Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of thyroid hormone receptor interactor 13 inhibits cell proliferation and survival in human chronic lymphocytic leukemia

Background The genetic regulation of apoptosis and cell proliferation plays a role in the growth of chronic lymphocytic leukemia (CLL), the most common form of leukemia in the Western hemisphere. Although thyroid hormone receptor interactors (TRIPs) are known to play roles in cell cycle, the potential involvement of the novel family member TRIP13 in CLL has not yet been investigated. Methods Quantitative PCR (qPCR) was used to detect expression of TRIP13 in 36 CLL patients and 33 healthy donors CD19+ B cells. Loss-of-function (siRNA) assays were used to alter TRIP13 expression levels. The effect of TRIP13 on cell proliferation and apoptosis was measured by MTT, Annexin V-based flow cytometry and Caspase 3/7 activity assay. Affymetrix GeneChip and Ingenuity Pathway Analysis (IPA) were used to describe an overview of TRIP13 potential biological function and downstream pathways. Dual-luciferase reporter assay was performed to assess the promoting effect of c-MYC on TRIP13 transcription. RESULTS The qPCR data showed that TRIP13 is significantly over-expressed in CLL patients. Microarray analyses indicated that the biological function of TRIP13 in CLL is majorly cell apoptosis and cell proliferation associated. TRIP13 siRNA expressing cells exhibited a slower cell proliferation rate and underwent apoptosis compared with control cells. TRIP13 knockdown induced CLL cells apoptosis through PUMA independent of p53. TRIP13 up-regulation is induced by c-MYC dependent transcriptional activation. Conclusion Overall, our data suggest the bio-function of TRIP13 in CLL cell for the first time, and that this gene might be a therapeutic target for CLL.
Optimization of sleep apnea detection using SpO2 and ANN

Repetitive respiratory disturbance during sleep is called Sleep Apnea Hypopnea Syndrome and causes various diseases. Different features and classifiers have been used by different researchers to detect sleep apnea. This study is undertaken to identify the better performing blood oxygen saturation features subset using an Artificial Neural Network classifier for sleep Apnea detection. A database of 8 subjects with one-minute annotation is used to test the proposed system. The optimized system has seven features chosen from a total set of sixty-one features presenting a high accuracy rate using a genetic algorithm. Artificial Neural Network was able to achieve 97.7 percentage of accuracy with only seven features chosen by the Genetic algorithm.
Dynamic characteristics and control of magnetorheological/electrorheological sandwich structures: A state-of-the-art review

During past four decades, applications of magnetorheological and electrorheological fluids in adaptive sandwich structures have been widely studied, primarily for the purpose of vibration control. The rapid response time of controllable magnetorheological/electrorheological fluids to an applied magnetic/electric field and reversible variations in their stiffness and damping properties have been the key motivations for adaptive structures applications. This article presents a comprehensive review of the reported studies on applications of magnetorheological/electrorheological fluids for realizing active and semi-active vibration suppression in sandwich structures. The review focuses on methods of characterizing the magnetorheological/electrorheological fluids in the pre-yield region, magnetic/electric field-dependent phenomenological models describing the storage and loss moduli of fluids, experimental and analytical methods developed for vibration analysis of sandwich structures with magnetorheological/electrorheological fluid treatments, analysis of structures with partial magnetorheological/electrorheological fluid treatments and optimal treatment locations, and developments in control strategies for vibration suppression of magnetorheological/electrorheological sandwich structures. The studies on dynamic responses of fully and partially treated magnetorheological/electrorheological-based sandwich beams, plates, shells, and panels are also discussed, including the mathematical modeling methods and associated assumptions, methods of solutions, and experimental methods.
Host Protein Moloney Leukemia Virus 10 (MOV10) Acts as a Restriction Factor of Influenza A Virus by Inhibiting the Nuclear Import of the Viral Nucleoprotein

