Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms

Commercial poultry abattoirs were evaluated to determine the efficacy of the multi-hurdle antimicrobial strategy employed to reduce the microbial load present on incoming broilers from the farm. As next generation sequencing (NGS) has been recently employed to characterize the poultry production system, this study utilized 16S High throughput sequencing (HTS) and quantitative plating data to profile the microbiota of chicken carcasses and determine the efficacy of the multi-hurdle antimicrobial system. Aerobic plate count (APC) and Enterobacteriaceae (EB) microbial counts were quantified from whole bird carcass rinsates (WBCR). The remaining rinsates underwent microbiome analysis using 16S rRNA gene fragments on an Illumina MiSeq and were analyzed by Quantitative Insights into Microbial Ecology (QIIME). The key stages of processing were determined to be at rehang, pre-chill, and post-chill as per the Salmonella Reduction Regulation (75 Fed. Reg. 27288–27294). The APC microbial data from rehang, pre-chill, and post-chill were mean log 4.63 CFU/mL, 3.21 CFU/mL, and 0.89 CFU/mL and EB counts were mean log 2.99 CFU/mL, 1.95 CFU/mL, and 0.35 CFU/mL. NGS of WBCR identified 222 Operational Taxonomic Units’ (OTU’s) of which only 23 OTU’s or 10% of the population was recovered post-chill. Microbiome data suggested a high relative abundance of Pseudomonas at post-chill. Additionally, Pseudomonas, Enterobacteriaceae, and Weeksellaceae Chryseobacterium have been identified as potential indicator organisms having been isolated from all processing abattoirs and sampling locations. This study provides insight into the microbiota of commercial broilers during poultry processing.
Dropout from cognitive‐behavioral therapy for eating disorders: A meta‐analysis of randomized, controlled trials

OBJECTIVE Cognitive-behavioral therapy (CBT) is efficacious for a range of eating disorder presentations, yet premature dropout is one factor that might limit CBTs effectiveness. Improved understanding of dropout from CBT for eating disorders is important. This meta-analysis aimed to study dropout from CBT for eating disorders in randomized controlled trials (RCTs), by (a) identifying the types of dropout definitions applied, (b) providing estimates of dropout, (c) comparing dropout rates from CBT to non-CBT interventions for eating disorders, and (d) testing moderators of dropout. METHOD RCTs of CBT for eating disorders that reported rates of dropout were searched. Ninety-nine RCTs (131 CBT conditions) were included. RESULTS Dropout definitions varied widely across studies. The overall dropout estimate was 24% (95% CI = 22-27%). Diagnostic type, type of dropout definition, baseline symptom severity, study quality, and sample age did not moderate this estimate. Dropout was highest among studies that delivered internet-based CBT and was lowest in studies that delivered transdiagnostic enhanced CBT. There was some evidence that longer treatment protocols were associated with lower dropout. No significant differences in dropout rates were observed between CBT and non-CBT interventions for all eating disorder subtypes. CONCLUSION Present study dropout estimates are hampered by the use of disparate dropout definitions applied. This meta-analysis highlights the urgency for RCTs to utilize a standardized dropout definition and to report as much information on patient dropout as possible, so that strategies designed to minimize dropout can be developed, and factors predictive of CBT dropout can be more easily identified.
Exploring resistive switching‐based memristors in the charge–flux domain: A modeling approach

We analyzed resistive switching‐based memristors by using the charge–flux relations instead of the traditional current–voltage approach. We employed simulated and experimental data to develop a model that can be easily included in circuit simulators. Physical simulations of devices with different conductive filament sizes were employed to fit the 3‐parameter model introduced. Later on, the relations between the model parameters and the conductive filament geometrical features were characterized in‐depth. In addition, a model to obtain the energy employed in the reset process was presented. Finally, we used the model to estimate the experimental conductive filament radius distribution using a set of 3000 reset cycles. Copyright © 2017 John Wiley & Sons, Ltd.
Self-management of oral anticoagulation in the elderly: Rationale, design, baselines and oral anticoagulation control after one year of follow-up

