopically grown breast tumors. These effects are entirely T cell- and natural killer cell-dependent, thereby justifying the testing of supplemental oxygen as an immunological coadjuvant to combine with existing immunotherapies for cancer.


A new model of the role of psychological and emotional distress in promoting obesity: conceptual review with implications for treatment and prevention.
The lack of significant treatment and prevention progress highlights the need for a more expanded strategy. Given the robust association between socioeconomic factors and obesity, combined with new insights into how socioeconomic disadvantage affects both behaviour and biology, a new causal model is proposed. The model posits that psychological and emotional distress is a fundamental link between socioeconomic disadvantage and weight gain. At particular risk are children growing up in a disharmonious family environment, mainly caused by parental socioeconomic disadvantage, where they are exposed to parental frustrations, relationship discord, a lack of support and cohesion, negative belief systems, unmet emotional needs and general insecurity. Without adequate resilience, such experiences increase the risk of psychological and emotional distress, including low self-esteem and self-worth, negative emotions, negative self-belief, powerlessness, depression, anxiety, insecurity and a heightened sensitivity to stress. These inner disturbances eventually cause a psycho-emotional overload, triggering a cascade of weight gain-inducing effects including maladaptive coping strategies such as eating to suppress negative emotions, chronic stress, appetite up-regulation, low-grade inflammation and possibly reduced basal metabolism. Over time, this causes obesity, circular causality and further weight gain. Tackling these proposed root causes of weight gain could potentially improve both treatment and prevention outcomes.


A network of chaperones prevents and detects failures in membrane protein lipid bilayer integration.
A fundamental step in membrane protein biogenesis is their integration into the lipid bilayer with a defined orientation of each transmembrane segment. Despite this, it remains unclear how cells detect and handle failures in this process. Here we show that single point mutations in the membrane protein connexin 32 (Cx32), which cause Charcot-Marie-Tooth disease, can cause failures in membrane integration. This leads to Cx32 transport defects and rapid degradation. Our data show that multiple chaperones detect and remedy this aberrant behavior: the ER-membrane complex (EMC) aids in membrane integration of low-hydrophobicity transmembrane segments. If they fail to integrate, these are recognized by the ER-lumenal chaperone BiP. Ultimately, the E3 ligase gp78 ubiquitinates Cx32 proteins, targeting them for degradation. Thus, cells use a coordinated system of chaperones for the complex task of membrane protein biogenesis, which can be compromised by single point mutations, causing human disease.


Development of ListeriaBase and comparative analysis of Listeria monocytogenes.
Listeria consists of both pathogenic and non-pathogenic species. Reports of similarities between the genomic content between some pathogenic and non-pathogenic species necessitates the investigation of these species at the genomic level to understand the evolution of virulence-associated genes. With Listeria genome data growing exponentially, comparative genomic analysis may give better insights into evolution, genetics and phylogeny of Listeria spp., leading to better management of the diseases caused by them. With this motivation, we have developed ListeriaBase, a web Listeria genomic resource and analysis platform to facilitate comparative analysis of Listeria spp. ListeriaBase currently houses 850,402 protein-coding genes, 18,113 RNAs and 15,576 tRNAs from 285 genome sequences of different Listeria strains. An AJAX-based real time search system implemented in ListeriaBase facilitates searching of this huge genomic data. Our in-house designed comparative analysis tools such as Pairwise Genome Comparison (PGC) tool allowing comparison between two genomes, Pathogenomics Profiling Tool (PathoProT) for comparing the virulence genes, and ListeriaTree for phylogenic classification, were customized and incorporated in ListeriaBase facilitating comparative genomic analysis of Listeria spp. Interestingly, we identified a unique genomic feature in the L. monocytogenes genomes in our analysis. The Auto protein sequences of the serotype 4 and the non-serotype 4 strains of L. monocytogenes possessed unique sequence signatures that can differentiate the two groups. We propose that the aut gene may be a potential gene marker for differentiating the serotype 4 strains from other serotypes of L. monocytogenes. ListeriaBase is a useful resource and analysis platform that can facilitate comparative analysis of Listeria for the scientific communities. We have successfully demonstrated some key utilities of ListeriaBase. The knowledge that we obtained in the analyses of L. monocytogenes may be important for functional works of this human pathogen in future. ListeriaBase is currently available at http://listeria.um.edu.my .


