Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and Lineage Diversity of Avian Haemosporidians from Three Distinct Cerrado Habitats in Brazil

Habitat alteration can disrupt host–parasite interactions and lead to the emergence of new diseases in wild populations. The cerrado habitat of Brazil is being fragmented and degraded rapidly by agriculture and urbanization. We screened 676 wild birds from three habitats (intact cerrado, disturbed cerrado and transition area Amazonian rainforest-cerrado) for the presence of haemosporidian parasites (Plasmodium and Haemoproteus) to determine whether different habitats were associated with differences in the prevalence and diversity of infectious diseases in natural populations. Twenty one mitochondrial lineages, including 11 from Plasmodium and 10 from Haemoproteus were identified. Neither prevalence nor diversity of infections by Plasmodium spp. or Haemoproteus spp. differed significantly among the three habitats. However, 15 of the parasite lineages had not been previously described and might be restricted to these habitats or to the region. Six haemosporidian lineages previously known from other regions, particularly the Caribbean Basin, comprised 50–80% of the infections in each of the samples, indicating a regional relationship between parasite distribution and abundance.
The prevalence of medication nonadherence in post-myocardial infarction survivors and its perceived barriers and psychological correlates: a cross-sectional study in a cardiac health facility in Malaysia

Background Although evidence-based practice has shown the benefits of prescribed cardioprotective drugs in post-myocardial infarction (MI) survivors, adherence rates remain suboptimal. The aim of this study was to determine the prevalence and factors associated with medication nonadherence among post-MI survivors in Malaysia. Materials and methods This cross-sectional study was conducted from February to September 2016 among 242 post-MI survivors aged 24–96 years at the cardiology outpatient clinic in a Malaysian cardiac specialist center. The study utilized an interviewer-administered questionnaire that consisted of items adapted and modified from the validated Simplified Medication Adherence Questionnaire, sociodemographics, health factors, perceived barriers, and novel psychological attributes, which employed the modified Confusion, Hubbub, and Order Scale and the Verbal Denial in Myocardial Infarction questionnaire. Results The prevalence of medication nonadherence was 74%. In the multivariable model, denial of illness (AOR 1.2, 95% CI 0.9–1.8; P=0.032), preference to traditional medicine (AOR 8.7, 95% CI 1.1–31.7; P=0.044), lack of information about illness (AOR 3.3, 95% CI 1.1–10.6; P=0.045), fear of side effects (AOR 6.4, 95% CI 2.5–16.6; P<0.001), and complex regimen (AOR 5.2, 95% CI 1.9–14.2; P=0.001) were statistically significant variables associated with medication nonadherence. Conclusion The relatively higher medication-nonadherence rate in this study was associated with patient-, provider-, and therapy-related factors and the novel psychological attribute denial of illness. Future research should explore these factors using robust methodological techniques to determine temporality among these factors.
Antidepressant Medication as a Risk Factor for Type 2 Diabetes and Impaired Glucose Regulation

OBJECTIVE Antidepressant use has risen sharply over recent years. Recent concerns that antidepressants may adversely affect glucose metabolism require investigation. Our aim was to assess the risk of type 2 diabetes associated with antidepressants through a systematic review. RESEARCH DESIGN AND METHODS Data sources were MEDLINE, Embase, PsycINFO, The Cochrane Library, Web of Science, meeting abstracts of the European Association for the Study of Diabetes, American Diabetes Association, and Diabetes UK, Current Controlled Trials, ClinicalTrials.gov, U.K. Clinical Research Network, scrutiny of bibliographies of retrieved articles, and contact with relevant experts. Relevant studies of antidepressant effects were included. Key outcomes were diabetes incidence and change in blood glucose (fasting and random). RESULTS Three systemic reviews and 22 studies met the inclusion criteria. Research designs included 1 case series and 21 observational studies comprising 4 cross-sectional, 5 case-control, and 12 cohort studies. There was evidence that antidepressant use is associated with type 2 diabetes. Causality is not established, but rather, the picture is confused, with some antidepressants linked to worsening glucose control, particularly with higher doses and longer duration, others linked with improved control, and yet more with mixed results. The more recent, larger studies, however, suggest a modest effect. Study quality was variable. CONCLUSIONS Although evidence exists that antidepressant use may be an independent risk factor for type 2 diabetes, long-term prospective studies of the effects of individual antidepressants rather than class effects are required. Heightened alertness to potential risks is necessary until these are complete.
Readiness to Manage Arthritis: A Pilot Study Using a Stages‐of‐Change Measure for Arthritis Rehabilitation