Summary Self-management is safe and reliable in patients with long-term oral anticoagulation (OAC). However, no study has yet assessed the safety and efficacy of OAC self-management in elderly patients with major thromboembolic and haemorrhagic complications as primary outcomes. In this multi-centre, open, randomised controlled trial, patients aged 60 years or more were randomised into the self-management group (SMG) (N=99) or routine care group (RCG) (N=96). We describe the rationale, design, baseline characteristics and interim analyses of oral anticoagulation control quality within the first year of follow-up. The medians of the squared international normalised ratio (INR) value deviations after six and 12 months were significantly lower in the SMG with medians of 0.16 and 0.16 compared to the RCG with medians of 0.25 and 0.25. The percentage of time within target range and the percentage of INR measurements within target range were significantly higher in the SMG versus the RCG within the first six months (medians 71% vs. 58% and 69% vs. 57%), and during the second six months of the study (75% vs. 67% and 72% vs. 57%). The numbers of all thromboembolic events requiring hospitalisation, major bleeding events, and deaths were similar in both groups. These preliminary results suggest that self-management of oral anticoagulation is safe and feasible for elderly patients willing to participate in a structured training programme.
Association of transcription factor 4 (TCF4) gene mRNA level with schizophrenia, its psychopathology, intelligence and cognitive impairments

Abstract Schizophrenia (SCZ), is considered as one of the most debilitating mental disorders around the world. Symptom-based clinical interview and numerous tests have been used to evaluate the diagnosis and also cognitive disturbances in patients with SCZ. All these tests measure phenotype-based functions. Thus, it seems accurate diagnosis of such complex disorders must rely on more valid and reliable factors. In this study, we evaluated the association of transcription factor 4 (TCF4) gene mRNA level in peripheral blood with SCZ, and also its psychopathology, cognitive and intellectual impairments. In this study, using real-time PCR, we compared TCF4 mRNA level between the case (70 unmedicated schizophrenia patients) and healthy control (n = 72) groups. In addition, all subjects underwent Psychopathology (PANSS) and cognitive and intelligence (WAIS, WMS, Stroop, WCST) assessments, and scores were compared between the two groups. Also, to determine the effect of TCF4 expression on psychopathology, cognitive and intellectual functions, the correlation between expression level and test scores was measured. The correlation between gene expression and age of onset and duration of the disorder was evaluated as well. Our results showed that the TCF4 mRNA level, psychopathology, cognitive and intellectual functions were significantly different in all, male, and female patients compared to healthy participants. Additionally, it was found that TCF4 level is positively correlated with scores of WAIS and WMS and is negatively correlated with Stroop and WCST errors and PANSS score. Our results showed that the mRNA level of TCF4 may be associated with SCZ, its psychopathology, IQ and cognitive impairments in an Iranian group of patients with SCZ. These results may help to better understanding the TCF4 role in the psychopathogenesis of SCZ and also may shed some light on the ongoing works conducted on peripheral biomarker-based diagnosis of complicated mental disorders.
Particle breakdown and rumen digestion of fresh ryegrass (Lolium perenne L.) and lucerne (Medicago sativa L.) fed to cows during a restricted feeding period

