Miracle-dz/UniFAR-FTUs huggingface dataset:
Sleep and Alertness in a Duty‐Hour Flexibility Trial in Internal Medicine

Background A purpose of duty‐hour regulations is to reduce sleep deprivation in medical trainees, but their effects on sleep, sleepiness, and alertness are largely unknown. Methods We randomly assigned 63 internal‐medicine residency programs in the United States to follow either standard 2011 duty‐hour policies or flexible policies that maintained an 80‐hour workweek without limits on shift length or mandatory time off between shifts. Sleep duration and morning sleepiness and alertness were compared between the two groups by means of a noninferiority design, with outcome measures including sleep duration measured with actigraphy, the Karolinska Sleepiness Scale (with scores ranging from 1 [extremely alert] to 9 [extremely sleepy, fighting sleep]), and a brief computerized Psychomotor Vigilance Test (PVT‐B), with long response times (lapses) indicating reduced alertness. Results Data were obtained over a period of 14 days for 205 interns at six flexible programs and 193 interns at six standard programs. The average sleep time per 24 hours was 6.85 hours (95% confidence interval [CI], 6.61 to 7.10) among those in flexible programs and 7.03 hours (95% CI, 6.78 to 7.27) among those in standard programs. Sleep duration in flexible programs was noninferior to that in standard programs (between‐group difference, ‐0.17 hours per 24 hours; one‐sided lower limit of the 95% confidence interval, ‐0.45 hours; noninferiority margin, ‐0.5 hours; P=0.02 for noninferiority), as was the score on the Karolinska Sleepiness Scale (between‐group difference, 0.12 points; one‐sided upper limit of the 95% confidence interval, 0.31 points; noninferiority margin, 1 point; P<0.001). Noninferiority was not established for alertness according to the PVT‐B (between‐group difference, ‐0.3 lapses; one‐sided upper limit of the 95% confidence interval, 1.6 lapses; noninferiority margin, 1 lapse; P=0.10). Conclusions This noninferiority trial showed no more chronic sleep loss or sleepiness across trial days among interns in flexible programs than among those in standard programs. Noninferiority of the flexible group for alertness was not established. (Funded by the National Heart, Lung, and Blood Institute and American Council for Graduate Medical Education; ClinicalTrials.gov number, NCT02274818.)
Immunometabolic disorders in the pathogenesis of systemic lupus erythematosus

Systemic lupus erythematosus is a chronic autoimmune disease connected with complex and unclear disorders of the immune system, which causes inflammation of body tissues and internal organs. It leads to the formation of anti-nuclear antibodies (ANA) and immune complexes. Numerous immune system disorders and dysfunctions in the biochemical processes can occur in the course of the disease, and a wide range of abnormalities associated with cellular respiratory processes and mitochondrial function have been documented. The following paper presents the current understanding of the contribution of these disorders to the pathogenesis of lupus.
Advances in Transfusion Medicine RCPath, November 2018

The 2018 Advances in Transfusion Medicine conference was held in the Royal College of Pathologists’ brand-new, state-of-the-art building situated in Aldgate, London, a stone’s throw from the Tower of London and Tower Bridge. The organisers did not disappoint, bringing together UK and international experts from a range of clinical disciplines and leaders in transfusion science. The speakers delivered thought-provoking insights of current developments in the field of transfusion. The proceedings were opened by the President of the Royal College of Pathologists, Prof. Jo Martin, who recognised the ‘stellar work undertaken in the transfusion specialty for patient safety that is unparalleled in the National Health Service’. Prof. Martin introduced the foundation lecture, focused on the age-old immunohaematology puzzle of warm autoantibodies (WAAs) and antigen matching. This was followed by sessions covering aspects of evidence-based practice, advances in transfusion science, advances in transfusion practice, transfusion safety, clinical practice and improving the impact of patient blood management.
Association between paraoxonase-1 gene Q192R and L55M polymorphisms and risk of gastric cancer: A case-control study from Iran

