Miracle-dz/UniFAR-FTUs huggingface dataset:
The Association Between the rs2975760 and rs3792267 Single Nucleotide Polymorphisms of Calpain 10 (CAPN10) and Gestational Diabetes Mellitus

Background This study aimed to investigate the association between the rs2975760 and rs3792267 single nucleotide polymorphisms (SNPs) of the calpain 10 (CAPN10) gene and gestational diabetes mellitus. Material/Methods The study included 138 patients with gestational diabetes mellitus and 152 healthy pregnant women. Venous blood was separated, and the DNA was extracted. The rs2975760 and rs3792267SNP polymorphisms of CAPN10 were detected using polymerase chain reaction (PCR). The frequencies of different genotypes in patients with gestational diabetes mellitus and healthy pregnant women were determined, and the relationship between different SNP genotypes and the risk of gestational diabetes mellitus was analyzed. Results There were no significant differences in the frequencies of the TT, CT and CC genotypes of rs2975760 and the frequencies of the GG, AG and AA genotypes of rs3792267 between the women with gestational diabetes and the controls. Expression of rs2975760 and rs3792267 were not associated with the risk of gestational diabetes in the dominant model, recessive model, and additive model. However, grade B and grade D diabetes in the CC and TC genotypes of rs2975760 were significantly different from those in the TT genotype (P<0.05). Grade B and grade D diabetes in the AA and AG genotypes of rs3792267 were significantly different compared with those in the GG genotype (P<0.05), and allele A was significantly increased compared with allele G (P<0.05). Conclusions The rs2975760 and rs3792267 SNP polymorphisms of CAPN10 showed no significant association with the incidence of gestational diabetes mellitus and only a mild association with the severity.
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction

Abstract Motivation Secondary structure prediction accuracy (SSPA) in the QuanTest benchmark can be used to measure accuracy of a multiple sequence alignment. SSPA correlates well with the sum-of-pairs score, if the results are averaged over many alignments but not on an alignment-by-alignment basis. This is due to a sub-optimal selection of reference and non-reference sequences in QuanTest. Results We develop an improved strategy for selecting reference and non-reference sequences for a new benchmark, QuanTest2. In QuanTest2, SSPA and SP correlate better on an alignment-by-alignment basis than in QuanTest. Guide-trees for QuanTest2 are more balanced with respect to reference sequences than in QuanTest. QuanTest2 scores correlate well with other well-established benchmarks. Availability and implementation QuanTest2 is available at http://bioinf.ucd. ie/quantest2.tar, comprises of reference and non-reference sequence sets and a scoring script. Supplementary information Supplementary data are available at Bioinformatics online
The role of high‐intensity focused ultrasound as a symptomatic treatment for Parkinson's disease

MR‐guided focused ultrasound is a novel, minimally invasive surgical procedure for symptomatic treatment of PD. With this technology, the ventral intermediate nucleus, STN, and internal globus pallidus have been targeted for therapeutic cerebral ablation, while also minimizing the risk of hemorrhage and infection from more invasive neurosurgical procedures. In a double‐blinded, prospective, sham‐controlled randomized controlled trial of MR‐guided focused ultrasound thalamotomy for treatment of tremor‐dominant PD, 62% of treated patients demonstrated improvement in tremor scores from baseline to 3 months postoperatively, as compared to 22% in the sham group. There has been only one open‐label trial of MR‐guided focused ultrasound subthalamotomy for patients with PD, demonstrating improvements of 71% for rigidity, 36% for akinesia, and 77% for tremor 6 months after treatment. Among the two open‐label trials of MR‐guided focused ultrasound pallidotomy for patients with PD, dyskinesia and overall motor scores improved up to 52% and 45% at 6 months postoperatively. Although MR‐guided focused ultrasound thalamotomy is now approved by the U.S. Food and Drug Administration for treatment of parkinsonian tremor, additional high‐quality randomized controlled trials are warranted and are underway to determine the safety and efficacy of MR‐guided focused ultrasound subthalamotomy and pallidotomy for treatment of the cardinal features of PD. These studies will be paramount to aid clinicians to determine the ideal ablative target for individual patients. Additional work will be required to assess the durability of MR‐guided focused ultrasound lesions, ideal timing of MR‐guided focused ultrasound ablation in the course of PD, and the safety of performing bilateral lesions. © 2019 International Parkinson and Movement Disorder Society
Medication errors in emergency departments: is electronic medical record an effective barrier?