&NA; The purpose of this pilot study was to evaluate the Readiness to Manage Arthritis Questionnaire (RMAQ), a new multibehavior measure of readiness for change in arthritis management. Data were obtained from 46 patients with chronic inflammatory arthritis admitted for intensive treatment. Test‐retest reliability, correlations with clinical variables and theoretically related constructs, and responsiveness to change were assessed. Test‐retest reliability indicated reasonable stability, with intraclass correlation coefficients ranging from 0.30 to 0.75. A significant association was observed between psychological well‐being and readiness status. Clinical variables of disease duration, disease severity, pain, and function were not related to readiness status. Correlations between stages‐of‐change scores and self‐efficacy for managing arthritis symptoms were mostly nonsignificant, with the exception of modest agreement between readiness to engage in physical activity and exercise self‐efficacy (0.43). Significant changes were observed in mean RMAQ scores from initial assessment to 12 weeks post‐treatment for the behaviors of using joint protection, dealing with frustration, learning about arthritis, engaging in physical activity, and stress management. Findings from this pilot study suggest that the RMAQ has adequate psychometric properties in patients with chronic inflammatory arthritis and can be used to assess an individual's readiness to adopt important arthritis self‐management behaviors.
Comparing representations in Chinese information retrieval

Three representation methods are empirically investigated for Chinese information retrieval: 1-gram (single character), bigram (two contiguous overlapping characters), and short-word indexing based on a simple segmentation of the text. The retrieval collection is the approximately 170 MB TREC-5 Chinese corpus of news articles, and 28 queries that are long and rich in wordings. Evaluation shows that 1-gram indexing is good but not sufficiently competitive, while bigram indexing works surprisingly well. Bigram indexing leads to a large index term space, three times that of short-word indexing, but is as good as short-word indexing in precision, and about 5% better in relevants retrieved. The best average non-interpolated precision is about 0.45, 17% better than 1-gram indexing and quite high for a mainly statistical approach.
Component age estimates for the Hell Gap Paleoindian site and methods for chronological modeling of stratified open sites - Response to commentary by C. Vance Haynes

The Hell Gap National Historic Landmark, located on the northwestern plains of Wyoming, is one of the most important Paleoindian archaeological sites in North America because it contains a stratified sequence of occupations spanning nearly the entirety of the Paleoindian period. Although Hell Gap is central to archaeological knowledge concerning North American Paleoindian chronology, consistently assigning component ages has been problematic due to conflicting radiocarbon determinations from individual strata, stratigraphic age reversals in age-depth relationships, and other issues related to the stratified open campsite. Toward resolving the Hell Gap chronology, we devised a procedure for correcting age-depth relationships for incorporation in chronostratigraphic models and then used the Bayesian age-depth modeling qprocedures in Bchron to estimate the ages of 11 stratified components present at Hell Gap Locality 1. We present these age estimates and discuss their significance to Paleoindian chronology. Notable aspects of our chronology include a revised age estimate for the Goshen complex, the identification of three Folsom components spanning the entirety of the Folsom temporal range, and relatively young age estimates for the Late Paleoindian Frederick/Lusk component(s) at Locality 1. More broadly, our study demonstrates a procedure for creating chronometric models of stratigraphically complicated open stratified sites of any type.
Meetings as Persistent Conversations that use ICTs and Face-to-Face to Build Social Capital