Identification of cross-reactive carbohydrate determinants in subjects reporting work-related respiratory symptoms.
The role of cross-reactive carbohydrate determinants (CCDs) in diagnostics of occupational allergy remains unclarified and its clinical relevance is still questioned. The aim of the study was to assess the frequency of positive response to CCDs in the subjects with suspected occupational allergy and the relationship between other diagnostic test results and final diagnosis. The study group included 201 patients. They underwent clinical examination, skin prick test (SPT) to common and occupational allergens, specific serum immunoglobulin (sIgE) determinations, spirometry and specific inhalation challenge test. Moreover, sIgE to CCDs from bromelain was assessed in all subjects. Occupational respiratory allergy was recognized in 64.3% of CCD-positive and 52.4% of CCD-negative patients. Positive SPT results to common and occupational allergens were found in 64.3% and 35.7% of CCD-positive subjects, respectively. In all subjects with CCDs, the sIgE to grass pollens as well as to occupational allergens were detected. The total IgE level > 100 kU/l was significantly associated with the presence of sIgE to CCDs. sIgE to CCDs were found in 7% of subjects suspected to suffer from occupational respiratory allergy. The presence of CCDs is not significantly associated with occupational respiratory allergy. It is also not more frequent in subjects reporting work-related respiratory symptoms in whom occupational allergy was not confirmed. The elevated total IgE level was related with CCD positivity. In patients with suspected occupational allergy, the presence of sIgE to CCDs in serum did not indicate the irrelevance of positive sIgE to occupational allergens.


Involving healthcare professionals and family carers in setting research priorities for end-of-life care.
It is important to ensure regional variances are considered when setting future end-of-life research priorities, given the differing demographics and service provision. This project sought to identify end-of-life research priorities within Greater Manchester (United Kingdom). Following an initial scoping exercise, six topics within the 10 national priorities outlined by The Palliative and end-of-life care Priority Setting Partnership were selected for exploration. A workshop involving 32 healthcare professionals and a consultation process with 26 family carers was conducted. Healthcare professionals and carers selected and discussed the topics important to them. The topics selected most frequently by both healthcare professionals and carers were 'Access to 24 hour care', 'Planning end-of-life care in advance' and 'Staff and carer education'. Healthcare professionals also developed research questions for their topics of choice which were refined to incorporate carers' views. These questions are an important starting point for future end-of-life research within Greater Manchester.


Human fetal cardiac function during the first trimester of pregnancy.
To investigate first trimester human fetal cardiac function in relation to cardiac volume blood flow, and peripheral arterial and venous blood flow patterns. Transvaginal Doppler ultrasonography was performed in 16 uncomplicated pregnancies at 6+, 7+, 8+, 9+, and 10+ gestational weeks. The shape of the inflow waveform and the presence of atrioventricular valve regurgitation (AVVR) were noted. The outflow mean velocity (Vmean) was calculated. The proportions of the isovolumetric relaxation (IRT%) and contraction times (ICT%) of the cardiac cycle were defined. Ductus venosus and umbilical artery pulsatility indices (PI) were obtained. Every inflow waveform was monophasic before 9+ weeks. At 9+ weeks 11 of 16 and at 10+ weeks all waveforms were biphasic. At 7+ and 8+ weeks AVVR was documented in one case. At 9+ and 10+ weeks AVVR was present in four and seven fetuses, respectively. Mean (SD) outflow Vmean increased between 6+ and 8+ weeks from 3.6 (1.5) to 8.4 (3.0) cm/s (p < 0.05). IRT% decreased significantly from 6+ to 7+ weeks (39.8 (2.6) to 19.2 (6.2), p < 0.001). ICT% decreased between 8+ and 9+ weeks from 13.2 (4.0) to 8.5 (2.5) (p < 0.05). Ductus venosus PIs were unchanged. Umbilical artery Vmean increased between 7+ and 10+ weeks from 1.59 (0.51) to 5.06 (1.06) cm/s (p < 0.001) and PIs remained unchanged. The first trimester of pregnancy is characterised by significant improvements in cardiac diastolic and systolic function with a concomitant increase in cardiac volume blood flow. At 10+ weeks AVVR is a common finding. Placental volume blood flow increases significantly with no change in the placental vascular impedance.