ABSTRACT The viral ribonucleoprotein (vRNP) complex of influenza A viruses (IAVs) contains an RNA-dependent RNA polymerase complex (RdRp) and nucleoprotein (NP) and is the functional unit for viral RNA transcription and replication. The vRNP complex is an important determinant of virus pathogenicity and host adaptation, implying that its function can be affected by host factors. In our study, we identified host protein Moloney leukemia virus 10 (MOV10) as an inhibitor of IAV replication, since depletion of MOV10 resulted in a significant increase in virus yield. MOV10 inhibited the polymerase activity in a minigenome system through RNA-mediated interaction with the NP subunit of vRNP complex. Importantly, we found that the interaction between MOV10 and NP prevented the binding of NP to importin-α, resulting in the retention of NP in the cytoplasm. Both the binding of MOV10 to NP and its inhibitory effect on polymerase activity were independent of its helicase activity. These results suggest that MOV10 acts as an anti-influenza virus factor through specifically inhibiting the nuclear transportation of NP and subsequently inhibiting the function of the vRNP complex. IMPORTANCE The interaction between the influenza virus vRNP complex and host factors is a major determinant of viral tropism and pathogenicity. Our study identified MOV10 as a novel host restriction factor for the influenza virus life cycle since it inhibited the viral growth rate. Conversely, importin-α has been shown as a determinant for influenza tropism and a positive regulator for viral polymerase activity in mammalian cells but not in avian cells. MOV10 disrupted the interaction between NP and importin-α, suggesting that MOV10 could also be an important host factor for influenza virus transmission and pathogenicity. Importantly, as an interferon (IFN)-inducible protein, MOV10 exerted a novel mechanism for IFNs to inhibit the replication of influenza viruses. Furthermore, our study potentially provides a new drug design strategy, the use of molecules that mimic the antiviral mechanism of MOV10.
Predictors of cognitive and physical fatigue in post-acute mild–moderate traumatic brain injury

ABSTRACT Post-traumatic fatigue (PTF) is a common, disabling, and often chronic symptom following traumatic brain injury (TBI). Yet, the impact of chronic cognitive and physical fatigue and their associations with psychiatric, sleep, cognitive, and psychosocial sequelae in mild–moderate TBI remain poorly understood. Sixty Veterans with a history of mild–moderate TBI and 40 Veteran controls (VC) were administered the Modified Fatigue Impact Scale, a validated measure of TBI-related cognitive and physical fatigue as well as measures of neuropsychiatric, psychosocial, sleep, and objective cognitive functioning. Compared to VC, TBI Veterans endorsed significantly greater levels of cognitive and physical fatigue. In TBI, psychiatric symptoms, sleep disturbance, and post-traumatic amnesia (PTA) were associated with both cognitive and physical fatigue, while loss of consciousness (LOC) and poor attention/processing speed were related to elevations in cognitive fatigue only. In regression analyses, anxiety, sleep disturbance, and LOC significantly predicted cognitive fatigue, while only post-traumatic stress symptoms and PTA contributed to physical fatigue. Cognitive and physical fatigue are problematic symptoms following mild–moderate TBI that are differentially associated with specific injury and psychiatric sequelae. Findings provide potential symptom targets for interventions aimed at ameliorating fatigue, and further underscore the importance of assessing and treating fatigue as a multi-dimensional symptom following TBI.
"Learning Relevance" as a Service for Improving Search Results in Technical Discussion Forums

Search results in technical forums are typically keyword based. The relevance of a link is usually gauged by closest content match. However, it has been shown in literature that users' click behavior is an integral part of deciding the relevance of a search result. Moreover, it is not just the number of clicks that matter, but time spent on a clicked link, order in which the links were clicked etc. also play an important role in the relevance decision. In this paper, we have developed a service that analyzes the click logs of searches performed in the technical forums and learns the new relevance scores for the search results with respect to a query. The computation model for relevance is an optimization problem, the constraints for which have been designed based on real user behavior study. We ingested StackOverflow data for few domains and designed a QA style search to carry out the study. We have developed heuristics to solve the optimization problem and have validated the relevance model using user behavior simulations. The relevance model is shown to yield efficient, robust and effective rank order using DCG (discounted cumulative gains) and stability metrics.
Towards Dataflow-Based Graph Accelerator

