Miracle-dz/UniFAR-FTUs huggingface dataset:
Abundance of Panamanian dry-forest birds along gradients of forest cover at multiple scales

Abstract: Community structure and species’ abundances may be strongly correlated to patterns of forest cover, although such patterns are poorly known for tropical dry-forest birds, especially for those in Panamanian dry forests. Birds were distance-sampled during point counts in five dry-forest fragments in Panama. Distance from point count to forest edge and forest coverage at three spatial scales (500, 1000 and 2000-m radius) were compared as covariate predictors of the abundance of avian species and guilds. Each covariate was selected in at least two models of species or guild abundance. Abundance patterns were consistent with previously reported habitat associations for only two of seven open-habitat or forest-preferring species that showed forest cover-abundance relationships. Null models best described the abundance of all forest species and the subset of uncommon forest species. Thus many of these species appear insensitive to the forest-cover gradients studied. Total abundance of open-habitat-preferring species increased in dry forests with increasing forest coverage within 500 m, suggesting that the relationship between their abundance and vegetation structure are spatial-scale and habitat dependent. Nectarivores had lower abundance as forest cover within 1000 m increased, supporting previous claims that this group is tolerant of forest edges.
Autocrine interleukin-23 promotes self-renewal of CD133+ ovarian cancer stem-like cells

Cancer stem cells (CSCs) are a group of cells which possess the ability of self-renewing and unlimited proliferation. And these CSCs are thought to be the cause of metastasis, recurrence and resistance. Recent study has found that pro-inflammatory cytokine and chemotactic factor mediate the self-renewing and differentiation of most of CSCs. Thus we speculate that ovarian cancer stem cells (OCSCs) can also maintain the ability of self-renewing and differentiation by releasing inflammatory factor. This report we discuss the biological characteristics and the specific molecular mechanism mediated by interleukin-23 (IL-23) and its receptor on the self-renewing of OCSCs. We found that OCSCs had high expression of IL-23 and IL-23R. IL-23 could promote the self-renewal ability of OCSCs and played a very important role to maintain the stable expression of stem cell markers in vitro. Moreover, we verified that IL-23 could maintain the potential tumorigenic of OCSCs in vivo and mediate the self-renewal ability and the formation of tumor in OCSCs by activating the signal pathways of STAT3 and NF-κB. In addition, human low differentiation tissues showed overexpression of IL-23. And IL-23 positively correlated to the expression level of CD133, Nanog and Oct4. In conclusion, Our discoveries demonstrate that autocrine IL-23 contribute to ovarian cancer malignancy through promoting the self-renewal of CD133+ ovarian cancer stem-like cells, and this suggests that IL-23 and its signaling pathway might serve as therapeutic targets for the treatment of ovarian cancer.
CLSI Methods Development and Standardization Working Group Best Practices for Evaluation of Antimicrobial Susceptibility Tests

ABSTRACT Effective evaluations of antimicrobial susceptibility tests (ASTs) require robust study design. The Clinical and Laboratory Standards Institute (CLSI) Subcommittee on Antimicrobial Susceptibility Testing has recognized that many published studies reporting the performance of commercial ASTs (cASTs) suffer from major design and/or analysis flaws, rendering the results difficult or impossible to interpret. This minireview outlines the current consensus of the Methods Development and Standardization Working Group of the CLSI Subcommittee on Antimicrobial Susceptibility Testing regarding best practices for systematic evaluation of the performance of an AST, including the analysis and presentation of essential data intended for publication.
A Material Point Method for Complex Fluids

We present a novel Material Point Method for simulating complex materials. The method achieves plasticity effects via the temporal evolution of the left elastic Cauchy-Green strain. We recast the upper-convected derivative of the strain in the Oldroyd-B constitutive model as a plastic flow and are able to simulate elastic and viscoelastic effects. Our model provides a volume-preserving rate-based description of plasticity that does not require singular value decompositions. Our semi-implicit discretization allows for high-resolution simulations. We also present novel discretizations of the temporal update of the left elastic Cauchy-Green strain for several constitutive models that preserve symmetry and positive-definiteness of the strain for use in the Material Point Method. A novel modification to a constitutive model is also presented that models material softening under plastic compression.
Cryptosporidiosis in children in the Indian subcontinent

