Miracle-dz/UniFAR-FTUs huggingface dataset:
Sex hormone levels by presence and severity of cirrhosis in women with chronic hepatitis C virus infection

Cirrhosis is associated with hormonal dysregulation, as evidenced by secondary amenorrhoea in reproductive‐aged women, and feminization of cirrhotic men. Whether hormone levels vary by severity of cirrhosis in women is not known. If identified, such changes may have important clinical relevance, particularly, as low sex hormone binding globulin (SHBG) and follicle stimulating hormone (FSH) are known to promote metabolic and cardiovascular disease in women. In a cohort of post‐menopausal women with chronic hepatitis C virus (HCV) infection, we compared comprehensive sex hormone levels by presence of cirrhosis, as well as across Child‐Turcotte‐Pugh (CTP) class. Results: There were n = 18 cirrhotic and n = 21 noncirrhotic women with a median age of 57 years (interquartile range [IQR] 53‐62). Compared to noncirrhotics, cirrhotic women had higher oestradiol (11.0 vs 6.0 pg/mL, P = 0.05) and oestrone levels (32.0 vs 8.0 ng/mL, P < 0.001), and lower sex hormone binding globulin (SHBG) (69.2 vs 155.6 nmol/L, P = 0.001), and FSH levels (4.9 vs 89.6 mIU/mL, P < 0.001). Among cirrhotic women, there was a progressive decline in FSH and SHBG and concurrent rise in oestrone levels from CTP class A to C (test of trend, P values ≤0.02). Cirrhosis is associated with lower FSH and SHBG levels in cirrhotic compared to noncirrhotic women with HCV infection. In cirrhotic women, these levels demonstrate steady decline by disease severity. Given known associations of low SHBG and FSH with cardio‐metabolic disease, the clinical implications of hormonal changes by cirrhosis severity in HCV‐infected women warrants investigation.
Shear Behavior of Hybrid Fiber Reinforced Concrete Deep Beams

Hybrid fiber reinforced concrete (HFRC) is based on a multilevel-reinforcement material design that improves both the compressive strength and tensile strength. Investigations of the mechanical performance of HFRC with two types of steel fibers were conducted experimentally. The investigated parameters were the volume fractions of the short steel fibers and long steel fibers. The compressive strength, tensile strength, and flexural strength of the HFRC were researched. The group with volume fractions of 1.5% for the long steel fibers and 0.5% for the short steel fibers exhibited the best flexural strength. The synergetic effect clearly was improved by combining different types of steel fiber. Four HFRC deep beams and one reinforced concrete (RC) deep beam were conducted to consider the shear behavior of these beams. The primary variables included the volume fraction of steel fibers and the web reinforcement ratio. The shear behavior was evaluated based on the cracking pattern, load-deflection behavior, and shear capacity. All of the beams failed due to the formation of diagonal cracks. The results indicated that hybrid fibers contribute greatly to the shear behavior of deep beams. The hybrid fibers led to the formation of multiple diagonal cracks in the deep beams and enhanced the damage tolerance. With the same web reinforcement ratio, the ultimate load and deformation of the HFRC deep beams were better than those of the RC deep beam.
EBP1 nuclear accumulation negatively feeds back on FERONIA-mediated RALF1 signaling

FERONIA (FER), a plasma membrane receptor-like kinase, is a central regulator of cell growth that integrates environmental and endogenous signals. A peptide ligand rapid alkalinization factor 1 (RALF1) binds to FER and triggers a series of downstream events, including inhibition of Arabidopsis H+-ATPase 2 activity at the cell surface and regulation of gene expression in the nucleus. We report here that, upon RALF1 binding, FER first promotes ErbB3-binding protein 1 (EBP1) mRNA translation and then interacts with and phosphorylates the EBP1 protein, leading to EBP1 accumulation in the nucleus. There, EBP1 associates with the promoters of previously identified RALF1-regulated genes, such as CML38, and regulates gene transcription in response to RALF1 signaling. EBP1 appears to inhibit the RALF1 peptide response, thus forming a transcription–translation feedback loop (TTFL) similar to that found in circadian rhythm control. The plant RALF1-FER-EBP1 axis is reminiscent of animal epidermal growth factor receptor (EGFR) signaling, in which EGF peptide induces EGFR to interact with and phosphorylate EBP1, promoting EBP1 nuclear accumulation to control cell growth. Thus, we suggest that in response to peptide signals, plant FER and animal EGFR use the conserved key regulator EBP1 to control cell growth in the nucleus.
The preregistration revolution needs to distinguish between predictions and analyses

