Miracle-dz/UniFAR-FTUs huggingface dataset:
The soluble extracellular domain of E‐cadherin interferes with EPEC adherence via interaction with the Tir:intimin complex

Enteropathogenic Escherichia coli (EPEC) causes watery diarrhea when colonizing the surface of enterocytes. The translocated intimin receptor (Tir):intimin receptor complex facilitates tight adherence to epithelial cells and formation of actin pedestals beneath EPEC. We found that the host cell adherens junction protein E‐cadherin (Ecad) was recruited to EPEC microcolonies. Live‐cell and confocal imaging revealed that Ecad recruitment depends on, and occurs after, formation of the Tir:intimin complex. Combinatorial binding experiments using wild‐type EPEC, isogenic mutants lacking Tir or intimin, and E. coli expressing intimin showed that the extracellular domain of Ecad binds the bacterial surface in a Tir:intimin‐dependent manner. Finally, addition of the soluble extracellular domain of Ecad to the infection medium or depletion of Ecad extracellular domain from the cell surface reduced EPEC adhesion to host cells. Thus, the soluble extracellular domain of Ecad may be used in the design of intervention strategies targeting EPEC adherence to host cells. —Login, F. H. , Jensen, H. H. , Pedersen, G. A. , Amieva, M. R. , Nejsum, L. N. The soluble extracellular domain of E‐cadherin interferes with EPEC adherence via interaction with the Tir:intimin complex. FASEB J. 32, 6860–6868 (2018). www.fasebj. org
Modeling Coordination and Productivity in Open-Source GitHub Projects

In open-source software development, coordination between globally separated developers is often structured in ways not immediately visible to them, such as implicit groupings of people working on similar code and related issues. This opacity is despite the availability and accessibility of a large quantity of low-level project activity data on platforms like GitHub. This paper uses this low-level data to construct meaningful indicators that could offer improved transparency into how coordination is conducted in open source. Prior work has shown the value of Socio-Technical Congruence for evaluating the quality of coordination in commercial software systems. However, little work has successfully translated this analysis to the domain of open source, primarily due to their less formal and inconsistent ways of partitioning work, assigning tasks and measuring success. We present a technique for distinguishing the active phases of coordination and define a measure of productivity for these projects. We perform a quantitative analysis of the influence of congruence on productivity in these phases demonstrating that the associations between our measure of productivity and the measures of congruence and other control variables are subtle but consistent with the prior work in commercial software development and discuss some applications of our work.
Functional Genetic Diversity and Culturability of Petroleum-Degrading Bacteria Isolated From Oil-Contaminated Soils

In this study, we compared the culturability of aerobic bacteria isolated from long-term oil-contaminated soils via enrichment and direct-plating methods; bacteria were cultured at 30°C or ambient temperatures. Two soil samples were collected from two sites in the Shengli oilfield located in Dongying, China. One sample (S0) was close to the outlet of an oil-production water treatment plant, and the other sample (S1) was located 500 m downstream of the outlet. In total, 595 bacterial isolates belonging to 56 genera were isolated, distributed in Actinobacteria, Firmicutes, Bacterioidetes, and Proteobacteria. It was interesting that Actinobacteria and Firmicutes were not detected from the 16S rRNA gene clone library. The results suggested the activation of rare species during culture. Using the enrichment method, 239 isolates (31 genera) and 96 (22 genera) isolates were obtained at ambient temperatures and 30°C, respectively, from S0 soil. Using the direct-plating method, 97 isolates (15 genera) and 163 isolates (20 genera) were obtained at ambient temperatures and 30°C, respectively, from two soils. Of the 595 isolates, 244 isolates (41.7% of total isolates) could degrade n-hexadecane. A greater number of alkane-degraders was isolated at ambient temperatures using the enrichment method, suggesting that this method could significantly improve bacterial culturability. Interestingly, the proportion of alkane degrading isolates was lower in the isolates obtained using enrichment method than that obtained using direct-plating methods. Considering the greater species diversity of isolates obtained via the enrichment method, this technique could be used to increase the diversity of the microbial consortia. Furthermore, phenol hydroxylase genes (pheN), medium-chain alkane monooxygenases genes (alkB and CYP153A), and long-chain alkane monooxygenase gene (almA) were detected in 60 isolates (11 genotypes), 91 isolates (27 genotypes) and 93 isolates (24 genotypes), and 34 isolates (14 genotypes), respectively. This study could provide new insights into microbial resources from oil fields or other environments, and this information will be beneficial for bioremediation of petroleum contamination and for other industrial applications.
Labor conditions and the meanings of nursing work in Barcelona

