Miracle-dz/UniFAR-FTUs huggingface dataset:
High‐quality human and rat spermatozoal RNA isolation for functional genomic studies

Sperm RNA is a sensitive monitoring endpoint for male reproductive toxicants, and a potential biomarker to assess male infertility and sperm quality. However, isolation of sperm RNA is a challenging procedure due to the heterogeneous population of cells present in the ejaculate, the low yield of RNA per spermatozoon, and the absence of 18S and 28S ribosomal RNA subunits. The unique biology of spermatozoa has created some uncertainty in the field about RNA isolation methods, indicating the need for rigorous quality control checks to ensure reproducibility of data generated from sperm RNA. Therefore, we developed a reliable and effective protocol for RNA isolation from rat and human spermatozoa that delivers highly purified and intact RNA, verified using RNA‐specific electrophoretic chips and molecular biology approaches such as RT‐PCR and Western blot analysis. The sperm RNA isolation technique was optimized using rat spermatozoa and then adapted to human spermatozoa. Three steps in the sperm isolation procedure, epididymal fluid collection, sperm purification, and spermatozoon RNA extraction, were evaluated and assessed. The sperm RNA extraction methodology consists of collection of rat epididymal fluid with repeated needle punctures of the epididymis, somatic cell elimination using detergent‐based somatic cell lysis buffer (SCLB) and the use of RNA isolation Kit. Rat sperm heads are more resistant to disruption than human spermatozoa, necessitating the addition of mechanical lysis with microbeads and heat in the rat protocol, whereas the human sperm protocol only required lysis buffer. In conclusion, this methodology results in reliable and consistent isolation of high‐quality sperm RNA. Using this technique will aid in translation of data collected from animal models, and reproducibility of clinical assessment of male factor fertility using RNA molecular biomarkers.
Dynamic Multi-View Hashing for Online Image Retrieval

Advanced hashing technique is essential to facilitate effective large scale online image organization and retrieval, where image contents could be frequently changed. Traditional multi-view hashing methods are developed based on batch-based learning, which leads to very expensive updating cost. Meanwhile, existing online hashing methods mainly focus on single-view data and thus can not achieve promising performance when searching real online images, which are multiple view based data. Further, both types of hashing methods can only produce hash code with fixed length. Consequently they suffer from limited capability to comprehensive characterization of streaming image data in the real world. In this paper, we propose dynamic multi-view hashing (DMVH), which can adaptively augment hash codes according to dynamic changes of image. Meanwhile, DMVH leverages online learning to generate hash codes. It can increase the code length when current code is not able to represent new images effectively. Moreover, to gain further improvement on overall performance, each view is assigned with a weight, which can be efficiently updated during the online learning process. In order to avoid the frequent updating of code length and view weights, an intelligent buffering scheme is also specifically designed to preserve significant data to maintain good effectiveness of DMVH. Experimental results on two real-world image datasets demonstrate superior performance of DWVH over several state-of-the-art hashing methods.
Joint developmental trajectories of internalizing and externalizing disorders between childhood and adolescence

Abstract This study sought to identify trajectories of DSM-IV based internalizing (INT) and externalizing (EXT) problem scores across childhood and adolescence and to provide insight into the comorbidity by modeling the co-occurrence of INT and EXT trajectories. INT and EXT were measured repeatedly between age 7 and age 15 years in over 7,000 children and analyzed using growth mixture models. Five trajectories were identified for both INT and EXT, including very low, low, decreasing, and increasing trajectories. In addition, an adolescent onset trajectory was identified for INT and a stable high trajectory was identified for EXT. Multinomial regression showed that similar EXT and INT trajectories were associated. However, the adolescent onset INT trajectory was independent of high EXT trajectories, and persisting EXT was mainly associated with decreasing INT. Sex and early life environmental risk factors predicted EXT and, to a lesser extent, INT trajectories. The association between trajectories indicates the need to consider comorbidity when a child presents with INT or EXT disorders, particularly when symptoms start early. This is less necessary when INT symptoms start at adolescence. Future studies should investigate the etiology of co-occurring INT and EXT and the specific treatment needs of these severely affected children.
Current Research on the Epidemiology, Pathogenesis, and Management of Necrotizing Enterocolitis