Nosek et al. (1) recently joined others in advocating for “widespread adoption of preregistration” as a tool for advancing science. The language they use in making this important argument, however, creates unnecessary confusion: Like many others discussing these issues, they seem to conflate the goal of theory falsification with the goal of constraining type I error. This masks a crucial distinction between two types of preregistration: preregistering a theoretical, a priori, directional prediction (which serves to clarify how a hypothesis is constructed) and preregistering an analysis plan (which serves to clarify how evidence is produced). Indeed, philosophers of science have identified elements of both how a hypothesis is constructed and how evidence is … [↵][1]1Email: aledgerwood{at}ucdavis.edu. [1]: #xref-corresp-1-1
Glutathione S-Transferase Gene Polymorphisms are Associated with an Improved Treatment Response to Cisplatin-Based Chemotherapy in Patients with Non-Small Cell Lung Cancer (NSCLC): A Meta-Analysis

Background Previous studies have shown an association with glutathione S-transferase (GST) gene polymorphisms in patients with non-small cell lung cancer (NSCLC) and treatment response. This study aimed to undertake a literature review and meta-analysis of GST gene polymorphisms, including GSTT1, GSTM1, and GSTP1 IIe105Val, and the treatment response to cisplatin-based chemotherapy in patients with NSCLC. Material/Methods A literature search was undertaken of the main medical publication databases for publications, up to March 2017, on the association between GSTT1, GSTM1, and GSTP1 IIe105Val polymorphisms and the clinical outcome in patients with NSCLC treated with cisplatin-based chemotherapy. A random fixed-effects model was used to calculate the pooled odds ratio (OR) and 95% confidence interval (CI) to evaluate the associations, considering multiple genetic models. A subgroup analysis according to ethnicity was performed. Results Twenty-three published studies were identified that showed that both the null GSTM1 and the GG genotype of GSTP1 IIe105Val were associated with improved treatment response to cisplatin-based chemotherapy (GSTT1 present/null: OR=1.328; 95% CI, 1.074–1.643) (GSTP1 GG + AG vs. AA: OR=0.596; 95% CI, 0.468–0.759). In subgroup analysis, the GSTP1 polymorphism was significantly associated with treatment response in East-Asian patients, but not in Caucasian patients. Conclusions Meta-analysis showed that the GG genotype of GSTP1 IIe105Val and the null GSTM1 genotype were associated with an improved treatment response to cisplatin-based chemotherapy in patients with NSCLC, especially in East-Asian patients.
The role of public health units in the delivery of HIV pre-exposure prophylaxis (PrEP)

Pre-exposure prophylaxis (PrEP) is an HIV prevention strategy involving the use of once daily antiretroviral medications to prevent HIV infection. Available research supports that PrEP, when used as prescribed, can prevent HIV transmission by upwards of 96%. Such findings have led to the development of research publications and guidelines supporting PrEP for individuals at high risk for HIV acquisition, such as men who have sex with men (MSM). Despite its benefit, current use of PrEP in clinical settings has been undermined by false impressions of poor efficacy of PrEP and concerns about increased risk-taking among MSM should PrEP be readily available. Furthermore, guidance for the role of public health units in PrEP access has not been well defined. While we maintain that PrEP should be available to any person who requests it, we feel that public health units should focus on those at highest risk for HIV acquisition, and, in doing so, possibly reduce local HIV rates. RésuméLa prophylaxie pré-exposition (PrEP) est une stratégie de prévention fondée sur la prise quotidienne de médicaments antirétroviraux pour prévenir le VIH. Selon les recherches disponibles, la PrEP, lorsqu'elle est prise telle que prescrite, peut prévenir la transmission du VIH dans une proportion de plus de 96%. Ces conclusions ont mené à l’élaboration de plusieurs publications et de lignes directrices à l’appui de la PrEP pour les personnes risquant fortement de contracter le VIH, comme les hommes ayant des relations sexuelles avec des hommes (HARSAH). Malgré ses avantages, l'utilisation de la PrEP en milieu clinique a été compromise par de fausses impressions quant à la faible efficacité de la PrEP et les inquiétudes concernant la prise de risque accrue chez les HARSAH si la PrEP était facilement accessible. De plus, les directives sur le rôle des unités de santé publique dans l'accès à la PrEP n'ont pas été bien définies. Bien que nous maintenions que la PrEP devrait être accessible à toute personne qui en fait la demande, nous pensons que les unités de santé publique devraient se concentrer sur les personnes les plus à risque, ce qui pourrait permettre de réduire l'incidence des cas de VIH au niveau local.
Memory T Cells in Flavivirus Vaccination