1. Five rumen-fistulated cows were given freshly cut ryegrass (Lolium perenne L.) and lucerne (Medicago sativa L.), on separate occasions, to compare rates of particle breakdown and aspects of rumen fermentation. 2. Cattle were required to consume their daily allowance (offered ad lib.) in two 2 h feeding periods daily. 3. During the first 2 h feeding period, dry matter (DM) intakes of ryegrass (4.75 kg) and lucerne (4.85 kg) were similar. Eating reduced 46% of ryegrass and 61 % of lucerne to a size able to pass a 2 mm sieve (P < 0.001). Rumen DM particles retained on the 2 and 4 mm sieves had a low probability of passage out of the rumen, and accounted for only 6 % of faecal DM with both feeds. 4. Ryegrass was cleared from the rumen more slowly than lucerne. During eating, rumen DM particles which could not pass the 2 mm sieve increased from 323 to 511 g/kg for ryegrass and from 201 to 389 g/kg for lucerne. The rate of particle size reduction for lucerne stem was similar to that for ryegrass. 5. When lucerne was eaten the increases in rumen volatile fatty acid (VFA) and ammonia concentrations were much greater than for ryegrass (P < 0.001). The proportions of plant chlorophyll released during eating were similar for both feeds (0.570 and 0.607), but 2 h after eating 22.3 g had been released from lucerne (79.1 %) compared with 15.0 g from ryegrass (63.8%). The flux of water from the rumen to the omasum was similar for ryegrass (10.2 litres/h) and lucerne (12.7 litres/h) during eating, but declined to 6.0 litres/h after eating with the lucerne diet.
Diagnostics and therapy of sudden hearing loss

This article reviews recent aspects of diagnostics, differential diagnostics, and evidence in systemic and local therapy of idiopathic sudden sensorineural hearing loss (ISSHL). Since a number of disorders can be accompanied by sudden hearing loss, a meaningful and targeted diagnostic strategy is of utmost importance. An important differential diagnosis of sudden hearing loss are intralabyrinthine schwannomas (ILS). The incidence of ILS is probably significantly underestimated. This may be due to the lack of awareness or lack of explicit search for an intralabyrinthine tumor on MRI or an inappropriate MRI technique for the evaluation of sudden hearing loss (“head MRI” instead of “temporal bone MRI” with too high slice thicknesses). Therefore, the request to the radiologist should specifically include the question for (or exclusion of) an ILS. With special MRI techniques, it is possibly today to visualize an endolymphatic hydrops. The evidence in the therapy of ISSHL is – with respect to the quality and not quantity of studies – unsatisfying. The value of systemically (low dose) or intratympanically applied corticosteroids in the primary treatment of ISSHL is still unclear. In order to investigate the efficacy and safety of high dose corticosteroids as primary therapy for ISSHL, a national, multicenter, three-armed, randomized, triple-blind controlled clinical trial is currently performed in Germany (http://hodokort-studie.hno.org/). After insufficient recovery of the threshold with systemic therapy of ISSHL, intratympanic corticosteroid therapy appears to be associated with a significantly higher chance of an improved hearing threshold than no therapy or placebo. Both, hearing gain and final hearing threshold, however, appear to be independent from the onset of secondary therapy. Based on currently available data from clinical studies, no recommendation can be made with respect to the type of corticosteroid and specifics of the intratympanic application protocol.
Cytotoxicity of Ciprofloxacin and Steroids in Mouse Tympanic Membrane Fibroblasts