ABSTRACT Objective: to analyze the relationship between the quantitative assessment of working conditions and the qualitative perception of one’s own work experience. Method: a sample of 1,760 nursing professionals from Barcelona answered a questionnaire assessing their working conditions and summarized their own current work experience in five key words. Results: the textual corpus of the meanings of nursing work included 8043 lexical forms, which were categorized and codified. Respondents who rated their work conditions the highest expressed a vision of their work in terms of autonomy, achievement and well-being, while those who rated their work conditions the lowest talked mostly of exhaustion, depersonalization and negative climate. A correspondence analysis showed a close relationship between the quantitative assessments of working conditions and the verbal codes of the meaning of work. Conclusions: the meanings given to work were not only consistent with the numerical evaluations of the working conditions but also made them more understandable. The information obtained poses challenges for reflection and indicates ways to promote the positive aspects and prevent the negative conditions of nursing work.
Structure‐activity relationship of heme and its analogues in membrane damage and inhibition of fusion

Under pathological conditions, such as sickle cell disease and malaria, heme concentration increases considerably, and it induces membrane damage. As sickled and normal erythrocytes contain high cholesterol: phospholipid ratio, we investigated the role of lipid composition, chain length, and unsaturation on the partitioning and leakage of hemin in phospholipid vesicles. To establish structure‐activity relationship in membrane damage, experiments with two other analogues, protoporphyrin‐IX and hematoporphyrin (HP) were also carried out. Hemin and its analogues localize differently in membranes and exhibit distinct roles in partitioning, leakage and fusion. Hemin and HP trigger more leakage in the presence of aminophospholipids, whereas cholesterol buffers the destabilizing effect remarkably. Inhibition of fusion by hemin further suggests its unexplored and important role in membrane trafficking, particularly under diseased conditions.
Identification of Acute Malnutrition in Children in Cambodia Requires Both Mid Upper Arm Circumference and Weight-For-Height to Offset Gender Bias of Each Indicator

Malnutrition remains a serious health problem in Cambodia with over 10% of children less than five years of age suffering from acute malnutrition. In addition to the presence of nutritional edema, two indicators are recommended by the World Health Organization for the diagnosis of acute malnutrition: weight-for-height Z-scores (WHZ; with acute malnutrition defined as WHZ < −2 Z-score) and mid-upper arm circumference (MUAC, with acute malnutrition defined as MUAC < 12.5 cm). Earlier, we showed that WHZ and MUAC identified different subgroups of children with acute malnutrition. To explore factors associated with both indicators of acute malnutrition, we analyzed baseline data from a longitudinal study in three provinces in Cambodia: Phnom Penh (capital, urban environment), Kratie (rural province), and Ratanakiri (hilly, rural province). Data was available for 4381 children below 30 months of age. Malnutrition rates were higher in the two rural provinces than in the capital. Although both MUAC and WHZ showed gender bias, with MUAC identifying more girls, and WHZ identifying more boys with acute malnutrition, the gender effect was strongest for MUAC. The gender bias of MUAC diminished with older age, but remained significant up to 30 months of age. Only using both MUAC and WHZ as indicators resulted in gender neutral identification of acute malnutrition. WHZ alone always identified more children with acute malnutrition than MUAC alone. In Phnom Penh, MUAC alone identified only 11% with acute malnutrition in addition to WHZ. To conclude, both MUAC and WHZ showed gender bias in this cohort of Cambodian children. In Cambodia, implementation of a MUAC-only or a WHZ-only program for the identification of acute malnutrition would be unethical as it will lead to many children remaining undiagnosed.
The Gains from Financial Inclusion: Theory and a Quantitative Assessment∗

This paper calibrates a general equilibrium model with contracting frictions, where agents differ in entrepreneurial ability and wealth, to study the benefits of financial inclusion. Alongside frictions due to moral hazard and limited liability, we also vary market access. As a benchmark, we calibrate the model to US default probabilities and the firm-size distribution. The calibrated counterfactuals that we generate show that financial inclusion is quantitatively much more important than contracting frictions. The main beneficiaries from extending credit market access are wage labourers; moving from aurtaky to full-inclusion increases the wage from 40% to 90% of the US wage. JEL Classification: E44, G28, O16
Epidemiology of Time-Loss Injuries in Senior and Under-18 Portuguese Male Rugby Players