Statistical monitoring of weak spots for improvement of normalization and ratio estimates in microarrays.
Several aspects of microarray data analysis are dependent on identification of genes expressed at or near the limits of detection. For example, regression-based normalization methods rely on the premise that most genes in compared samples are expressed at similar levels and therefore require accurate identification of nonexpressed genes (additive noise) so that they can be excluded from the normalization procedure. Moreover, key regulatory genes can maintain stringent control of a given response at low expression levels. If arbitrary cutoffs are used for distinguishing expressed from nonexpressed genes, some of these key regulatory genes may be unnecessarily excluded from the analysis. Unfortunately, no accurate method for differentiating additive noise from genes expressed at low levels is currently available. We developed a multistep procedure for analysis of mRNA expression data that robustly identifies the additive noise in a microarray experiment. This analysis is predicated on the fact that additive noise signals can be accurately identified by both distribution and statistical analysis. Identification of additive noise in this manner allows exclusion of noncorrelated weak signals from regression-based normalization of compared profiles thus maximizing the accuracy of these methods. Moreover, genes expressed at very low levels can be clearly identified due to the fact that their expression distribution is stable and distinguishable from the random pattern of additive noise.


Dynamic self-organization of side-propelling colloidal rods: experiments and simulations.
In recent years, there is a growing interest in designing artificial analogues of living systems, fueled not only by potential applications as 'smart micro-machines', but also by the demand for simple models that can be used to study the behavior of their more complex natural counterparts. Here, we present a facile, internally driven, experimental system comprised of fluorescently labeled colloidal silica rods of which the self-propulsion is powered by the decomposition of H2O2 catalyzed by a length-wise half Pt coating of the particles in order to study how shape anisotropy and swimming direction affect the collective behavior. We investigated the emerging structures and their time evolution for various particle concentrations in (quasi-)two dimensional systems for three aspect ratios of the rods on a single particle level using a combination of experiments and simulations. We found that the dynamic self-organization relied on a competition between self-propulsion and phoretic attractions induced by phoresis of the rods. We observed that the particle clustering behavior depends on the concentration as well as the aspect ratio of the rods. Our findings provide a more detailed understanding of dynamic self-organization of anisotropic particles and the role the propulsion direction plays in internally driven systems.


A highly thermostable trehalase from the thermophilic bacterium Rhodothermus marinus.
Trehalases play a central role in the metabolism of trehalose and can be found in a wide variety of organisms. A periplasmic trehalase (alpha,alpha-trehalose glucohydrolase, EC 18.104.22.168) from the thermophilic bacterium Rhodothermus marinus was purified and the respective encoding gene was identified, cloned and overexpressed in Escherichia coli. The recombinant trehalase is a monomeric protein with a molecular mass of 59 kDa. Maximum activity was observed at 88 degrees C and pH 6.5. The recombinant trehalase exhibited a K(m) of 0.16 mM and a V(max) of 81 micromol of trehalose (min)(-1) (mg of protein)(-1) at the optimal temperature for growth of R. marinus (65 degrees C) and pH 6.5. The enzyme was highly specific for trehalose and was inhibited by glucose with a K(i) of 7 mM. This is the most thermostable trehalase ever characterized. Moreover, this is the first report on the identification and characterization of a trehalase from a thermophilic bacterium.