Cryptosporidiosis is a leading cause of diarrheal disease among children under two in developing countries. Previous estimates have shown a high burden of cryptosporidial diarrhea in children from Sub-Saharan Africa and South Asia. Asymptomatic cryptosporidial infections which go undetected and untreated have been shown to result in significant malnutrition. In this review, we carried out a literature search of studies published on cryptosporidiosis in children in the Indian subcontinent from 1983 to 2016. Of the 154 publications identified, 54 were included for final analysis with both hospital-based and community-based studies. There were wide variations in reported prevalence rates from hospital studies and highlight the need to be carry out these studies with uniform sampling and molecular tools for detection, especially in countries with a dearth of information. Community-based studies, however, showed similarities in spite of differences in when (the late 1990s up until recently) and where (South India or Bangladesh) they were conducted. When more sensitive detection methods were used, cryptosporidial diarrhea accounted for 7%–9% of all diarrhea episodes and 20%–30% of children in these cohorts experienced at least one cryptosporidial diarrheal episode. High rates of asymptomatic infections with increased detection by serology and multiple infections (symptomatic and asymptomatic) were also documented in all cohorts. This overview brings to light the high burden of disease associated with cryptosporidiosis in children in the subcontinent and the gaps in knowledge to be addressed.
HepaRG cells: A human model to study mechanisms of acetaminophen hepatotoxicity

Acetaminophen (APAP) overdose is the leading cause of acute liver failure in Western countries. In the last four decades much progress has been made in our understanding of APAP‐induced liver injury through rodent studies. However, some differences exist in the time course of injury between rodents and humans. To study the mechanism of APAP hepatotoxicity in humans, a human‐relevant in vitro system is needed. Here we present evidence that the cell line HepaRG is a useful human model for the study of APAP‐induced liver injury. Exposure of HepaRG cells to APAP at several concentrations resulted in glutathione depletion, APAP‐protein adduct formation, mitochondrial oxidant stress and peroxynitrite formation, mitochondrial dysfunction (assessed by JC‐1 fluorescence), and lactate dehydrogenase (LDH) release. Importantly, the time course of LDH release resembled the increase in plasma aminotransferase activity seen in humans following APAP overdose. Based on propidium iodide uptake and cell morphology, the majority of the injury occurred within clusters of hepatocyte‐like cells. The progression of injury in these cells involved mitochondrial reactive oxygen and reactive nitrogen formation. APAP did not increase caspase activity above untreated control values and a pancaspase inhibitor did not protect against APAP‐induced cell injury. Conclusion: These data suggest that key mechanistic features of APAP‐induced cell death are the same in human HepaRG cells, rodent in vivo models, and primary cultured mouse hepatocytes. Thus, HepaRG cells are a useful model to study mechanisms of APAP hepatotoxicity in humans. (HEPATOLOGY 2011)
An Industry Perspective to Comparing the SQALE and Quamoco Software Quality Models

Context: We investigate the different perceptions of quality provided by leading operational quality models when used to evaluate software systems from an industry perspective. Goal: To compare and evaluate the quality assessments of two competing quality models and to develop an extensible solution to meet the quality assurance measurement needs of an industry stakeholder -The Construction Engineering Research Laboratory (CERL). Method: In cooperation with our industry partner TechLink, we operationalize the Quamoco quality model and employ a multiple case study design comparing the results of Quamoco and SQALE, two implementations of well known quality models. The study is conducted across current versions of several open source software projects sampled from GitHub and commercial software for sustainment management systems implemented in the C# language from our industry partner. Each project represents a separate embedded unit of study in a given context -open source or commercial. We employ inter-rater agreement and correlation analysis to compare the results of both models, focusing on Maintainability, Reliability, and Security assessments. Results: Our observations suggest that there is a significant disconnect between the assessments of quality under both quality models. Conclusion: In order to support industry adoption, additional work is required to bring competing implementations of quality models into alignment. This exploratory case study helps us shed light into this problem.
The Influence of Language on Memory for Object Location

