Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of domain on measures of semantic relatedness

Measures of semantic relatedness have been used in a variety of applications in information retrieval and language technology, such as measuring document similarity and cohesion of text. Definitions of such measures have ranged from using distance‐based calculations over WordNet or other taxonomies to statistical distributional metrics over document collections such as Wikipedia or the Web. Existing measures do not explicitly consider the domain associations of terms when calculating relatedness: This article demonstrates that domain matters. We construct a data set of pairs of terms with associated domain information and extract pairs that are scored nearly identical by a sample of existing semantic‐relatedness measures. We show that human judgments reliably score those pairs containing terms from the same domain as significantly more related than cross‐domain pairs, even though the semantic‐relatedness measures assign the pairs similar scores. We provide further evidence for this result using a machine learning setting by demonstrating that domain is an informative feature when learning a metric. We conclude that existing relatedness measures do not account for domain in the same way or to the same extent as do human judges.
Identification of transcription factor binding sites using Gaussian mixture models

Identification of transcription factor binding sites still remains a challenging problem even though many computational tools have been proposed in the literature for this specific task. In this study, a method to discover such DNA subsequences, that is, motifs, is proposed. The method uses Gaussian mixture models with expectation‐maximization algorithm. In order to show the potential of the proposed method, experiments are conducted by use of data sets extracted from the DNA sequences of various organisms. The proposed method is also compared with four other methods: MEME, MDScan, SOMBRERO and the fuzzy C‐means based motif finder. As a result, the proposed method proves itself as a promising tool in identifying over‐represented DNA motifs.
RNA‐virus proteases counteracting host innate immunity

Virus invasion triggers host immune responses, in particular, innate immune responses. Pathogen‐associated molecular patterns of viruses (such as dsRNA, ssRNA, or viral proteins) released during virus replication are detected by the corresponding pattern‐recognition receptors of the host, and innate immune responses are induced. Through production of type‐I and type‐III interferons as well as various other cytokines, the host innate immune system forms the frontline to protect host cells and inhibit virus infection. Not surprisingly, viruses have evolved diverse strategies to counter this antiviral system. In this review, we discuss the multiple strategies used by proteases of positive‐sense single‐stranded RNA viruses of the families Picornaviridae, Coronaviridae, and Flaviviridae, when counteracting host innate immune responses.
A Time-Based Receiver With 2-Tap Decision Feedback Equalizer for Single-Ended Mobile DRAM Interface

A time-based (TB) receiver (RX) with a 2-tap TB decision feedback equalizer (DFE) is proposed for mobile DRAM interface. The TB RX consists of a voltage-to-time converter (VTC), a TB DFE, and a time comparator. The VTC converts the RX input voltage to a time difference between two VTC outputs by using the difference in clock-to-Q delays between two latches with different input offset voltages. The TB DFE inserts an additional delay to one of the two VTC outputs and bypasses the other VTC output to increase the time opening. The time comparator makes a decision with the first arriving edge of the two outputs of the TB DFE. While the feedback loop delay must be less than 1 UI for proper operation in the conventional voltage-based DFE, the TB DFE allows the feedback loop delay up to 1.43 UI in this paper. A transmitter (TX) transmits a single-ended signal of 200-mV swing by using an n-over-n voltage-mode driver. The transceiver in a 65-nm CMOS process achieves a 12.5 Gb/s with a 0.8-V supply through a 15-inch FR-4 channel of 14-dB loss. The TX and RX chip consume 4.3 and 3.4 mA, respectively. The energy efficiency is 0.49 pJ/b.
The prognostic value of HER2 in ovarian cancer: A meta-analysis of observational studies