Despite decades of research on necrotizing enterocolitis, we still do not fully understand the pathogenesis of the disease, or how to prevent or how to treat it. However, as a result of recent significant advances in the microbiology, molecular biology, and cell biology of the intestine of preterm infants and infants with necrotizing enterocolitis, there is some hope that research into this devastating disease will yield some important translation into effective prevention, more rapid diagnosis, and novel therapies.
A Comparative Evaluation of the Frictional Resistance between Stainless Steel, TMA and Low Friction TMA Orthodontic Archwires - An In-Vitro Study

Aim: To understand the frictional forces between the orthodontic brackets and orthodontic wires and to evaluate the frictional resistance of different orthodontic wires. Materials and method: The test was divided into six groups comprising of fifteen samples each. Group I - stainless steel wires, Group II - TMA wires, Group III- low friction TMA wires, Group IV - colored low friction TMA wires aqua, Group V - colored low friction TMA wires purple, Group VI - colored low friction TMA wires honey dew. The measurements of friction between bracket and arch wire were done with the Instron Universal testing machine (model no.4701). The results were subjected to statistical analysis. Results: On analyzing the mean values of Groups I to VI it was clearly evident that the Group II (TMA) has the maximum frictional resistance and Group VI (colored low friction TMA - honey dew) has the lowest frictional resistance. Conclusion: The frictional resistance is highest in TMA, The frictional resistance is lowest in colored low friction TMA honeydew, and the frictional resistance of colored low friction TMA aqua is similar to that of stainless
Reduction of Proliferating Olfactory Cells and Low Expression of Extracellular Matrix Genes Are Hallmarks of the Aged Olfactory Mucosa

Background: The incidence of olfactory impairment increases with age; however, the detailed molecular and cellular mechanisms underlying this increase are yet to be determined. Methods: We examined the influence of aging on olfactory receptor neurons (ORNs), which are maintained by a unique stem cell system, from olfactory progenitor cells to mature ORNs, by histological comparisons of the physiological status of the olfactory epithelium between young adult and aged mice. Furthermore, we clarified the expression of genes encoding inflammatory cytokines, neurotrophins, growth factors, and extracellular matrix proteins to reveal the molecular mechanisms underlying olfactory impairment caused by aging. Results: The numbers of mature and immature ORNs, but not olfactory progenitors, decreased in the aged olfactory epithelium, with a concurrent reduction in Ki-67-positive proliferating cells. Transcriptome analyses revealed an increase in Il6, encoding a component of senescence-associated secretary phenotypes (SASP), and a decrease in Igf1, encoding a growth factor for ORNs, in the aged nasal mucosa. Interestingly, expression levels of several extracellular matrix genes, including Col1a2, decreased in the aged nasal mucosa. Consistent with the transcriptional changes, the number of Col1a2-GFP-positive cells decreased in the aged lamina propria. Conclusions: Our data suggest that reduction in ORN number and cell proliferation, reduced extracellular matrix gene expression, and increased SASP contribute to olfactory impairment during aging.
Multiplicative noise removal combining a total variation regularizer and a nonconvex regularizer

A novel variational model for removing multiplicative noise is proposed in this paper. In the model, a novel regularization term is elaborately designed which is inherently equivalent to a combination of the classical total variation regularizer and a nonconvex regularizer. The proposed regularization term, on the one hand, can better remove the noise in homogeneous regions of a noisy image and, on the other hand, can preserve edge details of the image during the denoising process. In order to solve the model efficiently, we design an alternating iteration process in which two coupling minimization problems are solved. For each of the two minimization problems, the existence and uniqueness of their solutions are proved under some necessary assumptions. Numerical results are reported to demonstrate the effectiveness of the proposed regularization term for multiplicative noise removal.
Exploiting multilinguality for creating mappings between thesauri