Attending meetings is a common activity where people accomplish tasks and extend their relationships. But what happens when a meeting is over? Is that the end of the meeting conversation? This study empirically demonstrates that meetings are not discrete events; rather they are a form of persistent conversation processes, involving combinations of ICTs and face-toface communication. Conversations between meetings contribute to a meeting process-perspective and link to the development of bonding and bridging social capital. The findings suggest that the frequency of face-to-face conversations and text messaging between meetings, positively impact bonding social capital. Peoples’ attitudes toward continuing conversations between meetings positively impacts bridging social capital. The frequency of using many contemporary ICTs—e.g., Facebook, Twitter, and GroupMe—between meetings was not a significant predictor in developing social capital, even in a sample of young adults.
Expression , Purification , and MALDI Analysis of RPE 65

METHODS. Human RPE65 was expressed in Sf9 cells using the baculovirus system. The subcellular localization was determined by Western blot analysis and immunocytochemistry. An ELISA was developed for RPE65 and used to measure levels in bovine RPE. Recombinant and native RPE65 were purified by affinity chromatography. Molecular mass was determined by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry.
The effect of feeding ractopamine (Paylean) on muscle quality and sensory characteristics in three diverse genetic lines of swine.

The present experiment utilized Berkshire (n = 76), Duroc (n = 81), and high-lean commercial crossbred (n = 75) barrows and gilts with an initial BW of approximately 85.1 kg. Pigs were fed a standard commercial diet (17.6% CP, 1.02% lysine) supplemented with ractopamine hydrochloride at a level of 0 or 10 ppm for 28 d. The experiment was conducted in a randomized complete block design, with animals blocked within genetic line according to litter, gender, and weight, for a total of four blocks per genetic line for each treatment. Pigs were harvested at a commercial abattoir and chilled for 24 h at 1 to 4 degrees C. At 24 h postmortem, wetness and firmness scores and ultimate muscle pH were measured in the center of the longissimus muscle (LM) at the 10th to 11th rib interface. Visual and instrumental color and marbling score were measured at 48 h postmortem on a fresh cut LM surface. Percentage of chemically extracted intramuscular fat (IMF) was measured, and a trained sensory panel evaluated cooked LM chops for juiciness, tenderness, and chewiness. Cooking loss (%) and instrumental measurement of tenderness also were measured on cooked LM chops. Ractopamine treatment increased ADG (P < 0.01) and LM area (P < 0.05), but had no effect (P > 0.05) on LM quality, sensory attributes, or instrumental measures of palatability. Berkshire LM received higher tenderness and juiciness (P < 0.05) scores and had lower cooking losses (P < 0.05) and instrumental tenderness (P < 0.05) than LM from the Duroc and high-lean lines. Loins from barrows were firmer (P < 0.05), had lower drip loss percentages (P < 0.05), and received greater tenderness scores (P < 0.05) than the LM from gilts. Genetic line x treatment and gender x treatment interactions were detected for IMF. The LM of Berkshire pigs fed ractopamine had lower (P < 0.05) IMF than Berkshires fed the control diet, with no interaction in the other lines. Purebred barrows (Berkshire and Duroc) had greater (P < 0.001 and P < 0.05, respectively) IMF than their respective purebred gilts, with no gender difference in IMF in the high-lean line. Results from the present study indicate that feeding ractopamine does not affect most muscle quality and palatability characteristics. However, the genetic line x treatment interaction for loin IMF suggests that feeding ractopamine might reduce IMF within the loin muscle of genetic lines that have a propensity to produce greater levels of IMF.
Relation of the Expression of Cyclooxygenase-2 in Colorectal Adenomas and Adenocarcinomas to Angiogenesis and Prognosis