Background The prognostic role of human epidermal growth factor receptor 2 (HER2) in ovarian cancer has been investigated in previous studies, but the results remain controversial. Here we present a meta-analysis to systematically review the association between HER2 expression and ovarian cancer prognosis. Method Observational studies published until July 2017 were searched in Pubmed, Embase, and Cochrane library databases. Hazard ratios (HRs) for survival with 95% confidence intervals (CIs), subgroup analyses, publication bias and sensitivity analyses were implemented under a standard manner. Estimates of overall survival (OS), progress-free survival (PFS) and disease-free survival (DFS) were weighted and pooled using Der Simonian-Laird random-effect model. Result Thirty-four studies that include 5180 ovarian cancer patients were collected for analysis. Expression of HER2 was negatively correlated with clinical prognosis of overall survival (HR = 1.57, 95% CI: 1.31 to 1.89, P < 0.001) and disease-free survival / progress-free survival (HR = 1.26, 95% CI = 1.06 to 1.49) in ovarian cancers. The association between HER2 expression and poor ovarian cancer prognosis in overall survival was also statistically significant in subgroups of unclassified ovarian cancer, Caucasian population and Asian population, while irrespective of detection method. Conclusion HER2 expression was related with poor prognosis in ovarian cancer patients and can be used as a predicting cancer prognostic biomarker in ovarian cancer patients.
Association Between Schizophrenia-Related Polygenic Liability and the Occurrence and Level of Mood-Incongruent Psychotic Symptoms in Bipolar Disorder

Importance Bipolar disorder (BD) overlaps schizophrenia in its clinical presentation and genetic liability. Alternative approaches to patient stratification beyond current diagnostic categories are needed to understand the underlying disease processes and mechanisms. Objective To investigate the association between common-variant liability for schizophrenia, indexed by polygenic risk scores (PRSs), and psychotic presentations of BD. Design, Setting, and Participants This case-control study in the United Kingdom used multinomial logistic regression to estimate differential PRS associations across categories of cases and controls. Participants included in the final analyses were 4436 cases of BD from the Bipolar Disorder Research Network. These cases were compared with the genotypic data for 4976 cases of schizophrenia and 9012 controls from the Type 1 Diabetes Genetics Consortium study and the Generation Scotland study. Data were collected between January 1, 2000, and December 31, 2013. Data analysis was conducted from March 1, 2016, to February 28, 2017. Exposures Standardized PRSs, calculated using alleles with an association threshold of P < . 05 in the second Psychiatric Genomics Consortium genome-wide association study of schizophrenia, were adjusted for the first 10 population principal components and genotyping platforms. Main Outcomes and Measures Multinomial logit models estimated PRS associations with BD stratified by Research Diagnostic Criteria subtypes of BD, by lifetime occurrence of psychosis, and by lifetime mood-incongruent psychotic features. Ordinal logistic regression examined PRS associations across levels of mood incongruence. Ratings were derived from the Schedules for Clinical Assessment in Neuropsychiatry interview and the Bipolar Affective Disorder Dimension Scale. Results Of the 4436 cases of BD, 2966 (67%) were female patients, and the mean (SD) age at interview was 46 [12] years. Across clinical phenotypes, there was an exposure-response gradient, with the strongest PRS association for schizophrenia (risk ratio [RR] = 1.94; 95% CI, 1.86-2.01), followed by schizoaffective BD (RR = 1.37; 95% CI, 1.22-1.54), bipolar I disorder subtype (RR = 1.30; 95% CI, 1.24-1.36), and bipolar II disorder subtype (RR = 1.04; 95% CI, 0.97-1.11). Within BD cases, there was an effect gradient, indexed by the nature of psychosis. Prominent mood-incongruent psychotic features had the strongest association (RR = 1.46; 95% CI, 1.36-1.57), followed by mood-congruent psychosis (RR = 1.24; 95% CI, 1.17-1.33) and BD with no history of psychosis (RR = 1.09; 95% CI, 1.04-1.15). Conclusions and Relevance For the first time to date, a study shows a polygenic-risk gradient across schizophrenia and BD, indexed by the occurrence and level of mood-incongruent psychotic symptoms.
The effect of a lifestyle intervention on metabolic health in young women