Abstract Rugby union has one of the highest injury incidence rates in team sports, however, most of the available data focus on the epidemiology of injuries in countries where rugby is popular. We aimed to report the incidence rate and relevant epidemiological aspects of injuries occurred in a group of Portuguese male rugby players. A prospective cohort study was conducted with a group of 45 senior and 32 under-18 male players (total of 77 players). Outcome measures included injury incidence, position, type, location and severity of injuries. The match injury incidence for all players was 55.84 per 1000 player match-hours (66.66 for seniors, 42.85 for under-18), while mean time-loss for injury was 20.79 days. No statistical differences were found between groups. Lower limb injuries accounted for 60.5% of all injuries, while joint/ligament injuries were the most prevalent type. Contact events were responsible for 65.1% of injuries. Despite the limitations, the obtained data are consistent with the literature. Time-loss injuries seem highly prevalent in rugby union and the incidence rates found in this Portuguese-based study were lower than the reported for international and senior men’s professional rugby union, but higher than those occurring in community rugby in tier-1 countries. The authors believe these data reinforce the need to develop and implement effective injury surveillance and prevention programs.
Activation of the Immune-Metabolic Receptor GPR84 Enhances Inflammation and Phagocytosis in Macrophages

GPR84 is a member of the metabolic G protein-coupled receptor family, and its expression has been described predominantly in immune cells. GPR84 activation is involved in the inflammatory response, but the mechanisms by which it modulates inflammation have been incompletely described. In this study, we investigated GPR84 expression, activation, and function in macrophages to establish the role of the receptor during the inflammatory response. We observed that GPR84 expression in murine tissues is increased by endotoxemia, hyperglycemia, and hypercholesterolemia. Ex vivo studies revealed that GPR84 mRNA expression is increased by LPS and other pro-inflammatory molecules in different murine and human macrophage populations. Likewise, high glucose concentrations and the presence of oxidized LDL increased GPR84 expression in macrophages. Activation of the GPR84 receptor with a selective agonist, 6-(octylamino) pyrimidine-2,4(1H,3H)-dione (6-n-octylaminouracil, 6-OAU), enhanced the expression of phosphorylated Akt, p-ERK, and p65 nuclear translocation under inflammatory conditions and elevated the expression levels of the inflammatory mediators TNFα, IL-6, IL-12B, CCL2, CCL5, and CXCL1. In addition, GPR84 activation triggered increased bacterial adhesion and phagocytosis in macrophages. The enhanced inflammatory response mediated by 6-OAU was not observed in GPR84−/− cells nor in macrophages treated with a selective GPR84 antagonist. Collectively, our results reveal that GPR84 functions as an enhancer of inflammatory signaling in macrophages once inflammation is established. Therefore, molecules that antagonize the GPR84 receptor may be potential therapeutic tools in inflammatory and metabolic diseases.
The influences of bariatric surgery on hemoglobin A1c in a sample of obese patients in Saudi Arabia

Background Although the frequency of surgical weight loss interventions has increased in Saudi Arabia, literature describing the clinical outcomes of bariatric surgery in Saudi Arabia is limited. This study aimed to assess whether weight loss intervention improves hemoglobin A1c (HbA1c) in obese patients and to identify its associated factors. Patients and methods A retrospective study was carried out on 318 patients with obesity class 1 or higher (body mass index [BMI] ≥ 30 kg/m2) who underwent laparoscopic sleeve gastrectomy or Roux-en-Y gastric bypass at King Abdulaziz Medical City in Riyadh, Saudi Arabia, between January 1, 2001 and March 31, 2017. Preoperatively and 12 months postoperatively, characteristics of patients were collected. BMI reduction was calculated, based on which patients were divided into three groups (0–9, 10–14, and >14 kg/m2). Results The postoperative HbA1c was 5.83±0.9, while the baseline level was 6.74±2.1 (P=0.001). Fifty-eight of the 318 patients had diabetes. We observed significantly higher HbA1c in diabetic than in non-diabetic patients preoperatively, whereas an insignificantly different HbA1c was observed postoperatively. Among those who had minimal reduction in BMI (0–9 kg/m2), we observed significantly higher HbA1c in diabetic than in non-diabetic patients, whereas among those who had large reduction in BMI (10–14 kg/m2) and (>14 kg/m2), we observed insignificant differences in HbA1c in diabetic than in non-diabetic patients. Conclusion Being a diabetic patient was related to a significant reduction in HbA1c levels postoperatively. The study suggests that the reduction in HbA1c levels could be modified by BMI, wherein greater reduction in BMI leads to greater reduction in HbA1c levels.
Sirtuin-4 (SIRT4), a therapeutic target with oncogenic and tumor-suppressive activity in cancer

Several members of the sirtuin (SIRT) family, a highly conserved family of NAD+-dependent enzymes, have been shown to play a critical role in both promoting and/or suppressing tumorigenesis. In this study, recent progress in the field concerning SIRT4 and cancer was reviewed, and the relationship between SIRT4 and tumors was investigated. Subsequently, we evaluated the role of SIRT4 with oncogenic or tumor-suppressive activity in cancer, which may provide insight in identifying the underlying mechanism of action of SIRT4 in cancer. Finally, we explored the potential of SIRT4 as a therapeutic target in cancer therapy.
Risk Factors for Depression in Long-Term Care: A Systematic Review