Flaviviruses include many medically important viruses, such as Dengue virus (DENV), Japanese encephalitis (JEV), tick-borne encephalitis (TBEV), West Nile (WNV), yellow fever (YFV), and Zika viruses (ZIKV). Currently, there are licensed human vaccines for DENV, JEV, TBEV and YFV, but not for WNV or ZIKV. Memory T cells play a central role in adaptive immunity and are important for host protection during flavivirus infection. In this review, we discuss recent findings from animal models and clinical trials and provide new insights into the role of memory T cells in host protective immunity upon vaccination with the licensed flavivirus vaccines.
The Influence of Globally Ungrammatical Local Syntactic Constraints on Real-Time Sentence Comprehension: Evidence From the Visual World Paradigm and Reading

We investigated the influence of globally ungrammatical local syntactic constraints on sentence comprehension, as well as the corresponding activation of global and local representations. In Experiment 1, participants viewed visual scenes with objects like a carousel and motorbike while hearing sentences with noun phrase (NP) or verb phrase (VP) modifiers like "The girl who likes the man (from London/very much) will ride the carousel. " In both cases, "girl" and "ride" predicted carousel as the direct object; however, the locally coherent combination "the man from London will ride…" in NP cases alternatively predicted motorbike. During "ride," local constraints, although ruled out by the global constraints, influenced prediction as strongly as global constraints: While motorbike was fixated less than carousel in VP cases, it was fixated as much as carousel in NP cases. In Experiment 2, these local constraints likewise slowed reading times. We discuss implications for theories of sentence processing.
Dyslipidaemias in women using hormonal contraceptives: a cross sectional study in Mulago Hospital Family Planning Clinic, Kampala, Uganda

Objective To determine the prevalence and factors associated with dyslipidaemias in women using hormonal contraceptives. Design Cross-sectional study Setting Mulago Hospital, Kampala, Uganda Participants Three hundred and eighty-four consenting women, aged 18–49 years, who had used hormonal contraceptives for at least 3 months prior to the study. Study outcome Dyslipidaemias (defined as derangements in lipid profile levels which included total cholesterol ≥200 mg/dL, high-density lipoprotein <40 mg/dL, triglyceride >150 mg/dL or low-density lipoprotein ≥160 mg/dL) for which the prevalence and associated factors were obtained. Results The prevalence of dyslipidaemias was 63.3% (95% CI: 58.4 to 68.1). Body mass index (BMI) (PR=1.33, 95% CI: 1.15 to 1.54, p<0.001) and use of antiretroviral therapy (ART) (PR=1.21, 95% CI: 1.03 to 1.42, p=0.020) were the factors significantly associated with dyslipidaemias. Conclusion Dyslipidaemias were present in more than half the participants, and this puts them at risk for cardiovascular diseases. The high-risk groups were women with a BMI greater than 25 Kg/m2 and those who were on ART. Therefore, lipid profiles should be assessed in women using hormonal contraceptives in order to manage them better.
Limited Genetic Structure of Gypsy Moth Populations Reflecting a Recent History in Europe