With the increasing obesity rates in Western countries, an effective lifestyle intervention for fat reduction and metabolic benefits is needed. High-intensity intermittent exercise (HIIE), Mediterranean eating habits (Mediet), and fish oil (ω-3) consumption positively impact metabolic health and adiposity, although the combined effect has yet to be determined. A 12-week lifestyle intervention on adiposity, insulin resistance, and interleukin-6 (IL-6) levels of young overweight women was administered. Thirty women with a body mass index of 26.6±0.5 kg/m2, blood pressure of 114/66±1.9/1.5 mmHg, and age of 22±0.8 years were randomly assigned to either an intervention group receiving Mediet advice, daily ω-3 supplementation, and HIIE 3 days/week for 12 weeks or a control group. The group receiving Mediet advice, daily ω-3 supplementation, and HIIE experienced a significant reduction in total body fat mass (P<0.001), abdominal adiposity (P<0.05), waist circumference (P<0.001), systolic blood pressure (P<0.05), fasting plasma insulin (P<0.05), IL-6 (P<0.001), and triglycerides (P<0.05). The greatest decreases in fasting plasma insulin (P<0.05) and IL-6 (P<0.001) occurred by week 6 of the intervention. Significant improvements in eating habits (P<0.05) and aerobic fitness (P<0.001) were also found following the intervention. A multifaceted 12-week lifestyle program comprising a Mediet, ω-3 supplementation, and HIIE induced significant improvements in fat loss, aerobic fitness, and insulin and IL-6 levels, positively influencing metabolic health.
Dental Blogs, Podcasts, and Associated Social Media: Descriptive Mapping and Analysis

Background Studies of social media in both medicine and dentistry have largely focused on the value of social media for marketing to and communicating with patients and for clinical education. There is limited evidence of how dental clinicians contribute to and use social media to disseminate and access information relevant to clinical care. Objective The purpose of this study was to inventory and assess the entry, growth, sources, and content of clinically relevant social media in dentistry. Methods We developed an inventory of blogs, podcasts, videos, and associated social media disseminating clinical information to dentists. We assessed hosts’ media activity in terms of their combinations of modalities, entry and exit dates, frequency of posting, types of content posted, and size of audience. Results Our study showed that clinically relevant information is posted by dentists and hygienists on social media. Clinically relevant information was provided in 89 blogs and podcasts, and topic analysis showed motives for blogging by host type: 55% (49 hosts) were practicing dentists or hygienists, followed by consultants (27 hosts, 30%), media including publishers and discussion board hosts (8 hosts, 9%), and professional organizations and corporations. Conclusions We demonstrated the participation of and potential for practicing dentists and hygienists to use social media to share clinical and other information with practicing colleagues. There is a clear audience for these social media sites, suggesting a changing mode of information diffusion in dentistry. This study was a first effort to fill the gap in understanding the nature and potential role of social media in clinical dentistry.
Merging Prototyping with Agile Software Development Methodology

Agile software development is a vast and rising discipline in field of software engineering that has gain importance in software industry. Due to flexibility of agile development, it is adopted by various organizations to develop software projects and is also a research area for software engineers. This paper introduces the concept of merging prototyping with agile software development methodology. The paper introduces a concept to reuse components from agile development by developing prototyping that could be reused. Hence, the available components would be reused instead of developing a component from scratch.
Dual Delivery of NGF and bFGF Coacervater Ameliorates Diabetic Peripheral Neuropathy via Inhibiting Schwann Cells Apoptosis

Diabetic neuropathy is a kind of insidious complications that impairs neural and vascular function and ultimately leads to somatic and visceral denervation. Basic fibroblast growth factor (bFGF) and nerve growth factor (NGF) are important neurotrophic factors for stimulating angiogenesis and improving peripheral nerve function. Administrating a single factor has good therapeutic effect on diabetic peripheral neuropathy (DPN). However, the short half-life and rapid diffusion of growth factors under physiological conditions limits its clinical applications. Here, we used a biodegradable coacervate, composed of heparin and polycation, to dominate the combined release of bFGF and NGF in a steady fashion. We found this combined growth factors (GFs) coacervate, administered as a single injection, improved motor and sensory functions, restored morphometric structure and decreased apoptosis of Schwann cells in a rat model of prolonged DPN. Similarly the GFs coacervate, as compared with free bFGF and NGF combination, markedly reduced the apoptosis level of a rat Schwann cell line, RSC 96 cells in vitro. We also demonstrated that neuroprotective effects of the GFs coacervate in both rat DPN model and hyperglycemia-induced RSC 96 cell model is likely due to suppression of endocytoplasmic reticulum stress (ERS).
Critical reanalysis of the methods that discriminate the activity of CDK2 from CDK1