Existing graph processing frameworks greatly improve the performance of memory subsystem, but they are still subject to the underlying modern processor, resulting in the potential inefficiencies for graph processing in the sense of low instruction level parallelism and high branch misprediction. These inefficiencies, in accordance with our comprehensive micro-architectural study, mainly arise out of a wealth of dependencies, serial semantic of instruction streams, and complex conditional instructions in graph processing. In this paper, we propose that a fundamental shift of approach is necessary to break through the inefficiencies of the underlying processor via the dataflow paradigm. It is verified that the idea of applying dataflow approach into graph processing is extremely appealing for the following two reasons. First, as the execution and retirement of instructions only depend on the availability of input data in dataflow model, a high degree of parallelism can be therefore provided to relax the heavy dependency and serial semantic. Second, dataflow is guaranteed to make it possible to reduce the costs of branch misprediction by simultaneously executing all branches of a conditional instruction. Consequently, we make the preliminary attempt to develop the dataflow insight into a specialized graph accelerator. We believe that our work would open a wide range of opportunities to improve the performance of computation and memory access for large-scale graph processing.
Epoxyalkane:Coenzyme M Transferase Gene Diversity and Distribution in Groundwater Samples from Chlorinated-Ethene-Contaminated Sites

ABSTRACT Epoxyalkane:coenzyme M transferase (EaCoMT) plays a critical role in the aerobic biodegradation and assimilation of alkenes, including ethene, propene, and the toxic chloroethene vinyl chloride (VC). To improve our understanding of the diversity and distribution of EaCoMT genes in the environment, novel EaCoMT-specific terminal-restriction fragment length polymorphism (T-RFLP) and nested-PCR methods were developed and applied to groundwater samples from six different contaminated sites. T-RFLP analysis revealed 192 different EaCoMT T-RFs. Using clone libraries, we retrieved 139 EaCoMT gene sequences from these samples. Phylogenetic analysis revealed that a majority of the sequences (78.4%) grouped with EaCoMT genes found in VC- and ethene-assimilating Mycobacterium strains and Nocardioides sp. strain JS614. The four most-abundant T-RFs were also matched with EaCoMT clone sequences related to Mycobacterium and Nocardioides strains. The remaining EaCoMT sequences clustered within two emergent EaCoMT gene subgroups represented by sequences found in propene-assimilating Gordonia rubripertincta strain B-276 and Xanthobacter autotrophicus strain Py2. EaCoMT gene abundance was positively correlated with VC and ethene concentrations at the sites studied. IMPORTANCE The EaCoMT gene plays a critical role in assimilation of short-chain alkenes, such as ethene, VC, and propene. An improved understanding of EaCoMT gene diversity and distribution is significant to the field of bioremediation in several ways. The expansion of the EaCoMT gene database and identification of incorrectly annotated EaCoMT genes currently in the database will facilitate improved design of environmental molecular diagnostic tools and high-throughput sequencing approaches for future bioremediation studies. Our results further suggest that potentially significant aerobic VC degraders in the environment are not well represented in pure culture. Future research should aim to isolate and characterize aerobic VC-degrading bacteria from these underrepresented groups.
CRISPR-Cas Targeting of Host Genes as an Antiviral Strategy

Currently, a new gene editing tool—the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) associated (Cas) system—is becoming a promising approach for genetic manipulation at the genomic level. This simple method, originating from the adaptive immune defense system in prokaryotes, has been developed and applied to antiviral research in humans. Based on the characteristics of virus-host interactions and the basic rules of nucleic acid cleavage or gene activation of the CRISPR-Cas system, it can be used to target both the virus genome and host factors to clear viral reservoirs and prohibit virus infection or replication. Here, we summarize recent progress of the CRISPR-Cas technology in editing host genes as an antiviral strategy.
Context is Everything: Finding Meaning Statistically in Semantic Spaces