Objective Ciprofloxacin, commonly given as eardrops, has been shown to adversely affect tympanic membrane fibroblasts. Dexamethasone potentiates this effect. A newly available eardrop contains ciprofloxacin and fluocinolone, a more potent steroid. We evaluated the cytotoxic effects of this preparation on mouse tympanic membrane fibroblasts. Study Design Prospective, in vitro. Setting Academic laboratory. Subjects and Methods In experiment 1, fibroblasts were exposed to 1:10 dilutions of commercially available 0.3% ofloxacin, 0.3% ciprofloxacin, 0.3% ciprofloxacin + 0.1% dexamethasone, 0.3% ciprofloxacin + 0.025% fluocinolone, or dilute hydrochloric acid (control), twice within 24 hours. In experiment 2, cells were also treated with the dilutions of the pure form of dexamethasone 0.1% or fluocinolone 0.025%, alone and in combination with ofloxacin or ciprofloxacin. Cells were exposed to the solutions for 2 hours each time and were placed back in growth media after the treatments. Cells were observed with phase-contrast microscope until the cytotoxicity assay was performed. Results Survival of fibroblasts treated with ofloxacin was not different from the control. Fibroblasts treated with ciprofloxacin, ciprofloxacin + dexamethasone, or ciprofloxacin + fluocinolone had much lower survival (all P < .0001). Cells treated with ciprofloxacin + fluocinolone had lower survival than ciprofloxacin (P < .0001) and ciprofloxacin + dexamethasone (P = .0001). Steroids alone also decreased fibroblast survival compared to control (P < .0001). The combination of dexamethasone or fluocinolone with ciprofloxacin, but not ofloxacin, further decreased fibroblast survival (P < .0001). Phase-contrast images mirrored the cytotoxicity findings. Conclusion Tympanic membrane fibroblast cytotoxicity of ciprofloxacin is potentiated by corticosteroids. This effect may be deleterious when treating a healing perforation but beneficial when treating granulation tissue on the tympanic membrane.
Influence of chemical treatments on the mechanical and water absorption properties of bamboo fiber composites

Chemical surface modification of woven bamboo mat with maleic anhydride, permanganate, benzoyl chloride, benzyl chloride, and pre-impregnation were carried out. These modified fibers were used as reinforcements in epoxy and polyester matrices. The effects of fiber modification on the tensile, flexural, impact, and water absorption properties of the composites were investigated. Flexural properties of maleic anhydride treated bamboo polyester composites improved by nearly 50%. The tensile strength and modulus of permanganate-treated bamboo polyester composite increased by 58% and 118%. The tensile strength and modulus of benzoylated bamboo fiber polyester composite improved by 71% and 118%, respectively. After benzoylation of the bamboo fiber, the water absorption is 16% for the bamboo-epoxy composite compared to 41% by untreated bamboo-epoxy composite. The water absorption by benzylated bamboo reinforced polyester composite was 16.8% compared to 51% by untreated bamboo-polyester composite. Pre-impregnation improved the mechanical and water resistant properties of both epoxy and polyester-based composites. SEM investigations of the tensile fracture surfaces show that modifications improved the fiber—matrix interaction.
Reinforcing effectiveness of midazolam, ethanol, and sucrose: behavioral economic comparison of a mixture relative to its component solutions

Benzodiazepines (BZs) are relatively safe when administered alone. However, these drugs can produce severe side effects when coadministered with ethanol. Despite these adverse consequences, rates of concurrent BZ and ethanol misuse are increasing, and it is unclear whether this behavior is maintained by an enhanced reinforcing effect of the mixture. To address this issue, the current study compared the reinforcing effectiveness of sucrose solutions mixed with midazolam, ethanol, or both. Eight male rats were trained to orally self-administer solutions of either sucrose (S), sucrose+midazolam (SM), sucrose+ethanol (SE), or sucrose+midazolam+ethanol (SME). The response requirement was increased between sessions until the number of reinforcers earned was zero and the relationship between response requirement and reinforcers earned was analyzed using the exponential model of demand. Although baseline intake was similar across drug conditions, consumption of SM was least affected by increases in cost, indicating that it possessed the highest reinforcing effectiveness (i.e. least elastic). The reinforcing effectiveness of S, SE, and SME did not differ significantly. The finding that the reinforcing effectiveness of the SME was less than that of SM does not support the supposition that BZ and ethanol coadministration is maintained by a higher reinforcing effectiveness of the mixture.
GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).
When is a Convolutional Filter Easy To Learn?