The definition of mappings between multilingual thesauri is a recent research topic concerning the application of the traditional schema mapping algorithms in conjunction with the use of multilingual resources. In this paper, we present a multilingual mapping approach aiming at defining matches between terms belonging to multilingual thesauri. The paper presents the approach as a variant of the schema mapping problem and discusses its evaluation on (i) domain-specific use cases and (ii) on a standard benchmark, namely MultiFarm benchmark, used for measuring the effectiveness of multilingual ontology mapping systems.
Comparison of Tracheal Wash and Bronchoalveolar Lavage Cytology in 154 Horses With and Without Respiratory Signs in a Referral Hospital Over 2009−2015

Most equine lower respiratory diseases present as increased airway neutrophilia, which can be detected in tracheal wash (TW) or bronchoalveolar lavage fluid (BALF) cytology samples. The aim was to compare the TW and BALF results in a population of client-owned horses with and without clinical respiratory disease signs. A secondary aim was to determine the sensitivity (Se) and specificity (Sp) of TW and BALF neutrophilia in detecting respiratory disease. The cutoff values for neutrophils were also evaluated. Retrospective data from 154 horses of various breeds that had been subject to both TW and bronchoalveolar lavage (BAL) sampling at rest during 2009−2015 were used. The horses were divided into three groups based on the presenting signs, physical examination, and endoscopy mucus score. Neutrophil counts of >20% in TW and >5% in BAL were considered abnormal. Cytology results between groups, correlations between TW and BALF cell types, and tracheal mucus score were analyzed. Two graph receiving operating characteristic (ROC) curves of the neutrophil percentage values of TW and BALF were created to determine the optimal cutoff values and to calculate the diagnostic Se and Sp for diagnosing airway inflammation in horses with and without clinical respiratory signs. The Se and Sp of TW and BALF neutrophil percentages were further estimated using a two-test one-population Bayesian latent class model. The two tests showed substantial agreement, and only 17.5% of the horses were classified differently (healthy vs. diseased). The neutrophil percentage was found to correlate between TW and BALF. The Se and Sp of TW were generally higher than for BAL when estimated with area under the curve or Bayesian model. Cutoff values of 17.7% for TW and 7% for BALF were indicated by the ROCs. We conclude that TW is a more sensitive and specific method in our patient population. We suggest that the current neutrophil cutoff values of 20% for TW and 5% for BALF would still be appropriate to use in clinical diagnosis of airway inflammation. However, further studies with other cell types and in other populations are warranted to determine the best sampling method for individual horses.
The EMT spectrum and therapeutic opportunities

Carcinomas are phenotypically arrayed along an epithelial–mesenchymal transition (EMT) spectrum, a developmental program currently exploited to understand the acquisition of drug resistance through a re‐routing of growth factor signaling. This review collates the current approaches employed in developing therapeutics against cancer‐associated EMT, and provides an assessment of their respective strengths and drawbacks. We reflect on the close relationship between EMT and chemoresistance against current targeted therapeutics, with a special focus on the epigenetic mechanisms that link these processes. This prompts the hypothesis that carcinoma‐associated EMT shares a common epigenetic pathway to cellular plasticity as somatic cell reprogramming during tissue repair and regeneration. Indeed, their striking resemblance suggests that EMT in carcinoma is a pathological adaptation of an intrinsic program of cellular plasticity that is crucial to tissue homeostasis. We thus propose a revised approach that targets the epigenetic mechanisms underlying pathogenic EMT to arrest cellular plasticity regardless of upstream cancer‐driving mutations.
Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir‐containing regimens

