Miracle-dz/UniFAR-FTUs huggingface dataset:
Bouts of Passive Stretching after Immobilization of the Rat Soleus Muscle Increase Collagen Macromolecular Organization and Muscle Fiber Area

This study evaluated the effect of short bouts of stretching on the soleus muscle after immobilization, by measuring the birefringence of the intramuscular connective tissue (ICT) and the muscle fiber area. Thirty rats were divided into five groups: the left soleus was immobilized in the shortened position; after immobilization the animals remained free; after immobilization, the soleus was stretched daily (10 stretches of 60 sec followed by 30 sec rest); after immobilization, the soleus was stretched 3 times a week; control. Immobilization caused a loss of birefringence of the ICT and of muscle fiber area and only daily stretching increased both compared with the control (p < 0.01). In conclusion, short daily bouts of stretching after immobilization induced molecular reorganization of the collagen bundles and muscle fiber hypertrophy in the rat soleus.
Natural stressors in uncontaminated sediments of shallow freshwaters: The prevalence of sulfide, ammonia, and reduced iron

Potentially toxic levels of 3 naturally occurring chemical stressors (dissolved sulfide, ammonia, and iron) can appear in freshwater sediments, although their roles in shaping ecosystem structure (i.e., plant and animal communities) and function (e.g., biologically mediated elemental cycles) have received little study. The present critical review discusses the prevalence and ecological effects of potentially toxic concentrations of sulfide, ammonia, and iron in uncontaminated freshwater sediments, including a review of the literature as well as a case study presenting previously unpublished data on sediment porewaters from a diverse set of shallow (<2 m) freshwater ecosystems in southwest Michigan, USA. Measured concentrations are compared with surface water quality criteria established by the US Environmental Protection Agency (USEPA) and with acute and chronic toxic thresholds in the published literature, where available. Based on USEPA criteria for aquatic life for these 3 stressors, the benthic environment of almost every freshwater ecosystem sampled was theoretically stressful to some component of aquatic life in some area or at some time (i.e., in at least 1 sample), and 54% of samples exceeded more than 1 criterion simultaneously. Organismal tolerances to chemical stressors vary, so the observed concentrations are likely shaping benthic animal communities and influencing rates of ecosystem processes. Consideration of the role of natural chemical stressors is important in shaping freshwater benthic environments and in developing bioassessments, restoration goals, and remediation plans. Environ Toxicol Chem 2015;34:467–479. © 2014 SETAC
A Controlled Experiment to Assess the Effectiveness of Eight Use Case Templates

Use case models, that include use case diagrams along with their documentations, are typically used to specify the functional requirements of the software systems. Use cases are usually semi-structured and documented using some natural language hence issues like ambiguity, inconsistency, and incompleteness are inevitably introduced in the specifications. There have been many efforts to formalize the use case template that make use of certain grammatical construction to guide the structure or style of the description. This paper describes an empirical work to assess the usefulness of eight such use case templates against a set of five judging criteria, namely, completeness, consistency, understandability, redundancy and fault proneness. We conducted a controlled experiment where a group of postgraduate students applied these use case templates on multiple problem specifications. In our results, Yue's template was found to be more consistent and less fault prone, Cockburn's template was found to be more complete and more understandable and, Tiwari's template was found to be less redundant as compared to the other use case templates, though the results were not statistically significant.
Use of Lipid-Lowering Medications at Discharge in Patients With Acute Myocardial Infarction: Data From the National Registry of Myocardial Infarction 3

