Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic susceptibility of eight nonsynonymous polymorphisms in HLA-DRB1 gene to hepatocellular carcinoma in Han Chinese

Backgrounds and Objective Mounting evidence suggests that human leukocyte antigen (HLA) plays a central role in anti-virus and tumor defense. To test whether genetic variation in HLA-DRB1 gene, a key component of HLA system, can predict its predisposition to hepatocellular carcinoma (HCC), we thereby conducted an association study by genotyping 8 nonsynonymous polymorphisms in HLA-DRB1 gene among 257 HCC patients and 264 controls. Results All polymorphisms respected the Hardy-Weinberg equilibrium. The genotypes and alleles of rs17879599 differed significantly between patients and controls after Bonferroni correction (both P < 0.001), and the power to detect this significance was 94.4%. After adjusting for age, gender, smoking, drinking and hepatitis infection, the mutant allele of rs17879702 was significantly associated with an increased risk for HCC under additive (odds ratio [OR] = 2.12, 95% confidence interval [CI]: 1.20-4.02, P = 0.004) and dominant (OR = 2.51, 95% CI: 1.39–2.96, P = 0.004) models. Haplotype analysis indicated that haplotype A-T-C-T-G-C-T-A (alleles ordered by rs199514452, rs201540428, rs201614260, rs17879702, rs17880292, rs17879599, rs17424145 and rs35445101) was overrepresented in patients and enhanced predisposition to HCC (adjusted OR = 2.72, 95% CI: 1.24–5.78, P = 0.004). In cumulative analysis, carriers of 7–9 unfavorable alleles had a 2.41-fold (95% CI: 1.18–4.92, P = 0.016) increased risk for HCC after adjusting for confounding factors relative to those possessing 4 or less unfavorable alleles. Materials and Methods Genotypes were determined by ligase detection reaction. HCC patients were newly diagnosed, histopathologically confirmed or previously untreated and controls were cancer-free. Conclusions Our findings suggest an independent leading contribution of rs17879599 in the 2nd exon of HLA-DRB1 gene to HCC risk in Han Chinese.
Costate-focused models for reinforcement learning.

Many recent algorithms for reinforcement learning are model-free and founded on the Bellman equation. Here we present a method founded on the costate equation and models of the state dynamics. We use the costate -- the gradient of cost with respect to state -- to improve the policy and also to "focus" the model, training it to detect and mimic those features of the environment that are most relevant to its task. We show that this method can handle difficult time-optimal control problems, driving deterministic or stochastic mechanical systems quickly to a target. On these tasks it works well compared to deep deterministic policy gradient, a recent Bellman method. And because it creates a model, the costate method can also learn from mental practice.
Microstructure and Compressive Strength of Magnesium-Zinc Alloy Reinforced with Different Percentage of Bio-Glass Content

The objective of this work is to fabricate composite Mg-Zn filled with 45S5 bio-glass (5, 10, and 15 wt. %) via powder metallurgy. The microstructure of the sintered composite was investigated using optical microscope and scanning electron microscope. The densities of the composites were also evaluated. The densities of the compacts are increasing with increasing bio-glass content. Compression test was done by the Instron machine. The result showed that bio-glass was dispersed in the Mg-Zn matrix. Compressive strength was decreased as the amount of bio-glass increased. However, the results are still comparable to natural bone, which is important to reduce the stress shielding effect.
A Review of Shaft Voltages and Bearing Currents in EV and HEV Motors

In most mechanical and electrical systems, reliability is paramount. Consumers, users and operators trust that their product will perform properly over its expected lifetime. Electric Vehicles (EVs) and Hybrid-Electric Vehicles (HEVs) are no exception to this statement. One of the most important components to consider when determining the reliability of EVs and HEVs is the electric motor. Within electric motors, many things can cause reduced reliability. This paper will focus on the most important component: the bearings. In this review paper, a general summary of bearing failure methods is provided along with an in-depth analysis of all facets relating to the shaft voltage and bearing current phenomenon with specific discussion relating to EV and HEV motors. Subsequently, this paper will provide a review of several mitigation techniques to render the bearing current failure mode obsolete.
Mimicry Attacks Against Wireless Link Signature and New Defense Using Time-Synched Link Signature

Wireless link signature is a physical layer authentication mechanism, using the multipath effect between a transmitter and a receiver to provide authentication of wireless signals. This paper identifies a new attack, called mimicry attack, against the existing wireless link signature schemes. An attacker can forge a legitimate transmitter's link signature as long as it knows the legitimate signal at the receiver's location, and the attacker does not have to be at exactly the same location as the legitimate transmitter. We also extend the mimicry attack to multiple-input multiple-output (MIMO) systems, and conclude that the mimicry attack is feasible only when the number of attacker' antennas is equal to or larger than that of the receiver's antennas. To defend against the mimicry attack, this paper proposes a novel construction for wireless link signature, called time-synched link signature, by integrating cryptographic protection and time factor into wireless physical layer features. Experimental results confirm that the mimicry attack is a real threat and the newly proposed time-synched link signatures are effective in physical layer authentication.
NL2Bash: A Corpus and Semantic Parser for Natural Language Interface to the Linux Operating System

We present new data and semantic parsing methods for the problem of mapping English sentences to Bash commands (NL2Bash). Our long-term goal is to enable any user to perform operations such as file manipulation, search, and application-specific scripting by simply stating their goals in English. We take a first step in this domain, by providing a new dataset of challenging but commonly used Bash commands and expert-written English descriptions, along with baseline methods to establish performance levels on this task.
A model‐based solution for observational errors in laboratory studies