In this study, the influence of two types of language on memory for object location was investigated: demonstratives (this, that) and possessives (my, your). Participants read instructions (containing this/that/my/your/the) to place objects at different locations. They then had to recall those object locations. Experiments 1 and 2 tested the contrasting predictions of two possible accounts of language on memory: the expectation model (Coventry, Griffiths, & Hamilton, 2014) and the congruence account (Bonfiglioli, Finocchiaro, Gesierich, Rositani, & Vescovi, 2009). In Experiment 3, the role of attention as a possible mechanism was investigated. The results across all three experiments show striking effects of language on object location memory; objects in the “that” and “your” condition were misremembered to be further away than objects in the “this” and “my” condition. The data favored the expectation model: expected location cued by language and actual location are concatenated leading to (mis)memory for object location.
Programmed death-ligand 1 is upregulated in intrahepatic lymphoepithelioma-like cholangiocarcinoma

Intrahepatic lymphoepithelioma-like cholangiocarcinoma (LELCC) is a rare variant of cholangiocarcinoma. Here, we report the largest single series of LELCC cases yet studied (n = 13). We retrospectively analyzed the clinical data of the 13 patients and measured the expression of programmed death-ligand 1 (PD-L1) in tumors using immunohistochemical staining. We also analyzed 15 cases of conventional intrahepatic cholangiocarcinoma (IHCC) for comparison. We found that eight patients with LELCC were infected with Epstein-Barr Virus (EBV), and EBV infection correlated with poor prognosis in LELCC. Four patients among the five (80.0%) without EBV had a history of chronic viral hepatitis B. None of the 15 cases of conventional cholangiocarcinoma were positive for EBV. PD-L1 was expressed in both the tumor cells and tumor-infiltrating immune cells in LELCC patients at higher levels than in IHCC patients (P < 0.05). These observations suggest that EBV infection may promote the development of LELCC, and that PD-L1 may be a potential therapeutic target for treatment of EBV-associated LELCC.
Weather Shocks and Climate Change

Previous research has shown that weather shocks, i.e. temperature deviations from the long-run normal values, have significant effect on economic outcomes, such as employment or income, even in developed economies such as the United States. This evidence is often interpreted as reflecting limits to adaptation. We document large differences in the sensitivity of economic activity to weather shocks across regions within the US. We interpret these differences as reflecting adaptation choices that regions make given their specific climate. This leads us to use these reduced form estimates to estimate a simple structural model of adaptation. We can then use the model to infer the effect of projected climate change on production. We find that both the median losses and the identity of the losers from climate change vary substantially once adaptation is taken into account.
A quantitative study of accuracy in system call-based malware detection

Over the last decade, there has been a significant increase in the number and sophistication of malware-related attacks and infections. Many detection techniques have been proposed to mitigate the malware threat. A running theme among existing detection techniques is the similar promises of high detection rates, in spite of the wildly different models (or specification classes) of malicious activity used. In addition, the lack of a common testing methodology and the limited datasets used in the experiments make difficult to compare these models in order to determine which ones yield the best detection accuracy. In this paper, we present a systematic approach to measure how the choice of behavioral models influences the quality of a malware detector. We tackle this problem by executing a large number of testing experiments, in which we explored the parameter space of over 200 different models, corresponding to more than 220 million of signatures. Our results suggest that commonly held beliefs about simple models are incorrect in how they relate changes in complexity to changes in detection accuracy. This implies that accuracy is non-linear across the model space, and that analytical reasoning is insufficient for finding an optimal model, and has to be supplemented by testing and empirical measurements.
Symptom rating scales and outcome in schizophrenia