Background—The present study aimed to assess use of lipid-lowering medication at discharge in a current national sample of patients hospitalized with acute myocardial infarction and to evaluate factors associated with prescribing patterns. Methods and Results—Demographic, procedural, and discharge medication data were collected from 138 001 patients with acute myocardial infarction discharged from 1470 US hospitals participating in the National Registry of Myocardial Infarction 3 from July 1998 to June 1999. Lipid-lowering medications were part of the discharge regimen in 31.7%. Among patients with prior history of CAD, revascularization, or diabetes, less than one half of the patients were discharged on treatment. In multivariate analysis, factors independently related to lipid-lowering use included history of hypercholesterolemia (odds ratio [OR] 4.93; 95% CI 4.79 to 5.07), cardiac catheterization during hospitalization (OR 1.29; 95% CI 1.24 to 1.34), care provided at a teaching hospital, (OR 1.26; 95% CI 1.22 to 1.32), use of &bgr;-blocker (OR 1.43; 95% CI 1.39 to 1.48), and smoking cessation counseling (OR 1.51; 95% CI 1.44 to 1.59). Lipid-lowering medications were given less often to patients who were older (65 to 74 versus <55 years of age; OR 0.82; 95% CI 0.78 to 0.86), those with a history of hypertension (OR 0.92; 95% CI 0.89 to 0.95), and those undergoing coronary artery bypass graft surgery (OR 0.58; 95% CI 0.55 to 0.60). Conclusions—Analysis of current practice patterns for the use of lipid-lowering medications in patients hospitalized with acute myocardial infarction reveals that a significant proportion of high-risk patients did not receive treatment at time of discharge.
The CERTH-UNITN Participation @ Verifying Multimedia Use 2015

We propose an approach that predicts whether a tweet, which is accompanied by multimedia content (image/video), is trustworthy or deceptive. We test dierent combinations of quality and trust-oriented features (tweet-based, userbased and forensics) in tandem with a standard classication and an agreement-retraining technique, with the goal of predicting the most likely label (fake or real) for each tweet. The experiments carried out on the Verifying Multimedia Use dataset show that the best performance is achieved when using all available features in combination with the agreement-retraining method.
The Burden of JAK2V617F Mutated Allele in Turkish Patients With Myeloproliferative Neoplasms

Background Studies regarding the impact of JAK2V617F allele burden on phenotypic properties and clinical course in Philadelphia-negative myeloproliferative neoplasms (Ph-negative MPNs) have reported variable results. We aimed to analyze the association of mutated JAK2V617F allele burden with laboratory characteristics and clinical phenotype in Turkish patients (107 essential thrombocythemia (ET) and 77 primary myelofibrosis (PMF)). Methods Peripheral blood samples of 184 patients with Ph-negative MPNs were analyzed for JAK2V617F allele status and burden. JAK2 MutaScreen assay (Ipsogen, Luminy Biotech, Marseille, France) was used to detect the JAK2V617F status and quantitative JAK2V617F allele burdens in genomic DNA using TaqMan allelic discrimination. Results Frequency of JAK2V617F-positive patients with high mutation load (allele burden > 50%) was higher in PMF compared to ET (23.4% and 4.7%, respectively; P = 0.001). We found significant association between ET patients with high JAK2V617F allele burden and lower hemoglobin (Hgb) and hematocrit (Hct), higher LDH levels and more prevalent massive splenomegaly (P = 0.001, P = 0.001, P = 0.012 and P = 0.015, respectively). ET patients with high mutation load displayed higher prevalence of bleeding compared to low mutation load and wild-type mutational status (P = 0.003). Rate of DVT was significantly higher in ET patients with mutant allele burden in upper half compared to lower half and wild-type (P = 0.029). We observed significant association between PMF patients with high JAK2V617F allele burden and higher Hgb, Hct levels and leukocyte counts (P = 0.003, P = 0.021 and P = 0.001, respectively). Conclusions Our study demonstrated JAK2V617F allele burden correlates with clinical features in ET and PMF. We conclude quantification of JAK2V617F mutation contributes to the workup of Ph-negative MPNs.
Distributed Document and Phrase Co-embeddings for Descriptive Clustering

Descriptive document clustering aims to automatically discover groups of semantically related documents and to assign a meaningful label to characterise the content of each cluster. In this paper, we present a descriptive clustering approach that employs a distributed representation model, namely the paragraph vector model, to capture semantic similarities between documents and phrases. The proposed method uses a joint representation of phrases and documents (i.e., a co-embedding) to automatically select a descriptive phrase that best represents each document cluster. We evaluate our method by comparing its performance to an existing state-of-the-art descriptive clustering method that also uses co-embedding but relies on a bag-of-words representation. Results obtained on benchmark datasets demonstrate that the paragraph vector-based method obtains superior performance over the existing approach in both identifying clusters and assigning appropriate descriptive labels to them.
Is Binge Drinking in Young Adults Associated with an Alcohol-Specific Impairment of Response Inhibition?