ABSTRACT Objective: To compare medication errors in two emergency departments with electronic medical record, to two departments that had conventional handwritten records at the same organization. Methods: A cross-sectional, retrospective, descriptive, comparative study of medication errors and their classification, according to the National Coordinating Council for Medication Error Reporting and Prevention, associated with the use of electronic and conventional medical records, in emergency departments of the same organization, during one year. Results: There were 88 events per million opportunities in the departments with electronic medical record and 164 events per million opportunities in the units with conventional medical records. There were more medication errors when using conventional medical record – in 9 of 14 categories of the National Coordinating Council for Medication Error Reporting and Prevention. Conclusion: The emergency departments using electronic medical records presented lower levels of medication errors, and contributed to a continuous improvement in patients´ safety.
Common Variants in Lipid Metabolism-Related Genes Associate with Fat Mass Changes in Response to Dietary Monounsaturated Fatty Acids in Adults with Abdominal Obesity.

BACKGROUND Different fatty acids (FAs) can vary in their obesogenic effect, and genetic makeup can contribute to fat deposition in response to dietary FA composition. However, the antiobesogenic effects of the interactions between dietary MUFAs and genetics have scarcely been tested in intervention studies. OBJECTIVE We evaluated the overall (primary outcome) and genetically modulated (secondary outcome) response in body weight and fat mass to different levels of MUFA consumption. METHODS In the Canola Oil Multicenter Intervention Trial II, a randomized, crossover, isocaloric, controlled-feeding multicenter trial, 44 men and 71 women with a mean age of 44 y and an increased waist circumference (men ∼108 cm and women ∼102 cm) consumed each of 3 oils for 6 wk, separated by four 12-wk washout periods. Oils included 2 high-MUFA oils-conventional canola and high-oleic canola (<7% SFAs, >65% MUFAs)-and 1 low-MUFA/high-SFA oil blend (40.2% SFAs, 22.0% MUFAs). Body fat was measured using DXA. Five candidate single-nucleotide polymorphisms (SNPs) were genotyped using qualitative PCR. Data were analyzed using a repeated measures mixed model. RESULTS No significant differences were observed in adiposity measures following the consumption of either high-MUFA diet compared with the low-MUFA/high-SFA treatment. However, when stratified by genotype, 3 SNPs within lipoprotein lipase (LPL), adiponectin, and apoE genes influenced, separately, fat mass changes in response to treatment (n = 101). Mainly, the LPL rs13702-CC genotype was associated with lower visceral fat (high-MUFA: -216.2 ± 58.6 g; low-MUFA: 17.2 ± 81.1 g; P = 0.017) and android fat mass (high-MUFA: -267.3 ± 76.4 g; low-MUFA: -21.7 ± 102.2 g; P = 0.037) following average consumption of the 2 high-MUFA diets. CONCLUSIONS Common variants in LPL, adiponectin, and apoE genes modulated body fat mass response to dietary MUFAs in an isocaloric diet in adults with abdominal obesity. These findings might eventually help in developing personalized dietary recommendations for weight control. The trial was registered at clinicaltrials.gov as NCT02029833 (https://www.clinicaltrials.gov/ct2/show/NCT02029833? cond=NCT02029833&rank=1).
Impact of age and pre-existing immunity on the induction of human antibody responses against influenza B viruses

ABSTRACT Pre-existing immunity to influenza is dependent on a number of factors and can vary greatly within and across influenza subtypes. In this study, volunteers (aged 18–85 years) were vaccinated with split, inactivated FluzoneTM in four consecutive influenza seasons from 2013 to 2016. The impact of repeat vaccination on breadth and durability of functional antibodies was assessed for total IgG and IgA anti-hemagglutinin (HA) binding antibodies and hemagglutination-inhibition (HAI) activity against both influenza B lineages. Many subjects were able to maintain high seroprotective titers to the vaccine strains in subsequent years, which resulted in low vaccine-induced seroconversion rates. This was especially evident in younger subjects who typically had higher titers and maintained these titers into the following season. In contrast, the HAI titers in elderly subjects were generally lower and more likely to decline prior to the start of the next influenza season. Immunological recall or ‘back-boosting’ to antigenically related viruses was associated with seroconversion. Overall, influenza vaccination in both younger and older people elicited broadly reactive immune responses within a lineage, as well as cross-reactive immune responses between lineages. This study exemplified the impact that age and influenza exposure history have on determining an individual’s ability to respond to future influenza infections.
Intuitive Honesty Versus Dishonesty: Meta-Analytic Evidence