Background Symptom rating scales are now well established in schizophrenia research buttheir scores are notthe same as outcome Aims To appraise the usefulness of symptom rating scales in evaluating the outcome of people with schizophrenia Method Literature on the use of the Brief Psychiatric Rating Scale (BPRS) the Positive and Negative Syndrome Scale (PANSS) and the Clinical Global Impression (CGI) in schizophrenia research was studied Results Scales were designed to make diagnoses, to categorise patients, syndromes or both, and to demonstrate antipsychotic efficacy, as well as to measure outcome. There is much redundancy both between and within scales. Early work suggests limited concurrent validity with external outcome variables. Data are at best ordinal and there are particular difficulties in equating outcome with percentage changes in scores. The concept of remission, which uses absolute item score thresholds with a duration criterion, is a promising outcome measure Conclusions Symptom rating scale scores can only comprise a limited part of outcome measurement. Standardised remission criteria may present advantages in outcome research
Brief eclectic psychotherapy v. eye movement desensitisation and reprocessing therapy for post-traumatic stress disorder: randomised controlled trial.

BACKGROUND Trauma-focused cognitive-behavioural therapy (CBT) and eye movement desensitisation and reprocessing therapy (EMDR) are efficacious treatments for post-traumatic stress disorder (PTSD), but few studies have directly compared them using well-powered designs and few have investigated response patterns. AIMS To compare the efficacy and response pattern of a trauma-focused CBT modality, brief eclectic psychotherapy for PTSD, with EMDR (trial registration: ISRCTN64872147). METHOD Out-patients with PTSD were randomly assigned to brief eclectic psychotherapy (n = 70) or EMDR (n = 70) and assessed at all sessions on self-reported PTSD (Impact of Event Scale - Revised). Other outcomes were clinician-rated PTSD, anxiety and depression. RESULTS Both treatments were equally effective in reducing PTSD symptom severity, but the response pattern indicated that EMDR led to a significantly sharper decline in PTSD symptoms than brief eclectic psychotherapy, with similar drop-out rates (EMDR: n = 20 (29%), brief eclectic psychotherapy: n = 25 (36%)). Other outcome measures confirmed this pattern of results. CONCLUSIONS Although both treatments are effective, EMDR results in a faster recovery compared with the more gradual improvement with brief eclectic psychotherapy.
Learning from Noisy Web Data with Category-Level Supervision

Learning from web data is increasingly popular due to abundant free web resources. However, the performance gap between webly supervised learning and traditional supervised learning is still very large, due to the label noise of web data as well as the domain shift between web data and test data. To fill this gap, most existing methods propose to purify or augment web data using instance-level supervision, which generally requires heavy annotation. Instead, we propose to address the label noise and domain shift by using more accessible category-level supervision. In particular, we build our deep probabilistic framework upon variational autoencoder (VAE), in which classification network and VAE can jointly leverage category-level hybrid information. Then, we extend our method for domain adaptation followed by our low-rank refinement strategy. Extensive experiments on three benchmark datasets demonstrate the effectiveness of our proposed method.
HETEROCLINIC SOLUTIONS TO AN ASYMPTOTICALLY AUTONOMOUS SECOND-ORDER EQUATION

We study the dierential equation ¨ x(t) = a(t)V 0 (x(t)), where V is a double-well potential with minima at x = ±1 and a(t) ! l > 0 as |t| ! 1. It is proven that under certain additional assumptions on a, there exists a heteroclinic solution x to the dierential equation with x(t) ! 1 as t ! 1 and x(t) ! 1 as t ! 1. The assumptions allow l a(t) to change sign for arbitrarily large values of |t|, and do not restrict the decay rate of |l a(t)| as |t| ! 1.
Examining the relationship between anxiety and depression and exacerbations of COPD which result in hospital admission: a systematic review