We analyze the convergence of (stochastic) gradient descent algorithm for learning a convolutional filter with Rectified Linear Unit (ReLU) activation function. Our analysis does not rely on any specific form of the input distribution and our proofs only use the definition of ReLU, in contrast with previous works that are restricted to standard Gaussian input. We show that (stochastic) gradient descent with random initialization can learn the convolutional filter in polynomial time and the convergence rate depends on the smoothness of the input distribution and the closeness of patches. To the best of our knowledge, this is the first recovery guarantee of gradient-based algorithms for convolutional filter on non-Gaussian input distributions. Our theory also justifies the two-stage learning rate strategy in deep neural networks. While our focus is theoretical, we also present experiments that illustrate our theoretical findings.
Targeting Cancer Stem Cells with Natural Killer Cell Immunotherapy

ABSTRACT Introduction: Standard cytoreductive cancer therapy, such as chemotherapy and radiotherapy, are frequently resisted by a small portion of cancer cells with ‘stem-cell’ like properties including quiescence and repopulation. Immunotherapy represents a breakthrough modality for improving oncologic outcomes in cancer patients. Since the success of immunotherapy is not contingent on target cell proliferation, it may also be uniquely suited to address the problem of resistance and repopulation exerted by cancer stem cells (CSCs). Areas covered: Natural killer (NK) cells have long been known for their ability to reject allogeneic hematopoietic stem cells, and there are increasing data demonstrating that NK cells can selectively identify and lyse CSCs. The authors review the current knowledge of CSCs and NK cells and highlight recent studies that support the concept that NK cells are capable of targeting CSC in solid tumors, especially in the context of combination therapy simultaneously targeting non-CSCs and CSCs. Expert opinion: Unlike cytotoxic cancer treatments, NK cells can target and eliminate quiescent/non-proliferating cells such as CSCs, and these enigmatic cells are an important source of relapse and metastasis. NK targeting of CSCs represents a novel and potentially high impact method to capitalize on the intrinsic therapeutic potential of NK cells
Calcium intake and the 10-year incidence of self-reported vertebral fractures in women and men: The Japan Public Health Centre-based Prospective Study

The purpose of this study was to evaluate the effect of low Ca intake on the 10-year incidence of vertebral fractures in cohorts I and II of the Japan Public Health Centre-based Prospective Study. The baseline studies were conducted in 1990–1994, with the follow-up studies conducted after 10 years. We analysed 33 970 subjects aged 40–59 years in cohort I and 41 664 subjects aged 40–69 years in cohort II. At baseline, the intake of Ca was assessed as a predictor, using validated FFQ. A meta-analysis was performed to estimate a summary relative risk (RR) for the two cohort studies. The 10-year cumulative incidences of self-reported vertebral fractures were 0·38 % for cohort I and 0·56 % for cohort II. In women, lower Ca intake was associated with a higher incidence of vertebral fractures (P for trend = 0·001), with the lowest quartile of Ca intake having a significantly higher incidence (0·89/1000 persons per year or RR 2·10 (95 % CI 1·25, 3·55)) than that (0·42/1000 persons per year) of the highest. In addition, the RR calculated using energy-adjusted Ca intake (by the residual method) as an outcome was 1·92 (95 % CI 1·28, 2·88). However, no such association was observed in men. An increase of Ca intake should be considered as a preventive strategy for vertebral fractures in peri- and post-menopausal women with a low Ca intake.
On Capacity Scaling Law of Cognitive Radio Ad Hoc Networks

Cognitive radio is envisioned to be an enabling radio technology for future wireless networks. In this paper, we study the capacity scaling laws for cognitive radio ad hoc networks (CRNs), i.e., how each individual node's capacity scales as the number of nodes in the network increases. This effort is critical to the fundamental understanding of the scalability of such network. However, due to the heterogeneity in available frequency bands at each node, the asymptotic capacity is much more difficult to develop than prior efforts for other types of wireless networks. To overcome this difficulty, we introduce two auxiliary networks $\zeta$ and $\alpha$ to analyze the capacity upper bound and lower bound. We derive the capacity results under both the protocol model and the physical model. Further, we show that the results developed by Gupta and Kumar for the simple single-channel single-radio (SC-SR) networks are special cases under the results for CRNs.