ABSTRACT Objectives: Depression rates are substantially higher among older adults in long-term care when compared with older adults in the community. Furthermore, the needs of older adults in long-term care are increasingly complex, and risk factors that contribute to depression in this population are unclear. This limits not only the identification of those at risk for depression but also the development of therapeutic interventions. This review summarizes the evidence on risk factors for depression. Methods: Searches were performed using CINAHL, Cochrane Library, Ovid Medline, PsycINFO and Scopus for research published 1980–2017. Data were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Results: Eleven studies met the inclusion criteria, representing a total of 11,703 participants, with a mean sample size of 1,064. The most consistently supported risk factor was cognitive impairment, followed by functional impairment and baseline depression score. Conclusions: The studies lacked a systematic approach to investigating risk factors for depression, and the research remains largely atheoretical. Few risk factors were consistently studied, with over 20 risk factors examined no more than once each. Psychological and environmental risk factors, which may be modifiable and have the potential to inform therapeutic interventions and preventative strategies, remain under-studied. Clinical Implications: The most consistently supported risk factors—cognitive impairment, functional disability and baseline depression score—have the potential to inform screening protocols and should be monitored longitudinally. When developing psychotherapeutic interventions, close consideration should be given to cognitive and functional impairment as barriers to implementation and uptake.
Instance-Level Explanations for Fraud Detection: A Case Study

Fraud detection is a difficult problem that can benefit from predictive modeling. However, the verification of a prediction is challenging; for a single insurance policy, the model only provides a prediction score. We present a case study where we reflect on different instance-level model explanation techniques to aid a fraud detection team in their work. To this end, we designed two novel dashboards combining various state-of-the-art explanation techniques. These enable the domain expert to analyze and understand predictions, dramatically speeding up the process of filtering potential fraud cases.
How do we fit underground coal mining work boots?

Abstract Acceptable footwear fit, particularly width, is subjective and vaguely quantified. Proper shoe fit is important because it affects both comfort and the potential to prevent injury. Although mismatches between the feet of underground coal miners and their internal boot dimensions are known, no research has been undertaken to determine the impact of these mismatches on worker perceptions of fit, comfort and pain. This study aimed to quantitatively assess mining work boot fit relative to underground coal miners’ subjectively rated work boot fit and comfort, reported foot problems, lower limb pain and lower back pain in order to develop evidence-based work boot fit recommendations. Traditional footwear fitting methods based predominantly on foot length are insufficient for underground coal mining-specific footwear. Instead, fit at the heel, instep and forefoot must be considered when fitting underground coal mining work boots, in conjunction with the traditional length measurement.Practitioner summary: Underground coal miners report their work boots fit but are uncomfortable. This study assessed actual fit relative to perceived fit, comfort, foot problems, lower limb pain and lower back pain of 197 miners. Fit at the heel, instep and forefoot must be considered when fitting mining work boots.
Seasonal changes of &dgr;D and &dgr;18O in tree-ring cellulose of Quercus crispula suggest a change in post-photosynthetic processes during earlywood growth

Leaf photosynthetic and post-photosynthetic processes modulate the isotope ratios of tree-ring cellulose. Post-photosynthetic processes, such as the remobilization of stored starch in early spring, are important to understanding the mechanisms of xylem formation in tree stems; however, untangling the isotope ratio signals of photosynthetic and post-photosynthetic processes imprinted on tree rings is difficult. Portions of carbon-bound hydrogen and oxygen atoms are exchanged with medium water during post-photosynthetic processes. We investigated the δD and δ18O values of tree-ring cellulose using Quercus crispula Blume trees in two different habitats to evaluate seasonal changes in the exchange rate (f-value) of hydrogen or oxygen with medium water, and examined the associations of the post-photosynthetic processes. Theoretically, if the f-value is constant, δD and δ18O would be positively correlated due to meteorological factors, while variation in the f-value will create a discrepancy and weak correlation between δD and δ18O due to the exchange of carbon-bound hydrogen and oxygen with medium water. The values of δD decreased drastically from earlywood to latewood, while those of δ18O increased to a peak and then decreased toward the latewood. The estimated seasonal f-value was high at the beginning of earlywood and decreased toward the latewood. The post-photosynthetic processes associated with changes in the f-value were the remobilization of stored starch and triose cycling during cellulose synthesis because of the shortage of photo-assimilates in early spring. Although we did not evaluate relevant physiological parameters, the seasonal pattern of δD and δ18O in tree-ring cellulose of Q. crispula was clear, suggesting that the dual isotope (δD and δ18O) approach can be used to reveal the resource allocation mechanisms underlying seasonal xylem formation.