Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term social dynamics drive loss of function in pathogenic bacteria

Significance Laboratory experiments show that bacteria have surprisingly complex social lives: Like humans, they can cooperate but also cheat each other. Cooperation could benefit bacteria causing infection by coordinating attack and producing toxins in a collective effort. But can cheaters, exploiting the work of others, affect the outcome of infection? We show that populations of bacteria causing chronic lung infections in cystic fibrosis patients contain cheaters that freeload to the point where cooperation no longer pays off by not producing a compound that helps them steal iron from blood. Bad news for bacteria but good for us if we can find ways to meddle in their social lives. Laboratory experiments show that social interactions between bacterial cells can drive evolutionary change at the population level, but significant challenges limit attempts to assess the relevance of these findings to natural populations, where selection pressures are unknown. We have increasingly sophisticated methods for monitoring phenotypic and genotypic dynamics in bacteria causing infectious disease, but in contrast, we lack evidence-based adaptive explanations for those changes. Evolutionary change during infection is often interpreted as host adaptation, but this assumption neglects to consider social dynamics shown to drive evolutionary change in vitro. We provide evidence to show that long-term behavioral dynamics observed in a pathogen are driven by selection to outcompete neighboring conspecific cells through social interactions. We find that Pseudomonas aeruginosa bacteria, causing lung infections in patients with cystic fibrosis, lose cooperative iron acquisition by siderophore production during infection. This loss could be caused by changes in iron availability in the lung, but surprisingly, we find that cells retain the ability to take up siderophores produced by conspecifics, even after they have lost the ability to synthesize siderophores. Only when cooperative producers are lost from the population is the receptor for uptake lost. This finding highlights the potential pitfalls of interpreting loss of function in pathogenic bacterial populations as evidence for trait redundancy in the host environment. More generally, we provide an example of how sequence analysis can be used to generate testable hypotheses about selection driving long-term phenotypic changes of pathogenic bacteria in situ.
Gender Differences in Outcomes after Ischemic Stroke: Role of Ischemic Lesion Volume and Intracranial Large-Artery Occlusion

Background: The reasons for gender disparities in stroke outcome remain unclear, and little is known about the value of acute neuroimaging characteristics in elucidating differential stroke outcomes between the sexes. Methods: We prospectively evaluated consecutive patients with acute ischemic stroke. CT angiography (CTA) was performed in all patients within 24 h of symptom onset. CTA source images were used to evaluate lesion volume. The primary outcome measure was a modified Rankin scale (mRS) score ≧3 at 6 months. Results: We evaluated 676 consecutive patients (322 women). Women were older than men (p < 0.01), more frequently had a prestroke mRS >0 (p < 0.01), and had higher admission National Institutes of Health Stroke scale scores (p = 0.01). More women had intracranial artery occlusions than men (46 vs. 33.1%, p = 0.01), but there was no significant difference between ischemic lesion volumes (p = 0.21). Using multiple regression, female gender remained an independent predictor of poor mRS scores at 6 months (odds ratio 1.57; 95% confidence interval 1.02–2.36) after adjustment for clinical and imaging covariates. Conclusion: Compared with men, women are less likely to achieve independence after acute ischemic stroke. The disparity in stroke outcome is not explained by differences in ischemic lesion volume or the presence of intracranial artery occlusions.
Decellularization and Solubilization of Porcine Liver for Use as a Substrate for Porcine Hepatocyte Culture