Is self-serving lying intuitive? Or does honesty come naturally? Many experiments have manipulated reliance on intuition in behavioral-dishonesty tasks, with mixed results. We present two meta-analyses (with evidential value) testing whether an intuitive mind-set affects the proportion of liars (k = 73; n = 12,711) and the magnitude of lying (k = 50; n = 6,473). The results indicate that when dishonesty harms abstract others, promoting intuition causes more people to lie, log odds ratio = 0.38, p = . 0004, and people to lie more, Hedges’s g = 0.26, p < . 0001. However, when dishonesty inflicts harm on concrete others, promoting intuition has no significant effect on dishonesty (p > .63). We propose one potential explanation: The intuitive appeal of prosociality may cancel out the intuitive selfish appeal of dishonesty, suggesting that the social consequences of lying could be a promising key to the riddle of intuition’s role in honesty. We discuss limitations such as the relatively unbalanced distribution of studies using concrete versus abstract victims and the overall large interstudy heterogeneity.
Prevalence of and Risk Factors for Anal High-grade Squamous Intraepithelial Lesions in Women Living with Human Immunodeficiency Virus.

BACKGROUND Women living with human immunodeficiency virus (WLHIV) have disproportionately high rates of squamous cell carcinoma of the anus compared with the general population of women. Anal high-grade squamous intraepithelial lesions (HSILs) precede anal cancer, and accurate studies of HSIL prevalence among WLHIV in the United States are lacking. METHODS The AIDS Malignancy Consortium 084 study was a multicenter national trial to evaluate the prevalence of and risk factors for anal HSIL in a US cohort. Eligible participants were WLHIV aged ≥18 years with no history of anal HSIL. Study participants had an examination including collection of cervical/vaginal and anal specimens, followed by high-resolution anoscopy with biopsy. RESULTS We enrolled 256 women with evaluable anal pathology. The mean age was 49.4 years, 64% women were non-Hispanic black, 67% were former or current smokers, and 56% reported ever having anal sex with a man. The median CD4 T-cell count was 664 cells/μL. The prevalence of anal histologic HSIL (hHSIL) was 27% (95% confidence interval [CI], 22%-33%). There was a strong concordance (240/254) between local and consensus pathologists for hHSIL vs less than hHSIL (κ = 0.86 [95% CI, .79-.93]). Current CD4 count of ≤200 cells/μL was the strongest predictor of consensus anal hHSIL diagnosis (adjusted odds ratio [aOR], 10.34 [95% CI, 3.47-30.87]). History of anoreceptive intercourse was also associated with hHSIL (aOR, 2.44 [95% CI, 1.22-4.76]). CONCLUSIONS The prevalence of anal hHSIL in WLHIV in the United States was 27% in this study where all participants received high-resolution anoscopy and biopsy.
Personal protective equipment doffing practices of healthcare workers

Abstract During the doffing of personal protective equipment (PPE), pathogens can be transferred from the PPE to the bodies of healthcare workers (HCWs), putting HCWs and patients at risk of exposure and infection. PPE doffing practices of HCWs who cared for patients with viral respiratory infections were observed at an acute care hospital from March 2017 to April 2018. A trained observer recorded doffing performance of HCWs inside the patient rooms using a pre-defined checklist based on the Centers for Disease Control and Prevention (CDC) guideline. Doffing practices were observed 162 times during care of 52 patients infected with respiratory viral pathogens. Out of the 52 patients, 30 were in droplet and contact isolation, 21 were in droplet isolation, and 1 was in contact isolation. Overall, 90% of observed doffing was incorrect, with respect to the doffing sequence, doffing technique, or use of appropriate PPE. Common errors were doffing gown from the front, removing face shield of the mask, and touching potentially contaminated surfaces and PPE during doffing. Deviations from the recommended PPE doffing protocol are common and can increase potential for contamination of the HCW’s clothing or skin after providing care. There is a clear need to change the approach used to training HCWs in PPE doffing practices.
Label‐Free Analysis of Red Blood Cell Storage Lesions Using Imaging Flow Cytometry