Abstract The aim of the present study was to examine the relation between two paraoxonase1 (PON1) polymorphisms, Q192R and L55M and susceptibility to gastric cancer in an Iranian population. In this case-control study the PON1 polymorphisms were assessed in 90 gastric cancer patients and 90 healthy controls by polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) method. Regarding PON1 Q192R polymorphism, a significant increase in the R allele in the patient group compared with the controls (p value = 0.0006) While the Q allele was more frequent in the control group. No significant difference was found in the genotype or allele frequency of the L55M polymorphism between healthy individuals and patients with gastric cancer. Our results demonstrated the protective effect of Q allele against gastric cancer.
Spatial Association of Food Sales in Supermarkets with the Mean BMI of Young Men: An Ecological Study

Supermarket food sales data might serve as a simple indicator of population-level dietary habits that influence the prevalence of excess weight in local environments. To test this possibility, we investigated how variation in store-level food sales composition across Switzerland is associated with the mean Body Mass Index (BMI) of young men (Swiss Army conscripts) living near the stores. We obtained data on annual food sales (2011) for 553 stores from the largest supermarket chain in Switzerland, identified foods commonly regarded as “healthy” or “unhealthy” based on nutrient content, and determined their contribution to each store’s total sales (Swiss francs). We found that the sales percentages of both “healthy” and “unhealthy” food types varied by 2- to 3-fold among stores. Their balance ranged from −15.3% to 18.0% of total sales; it was positively associated with area-based socioeconomic position (r = 0.63) and negatively associated with the mean BMI of young men in the area (r = −0.42). Thus, even though we compared supermarkets from a single chain, different shopping behaviors of customers caused stores in privileged areas to sell relatively more healthy food. Knowledge about such patterns could help in designing in-store interventions for healthier nutrition and monitoring their effects over time.
Radiation Responses of Human Mesenchymal Stem Cells Derived From Different Sources

Mesenchymal stem cells (MSCs) derived from different tissues may aid in the regeneration of radiation-induced organ lesions; however, the radiation responses of human MSCs from different sources are unknown. In our study, a comparison of the results from cell proliferation, apoptosis, cell cycle, DNA damage, and DNA repair assays consistently showed that MSCs derived from adipose tissue possess a significantly stronger radiation resistance capacity than MSCs derived from umbilical cord and gingival, which is accompanied by a higher level of phosphorylated signal transducer and activator of transcription 3 (Stat3) expression. This reminds us Stat3 could be a potential biomarker of radiation resistance. These findings provide a better understanding of radiation-induced biologic responses in MSCs and may lead to the development of better strategies for stem cell treatment and cancer therapy.
Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery

ABSTRACT Prevailing agro-ecological conditions and intermingling of human and animals in intensive farms in urban and peri-urban areas in Africa favour cross species transmission of pathogens at the human-animal interface. However, molecular epidemiology studies of zoonotic swine influenza viruses in this region are limited. In this study, isolates of pandemic influenza virus (H1N1pdm09) obtained from pigs in Nigeria were fully sequenced. BLAST of swine influenza virus genes from Nigeria was carried out in GenBank and gene alignment was done using MEGA version 7. Maximum likelihood method (PhyML program) was used to determine gene evolutionary relationships with other viruses and phylogenetic trees were constructed to infer genomic clusters and relationship. Swine influenza viruses isolated and sequenced in this study were monophyletic and 99% congenetic with human isolates from Nigeria, Cameroon, Ghana and USA suggesting reverse zoonotic transmission from humans to pigs in intensive husbandry. A Q240R and S31N substitution among others were detected in the haemagglutinin and matrix genes, respectively, indicating potentials for mutations during interspecies co-mingling and transmission. The A/H1N1pdm09 viruses circulating in pigs that are also exposed to avian influenza in the same epidemiological zones could engender emergence of novel viruses with zoonotic or pandemic potential requiring enhanced surveillance and monitoring.
Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics

This study has two novel findings: it is not only the first to deduct potential genes involved in scleral growth repression upon atropine instillation from a prevention point of view, but also the first to demonstrate that only slight changes in scleral gene expression were found after atropine treatment as side effects and safety reasons of the eye drops are of concern. The sclera determines the final ocular shape and size, constituting of scleral fibroblasts as the principal cell type and the major regulator of extracellular matrix. The aim of our study was to identify differentially expressed genes and microRNA regulations in atropine-treated scleral fibroblasts that are potentially involved in preventing the onset of excessive ocular growth using next-generation sequencing and bioinformatics approaches. Differentially expressed genes were functionally enriched in anti-remodeling effects, comprising of structural changes of extracellular matrix and metabolic pathways involving cell differentiation. Significant canonical pathways were correlated to inhibition of melatonin degradation, which was compatible with our clinical practice as atropine eye drops are instilled at night. Validation of the dysregulated genes with previous eye growth-related arrays and through microRNA-mRNA interaction predictions revealed the association of hsa-miR-2682-5p-KCNJ5 and hsa-miR-2682-5p-PRLR with scleral anti-remodeling and circadian rhythmicity. Our findings present new insights into understanding the anti-myopic effects of atropine, which may assist in prevention of myopia development.
Data Expedition into the Swiss Twitter Corpus

Data Expeditions are short, collaborative events focusing on ﬁnding interesting patterns and insights in a dataset through interdisciplinary teams. This is a report of the Data Expedition into the Swiss Twitter Corpus ex-pedition hosted by SpinningBytes AG at the SwissText 2018 conference. The aim was to research interesting topics related to Switzer-land in the Swiss Twitter Corpus 1 . Two teams with a total of 11 participants were given 140’521 Switzerland-related Tweets with relevant metadata and analyzed topics of their choice during the 4 hour workshop. We explain how the data expedition was organized and discuss some of the results and lessons learned.
Attitudes and Motivations of Consumers in Sharing Economy

This study first provides a brief overview of the theoretical background of sharing economy, then it discloses the main results of our research related to consumer behaviour and consumer attitudes. By using our qualitative results, we have identified the main consumer motivation factors that we later used in our country-wide quantitative research for the classification of sharing economy users into 4 groups. The first group includes those enthusiastic frequent users who are less motivated by the economic benefits, they rather pursuit the good experience in using these services. The second group consists of users who are definitely motivated by better prices. The third group is made up of environmentally conscious consumers who support sustainability not just on the level of attitude, but also on the level of actions. The fourth group embraces occasional users, not necessarily enjoying the personal touch, they rather use sharing-based services only in the case of attractive offers.
Business as usual? On the nature of relationships in enterprise software platform ecosystems

To obtain measurable benefit from an ecosystem, partners need to overcome the challenges they face when they join. This research aims to provide insight into whether partners are influenced by the keystone through power forms and how the partners perceive these influences. Subsequently, this research identifies possible perceived software ecosystem benefits and disadvantages that these partners experience after joining. Semi-structured interviews were conducted with both a keystone company and multiple partners within a single ecosystem. The most frequently observed power forms are reward and legitimate power. Finally, various SECO benefits and disadvantages have been identified for each partner. Thus, this research contributes to an improved understanding of partner-keystone dynamics within a single software ecosystem and provides insights beneficial to the industry.
Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair

The transcription factor Ets-1 (ETS proto-oncogene 1) shows low expression levels except in specific biological processes like haematopoiesis or angiogenesis. Elevated levels of expression are observed in tumor progression, resulting in Ets-1 being named an oncoprotein. It has recently been shown that Ets-1 interacts with two DNA repair enzymes, PARP-1 (poly(ADP-ribose) polymerase 1) and DNA-PK (DNA-dependent protein kinase), through two different domains and that these interactions play a role in cancer. Considering that Ets-1 can bind to distinctly different domains of two DNA repair enzymes, we hypothesized that the interaction can be transposed onto homologs of the respective domains. We have searched for sequence and structure homologs of the interacting ETS(Ets-1), BRCT(PARP-1) and SAP(DNA-PK) domains, and have identified several candidate binding pairs that are currently not annotated as such. Many of the Ets-1 partners are associated to DNA repair mechanisms. We have applied protein-protein docking to establish putative interaction poses and investigated these using centrality analyses at the protein residue level. Most of the identified poses are virtually similar to our recently established interaction model for Ets-1/PARP-1 and Ets-1/DNA-PK. Our work illustrates the potentially high number of interactors of Ets-1, in particular involved in DNA repair mechanisms, which shows the oncoprotein as a potential important regulator of the mechanism.
AMPK variant, a candidate of novel predictor for chemotherapy in metastatic colorectal cancer: A meta‐analysis using TRIBE, MAVERICC and FIRE3

AMP‐activated protein kinase (AMPK) is a key sensor of energy homeostasis and regulates cell metabolism, proliferation and chemotherapy/radiotherapy sensitivities. This study aimed to explore the relationship between the AMPK pathway‐related single nucleotide polymorphisms (SNPs) and clinical outcomes in patients with metastatic colorectal cancer (mCRC). We analyzed a total of 884 patients with mCRC enrolled in three randomized clinical trials (TRIBE, MAVERICC and FIRE‐3: where patients were treated with FOLFIRI, mFOLFOX6 or FOLFOXIRI combined with bevacizumab or cetuximab as the first‐line chemotherapy). The association between AMPK pathway‐related SNPs and clinical outcomes was analyzed across the six treatment cohorts, using a meta‐analysis approach. Our meta‐analysis showed that AMPK pathway had significant associations with progression‐free survival (PFS; p < 0.001) and overall survival (OS; p < 0.001), but not with tumor response (TR; p = 0.220): PRKAA1 rs13361707 was significantly associated with favorable PFS (log HR = −0.219, SE = 0.073, p = 0.003), as well as PRKAA1 rs10074991 (log HR = −0.215, SE = 0.073, p = 0.003), and there were suggestive associations of PRKAG1 rs1138908 with unfavorable OS (log HR = 0.170, SE = 0.083, p = 0.041), and of UBE2O rs3803739 with unfavorable PFS (log HR = 0.137, SE = 0.068, p = 0.042) and OS (log HR = 0.210, SE = 0.077, p = 0.006), although these results were not significant after false discovery rate adjustment. AMPK pathway‐related SNPs may be predictors for chemotherapy in mCRC. Upon validation, our findings would provide novel insight for selecting treatment strategies.
Identification of TCP Congestion Control Algorithms from Unidirectional Packet Traces

Recently, according to the diversification of network environments, various TCP congestion control mechanisms have been introduced. Since the TCP congestion control algorithms affect the traffic characteristic in the Internet, it is important to analyze which algorithms are used widely. This paper proposes a method to identify a congestion control algorithm from passively collected packet traces that include only unidirectional packet traces. In unidirectional traces, it is hard to map a data segment and the ACK segment corresponding to it and to estimate round-trip time. So, the proposed method uses the curve fitting for sequence number vs. time graphs by applying the least squares method with linear through quartic functions, and maps the first-order and second-order differentiations. This paper applies the proposed method to various TCP congestion control algorithms including TCP Reno, CUBIC TCP, Hamilton TCP, TCP Vegas, and TCP Veno.
Antileishmanial Compounds Isolated from Psidium Guajava L. Using a Metabolomic Approach