Purpose Recent studies have shown that cyclooxygenase (COX)-2 may be involved in tumor growth, invasion and apoptosis in various carcinomas. Vascular endothelial growth factor (VEGF) has a potent angiogenic activity, and COX-2 promotes angiogenesis by modulating angiogenic factors, including VEGF. Endothelial growth factor receptor (EGFR) is considered as a factor of cell growth, maturation and cell death. The current study was designed to investigate the possible roles of COX-2 in colorectal tumor progression and angiogenesis. Methods Fifty colorectal adenomas and forty adenocarcinomas were investigated by using immunohistochemical staining for COX-2, VEGF and EGFR. The correlations of COX-2, VEGF and EGFR with the grade of dysplasia, the size of the adenoma, and various clinicopathologic factors were studied. Results The expressions of COX-2, VEGF and EGFR were each significantly correlated with carcinomatous transformation, and the expressions of COX-2 and VEGF were significantly correlated. COX-2 and EGFR showed correlations with adenomas rather than adenocarcinomas. However, no correlations of COX-2, VEGF and EGFR expression to other clinicopathologic factors, except tumor size in EGFR expression, were detected. Conclusion These results suggest that COX-2 may play an important role in carcinogenesis through interaction with VEGF and EGFR in human colorectal cancer.
Forget It !

We encountered the need for a theory of forgetting in our work on Cognitive Robotics.1 In our effort to control an autonomous robot, we imagine the robot has a knowledge base representing the initial world state. As the robot performs actions, she needs to bring the knowledge base up to date. To do so, she needs to forget about all the facts that are no longer true, and in such a way that this will not affect any of her possible future actions (Lin and Reiter [3; 3]). This paper describes in general terms the particular forms of forgetting used in (Lin and Reiter [3; 3]). Specifically, we propose a logical theory to account for: forgetting about a fact (forget that John is a student), and forgetting about a relation (forget the student relation). We then apply our notion of forgetting in defining various notion of relevance.
Revealing the hidden structure of dynamic ecological networks

In ecology, recent technological advances and long-term data studies now provide longitudinal interaction data (e.g. between individuals or species). Most often, time is the parameter along which interactions evolve but any other one-dimensional gradient (temperature, altitude, depth, humidity, etc.) can be considered. These data can be modelled through a sequence of different snapshots of an evolving ecological network, i.e. a dynamic network. Here, we present how the dynamic stochastic block model approach developed by Matias & Miele (Matias & Miele In press J. R. Stat. Soc. B (doi:10.1111/rssb.12200)) can capture the complexity and dynamics of these networks. First, we analyse a dynamic contact network of ants and we observe a clear high-level assembly with some variations in time at the individual level. Second, we explore the structure of a food web evolving during a year and we detect a stable predator–prey organization but also seasonal differences in the prey assemblage. Our approach, based on a rigorous statistical method implemented in the R package dynsbm, can pave the way for exploration of evolving ecological networks.
Return periods of losses associated with European

Possible future changes of clustering and return periods (RPs) of European storm series with high potential losses are quantified. Historical storm series are identified using 40 winters of reanalysis. Time series of top events (1, 2 or 5 year return levels (RLs)) are used to assess RPs of storm series both empirically and theoretically. Additionally, 800 winters of general circulation model simulations for present (1960–2000) and future (2060–2100) climate conditions are investigated. Clustering is identified for most countries, and estimated RPs are similar for reanalysis and present day simulations. Future changes of RPs are estimated for fixed RLs and fixed loss index thresholds. For the former, shorter RPs are found for Western Europe, but changes are small and spatially heterogeneous. For the latter, which combines the effects of clustering and event ranking shifts, shorter RPs are found everywhere except for Mediterranean countries. These changes are generally not statistically significant between recent and future climate. However, the RPs for the fixed loss index approach are mostly beyond the range of preindustrial natural climate variability. This is not true for fixed RLs. The quantification of losses associated with storm series permits a more adequate windstorm risk assessment in a changing climate. S Online supplementary data available from stacks.iop. org/ERL/9/124016/mmedia
Autologous Melanoma Vaccine Induces Antitumor and Self-Reactive Immune Responses That Affect Patient Survival and Depend on MHC Class II Expression on Vaccine Cells