Deleterious changes, collectively termed as storage lesions, alter the characteristics of red blood cell (RBC) morphology during in vitro storage. Due to gradual loss of cellular membrane, RBCs lose their original biconcave disk shape and begin a process of spherical deformation that is characterized by well‐defined morphological criteria. At the spheroechinocyte stage, the structure of RBC is irreversibly damaged and lacks the elasticity necessary to efficiently deliver oxygen. Quantifying the prevalence of spheroechinocytes could provide an important morphological measure of the quality of stored blood products. Unlike the conventional RBC morphology characterization assay involving light microscopy, we introduce a label‐free assay using imaging flow cytometry (IFC). The technique captures 100,000 images of a sample and calculates a relative measure of spheroechinocyte population in a fraction of the time required by the conventional method. A comparative method study, measuring a morphological index for 11 RCC units through storage, found that the two techniques measured similar trends with IFC reporting the metric at an average of 3.9% higher. We monitored 18 RCC units between Weeks 1 and 6 of storage and found that the spheroechinocyte population increased by an average of 26.2%. The large (3.5–64.1%) variation between the units' spheroechinocyte population percentage at Week 1 suggests a possible dependence of blood product quality on donor characteristics. Given our method's ability to rapidly monitor large samples and refine morphological characterization beyond conventional methods, we believe our technique offers good potential for studying the underlying relationships between RBC morphology and blood storage lesions. © 2019 International Society for Advancement of Cytometry
Caribbean climate change vulnerability: Lessons from an aggregate index approach

The study examines the potential influence of sub-regional variations in climate, and specifically heavy rain events, in determining relative vulnerabilities of locations in twelve Caribbean countries. An aggregate vulnerability index, referred to as the Caribbean Vulnerability Score (CVS), is created using historical demographic and socioeconomic data and climate data representing extreme rain events. Four scenarios are explored. Firstly, comparative vulnerabilities are determined when heavy rainfall is incorporated in CVS versus when it is excluded. The impact of climate change is also investigated using future climate data derived from statistical downscaling but holding demographic and socioeconomic sub-indices constant. The analysis is repeated with projections of future demographic structure from the Shared Socioeconomic Pathway data (SSP3), future climate projections and constant socioeconomic. Finally, the sensitivity of the results is examined with respect to applying different weights i.e. versus using equal weights for the climate and non-climatic components of CVS as is done for the first three scenarios. Results suggest that the inclusion of historical susceptibility to rainfall extremes influences relative vulnerabilities within the Caribbean when compared to the rankings of vulnerability derived using only socioeconomic and demographic inputs. In some cases significant increases in relative rankings are noted. Projected changes in the intensity of rain events across the Caribbean region in the 2030s and 2050s, do not significantly alter the top and lowest ranked vulnerable locations when demographic and socioeconomic indices are held constant. Changes may however occur in the order of the top ranked locations dependent on scenario and time slice. In general, future shifts in relative vulnerabilities were found to be dependent on (i) changes in both future climate and demographic scenarios, (ii) the time horizons being considered, and (iii) the weighting assigned to climate in the future.
Lower long-term mortality in obese patients with community-acquired pneumonia: possible role of CRP