Objectives Exacerbations of chronic obstructive pulmonary disease (COPD) are the third largest cause of emergency hospital admissions in the UK. This systematic literature review explored the relationship between the hospitalization rates and the COPD comorbidities, anxiety, and depression. Methods The Centre for Research Dissemination’s framework for systematic reviews was followed using search terms relating to COPD, anxiety, depression, and hospital admission. Papers identified were assessed for relevance and quality, using a suitable Critical Appraisal Skills Programme tool and Mixed Methods Assessment Tool. Results Twenty quantitative studies indicated that anxiety and depression led to a statistically significant increase in the likelihood of COPD patients being hospitalized. These comorbidities also led to an increased length of stay and a greater risk of mortality postdischarge. Other significant factors included lower Body-Mass Index, Airflow Obstruction, Dyspnea, and Exercise scores, female gender, lower socioeconomic status, poorer patient perceived quality of life, increased severity of lung function, and less improvement in dyspnea from admission to discharge. It was also highlighted that only 27%–33% of those with depression were being treated for it. Four qualitative studies revealed that patients saw anxiety and depression as a major factor that affected their ability to cope with and self-manage their condition. Implications Findings from the systematic review have highlighted a need for better recognition and treatment of anxiety and depression amongst individuals with COPD. Ongoing research will develop and test strategies for promoting better management and self-management as a means of reducing hospital admissions.
Die-Attachment on Copper by Nanosilver Sintering: Processing, Characterization and Reliability

Die-attachment, as the first level of electronics packaging, plays a key role for the overall performance of the power electronics packages. Nanosilver sintering has becoming an emerging solder-free, environmental friendly die-attach technology. Researchers have demonstrated the feasibility of die-attachment on silver (Ag) or gold (Au) surfaces by pressure-less or low-pressure (< 5 MPa) nanosilver sintering. This study extended the application of nanosilver sintering dieattach technique to copper (Cu) surface. The main challenge of nanosilver sintering on Cu is the formation of thick Cu oxide during processing, which may lead to weak joints. In this study, different processes were developed based on the die size: for small-area dice (< 5 × 5 mm), different sintering atmospheres (e.g. forming gas) were applied to protect Cu surface from oxidation; for large-area dice (> 5 × 5 mm), a double-print, low-pressure (< 5 MPa) assisted sintering process was developed. For both processes, die-shear tests demonstrated die-shear strength can reach 40 MPa. The effects of different sintering parameters of the processing were analyzed by different material characterization techniques. With forming gas as sintering atmosphere, not only Cu surface was protected from oxidation, but also the organics in the paste were degraded with nanosilver particles as catalyst. External pressure applied in the processing not only increased the density of sintered Ag, but also enhanced the contact area of sintered-Ag/Cu interface. Microstructure of Ag/Cu interface were characterized by transmission electron microscopy
Towards a Similarity between Qualitative Image Descriptions for Comparing Real Scenes

In this paper, qualitative descriptors of shape, color, topology and location are applied to describe images of real scenes. Then, an approach for obtaining a similarity measure between two qualitative image descriptions (SimQID) is presented. As a proof-of-concept, this approach is tested on real digital images taken by a robot camera at the corridors of TI building at Universitat Jaume I. The results obtained are analyzed and a discussion is provided.
MicroRNA-376a inhibits cell proliferation and invasion in glioblastoma multiforme by directly targeting specificity protein 1

Glioblastoma multiforme (GBM), a World Health Organization grade IV glioma, is the most common and aggressive primary brain tumor in humans. microRNAs (miRNAs) are aberrantly expressed in numerous cancer types, including GBM. Abnormally expressed miRNAs are commonly associated with malignant characteristics of GBM, including malignant growth, proliferation, apoptosis, invasion, metastasis and resistance to chemotherapy. miRNA (miR)-376a is abnormally expressed in multiple human cancers; however, the expression pattern and role of miR-376a in GBM, and the underlying molecular mechanisms by which miR-376a exerts its functions remain to be elucidated. Therefore, the aim of this study was to measure miR-376a expression and determine its biological roles in GBM as well as its associated molecular mechanism. In the present study, miR-376a expression was markedly downregulated in GBM tissues and cell lines. Overexpression of miR-376a markedly decreased the proliferation and invasion of GBM cells in vitro. In the present study, specificity protein 1 (SP1) was demonstrated to be a direct target of miR-376a. In addition, a negative association between SP1 mRNA and miR-376a expression was observed in GBM tissues. SP1 upregulation reduced the effects of miR-376a overexpression on GBM cell proliferation and invasion. miR-376a may be a therapeutic target for the treatment of patients with GBM.