Biologic substrates, prepared by decellularizing and solubilizing tissues, have been of great interest in the tissue engineering field because of the preservation of complex biochemical constituents found in the native extracellular matrix (ECM). The integrity of the ECM is critical for cell behavior, adhesion, migration, differentiation, and proliferation that in turn affect homeostasis and tissue regeneration. Previous studies have shown that various processing methods have a distinctive way of affecting the composition of the decellularized ECM. In this study, we developed a bioactive substrate for hepatocytes in vitro, made of decellularized and solubilized liver tissue. The present work is a comparative approach of 2 different methods. First, we decellularized porcine liver tissue with ammonium hydroxide versus a sodium deoxycholate method, then characterized the decellularized tissue using various methods including double stranded DNA (dsDNA) content, DNA size, immunogenicity, and mass spectrometry. Second, we solubilized the decellularized porcine liver with hydrochloric acid versus acetic acid (AA) and characterized the resultant solubilized tissues using relevant methodologies including protein yield, immunogenicity, and bioactivity. Finally, we isolated primary porcine hepatocytes, cultured, and evaluated their bioactivity on the optimized decellularized–solubilized liver substrate. The decellularized porcine liver ECM processed by the ammonium hydroxide method and solubilized with AA displayed higher ECM integrity, low dsDNA, no evidence of intact nuclei, low human monocyte chemoattraction, and the presence of key molecules typically found in the native liver, a very important element for normal cell function. In addition, primary porcine hepatocytes showed enhanced functionality including albumin and urea production and bile canaliculi formation when cultured on the developed liver substrate compared to type I collagen.
Interpreting CNN Models for Apparent Personality Trait Regression

This paper addresses the problem of automatically inferring personality traits of people talking to a camera. As in many other computer vision problems, Convolutional Neural Networks (CNN) models have shown impressive results. However, despite of the success in terms of performance, it is unknown what internal representation emerges in the CNN. This paper presents a deep study on understanding why CNN models are performing surprisingly well in this complex problem. We use current techniques on CNN model interpretability, combined with face detection and Action Unit (AUs) recognition systems, to perform our quantitative studies. Our results show that: (1) face provides most of the discriminative information for personality trait inference, and (2) the internal CNN representations mainly analyze key face regions such as eyes, nose, and mouth. Finally, we study the contribution of AUs for personality trait inference, showing the influence of certain AUs in the facial trait judgments.
Advances in tracking hematopoiesis at the single-cell level

Purpose of reviewStudying heterogeneous populations, such as hematopoietic stem cells (HSCs), requires continuous long-term observation of living cells at the single-cell level. The purpose of this review is to discuss recent advances in technologies required for continuous single-cell analysis and the contribution of this approach to find answers in hematopoiesis research. Recent findingsContinuous long-term imaging at the single-cell level still requires custom-made hardware, software and manual in-depth analysis of large amounts of data. Despite these technical difficulties, continuous time-lapse imaging and single-cell tracking are increasingly used in hematopoiesis research. It has already contributed to answering decades-old questions. SummaryContinuous long-term single-cell analysis is indispensable for a comprehensive analysis of dynamic processes in heterogeneous cell populations. Despite many remaining technological hurdles, this approach is increasingly used in hematopoiesis research.
Endometriosis: Diagnosis and Management

Objective To improve the understanding of endometriosis and to provide evidence-based guidelines for the diagnosis and management of endometriosis. Outcomes Outcomes evaluated include the impact of the medical and surgical management of endometriosis on women's experience of morbidity and infertility. Methods Members of the guideline committee were selected on the basis of individual expertise to represent a range of practical and academic experience in terms of both location in Canada and type of practice, as well as subspecialty expertise along with general gynaecology background. The committee reviewed all available evidence in the English and French medical literature and available data from a survey of Canadian women. Recommendations were established as consensus statements. The final document was reviewed and approved by the Executive and Council of the SOGC. Results This document provides a summary of up-to-date evidence regarding diagnosis, investigations, and medical and surgical management of endometriosis. The resulting recommendations may be adapted by individual health care workers when serving women with this condition. Conclusions Endometriosis is a common and sometimes debilitating condition for women of reproductive age. A multidisciplinary approach involving a combination of lifestyle modifications, medications, and allied health services should be used to limit the impact of this condition on activities of daily living and fertility. In some circumstances surgery is required to confirm the diagnosis and provide therapy to achieve the desired goal of pain relief or improved fecundity. Women who find an acceptable management strategy for this condition may have an improved quality of life or attain their goal of successful pregnancy. Evidence Medline and Cochrane databases were searched for articles in English and French on subjects related to endometriosis, pelvic pain, and infertility from January 1999 to October 2009 in order to prepare a Canadian consensus guideline on the management of endometriosis. Values The quality of evidence was rated with use of the criteria described by the Canadian Task Force on Preventive Health Care. Recommendations for practice were ranked according to the method described by the Task Force. See Table 1. Benefits, harms, and costs Implementation of the guideline recommendations will improve the care of women with pain and infertility associated with endometriosis.
Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus

Positive-strand RNA viruses are the largest virus class and include many pathogens such as hepatitis C virus and the severe acute respiratory syndrome coronavirus (SARS). Brome mosaic virus (BMV) is a representative positive-strand RNA virus whose RNA replication, gene expression, and encapsidation have been reproduced in the yeast Saccharomyces cerevisiae. By using traditional yeast genetics, host genes have been identified that function in controlling BMV translation, selecting BMV RNAs as replication templates, activating the replication complex, maintaining a lipid composition required for membrane-associated RNA replication, and other steps. To more globally and systematically identify such host factors, we used engineered BMV derivatives to assay viral RNA replication in each strain of an ordered, genome-wide set of yeast single-gene deletion mutants. Each deletion strain was transformed to express BMV replicase proteins and a BMV RNA replication template with the capsid gene replaced by a luciferase reporter. Luciferase expression, which is dependent on viral RNA replication and RNA-dependent mRNA synthesis, was measured in intact yeast cells. Approximately 4,500 yeast deletion strains (≈80% of yeast genes) were screened in duplicate and selected strains analyzed further. This functional genomics approach revealed nearly 100 genes whose absence inhibited or stimulated BMV RNA replication and/or gene expression by 3- to >25-fold. Several of these genes were shown previously to function in BMV replication, validating the approach. Newly identified genes include some in RNA, protein, or membrane modification pathways and genes of unknown function. The results further illuminate virus and cell pathways. Further refinement of virus screening likely will reveal contributions from additional host genes.
The relationship between TQM factors and successful ERP implementation

ERP system is a generic term for a broad set of activities supported by multi-module application software which helps organizations to manage their own resources. ERP system has been proved to be able to provide significant improvements in efficiency, productivity and service quality, and to lead to a reduction in service costs as well as to make decisions more effective. ERP systems can integrate enterprise wide systems, which automate core corporate activities such as manufacturing, human resources, finance, supply chain management, etc. by using this system companies can enhance a considerable improvement in easier access to reliable information, elimination of redundant data and operations, reduction of cycle times and increased efficiency which finally cause cost reduction. Recently, one of the main challenges of managers in organizations is ERP implementation successfully. Since ERP influences all the aspect of organization, there are many barriers in implementation of ERP successfully. Total Quality Management (TQM) as a comprehensive philosophy encompasses all the dimensions of organization and can prepare the pre-requisites in organization. This paper analyzes the critical factors included in both TQM and ERP. Findings imply that there are common factors in the both mentioned approaches such as communication, training, top management support, etc.
CFL1, a WW Domain Protein, Regulates Cuticle Development by Modulating the Function of HDG1, a Class IV Homeodomain Transcription Factor, in Rice and Arabidopsis[W]