Background/Aims: Little is known about the association of binge drinking with impulsivity related to trait- or state-like aspects of behavior. The aim of the present study was therefore to investigate whether binge drinkers show an impairment of inhibitory control in comparison to non-binge drinkers when confronted with alcohol-associated or control stimuli, and whether this is reflected in self-reported impulsivity. Methods: A go/no-go task with pictures of alcoholic and nonalcoholic beverages as well as control stimuli was administered to binge drinkers and a gender-matched group of non-binge drinkers. All participants also completed the Barratt Impulsiveness Scale (BIS-11). Results: We found an alcohol-specific impairment of response inhibition for binge drinkers only, while the groups did not differ with regard to overall response inhibition to the experimental stimuli or self-reported impulsiveness (BIS-11). In addition, the number of commission errors in response to alcohol-associated stimuli was the only significant predictor of binge drinking. Conclusion: The findings of the present study suggest that when young adults have established binge drinking as a common drinking pattern, impairment of inhibition in response to alcoholic stimuli is the only significant predictor of binge drinking, but not general impulsive behavior. i 2014 S. Karger AG, Basel
Home Production and Social Security Reform

This paper incorporates home production into a dynamic general equilibrium model of overlapping generations with endogenous retirement to study Social Se- curity reforms. As such, the model dierentiates both consumption goods and labor eort according to their respective roles in home production and market activities. Using a calibrated model, we …nd that eliminating the current pay-as- you-go Social Security system has important implications for both labor supply and consumption decisions and that these decisions are in‡uenced by the presence of a home production technology. Comparing our benchmark economy to one with dierentiated goods but no home production, we …nd that eliminating Social Security bene…ts generates larger welfare gains in the presence of home produc- tion. This result is due to the self insurance aspects generated by the presence of home production. Comparing our economy to a one-good economy without home production, we show that the welfare gains of eliminating Social Security are magni…ed even further. These policy analyses suggest the importance of mod- eling home production and distinguishing between both time use and consumption goods depending on whether they are involved in market or home production.
ICC density predicts bacterial overgrowth in a rat model of post-infectious IBS.

AIM To investigate the interstitial cells of Cajal (ICC) number using a new rat model. METHODS Sprague-Dawley rats were assigned to two groups. The first group received gavage with Campylobacter jejuni (C. jejuni) 81-176. The second group was gavaged with placebo. Three months after clearance of Campylobacter from the stool, precise segments of duodenum, jejunum, and ileum were ligated in self-contained loops of bowel that were preserved in anaerobic bags. Deep muscular plexus ICC (DMP-ICC) were quantified by two blinded readers assessing the tissue in a random, coded order. The number of ICC per villus was compared among controls, Campylobacter recovered rats without small intestinal bacterial overgrowth (SIBO), and Campylobacter recovered rats with SIBO. RESULTS Three months after recovery, 27% of rats gavaged with C. jejuni had SIBO. The rats with SIBO had a lower number of DMP-ICC than controls in the jejunum and ileum. Additionally there appeared to be a density threshold of 0.12 DMP-ICC/villus that was associated with SIBO. If ileal density of DMP-ICC was < 0.12 ICC/villus, 54% of rats had SIBO compared to 9% among ileal sections with > 0.12 (P < 0.05). If the density of ICC was < 0.12 DMP-ICC/villus in more than one location of the bowel, 88% of these had SIBO compared to 6% in those who did not (P < 0.001). CONCLUSION In this post-infectious rat model, the development of SIBO appears to be associated with a reduction in DMP-ICC. Further study of this rat model might help understand the pathophysiology of post-infectious irritable bowel syndrome.
Abdominal Tuberculosis: An Immigrant's Disease in the United States