Treatment with the direct‐acting antiviral agent (DAA) sofosbuvir (SOF), an NS5B inhibitor, and velpatasvir (VEL), an NS5A inhibitor, demonstrates viral cure rates of ≥95% in hepatitis C virus (HCV) genotypes (GT) 1‐6. Here, we investigated intrapatient HCV diversity in NS5A and NS5B using Shannon entropy to examine the relationship between viral diversity and treatment outcome. At baseline, HCV diversity was lowest in patients infected with HCV GT3 as compared to the other GTs, and viral diversity was greater in NS5A than NS5B (P < .0001). Treatment outcome with SOF/VEL or the comparator regimen of SOF with ribavirin (RBV) was not correlated with baseline diversity. However, among persons treated with SOF/VEL, a decrease in diversity from baseline was observed at relapse in the majority virologic failures, consistent with a viral bottleneck event at relapse. In contrast, an increase in diversity was observed in 27% of SOF+RBV virologic failures. We investigated whether the increase in diversity was due to an increase in the transition rate, one mode of potential RBV‐mediated mutagenesis; however, we found no evidence of this mechanism. Overall, we did not observe that viral diversity at baseline influenced treatment outcome, but the diversity changes observed at relapse can improve our understanding of RBV viral suppression in vivo.
Fast Parametric Learning with Activation Memorization

Neural networks trained with backpropagation often struggle to identify classes that have been observed a small number of times. In applications where most class labels are rare, such as language modelling, this can become a performance bottleneck. One potential remedy is to augment the network with a fast-learning non-parametric model which stores recent activations and class labels into an external memory. We explore a simplified architecture where we treat a subset of the model parameters as fast memory stores. This can help retain information over longer time intervals than a traditional memory, and does not require additional space or compute. In the case of image classification, we display faster binding of novel classes on an Omniglot image curriculum task. We also show improved performance for word-based language models on news reports (GigaWord), books (Project Gutenberg) and Wikipedia articles (WikiText-103) --- the latter achieving a state-of-the-art perplexity of 29.2.
Fungal burden exposure assessment in podiatry clinics from Ireland

ABSTRACT Fungi are amongst the bioaerosols of most importance, as indicated by the growing interest in this field of research. The aim was to characterize the exposure to fungal burden in podiatry clinics using culture-based and molecular methods. Methods: Airborne fungi were collected using an impaction air sampler and surface samples were also performed. Fourteen air samples were collected for direct detection of fungal DNA from filamentous fungi and dermatophytes. Overall, 63.6 % of the evening samples and 46 % of the morning samples surpassed the threshold values (150 CFU/m3). Molecular detection, by real time PCR, of the target fungal species/strains (Aspergillus and Stachybotrys species) was negative for all samples collected. Trichophyton rubrum was detected by PCR analysis in one DNA sample collected on day six. Results suggest the use of both culture-based and molecular methodologies are desirable for a complete evaluation of fungal burden in this particular health care setting.
Amyloid-β Acts as a Regulator of Neurotransmitter Release Disrupting the Interaction between Synaptophysin and VAMP2

Background It is becoming increasingly evident that deficits in the cortex and hippocampus at early stages of dementia in Alzheimer’s disease (AD) are associated with synaptic damage caused by oligomers of the toxic amyloid-β peptide (Aβ42). However, the underlying molecular and cellular mechanisms behind these deficits are not fully understood. Here we provide evidence of a mechanism by which Aβ42 affects synaptic transmission regulating neurotransmitter release. Methodology/Findings We first showed that application of 50 nM Aβ42 in cultured neurones is followed by its internalisation and translocation to synaptic contacts. Interestingly, our results demonstrate that with time, Aβ42 can be detected at the presynaptic terminals where it interacts with Synaptophysin. Furthermore, data from dissociated hippocampal neurons as well as biochemical data provide evidence that Aβ42 disrupts the complex formed between Synaptophysin and VAMP2 increasing the amount of primed vesicles and exocytosis. Finally, electrophysiology recordings in brain slices confirmed that Aβ42 affects baseline transmission. Conclusions/Significance Our observations provide a necessary and timely insight into cellular mechanisms that underlie the initial pathological events that lead to synaptic dysfunction in Alzheimer’s disease. Our results demonstrate a new mechanism by which Aβ42 affects synaptic activity.
Necessity of electrically conductive pili for methanogenesis with magnetite stimulation