This paper introduces Contextual Salience (CoSal), a simple and explicit measure of a word's importance in context which is a more theoretically natural, practically simpler, and more accurate replacement to tf-idf. CoSal supports very small contexts (20 or more sentences), out-of context words, and is easy to calculate. A word vector space generated with both bigram phrases and unigram tokens reveals that contextually significant words disproportionately define phrases. This relationship is applied to produce simple weighted bag-of-words sentence embeddings. This model outperforms SkipThought and the best models trained on unordered sentences in most tests in Facebook's SentEval, beats tf-idf on all available tests, and is generally comparable to the state of the art. This paper also applies CoSal to sentence and document summarization and an improved and context-aware cosine distance. Applying the premise that unexpected words are important, CoSal is presented as a replacement for tf-idf and an intuitive measure of contextual word importance.
Eight-minute self-regulation intervention raises educational attainment at scale in individualist but not collectivist cultures

Significance High attrition from educational programs is a major obstacle to social mobility and a persistent source of economic inefficiency. Over two-thirds of students entering a 2-y institution fail to earn a credential in the United States. In online courses, attrition rates are even higher. In two large field experiments, we tested the conditions under which a writing activity that facilitates goal commitment and goal-directed behavior reduces attrition in online courses. The activity raised completion rates by up to 78% for members of individualist cultures and primarily for those who contended with predictable and surmountable obstacles in the form of everyday obligations, but it was ineffective in collectivist cultures and for people contending with other types of obstacles. Academic credentials open up a wealth of opportunities. However, many people drop out of educational programs, such as community college and online courses. Prior research found that a brief self-regulation strategy can improve self-discipline and academic outcomes. Could this strategy support learners at large scale? Mental contrasting with implementation intentions (MCII) involves writing about positive outcomes associated with a goal, the obstacles to achieving it, and concrete if–then plans to overcome them. The strategy was developed in Western countries (United States, Germany) and appeals to individualist tendencies, which may reduce its efficacy in collectivist cultures such as India or China. We tested this hypothesis in two randomized controlled experiments in online courses (n = 17,963). Learners in individualist cultures were 32% (first experiment) and 15% (second experiment) more likely to complete the course following the MCII intervention than a control activity. In contrast, learners in collectivist cultures were unaffected by MCII. Natural language processing of written responses revealed that MCII was effective when a learner’s primary obstacle was predictable and surmountable, such as everyday work or family obligations but not a practical constraint (e.g., Internet access) or a lack of time. By revealing heterogeneity in MCII’s effectiveness, this research advances theory on self-regulation and illuminates how even highly efficacious interventions may be culturally bounded in their effects.
Plantar heel pain and plantar fasciitis.

INTRODUCTION Plantar heel pain, also known as plantar fasciitis, causes soreness or tenderness of the sole of the foot under the heel, which sometimes extends into the medial arch. Pain associated with the condition may cause substantial disability and poor health-related quality of life. The prevalence and prognosis are unclear, but the symptoms seem to resolve over time in most people. METHODS AND OUTCOMES We conducted a systematic overview, aiming to answer the following clinical questions: What are the effects of conservative treatments for plantar heel pain? What are the effects of non-conservative treatments for plantar heel pain? We searched: Medline, Embase, The Cochrane Library and other important databases up to November 2013 (Clinical Evidence reviews are updated periodically, please check our website for the most up-to-date version of this review). RESULTS At this update, searching of electronic databases retrieved 162 studies. After deduplication and removal of conference abstracts, 84 records were screened for inclusion in the overview. Appraisal of titles and abstracts led to the exclusion of 39 studies and the further review of 45 full articles. Of the 45 full articles evaluated, five systematic reviews and nine RCTs were included at this update. We performed a GRADE evaluation for 30 PICO combinations. CONCLUSIONS In this systematic overview, we categorised the efficacy for 12 interventions based on information relating to the effectiveness and safety of corticosteroid injection alone (both short-term and longer-term effects), corticosteroid injections plus local anaesthetic injection (both short-term and longer-term effects), customised foot orthoses, extracorporeal shock wave therapy, heel pads and cups, local anaesthetic injection alone, night splints, stretching exercises, surgery, and taping.
Rearrangement of Influenza Virus Spliced Segments for the Development of Live-Attenuated Vaccines