This study identifies CFL1 as a negative regulator of cuticle development in rice and Arabidopsis. CFL1 interacts with a class IV homeodomain-leucine zipper transcription factor to modulate the expression of two genes known to be involved in cuticle development. Plants have a chemically heterogeneous lipophilic layer, the cuticle, which protects them from biotic and abiotic stresses. The mechanisms that regulate cuticle development are poorly understood. We identified a rice (Oryza sativa) dominant curly leaf mutant, curly flag leaf1 (cfl1), and cloned CFL1, which encodes a WW domain protein. We overexpressed both rice and Arabidopsis CFL1 in Arabidopsis thaliana; these transgenic plants showed severely impaired cuticle development, similar to that in cfl1 rice. Reduced expression of At CFL1 resulted in reinforcement of cuticle structure. At CFL1 was predominantly expressed in specialized epidermal cells and in regions where dehiscence and abscission occur. Biochemical evidence showed that At CFL1 interacts with HDG1, a class IV homeodomain-leucine zipper transcription factor. Suppression of HDG1 function resulted in similar defective cuticle phenotypes in wild-type Arabidopsis but much alleviated phenotypes in At cfl1-1 mutants. The expression of two cuticle development-associated genes, BDG and FDH, was downregulated in At CFL1 overexpressor and HDG1 suppression plants. HDG1 binds to the cis-element L1 box, which exists in the regulatory regions of BDG and FDH. Our results suggest that rice and Arabidopsis CFL1 negatively regulate cuticle development by affecting the function of HDG1, which regulates the downstream genes BDG and FDH.
Ascorbic Acid Promotes the Stemness of Corneal Epithelial Stem/Progenitor Cells and Accelerates Epithelial Wound Healing in the Cornea

High concentration of ascorbic acid (vitamin C) has been found in corneal epithelium of various species. However, the specific functions and mechanisms of ascorbic acid in the repair of corneal epithelium are not clear. In this study, it was found that ascorbic acid accelerates corneal epithelial wound healing in vivo in mouse. In addition, ascorbic acid enhanced the stemness of cultured mouse corneal epithelial stem/progenitor cells (TKE2) in vitro, as shown by elevated clone formation ability and increased expression of stemness markers (especially p63 and SOX2). The contribution of ascorbic acid on the stemness enhancement was not dependent on the promotion of Akt phosphorylation, as concluded by using Akt inhibitor, nor was the stemness found to be dependent on the regulation of oxidative stress, as seen by the use of two other antioxidants (GMEE and NAC). However, ascorbic acid was found to promote extracellular matrix (ECM) production, and by using two collagen synthesis inhibitors (AzC and CIS), the increased expression of p63 and SOX2 by ascorbic acid was decreased by around 50%, showing that the increased stemness by ascorbic acid can be attributed to its regulation of ECM components. Moreover, the expression of p63 and SOX2 was elevated when TKE2 cells were cultured on collagen I coated plates, a situation that mimics the in vivo situation as collagen I is the main component in the corneal stroma. This study shows direct therapeutic benefits of ascorbic acid on corneal epithelial wound healing and provides new insights into the mechanisms involved. Stem Cells Translational Medicine 2017;6:1356–1365
The aetiology of vaginal symptoms in rural Haiti

Vaginal symptoms are a common chief complaint amongst women visiting outpatient clinics in rural Haiti. A systematic sample of 206 consecutive women over age 18 with gynaecological symptoms underwent gynaecologic examination and laboratory testing for chlamydia, gonorrhoea, syphilis, HIV infection, trichomoniasis, candidiasis, and bacterial vaginosis. Among 206 women, 174 (84%) presented with vaginal discharge, 165 (80%) with vaginal itching, 123 (60%) with vaginal pain or dysuria, and 18 (9%) with non-traumatic vaginal sores or boils. Laboratory results were positive for Chlamydia trachomatis in 5.4% (11/203), syphilis in 3.5% (7/202), HIV in 1.0% (2/200), and Neisseria gonorrhoeae in 1.0% (2/203). Among those that had microscopy, hyphae suggestive of candidiasis were visualized in 2.2% (1/45) and no cases of trichomoniasis were diagnosed 0% (0/45). Bacterial vaginosis was diagnosed in 28.3% (13/46). The prevalence of chlamydia was 4.9 (95% CI: 1.3–17.7) times greater among those 25 years of age and under (10.8%) than those older (2.3%). Chlamydia and bacterial vaginosis were the most common sexually transmitted infection and vaginal condition, respectively, in this study of rural Haitian adult women. The higher risk of chlamydia in younger women suggests education and screening programmes in young women should be considered.
Self-motivation and physical activity among black and white adolescent girls.