Polyarticular septic arthritis caused by Staphylococcus lugdunensis in a patient with systemic lupus erythematosus.
Septic arthritis in patients with systemic lupus erythematosus (SLE) is rare and is reported in only 3% of patients. Contrary to lupus arthritis, which tends to be polyarticular in nature, primarily involving the small joints of the hands, septic arthritis is commonly monoarticular. Here, we present an unusual case of a patient with SLE, who developed oligoarticular inflammatory arthritis caused by a rare native joint pathogen Staphylococcus lugdunensis. The infection resulted in extensive early damage to the joints involved, highlighting the need for early diagnosis and treatment.


A proliferation saturation index to predict radiation response and personalize radiotherapy fractionation.
Although altered protocols that challenge conventional radiation fractionation have been tested in prospective clinical trials, we still have limited understanding of how to select the most appropriate fractionation schedule for individual patients. Currently, the prescription of definitive radiotherapy is based on the primary site and stage, without regard to patient-specific tumor or host factors that may influence outcome. We hypothesize that the proportion of radiosensitive proliferating cells is dependent on the saturation of the tumor carrying capacity. This may serve as a prognostic factor for personalized radiotherapy (RT) fractionation. We introduce a proliferation saturation index (PSI), which is defined as the ratio of tumor volume to the host-influenced tumor carrying capacity. Carrying capacity is as a conceptual measure of the maximum volume that can be supported by the current tumor environment including oxygen and nutrient availability, immune surveillance and acidity. PSI is estimated from two temporally separated routine pre-radiotherapy computed tomography scans and a deterministic logistic tumor growth model. We introduce the patient-specific pre-treatment PSI into a model of tumor growth and radiotherapy response, and fit the model to retrospective data of four non-small cell lung cancer patients treated exclusively with standard fractionation. We then simulate both a clinical trial hyperfractionation protocol and daily fractionations, with equal biologically effective dose, to compare tumor volume reduction as a function of pretreatment PSI. With tumor doubling time and radiosensitivity assumed constant across patients, a patient-specific pretreatment PSI is sufficient to fit individual patient response data (R(2) = 0.98). PSI varies greatly between patients (coefficient of variation >128 %) and correlates inversely with radiotherapy response. For this study, our simulations suggest that only patients with intermediate PSI (0.45-0.9) are likely to truly benefit from hyperfractionation. For up to 20 % uncertainties in tumor growth rate, radiosensitivity, and noise in radiological data, the absolute estimation error of pretreatment PSI is <10 % for more than 75 % of patients. Routine radiological images can be used to calculate individual PSI, which may serve as a prognostic factor for radiation response. This provides a new paradigm and rationale to select personalized RT dose-fractionation.


Human mate choice and the wedding ring effect : Are married men more attractive?
Individuals are often restricted to indirect cues when assessing the mate value of a potential partner. Females of some species have been shown to copy each other's choice; in other words, the probability of a female choosing a particular male increases if he has already been chosen by other females. Recently it has been suggested that mate-choice copying could be an important aspect of human mate choice as well. We tested one of the hypotheses, the so-called wedding ring effect-that women would prefer men who are already engaged or married-in a series of live interactions between men and women. The results show that women do not find men signaling engagement, or being perceived as having a partner, more attractive or higher in socioeconomic status. Furthermore, signs of engagement did not influence the women's reported willingness to engage in short-term or long-term relationships with the men. Thus, this study casts doubt on some simplified theories of human mate-choice copying, and alternative, more complex scenarios are outlined and discussed.