Purpose: Autologous melanoma cells display a broad variety of tumor antigens and were used for treatment of American Joint Committee on Cancer stages III and IV melanoma as an adjuvant or active therapy. Survival data and immune response were evaluated in vaccinated patients. Experimental Design: Forty-seven patients received 2,4-dinitrophenyl–conjugated autologous melanoma vaccine as an adjuvant (23 patients) or therapy (24 patients). CD4 and CD8 T-cell response in blood sampled before vaccination and after five or eight vaccine doses was evaluated against melanoma cells and autologous peripheral blood mononuclear cells using IFNγ enzyme–linked immunospot. Serum levels of antilivin, an inhibitor of apoptosis, and anti-gp100 IgG were determined. Results: The immunologic effect of the vaccine differed between the two groups of patients. In the adjuvant group, there was a significant increase in CD8 melanoma-reactive T cells (P = 0.035) after vaccination and an increase in antimelanoma CD4 T cells correlating with improved overall survival (P = 0.04). In the therapeutic group, there was no objective tumor regression; antimelanoma T-cell reactivity increased by a small amount, stayed the same, or in some cases decreased. In all patients, a significant increase was noted in CD4 T-cell reactivity against autologous peripheral blood mononuclear cells (P = 0.02), which did not affect survival. Increased antilivin IgG was associated with improved survival. Expression of MHC class II on melanoma cells was vital for the immunogenicity of the vaccine. Conclusion: Autologous melanoma cell vaccine is capable of inducing effective antimelanoma CD4 T-cell activity associated with improved survival. Patients with active metastatic disease generally displayed reduced immune response and gained little from active immunization.
Helper effects on pup lifetime fitness in the cooperatively breeding red wolf (Canis rufus)

The evolutionary maintenance of cooperative breeding systems is thought to be a function of relative costs and benefits to breeders, helpers and juveniles. Beneficial effects of helpers on early-life survivorship and performance have been established in several species, but lifetime fitness benefits and/or costs of being helped remain unclear, particularly for long-lived species. We tested for effects of helpers on early- and late-life traits in a population of reintroduced red wolves (Canis rufus), while controlling for ecological variables such as home-range size and population density. We found that the presence of helpers in family groups was positively correlated with pup mass and survival at low population density, but negatively correlated with mass/size at high density, with no relation to survival. Interestingly, mass/size differences persisted into adulthood for both sexes. While the presence of helpers did not advance age at first reproduction for pups of either sex, females appeared to garner long-term fitness benefits from helpers through later age at last reproduction, longer reproductive lifespan and a greater number of lifetime reproductive events, which translated to higher lifetime reproductive success. In contrast, males with helpers exhibited diminished lifetime reproductive performance. Our findings suggest that while helper presence may have beneficial short-term effects in some ecological contexts, it may also incur long-term sex-dependent costs with critical ramifications for lifetime fitness.
Any open bounded subset of Rn has the same homotopy type than its medial axis

Medial Axis Transform is sometimes used as an intermediate representation in algorithms for meshing or recognition of shapes from digitized data. This raises the question whether the Medial Axis captures fundamental topological invariants of the object. The (positive) answer has been known already in the case of smooth objects. The main result presented here is the homotopy equivalence of any bounded open subset of Rn with its Medial Axis.
Crystal structure of a pair of follistatin‐like and EF‐hand calcium‐binding domains in BM‐40

BM‐40 (also known as SPARC or osteonectin) is an anti‐adhesive secreted glycoprotein involved in tissue remodelling. Apart from an acidic N‐terminal segment, BM‐40 consists of a follistatin‐like (FS) domain and an EF‐hand calcium‐binding (EC) domain. Here we report the crystal structure at 3.1 Å resolution of the FS–EC domain pair of human BM‐40. The two distinct domains interact through a small interface that involves the EF‐hand pair of the EC domain. Residues implicated in cell binding, inhibition of cell spreading and disassembly of focal adhesions cluster on one face of BM‐40, opposite the binding epitope for collagens and the N‐linked carbohydrate. The elongated FS domain is structurally related to serine protease inhibitors of the Kazal family. Notable differences are an insertion into the inhibitory loop in BM‐40 and a protruding N‐terminal β‐hairpin with striking similarities to epidermal growth factor. This hairpin is likely to act as a rigid spacer in proteins containing tandemly repeated FS domains, such as follistatin and agrin, and forms the heparin‐binding site in follistatin.