Background: Abdominal tuberculosis (TB) is an uncommon condition in the United States (US) except for patients with human immunodeficiency virus (HIV). An increasing number of cases have been reported in western countries amongst immigrants. It is important to be aware of the data and clinical characteristics in the immigrant population. Aims: The purpose of this study is to determine the epidemiologic characteristics of abdominal TB among immigrants in the US and to review the clinical presentations of abdominal TB with a focus particularly on unusual features. Materials and Methods: In a community teaching hospital in New Jersey, patients diagnosed with abdominal TB were examined and included in this report. All nine patients were immigrants from countries with high prevalence of TB and a majority had resided in the US for at least 5 years. None had clinical evidence of HIV and those that were tested were not found to be positive for HIV. Initial examination, diagnostic workup, and response to therapy were all pertinent to the management and diagnosis of these patients. Results: Three patients had atypical clinical presentations with normal chest X-rays and either negative or unknown tuberculin tests leading to delayed diagnosis and inappropriate therapy in at least one patient. With antituberculous therapy, all except for one patient had satisfactory outcomes. Immigrant patients with a diagnosis of abdominal TB had no evidence of HIV infection or other associated conditions in contrast to native-born individuals. Conclusion: Atypical presentations may cause diagnostic difficulties. Failure to perform appropriate tests may lead to inappropriate therapy with adverse outcomes. Although there is a decline in the number of TB cases in the US and screening for latent pulmonary infection in foreigners has been implemented effectively, the diagnosis of abdominal TB continues to be under diagnosed.
Identification and Characterization of Novel Human Cav2.2 (α1B) Calcium Channel Variants Lacking the Synaptic Protein Interaction Site

The physical interaction between the presynaptic vesicle release complex and the large cytoplasmic region linking domains II and III of N-type (Cav2.2) calcium channel α1B subunits is considered to be of fundamental importance for efficient neurotransmission. By PCR analysis of human brain cDNA libraries and IMR32 cell mRNA, we have isolated novel N-type channel variants, termed Cav2.2-Δ1 and Δ2, which lack large parts of the domain II–III linker region, including the synaptic protein interaction site. They appear to be widely expressed across the human CNS as indicated by RNase protection assays. When expressed in tsA-201 cells, both novel variants formed barium-permeable channels with voltage dependences and kinetics for activation that were similar to those observed with the full-length channel. All three channel types exhibited the hallmarks of prepulse facilitation, which interestingly occurred independently of G-protein βγ subunits. By contrast, the voltage dependence of steady-state inactivation seen with both Δ1 and Δ2 channels was shifted toward more depolarized potentials, and recovery from inactivation of Δ1 and Δ2 channels occurred more rapidly than that of the full-length channel. Moreover, the Δ1 channel was dramatically less sensitive to both ω-conotoxin MVIIA and GVIA than either the Δ2 variant or the full-length construct. Finally, the domain II–III linker region of neither variant was able to effectively bind syntaxin in vitro. These results suggest that the structure of the II–III linker region is an important determinant of N-type channel function and pharmacology. The lack of syntaxin binding hints at a unique physiological function of these channels.
Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString® barcode probes to specific mRNA targets

A DNA profile from the perpetrator does not reveal, per se, the circumstances by which it was transferred. Body fluid identification by mRNA profiling may allow extraction of contextual ‘activity level’ information from forensic samples. Here we describe the development of a prototype multiplex digital gene expression (DGE) method for forensic body fluid/tissue identification based upon solution hybridization of color-coded NanoString® probes to 23 mRNA targets. The method identifies peripheral blood, semen, saliva, vaginal secretions, menstrual blood and skin. We showed that a simple 5 minute room temperature cellular lysis protocol gave equivalent results to standard RNA isolation from the same source material, greatly enhancing the ease-of-use of this method in forensic sample processing. We first describe a model for gene expression in a sample from a single body fluid and then extend that model to mixtures of body fluids. We then describe calculation of maximum likelihood estimates (MLEs) of body fluid quantities in a sample, and we describe the use of likelihood ratios to test for the presence of each body fluid in a sample. Known single source samples of blood, semen, vaginal secretions, menstrual blood and skin all demonstrated the expected tissue-specific gene expression for at least two of the chosen biomarkers. Saliva samples were more problematic, with their previously identified characteristic genes exhibiting poor specificity. Nonetheless the most specific saliva biomarker, HTN3, was expressed at a higher level in saliva than in any of the other tissues. Crucially, our algorithm produced zero false positives across this study’s 89 unique samples. As a preliminary indication of the ability of the method to discern admixtures of body fluids, five mixtures were prepared. The identities of the component fluids were evident from the gene expression profiles of four of the five mixtures. Further optimization of the biomarker ‘CodeSet’ will be required before it can be used in casework, particularly with respect to increasing the signal-to-noise ratio of the saliva biomarkers. With suitable modifications, this simplified protocol with minimal hands on requirement should facilitate routine use of mRNA profiling in casework laboratories.
Effectiveness of tacrolimus in comparison with methotrexate or biologics in propensity score-matched patients with rheumatoid arthritis