ABSTRACT Cyclin dependent kinases 1 and 2 (CDK1 and CDK2) play crucial roles in regulating cell cycle progression from G1 to S, through S, and G2 to M phase. Both inhibition and aberrant activation of CDK1/2 can be detrimental to cancer cell growth. However, the tools routinely employed to discriminate between the activities of these 2 kinases do not have the selectivity commonly attributed to them. Activation of these kinases is often assayed as a decrease of the inhibitory tyrosine-15 phosphorylation, yet the antibodies used cannot discriminate between phosphorylated CDK1 and CDK2. Inhibitors of these kinases, while partially selective against purified kinases, may lack selectivity when applied to intact cells. High levels of cyclin E are often considered a marker of increased CDK2 activity, yet active CDK2 targets cyclin E for degradation, hence high levels usually reflect inactive CDK2. Finally, inhibition of CDK2 does not arrest cells in S phase suggesting CDK2 is not required for S phase progression. Furthermore, activation of CDK2 in S phase can rapidly induce DNA double-strand breaks in some cell lines. The misunderstandings associated with the use of these tools has led to misinterpretation of results. In this review, we highlight these challenges in the field.
SD3: a trust management system with certified evaluation

We introduce SD3, a trust management system consisting of a high-level policy language, a local policy evaluation, and a certificate retrieval system. A unique feature of SD3 is its certified evaluator. As the evaluator computes the answer to a query, it also computes a proof that the answer follows from the security policy. Before the answer is returned, the proof is passed through a simple checker and incorrect proofs are reported as errors. The certified evaluator reduces the trusted computing base and greatly increases our confidence that the answers produced by the evaluator follow from the specification, despite complex optimizations. To illustrate SD3's capabilities, we show how to implement a secure name service, similar to DNSSEC, entirely in SD3.
Transplantation of allogenic nucleus pulposus cells attenuates intervertebral disc degeneration by inhibiting apoptosis and increasing migration

Transplantation of nucleus pulposus cells (NPCs) into the intervertebral disc (IVD) has been demonstrated to be an effective treatment of degenerative disc disease (DDD). However, the underlying mechanisms have remained to be sufficiently elucidated. The aim of the present study was to explore the potential cell migration and anti-apoptosis efficacy of NPCs in the treatment of DDD. NPCs cultured from rats expressing green fluorescent protein (GFP-NPCs) were transplanted into the degenerated IVD, and the migration of GFP-NPCs, as well as the degeneration and apoptosis of the IVD were detected to evaluate the therapeutic effect in vivo. In vitro, disc chondrocytes (DCs) and annulus fibrosus cells (AFCs) were co-cultured to explore the underlying mechanism. The results demonstrated that injection of NPCs suppressed DDD by inhibiting apoptosis and increasing extracellular matrix in vivo and in vitro. NPCs migrated into the inner AF in vivo, and NPC migration was observed to be promoted by AFCs and DCs in vitro, particularly by damaged AFCs. These results demonstrated the anti-apoptotic effects and migratory capacity of allogenic NPCs transplanted into the IVD, which evidences the contribution of NPCs to disc regeneration and provide a novel strategy for treating DDD.
Characterization of Carbon Nanostructures Based on Transmission Line Model.