The roles of ecological fitting, phylogeny and physiological equivalence in understanding realized and fundamental host ranges in endoparasitoid wasps.
Co-evolutionary theory underpins our understanding of interactions in nature involving plant-herbivore and host-parasite interactions. However, many studies that are published in the empirical literature that have explored life history and development strategies between endoparasitoid wasps and their hosts are based on species that have no evolutionary history with one another. Here, we investigated novel associations involving two closely related solitary endoparasitoids that originate from Europe and North America and several of their natural and factitious hosts from both continents. The natural hosts of both species are also closely related, all being members of the same family. We compared development and survival of both parasitoids on the four host species and predicted that parasitoid performance is better on their own natural hosts. In contrast with this expectation, survival, adult size and development time of both parasitoids were similar on all (with one exception) hosts, irrespective as to their geographic origin. Our results show that phylogenetic affinity among the natural and factitious hosts plays an important role in their nutritional suitability for related parasitoids. Evolved traits in parasitoids, such as immune suppression and development, thus enable them to successfully develop in novel host species with which they have no evolutionary history. Our results show that host suitability for specialized organisms like endoparasitoids is closely linked with phylogenetic history and macro-evolution as well as local adaptation and micro-evolution. We argue that the importance of novel interactions and 'ecological fitting' based on phylogeny is a greatly underappreciated concept in many resource-consumer studies.


Atherosclerosis and endothelial dysfunction in patients with ankylosing spondylitis.
Ankylosing spondylitis (AS) is a systemic inflammatory rheumatic disease characterized primarily by axial joint involvement, sacroiliitis and various extra-articular manifestations. High cardiovascular mortality in AS has led many researchers to investigate possible risk factors involved with cardiovascular disease in these patients. This review summarizes published data concerning endothelial dysfunction and atherosclerosis in patients with AS. The author discusses current limitations and problems related to a better assessment of these two possible changes in AS.


Cost-effectiveness of using a gene expression profiling test to aid in identifying the primary tumour in patients with cancer of unknown primary.
We aimed to investigate the cost-effectiveness of a 2000-gene-expression profiling (GEP) test to help identify the primary tumor site when clinicopathological diagnostic evaluation was inconclusive in patients with cancer of unknown primary (CUP). We built a decision-analytic-model to project the lifetime clinical and economic consequences of different clinical management strategies for CUP. The model was parameterized using follow-up data from the Manitoba Cancer Registry, cost data from Manitoba Health administrative databases and secondary sources. The 2000-GEP-based strategy compared to current clinical practice resulted in an incremental cost-effectiveness ratio (ICER) of $44,151 per quality-adjusted life years (QALY) gained. The total annual-budget impact was $36.2 million per year. A value-of-information analysis revealed that the expected value of perfect information about the test's clinical impact was $4.2 million per year. The 2000-GEP test should be considered for adoption in CUP. Field evaluations of the test are associated with a large societal benefit.


Facilitation can increase the phylogenetic diversity of plant communities.
With the advent of molecular phylogenies the assessment of community assembly processes has become a central topic in community ecology. These processes have focused almost exclusively on habitat filtering and competitive exclusion. Recent evidence, however, indicates that facilitation has been important in preserving biodiversity over evolutionary time, with recent lineages conserving the regeneration niches of older, distant lineages. Here we test whether, if facilitation among distant-related species has preserved the regeneration niche of plant lineages, this has increased the phylogenetic diversity of communities. By analyzing a large worldwide database of species, we showed that the regeneration niches were strongly conserved across evolutionary history. Likewise, a phylogenetic supertree of all species of three communities driven by facilitation showed that nurse species facilitated distantly related species and increased phylogenetic diversity.


Comparison of the effects of medium and long chain triglyceride containing liquid meals on gall bladder and small intestinal function in normal man.
We investigated the effects of medium (MCT) and long (LCT) chain triglyceride test meals on gall bladder contraction (using ultrasonography) and small intestinal bile acid concentrations and ileal flow rates (using intubation techniques) in normal individuals. Comparing the effects of ingesting medium chain triglyceride and long chain triglyceride meals, the gall bladder volume was reduced by 23.4 +/- 33.6% and 59.0 +/- 17.1% respectively (mean +/- SD, p less than 0.01, n = 13), the jejunal bile acid concentrations increased significantly only after the ingestion of long chain triglyceride (p less than 0.05, n = 5), while the volume of the postprandial jejunal contents was not significantly different (540 +/- 150, 522 +/- 169 ml, medium chain triglyceride vs long chain triglyceride, p = 0.2, n = 5). The postprandial colonic inflow was 48.5 +/- 12.5 and 123.4 +/- 35.2 ml/h (medium chain triglyceride vs long chain triglyceride, p less than 0.01, n = 5). Thus medium chain triglyceride, compared with long chain triglyceride, produces a smaller input of bile acids into the small intestine and a smaller volume of fluid delivered to the colon. These observations may be relevant to the beneficial effects of medium chain triglyceride substitution for long chain triglyceride in the treatment of diarrhoea in patients with small intestinal disease.