The gypsy moth, Lymantria dispar, a prominent polyphagous species native to Eurasia, causes severe impacts in deciduous forests during irregular periodical outbreaks. This study aimed to describe the genetic structure and diversity among European gypsy moth populations. Analysis of about 500 individuals using a partial region of the mitochondrial COI gene, L. dispar was characterized by low genetic diversity, limited population structure, and strong evidence that all extant haplogroups arose via a single Holocene population expansion event. Overall 60 haplotypes connected to a single parsimony network were detected and genetic diversity was highest for the coastal populations Croatia, Italy, and France, while lowest in continental populations. Phylogenetic reconstruction resulted in three groups that were geographically located in Central Europe, Dinaric Alps, and the Balkan Peninsula. In addition to recent events, the genetic structure reflects strong gene flow and the ability of gypsy moth to feed on about 400 deciduous and conifer species. Distinct genetic groups were detected in populations from Georgia. This remote population exhibited haplotypes intermediate to the European L. dispar dispar, Asian L. dispar asiatica, and L. dispar japonica clusters, highlighting this area as a possible hybridization zone of this species for future studies applying genomic approaches.
Short-term cortisol exposure alters cardiac hypertrophic and non-hypertrophic signalling in a time-dependent manner in rainbow trout

ABSTRACT Cardiac disease is a growing concern in farmed animals, and stress has been implicated as a factor for myocardial dysfunction and mortality in commercial fish rearing. We recently showed that the stress hormone cortisol induces pathological cardiac remodelling in rainbow trout. Wild and farmed salmonids are exposed to fluctuations and sometimes prolonged episodes of increased cortisol levels. Thus, studying the timeframe of cortisol-induced cardiac remodelling is necessary to understand its role in the pathogenesis of cardiovascular disease in salmonids. We here establish that 3 weeks of cortisol exposure is sufficient to increase relative ventricular mass (RVM) by 20% in rainbow trout. Moreover, increased RVMs are associated with altered expression of hypertrophic and non-hypertrophic remodelling markers. Further, we characterised the time course of cortisol-induced cardiac remodelling by feeding rainbow trout cortisol-containing feed for 2, 7 and 21 days. We show that the effect of cortisol on expression of hypertrophic and non-hypertrophic remodelling markers is time-dependent and in some cases acute. Our data indicate that short-term stressors and life cycle transitions associated with elevated cortisol levels can potentially influence hypertrophic and non-hypertrophic remodelling of the trout heart. Summary: Here we indicate that short-term cortisol exposure can induce cardiac hypertrophic and non-hypertrophic remodelling and that certain pro-hypertrophic effects of cortisol are time-dependent in rainbow trout.
Leveraging Breadth and Depth: Strategies to Characterize Population Diversity to Address Cancer Disparities in the DF/HCC Catchment Area

Background: NCI-Designated Cancer Centers provide key cancer research, prevention, and treatment services to members of their catchment area. Characterization of these areas may be complex given the diverse needs of the populations within, particularly those from low socioeconomic position (SEP). The purpose of this paper is to describe the characterization of the Dana-Farber/Harvard Cancer Center (DF/HCC) catchment area through using a two-pronged approach. Methods: Participants (n = 1,511) were recruited through (i) an online, probability-based survey (n = 1,013) and (ii) a supplementary, in-person survey from priority groups (African Americans, Latinos, blue-collar workers, low SEP, homeless; n = 498) within Massachusetts. Study staff worked closely with community partners across the state to reach individuals who may not usually be included in online surveys. Results: There were several differences across samples, with the community-based sample having a higher percentage of low SEP, low education, African Americans, and Latinos compared with the online sample. Differences were also noted in the cancer-related behaviors of the samples, with the community-based sample having higher rates of smoking, particularly within those who were homeless or make less than $20,000 per year. Fewer community-based subgroups were current with cancer screenings, and more showed more indication of potential communication inequalities compared with statewide estimates. Conclusions: The sampling strategy used to characterization of the DF/HCC catchment area provided broad, statewide estimates and additional focus on vulnerable populations, highlighting several potential areas for intervention. Impact: This study provides data to highlight the value of using multiple sampling strategies when characterizing cancer center catchment areas.
Partial Discharge Recognition with a Multi-Resolution Convolutional Neural Network