PURPOSE The psychometric properties of the Self-Motivation Inventory for children (SMI-C) were established using tests of factorial validity, factorial invariance, latent mean structure, and predictive validity. METHODS Adolescent girls from two cohorts (N = 955 and 1797) completed the SMI-C and measures of physical activity, team sport involvement, cardiorespiratory endurance, and body fatness in the 8th grade; participants in cohort 2 ( N= 1658) also completed the measures 1 yr later in the 9th grade. The data were analyzed with exploratory and confirmatory (CFA) factor analysis and structural equation modeling (SEM). RESULTS The 20-item SMI-C was best represented by a single substantive factor, but there were method effects among the negatively worded items. CFA indicated that a single-factor model fit the nine positively worded items and exhibited strong evidence of cross-validity and factorial invariance between races and across 1 yr; there were no differences in latent means between black and white girls. SEM indicated that the nine-item SMI-C had direct effects on moderate (gamma(11) = 0.16) and vigorous (gamma(21) = 0.22) physical activity and team sport involvement (gamma(31) = 0.29); the effects were invariant between black and white girls, independent of cardiorespiratory endurance and body fatness, and consistent across a 1-yr period. CONCLUSION The positively worded nine-item version of the SMI-C can be used in cross-sectional, prospective cohort, and intervention studies that examine self-motivation as a putative moderator or mediator of physical activity among black and white adolescent girls.
Analysis of time to a silent event whose occurrence is monitored with error, with application to mother‐to‐child HIV transmission

Inferences about the distribution of time to HIV infection in infants are complicated because infection is a silent event and imperfect diagnostic tests are used to detect its occurrence, leading to false‐positive and false‐negative results. Nonparametric likelihood approaches are computationally hampered by a large number of parameters and a possibly nonconcave likelihood function. To overcome these difficulties, we develop one‐sample and regression methods based on profile likelihood and Markov chain Monte Carlo techniques. The methods also provide a useful diagnostic for assessing the infection status of individual subjects, and are illustrated using results from a recent clinical trial for the prevention of mother‐to‐child HIV transmission. Copyright © 2007 John Wiley & Sons, Ltd.
Breast MRI at 3.0 T in a high-risk familial breast cancer screening cohort: comparison with 1.5 T screening studies.

OBJECTIVES The sensitivity of X-ray mammography for the detection of breast malignancy in younger females is lower than that of breast MRI; consequently, guidelines recommend annual MRI for patients with a significantly elevated lifetime risk. The improved signal-to-noise ratio obtainable at 3.0 T should result in data superior to those obtainable at 1.5 T. However, breast imaging on higher field strength systems poses specific problems. As a result, caution has been urged in the implementation of breast MRI at 3.0 T. The aim of this study was to determine if it is appropriate to use 3.0 T MRI in the screening of patients by comparing the summary statistics achieved by this 3.0 T MRI programme against the published results of 1.5 T screening studies. METHODS Over a 20-month period, 291 patients referred with an elevated familial risk of breast cancer were examined at 3.0 T. Resulting images were scored based on the Royal College of Radiologists Breast Group imaging classification. The reference standard was a combination of histology and follow-up imaging. RESULTS Follow-up data were available in 267 patients. Analysis revealed positive and negative post-test probabilities of 28% [95% confidence intervals (CI); range, 10-60%] and 1% (95% CI; range, 0-2%), respectively. These results compared favourably against those of a recent meta-analysis [25.3% (95% CI; range, 18.4-33.8%) and 0.4% (95% CI; range, 0.2-0.9%), respectively]. CONCLUSION Given the similar summary statistics between this work and the 1.5 T results, it would appear that screening of high-risk patients at 3.0 T has potential. Further studies should be undertaken to verify this result.