With an estimated annual incidence of one million cases, leishmaniasis is one of the top five vector-borne diseases. Currently available medical treatments involve side effects, including toxicity, non-specific targeting, and resistance development. Thus, new antileishmanial chemical entities are of the utmost interest to fight against this disease. The aim of this study was to obtain potential antileishmanial natural products from Psidium guajava leaves using a metabolomic workflow. Several crude extracts from P. guajava leaves harvested from different locations in the Lao People’s Democratic Republic (Lao PDR) were profiled by liquid chromatography coupled to high-resolution mass spectrometry, and subsequently evaluated for their antileishmanial activities. The putative active compounds were highlighted by multivariate correlation analysis between the antileishmanial response and chromatographic profiles of P. guajava mixtures. The results showed that the pooled apolar fractions from P. guajava were the most active (IC50 = 1.96 ± 0.47 µg/mL). Multivariate data analysis of the apolar fractions highlighted a family of triterpenoid compounds, including jacoumaric acid (IC50 = 1.318 ± 0.59 µg/mL) and corosolic acid (IC50 = 1.01 ± 0.06 µg/mL). Our approach allowed the identification of antileishmanial compounds from the crude extracts in only a small number of steps and can be easily adapted for use in the discovery workflows of several other natural products.
Identifying and addressing mental health providers' perceived barriers to clinical video telehealth utilization.

OBJECTIVE Clinical video telehealth (CVT) is an innovative modality to provide care directly to Veterans' homes. Despite prior training initiatives, CVT remains underutilized. This project sought to better understand barriers to implementation and to compare responses of CVT utilizers versus nonutilizers. METHOD Mental health staff were invited to complete an online anonymous survey on their use of CVT in clinical practice. RESULTS A total of 159 mental health staff completed the survey. Although the majority of the sample endorsed personal use of a video chat program, less than half reported using CVT for patient care. Among nonutilizers, lack of training was the most frequently endorsed barrier to CVT use whereas administrative burden was the most frequently endorsed barrier by utilizers. CONCLUSIONS This study extends existing literature by determining barriers to CVT adoption. It identifies several barriers among utilizers versus nonutilizers. Discussion includes potential guidelines for overcoming barriers to CVT utilization.
COPD and the risk of mild cognitive impairment and dementia: a cohort study based on the Chinese Longitudinal Health Longevity Survey

Background COPD may lead to cognitive impairment or even dementia. However, the current conclusions are inconsistent with little evidence from prospective, large-sample studies. This study was designed to explore the association of COPD with mild cognitive impairment (MCI) and dementia risk based on a cohort study. Patients and methods All participants were from the Chinese Longitudinal Health Longevity Survey (CLHLS) 2011/2012 waves. The follow-up survey was conducted in 2014 and the incidence of MCI and dementia were recorded. Results During the 3-year follow-up period, 712 new cases of MCI and 83 new cases of dementia were diagnosed. The incidence of MCI and dementia were higher in those with COPD than those without COPD at baseline. Cox analysis showed that the HRs of COPD for MCI and dementia incidence were 1.486 (95% CI: 1.207–1.855) and 1.896 (95% CI: 1.079–3.330), respectively after adjusting for related covariates. For different baseline smoking status, those who were current smokers had the highest HRs of COPD for MCI and dementia. Conclusion Baseline COPD was independently associated with increased risk of MCI and dementia incidence among Chinese elderly, and the association was more pronounced among those who were current smokers.
3D-Printed Solid Dispersion Drug Products

With the well-known advantages of additive manufacturing methods such as three-dimensional (3D) printing in drug delivery, it is disappointing that only one product has been successful in achieving regulatory approval in the past few years. Further research and development is required in this area to introduce more 3D printed products into the market. Our study investigates the potential of fixed dose combination solid dispersion drug products generated via 3D printing. Two model drugs—fluorescein sodium (FS) and 5-aminosalicyclic acid (5-ASA)—were impregnated onto a polyvinyl alcohol (PVA) filament, and the influence of solvent choice in optimal drug loading as well as other influences such as the physicochemical and mechanical properties of the resultant filaments were investigated prior to development of the resultant drug products. Key outcomes of this work included the improvement of filament drug loading by one- to threefold due to solvent choice on the basis of its polarity and the generation of a 3D-printed product confirmed to be a solid dispersion fixed dose combination with the two model drugs exhibiting favourable in vitro dissolution characteristics.