Background Magnetite-mediated direct interspecies electron transfer (DIET) between Geobacter and Methanosarcina species is increasingly being invoked to explain magnetite stimulation of methane production in anaerobic soils and sediments. Although magnetite-mediated DIET has been documented in defined co-cultures reducing fumarate or nitrate as the electron acceptor, the effects of magnetite have only been inferred in methanogenic systems. Methods Concentrations of methane and organic acid were analysed with a gas chromatograph and high-performance liquid chromatography, respectively. The concentration of HCl-extractable Fe(II) was determined by the ferrozine method. The association of the defined co-cultures of G. metallireducens and M. barkeri with magnetite was observed with transmission electron micrographs. Results Magnetite stimulated ethanol metabolism and methane production in defined co-cultures of G. metallireducens and M. barkeri; however, magnetite did not promote methane production in co-cultures initiated with a culture of G. metallireducens that could not produce electrically conductive pili (e-pili), unlike the conductive carbon materials that facilitate DIET in the absence of e-pili. Transmission electron microscopy revealed that G. metallireducens and M. barkeri were closely associated when magnetite was present, as previously observed in G. metallireducens/G. sulfurreducens co-cultures. These results show that magnetite can promote DIET between Geobacter and Methanosarcina species, but not as a substitute for e-pili, and probably functions to facilitate electron transfer from the e-pili to Methanosarcina. Conclusion In summary, the e-pili are necessary for the stimulation of not only G. metallireducens/G. sulfurreducens, but also methanogenic G. metallireducens/M. barkeri co-cultures with magnetite.
Ligation versus no ligation of spontaneous portosystemic shunts during liver transplantation: Audit of a prospective series of 66 consecutive patients

The management of large spontaneous portosystemic shunt (SPSS) during liver transplantation (LT) is a matter of debate. The aim of this study is to compare the short‐term and longterm outcomes of SPSS ligation versus nonligation during LT, when both options are available. From 2011 to 2017, 66 patients with SPSS underwent LT: 56 without and 10 with portal vein thrombosis (PVT), all of whom underwent successful thrombectomy and could have portoportal reconstruction. The SPSS were either splenorenal (n = 40; 60.6%), left gastric (n = 16; 24.2%), or mesenterico‐iliac (n = 10; 15.1%). Following portoportal anastomosis, the SPSS was ligated in 36 (54.4%) patients and left in place in 30 (45.5%) patients, based on the effect of the SPSS clamping/unclamping test on portal vein flow during the anhepatic phase. Intraoperatively, satisfactory portal flow was obtained in both groups. Primary nonfunction (PNF) and primary dysfunction (PDF) rates did not differ significantly between the 2 groups. Nonligation of SPSS was significantly associated with a higher rate of postoperative encephalopathy (P < 0.001) and major postoperative morbidity (P = 0.02). PVT occurred in 0 and 3 patients in the ligated and nonligated shunt group, respectively (P = 0.08). A composite end point, which included the relevant complications in the setting of SPSS in LT (ie, PNF and PDF, PVT, and encephalopathy) was present in 16 (44.4%) and 22 (73.3%) patients of the ligated and nonligated shunt group, respectively (P = 0.02). Patient (P = 0.05) and graft (P = 0.02) survival rates were better in the ligated shunt group. In conclusion, the present study supports routine ligation of large SPSS during LT whenever feasible. Liver Transplantation 24 505–515 2018 AASLD.
Energy consumption in Java: An early experience

There has been a 10,000-fold increase in performance of supercomputers since 1992 but only 300-fold improvement in performance per watt. Dynamic adaptation of hardware techniques such as fine-grain clock gating, power gating and dynamic voltage/frequency scaling, are used for many years to improve the computer's energy efficiency. However, recent demands of exascale computation, as well as the increasing carbon footprint, require new breakthrough to make ICT systems more energy efficient. Energy efficient software has not been well studied in the last decade. In this paper, we take an early step to investigate the energy efficiency of Java which is one of the most common languages used in ICT systems. We evaluate energy consumption of data types, operators, control statements, exception, and object in Java at a granular level. Intel Running Average Power Limit (RAPL) technology is applied to measure the relative power consumption of small code snippets. Several observations are found, and these results will help in standardizing the energy consumption traits of Java which can be leveraged by software developers to generate energy efficient code in future.