Chromatin organisation and cancer prognosis: a pan-cancer study.
Chromatin organisation affects gene expression and regional mutation frequencies and contributes to carcinogenesis. Aberrant organisation of DNA has been correlated with cancer prognosis in analyses of the chromatin component of tumour cell nuclei using image texture analysis. As yet, the methodology has not been sufficiently validated to permit its clinical application. We aimed to define and validate a novel prognostic biomarker for the automatic detection of heterogeneous chromatin organisation. Machine learning algorithms analysed the chromatin organisation in 461 000 images of tumour cell nuclei stained for DNA from 390 patients (discovery cohort) treated for stage I or II colorectal cancer at the Aker University Hospital (Oslo, Norway). The resulting marker of chromatin heterogeneity, termed Nucleotyping, was subsequently independently validated in six patient cohorts: 442 patients with stage I or II colorectal cancer in the Gloucester Colorectal Cancer Study (UK); 391 patients with stage II colorectal cancer in the QUASAR 2 trial; 246 patients with stage I ovarian carcinoma; 354 patients with uterine sarcoma; 307 patients with prostate carcinoma; and 791 patients with endometrial carcinoma. The primary outcome was cancer-specific survival. In all patient cohorts, patients with chromatin heterogeneous tumours had worse cancer-specific survival than patients with chromatin homogeneous tumours (univariable analysis hazard ratio [HR] 1·7, 95% CI 1·2-2·5, in the discovery cohort; 1·8, 1·0-3·0, in the Gloucester validation cohort; 2·2, 1·1-4·5, in the QUASAR 2 validation cohort; 3·1, 1·9-5·0, in the ovarian carcinoma cohort; 2·5, 1·8-3·4, in the uterine sarcoma cohort; 2·3, 1·2-4·6, in the prostate carcinoma cohort; and 4·3, 2·8-6·8, in the endometrial carcinoma cohort). After adjusting for established prognostic patient characteristics in multivariable analyses, Nucleotyping was prognostic in all cohorts except for the prostate carcinoma cohort (HR 1·7, 95% CI 1·1-2·5, in the discovery cohort; 1·9, 1·1-3·2, in the Gloucester validation cohort; 2·6, 1·2-5·6, in the QUASAR 2 cohort; 1·8, 1·1-3·0, for ovarian carcinoma; 1·6, 1·0-2·4, for uterine sarcoma; 1·43, 0·68-2·99, for prostate carcinoma; and 1·9, 1·1-3·1, for endometrial carcinoma). Chromatin heterogeneity was a significant predictor of cancer-specific survival in microsatellite unstable (HR 2·9, 95% CI 1·0-8·4) and microsatellite stable (1·8, 1·2-2·7) stage II colorectal cancer, but microsatellite instability was not a significant predictor of outcome in chromatin homogeneous (1·3, 0·7-2·4) or chromatin heterogeneous (0·8, 0·3-2·0) stage II colorectal cancer. The consistent prognostic prediction of Nucleotyping in different biological and technical circumstances suggests that the marker of chromatin heterogeneity can be reliably assessed in routine clinical practice and could be used to objectively assist decision making in a range of clinical settings. An immediate application would be to identify high-risk patients with stage II colorectal cancer who might have greater absolute benefit from adjuvant chemotherapy. Clinical trials are warranted to evaluate the survival benefit and cost-effectiveness of using Nucleotyping to guide treatment decisions in multiple clinical settings. The Research Council of Norway, the South-Eastern Norway Regional Health Authority, the National Institute for Health Research, and the Wellcome Trust.