Partial discharge (PD) is not only an important symptom for monitoring the imperfections in the insulation system of a gas-insulated switchgear (GIS), but also the factor that accelerates the degradation. At present, monitoring ultra-high-frequency (UHF) signals induced by PDs is regarded as one of the most effective approaches for assessing the insulation severity and classifying the PDs. Therefore, in this paper, a deep learning-based PD classification algorithm is proposed and realized with a multi-column convolutional neural network (CNN) that incorporates UHF spectra of multiple resolutions. First, three subnetworks, as characterized by their specified designed temporal filters, frequency filters, and texture filters, are organized and then intergraded by a fully-connected neural network. Then, a long short-term memory (LSTM) network is utilized for fusing the embedded multi-sensor information. Furthermore, to alleviate the risk of overfitting, a transfer learning approach inspired by manifold learning is also present for model training. To demonstrate, 13 modes of defects considering both the defect types and their relative positions were well designed for a simulated GIS tank. A detailed analysis of the performance reveals the clear superiority of the proposed method, compared to18 typical baselines. Several advanced visualization techniques are also implemented to explore the possible qualitative interpretations of the learned features. Finally, a unified framework based on matrix projection is discussed to provide a possible explanation for the effectiveness of the architecture.
Symptoms and feelings valued by patients after a percutaneous coronary intervention: a discrete-choice experiment to inform development of a new patient-reported outcome

Objective To inform the development of a patient-reported outcome measure, the aim of this study was to identify which symptoms and feelings following percutaneous coronary intervention (PCI) are most important to patients. Design Discrete-choice experiment consisting of two hypothetical scenarios of 10 symptoms and feelings (pain or discomfort; shortness of breath; concern/worry about heart problems; tiredness; confidence to do usual activities; ability to do usual activities; happiness; sleep disturbance; dizziness or light-headedness and bruising) experienced after PCI, described by three levels (never, some of the time, most of the time). Preference weights were estimated using a conditional logit model. Setting Four Australian public hospitals that contribute to the Victorian Cardiac Outcomes Registry (VCOR) and a private insurer’s claim database. Participants 138 people aged >18 years who had undergone a PCI in the previous 6 months. Main outcome measures Patient preferences via trade-offs between 10 feelings and symptoms. Results Of the 138 individuals recruited, 129 (93%) completed all 16 choice sets. Conditional logit parameter estimates were mostly monotonic (eg, moving to worse levels for each individual symptom and feeling made the option less attractive). When comparing the magnitude of the coefficients (based on the coefficient of the worst level relative to best level in each item), feeling unhappy was the symptom or feeling that most influenced perception of a least-preferred PCI outcome (OR 0.42, 95% CI 0.34 to 0.51, p<0.0001) and the least influential was bruising (OR 0.81, 95% CI 0.67 to 0.99, p=0.04). Conclusion This study provides new insights into how patients value symptoms and feelings they experience following a PCI.
Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients

Selecting among alternative scenarios of human evolution is nowadays a common methodology to investigate the history of our species. This strategy is usually based on computer simulations of genetic data under different evolutionary scenarios, followed by a fitting of the simulated data with the real data. A recent trend in the investigation of ancestral evolutionary processes of modern humans is the application of genetic gradients as a measure of fitting, since evolutionary processes such as range expansions, range contractions, and population admixture (among others) can lead to different genetic gradients. In addition, this strategy allows the analysis of the genetic causes of the observed genetic gradients. Here, we review recent findings on the selection among alternative scenarios of human evolution based on simulated genetic gradients, including pros and cons. First, we describe common methodologies to simulate genetic gradients and apply them to select among alternative scenarios of human evolution. Next, we review previous studies on the influence of range expansions, population admixture, last glacial period, and migration with long-distance dispersal on genetic gradients for some regions of the world. Finally, we discuss this analytical approach, including technical limitations, required improvements, and advice. Although here we focus on human evolution, this approach could be extended to study other species.