Abstract Objective: To analyze the effectiveness of tacrolimus (TAC) in comparison with methotrexate (MTX) or biologics in propensity score (PS)-matched rheumatoid arthritis (RA) patients. Methods: RA patients with moderate or high disease activity as defined by the 28-joint disease activity score (DAS28) and who had completed at least two successive biannual RA cohort surveys were analyzed. Patients were assigned in a stepwise fashion to one of four groups (Biologics, MTX, TAC, or Control) according to medication changes during a 6-month period. A PS was generated for each of three conditions (Biologics, MTX or Control group versus the TAC group, respectively), followed by the assignment of PS-matched patients. At 1 year, the DAS28 in each treatment versus TAC group was analyzed using a mixed effect model with repeated measures. Results: Compared with the respective PS-matched TAC group, the difference in DAS28 at 1 year was −0.398 [95% confidence interval (CI) − 0.660 to −0.136, p < 0.005] in the Biologics group (N = 120), −0.045 (95% CI −0.222 to 0.133, p = 0.622) in the MTX group (N = 465), and 0.182 (95% CI 0.010 to 0.353, p < 0.05) in the Control group (N = 462). Conclusion: TAC may provide a potential therapeutic option for RA patients with moderate to high disease activity.
The Bull Sperm MicroRNAome and the Effect of Fescue Toxicosis on Sperm MicroRNA Expression

Tall fescue [Schedonorus phoenix (Scop.) Holub] accounts for nearly 16 million hectares of pasture in the Southeastern and Mid-Atlantic U.S. due to its heat, drought, and pest resistance, conferred to the plant by its symbiotic relationship with the endophyte Neotyphodium coenophialum. The endophyte produces ergot alkaloids that have negative effects on the growth and reproduction of animals, resulting in the syndrome known as fescue toxicosis. The objectives of our study were to identify microRNA (miRNA) present in bovine sperm and to evaluate the effects of fescue toxicosis on sperm miRNA expression. Angus bulls were assigned to treatments of either toxic or non-toxic fescue seed diets. Semen was collected and subjected to RNA isolation. Three samples from each treatment group were chosen and pooled for deep sequencing. To compare miRNA expression between treatment groups, a microarray was designed and conducted. For each of the top ten expressed miRNA, target prediction analysis was conducted using TargetScan. Gene ontology enrichment was assessed using the Database for Annotation, Visualization and Integrated Discovery. Sequencing results elucidated the presence of 1,582 unique small RNA present in sperm. Of those sequences, 382 were known Bos taurus miRNA, 22 were known but novel to Bos taurus, and 816 were predicted candidate miRNA that did not map to any currently reported miRNA. Of the sequences chosen for microarray, twenty-two showed significant differential expression between treatment groups. Gene pathways of interest included: regulation of transcription, embryonic development (including blastocyst formation), Wnt and Hedgehog signaling, oocyte meiosis, and kinase and phosphatase activity. MicroRNA present in mature sperm appears to not only be left over from spermatogenic processes, but may actually serve important regulatory roles in fertilization and early developmental processes. Further, our results indicate the possibility that environmental changes may impact the expression of specific miRNA.