In the past two decades carbon nanotubes and graphene have attracted a lot of research attention due to their exceptional electronic properties. The research focus on improving the synthesising techniques will eventually lead to their applications in terahertz wave, millimetre wave and microwave frequencies. In this thesis, a modelling technique based on the transmission line theory is proposed to calculate the 2-port S-parameters of vertically aligned CNT arrays with finite sizes and arbitrary cross sections. The process takes into account all the coupling in the array and gives the analytical solution of S-parameters. The simulation results from the proposed technique are compared with results obtained by effective single conductor model and shows a good matching for small arrays and an increasing difference with the increase of array sizes. From the S-parameters, the fundamental properties of CNT arrays such as input impedance and absorption are obtained and compared with measurement results in microwave frequencies. The dependence of these properties on ambient temperature and host medium are also presented to explore the tunability of CNT arrays. From the Fabry-Perot the wave propagating velocity is also calculated for arrays with different sizes and fitted with a power function. The S-parameters allows the extraction of the complex permittivity, permeability and conductivity of the CNT array. The extracted permittivity and absorption are compared with measurement results. The graphene nanoribbons are simulated in the same manner. The graphene sheet on top of a microstrip gap is simulated using transmission line model at microwave frequencies to show the impact of parasitics and contact resistances. Finally, a graphene based microwave absorber is proposed and modelled under both electric and magnetic bias. The absorber shows good broadband absorption rate and a potential for turning transparent and opaque to microwaves under both electric and magnetic bias.
Challenging Cytokine Redundancy: Inflammatory Cell Movement and Clinical Course of Experimental Autoimmune Encephalomyelitis Are Normal in Lymphotoxin-deficient, but Not Tumor Necrosis Factor–deficient, Mice

Lymphotoxin (LT) is widely regarded as a proinflammatory cytokine with activities equivalent to tumor necrosis factor (TNF). The contribution of LT to experimental autoimmune encephalomyelitis (EAE) was examined using TNF/LTα−/− mice, TNF−/− mice, and a new LTα−/− line described here. All mice were generated directly in the C57BL/6 strain and used for the preparation of radiation bone marrow chimeras to reconstitute peripheral lymphoid organs and restore immunocompetence. This approach overcame the problems related to the lack of lymph nodes that results from LTα gene targeting. We show here that when LT is absent but TNF is present, EAE progresses normally. In contrast, when TNF is absent but LT is present, EAE is delayed in onset and inflammatory leukocytes fail to move normally into the central nervous system parenchyma, even at the peak of disease. In the absence of both cytokines, the clinical and histological picture is identical to that seen when TNF alone is deficient, including demyelination. Furthermore, the therapeutic inhibition of TNF and LTα with soluble TNF receptor in unmanipulated wild-type or TNF−/− mice exactly reproduces these outcomes. We conclude from these studies that TNF and LT are functionally distinct cytokines in vivo, and despite sharing common receptors, show no redundancy of function nor mutual compensation.
Budgetary Policy and Unemployment Dynamics in an OLG Model with Collective Bargaining

We consider a dynamic general equilibrium model with capital accumulation and collective wage bargaining and investigate how unemployment responds to structural shocks under two stylised budgetary policies. Under balanced budgets, tax adjustments lead to higher unemployment on impact but enable a quick recovery of employment. By contrast, unbalanced budgets mitigate unemployment effects on impact but dynamics are more persistent due to weaker capital accumulation and future fiscal consolidations. These results are consistent with empirical evidence on a positive cross-country relationship between government borrowing and unemployment persistence. This paper starts out from the well-known fact that many European countries have suffered from persistently high unemployment over the past two decades. There is a large literature which attempts to explain this development as resulting from a combination of structural shocks and mechanisms which make the effects of any such shifts more persistent. One prominent branch of this literature stresses that adverse structural shocks tend to induce a slowdown in capital accumulation which reinforces the employment losses and adds to unemployment persistence (Bean, 1989; Benassy, 1997; Blanchard, 1997; Burda, 1988; Caballero and Hammour, 1998; Daveri and Tabellini, 2000). Similarly, these studies point out that, when the shock is over, the recovery of employment depends critically on the speed with which investments in capital respond to the new situation. The purpose of this paper is to reconsider this ‘capital-shortage hypothesis’ by linking it explicitly to the stance of fiscal policy. To see the importance of fiscal policy in this context, consider a government which faces an adverse structural shock (such as a drop in employment due to a wage-setting shock) and decides whether it should keep its budget balanced or not. This decision will affect the overall structure of assets in the economy (i.e. the mix between capital and government bonds), and this mix will in turn be an important determinant of the speed with which the economy can create employment once the shock is over. In particular, according to the capital-shortage hypothesis, the recovery in terms of employment is likely to take longer under a policy which temporarily accepts structural budget deficits, particularly when crowding out effects have been substantial.