ABSTRACT Influenza viral infections represent a serious public health problem, with influenza virus causing a contagious respiratory disease which is most effectively prevented through vaccination. Segments 7 (M) and 8 (NS) of the influenza virus genome encode mRNA transcripts that are alternatively spliced to express two different viral proteins. This study describes the generation, using reverse genetics, of three different recombinant influenza A/Puerto Rico/8/1934 (PR8) H1N1 viruses containing M or NS viral segments individually or modified M or NS viral segments combined in which the overlapping open reading frames of matrix 1 (M1)/M2 for the modified M segment and the open reading frames of nonstructural protein 1 (NS1)/nuclear export protein (NEP) for the modified NS segment were split by using the porcine teschovirus 1 (PTV-1) 2A autoproteolytic cleavage site. Viruses with an M split segment were impaired in replication at nonpermissive high temperatures, whereas high viral titers could be obtained at permissive low temperatures (33°C). Furthermore, viruses containing the M split segment were highly attenuated in vivo, while they retained their immunogenicity and provided protection against a lethal challenge with wild-type PR8. These results indicate that influenza viruses can be effectively attenuated by the rearrangement of spliced segments and that such attenuated viruses represent an excellent option as safe, immunogenic, and protective live-attenuated vaccines. Moreover, this is the first time in which an influenza virus containing a restructured M segment has been described. Reorganization of the M segment to encode M1 and M2 from two separate, nonoverlapping, independent open reading frames represents a useful tool to independently study mutations in the M1 and M2 viral proteins without affecting the other viral M product. IMPORTANCE Vaccination represents our best therapeutic option against influenza viral infections. However, the efficacy of current influenza vaccines is suboptimal, and novel approaches are necessary for the prevention of disease caused by this important human respiratory pathogen. In this work, we describe a novel approach to generate safer and more efficient live-attenuated influenza virus vaccines (LAIVs) based on recombinant viruses whose genomes encode nonoverlapping and independent M1/M2 (split M segment [Ms]) or both M1/M2 and NS1/NEP (Ms and split NS segment [NSs]) open reading frames. Viruses containing a modified M segment were highly attenuated in mice but were able to confer, upon a single intranasal immunization, complete protection against a lethal homologous challenge with wild-type virus. Notably, the protection efficacy conferred by our viruses with split M segments was better than that conferred by the current temperature-sensitive LAIV. Altogether, these results open a new avenue for the development of safer and more protective LAIVs on the basis of the reorganization of spliced viral RNA segments in the genome.
The Joint Effects of Tweet Content Similarity and Tweet Interactions for Topic Derivation

Interactions among tweets, i.e., mentions, retweets, replies, are important factors contributing to the quality of topic derivation on Twitter. If applied correctly, the incorporation of tweet interactions can significantly improve the quality of topic derivation in comparison with approaches that are mainly based on the content similarity analysis. However, how interactions can be measured and integrated with content similarity for topic derivation remains a challenge. In previous work, the strength of tweet-to-tweet relationship has been computed by simply adding measures for content similarity, mentions, and reply-retweets. This simple linear addition does not accurately reflect the various impacts these factors have on tweet relationships. In order to address this issue, we propose a joint probability model that can effectively integrate the effects of the content similarity, mentions, and reply-retweets to measure the tweet relationship for the purpose of topic derivation. The proposed method is based on matrix factorization techniques, which enables a flexible implementation on a distributed system in an incremental manner. Experimental results show that the proposed model results in a significant improvement in the quality of topic derivation over existing methods.