OBJECTIVE: The present study aimed to investigate the relationship between obesity and mortality in patients with community-acquired pneumonia (CAP) in China. METHODS: In total, 909 patients with CAP were recruited for this study from January 2010 to June 2015. All patients were selected and divided into 4 groups according to their body mass index (BMI) values. All patients' clinical information was recorded. The associations among mortality; BMI; the 30-day, 6-month and 1-year survival rates for different BMI classes; the etiology of pneumonia in each BMI group; and the risk factors for 1-year mortality in CAP patients were analyzed. RESULT: With the exception of the level of C-reactive protein (CRP), no other clinical indexes showed significant differences among the different BMI groups. No significant differences were observed among all groups in terms of the 30-d and 6-month mortality rates (p>0.05). There was a significantly lower risk of 1-year mortality in the obese group than in the nonobese group, (p<0.05). Logistic regression analysis showed that there were seven independent risk factors for 1-year mortality in CAP patients, namely, age, cardiovascular disease, cerebrovascular disease, obesity, APACHE II score, level of CRP and CAP severity. CONCLUSION: Compared with nonobese patients with CAP, obese CAP patients may have a lower mortality rate, especially with regard to 1-year mortality, and CRP may be associated with the lower mortality rate in obese individuals than in nonobese individuals.
The tumor cell‐secreted matricellular protein WISP1 drives pro‐metastatic collagen linearization

Collagen linearization is a hallmark of aggressive tumors and a key pathogenic event that promotes cancer cell invasion and metastasis. Cell‐generated mechanical tension has been proposed to contribute to collagen linearization in tumors, but it is unknown whether other mechanisms play prominent roles in this process. Here, we show that the secretome of cancer cells is by itself able to induce collagen linearization independently of cell‐generated mechanical forces. Among the tumor cell‐secreted factors, we find a key role in this process for the matricellular protein WISP1 (CCN4). Specifically, WISP1 directly binds to type I collagen to promote its linearization in vitro (in the absence of cells) and in vivo in tumors. Consequently, WISP1‐induced type I collagen linearization facilitates tumor cell invasion and promotes spontaneous breast cancer metastasis, without significantly affecting gene expression. Furthermore, higher WISP1 expression in tumors from cancer patients correlates with faster progression to metastatic disease and poor prognosis. Altogether, these findings reveal a conceptually novel mechanism whereby pro‐metastatic collagen linearization critically depends on a cancer cell‐secreted factor.
Sharing of clinical trial data and results reporting practices among large pharmaceutical companies: cross sectional descriptive study and pilot of a tool to improve company practices

Abstract Objectives To develop and pilot a tool to measure and improve pharmaceutical companies’ clinical trial data sharing policies and practices. Design Cross sectional descriptive analysis. Setting Large pharmaceutical companies with novel drugs approved by the US Food and Drug Administration in 2015. Data sources Data sharing measures were adapted from 10 prominent data sharing guidelines from expert bodies and refined through a multi-stakeholder deliberative process engaging patients, industry, academics, regulators, and others. Data sharing practices and policies were assessed using data from ClinicalTrials.gov, Drugs@FDA, corporate websites, data sharing platforms and registries (eg, the Yale Open Data Access (YODA) Project and Clinical Study Data Request (CSDR)), and personal communication with drug companies. Main outcome measures Company level, multicomponent measure of accessibility of participant level clinical trial data (eg, analysis ready dataset and metadata); drug and trial level measures of registration, results reporting, and publication; company level overall transparency rankings; and feasibility of the measures and ranking tool to improve company data sharing policies and practices. Results Only 25% of large pharmaceutical companies fully met the data sharing measure. The median company data sharing score was 63% (interquartile range 58-85%). Given feedback and a chance to improve their policies to meet this measure, three companies made amendments, raising the percentage of companies in full compliance to 33% and the median company data sharing score to 80% (73-100%). The most common reasons companies did not initially satisfy the data sharing measure were failure to share data by the specified deadline (75%) and failure to report the number and outcome of their data requests. Across new drug applications, a median of 100% (interquartile range 91-100%) of trials in patients were registered, 65% (36-96%) reported results, 45% (30-84%) were published, and 95% (69-100%) were publicly available in some form by six months after FDA drug approval. When examining results on the drug level, less than half (42%) of reviewed drugs had results for all their new drug applications trials in patients publicly available in some form by six months after FDA approval. Conclusions It was feasible to develop a tool to measure data sharing policies and practices among large companies and have an impact in improving company practices. Among large companies, 25% made participant level trial data accessible to external investigators for new drug approvals in accordance with the current study’s measures; this proportion improved to 33% after applying the ranking tool. Other measures of trial transparency were higher. Some companies, however, have substantial room for improvement on transparency and data sharing of clinical trials.