Molecular techniques for detecting microorganisms, macroorganisms and infectious agents are susceptible to false‐negative and false‐positive errors. If left unaddressed, these observational errors may yield misleading inference concerning occurrence, prevalence, sensitivity, specificity and covariate relationships. Occupancy models are widely used to account for false‐negative errors and more recently have even been used to address false‐positive errors, too. Current modelling options assume false‐positive errors only occur in truly negative samples, an assumption that yields biased inference concerning detection because a positive sample could be classified as such not because the target agent was successfully detected, but rather due to a false‐positive test result. We present an extension to the occupancy modelling framework that allows false‐positive errors in both negative and positive samples, thereby providing unbiased inference concerning occurrence and detection, as well as reliable conclusions about the efficacy of sampling designs, handling protocols and diagnostic tests. We apply the model to simulated data, showing that it recovers known parameters and outperforms other approaches that are commonly used when confronted with observation errors. We then apply the model to an experimental data set on Batrachochytrium dendrobatidis, a pathogenic fungus that is implicated in the global decline or extinction of hundreds of amphibian species. The model‐based approach we present is not only useful for obtaining reliable inference when data are contaminated with observational errors, but also eliminates the need for establishing arbitrary thresholds or decision rules that have hidden and unintended consequences.
Validation of the Center for Epidemiological Studies Depression Scale among Korean Adolescents

Objective The Center for Epidemiological Studies Depression Scale (CES-D) is designed to measure the current level of depressive symptomatology in the general population. However, no review has examined whether the scale is reliable and valid among children and adolescents in Korea. The purpose of this study was to test whether the Korean form of the CES-D is valid in adolescents. Methods Data were obtained from 1,884 adolescents attending grades 1–3 in Korean middle schools. Reliability was evaluated by internal consistency (Cronbach’s alpha). Concurrent validity was evaluated by a correlation analysis between the CES-D and other scales. Construct validity was evaluated by exploratory factor and confirmatory factor analyses. Results The internal consistency coefficient for the entire group was 0.88. The CES-D was positively correlated with scales that measure negative psychological constructs, such as the State Anxiety Inventory for Children, the Korean Social Anxiety Scale for Children and Adolescents, and the Reynold Suicidal Ideation Questionnaire, but it was negatively correlated with scales that measure positive psychological constructs, such as the Korean version of the Rosenberg Self-Esteem Scale and the Connor-Davidson Resilience Scale-2. The CES-D was examined by three-dimensional exploratory factor analysis, and the three-factor structure of the scale explained 53.165% of the total variance. The variance explained by factor I was 24.836%, that explained by factor II was 15.988%, and that explained by factor III was 12.341%. The construct validity of the CES-D was tested by confirmatory factor analysis, and we applied the entire group’s data using a three-factor hierarchical model. The fit index showed a level similar to those of other countries’ adolescent samples. Conclusion The CES-D has high internal consistency and addresses psychological constructs similar to those addressed by other scales. The CES-D showed a three-factor structure in an exploratory factor analysis. The present findings suggest that the CES-D is a useful and reliable tool for measuring depression in Korean adolescents.
Structural performance of pretensioned member with Ultra High Strength Fiber Reinforced Concrete

The authors have developed a kind of Ultra High Strength Fiber Reinforced Concrete (UFC) with high compressive strength and high tensile ductility and have been studying for practical use. UFC makes it possible to reduce the weight of prestressed concrete structures. Particularly in case that UFC is applied to pretensioned members, high bond strength can also be expected to reduce the transfer length. Autogenous shrinkage and creep in early age of UFC, however, reduces effective prestress. In this study, its basic mechanical properties concerning effective prestress such as shrinkage and creep in early age were investigated to get design values for the material. Prestressing tests were also conducted to determine transfer length and effective stress. Furthermore, flexural and shear tests using beam members were conducted and it was revealed that flexural and shear capacity could be estimated using the formula shown in “Recommendations for Design and Construction of Ultra High Strength Fiber Reinforced Concrete Structures, -Draft” by Japan Society of Civil Engineers.
Effect of surface treatment on the morphology of sisal fibers in sisal/polylactic acid composites

Sisal fibers were pretreated by alkali and alkylation, and then mixed with polylactic acid to make sisal fiber-reinforced polylactic acid composites, respectively. The architecture and aspect ratio of sisal fibers before and after mixing, the micro-morphology of fracture surface, and the properties of composites were investigated. The results showed that surface treatment greatly impacted the fiber fracture behavior. Shearing fracture occurred to the untreated sisal fibers and alkali-treated sisal fibers, which led to a sharp reduction in the length of the fiber, while the shear-tear facture occurred to the alkylation-treated sisal fibers and resulted in obvious decrease in both length and diameter of alkylation-treated sisal fibers. The fiber aspect ratio of sisal fibers was affected first by the pretreatment method, then by the processing temperature, and the sisal fiber content. Furthermore, the mechanical properties of reinforcing fibers and sisal fiber-reinforced polylactic acid composites were influenced fundamentally by the pretreatment method.
Fuzzy information granules in time series data

It is often desirable to summarize a set of time series through typical shapes in order to analyze them. The algorithm presented here compares pieces of different time series in order to find similar shapes. The use of a fuzzy clustering technique based on fuzzy c-means allows us to consider such subsets belonging to typical shapes with a degree of membership. Additionally, this matching is invariant with respect to a scaling of the time series. The algorithm is demonstrated on a widely known set of data taken from the ECG rhythm analysis experiments performed at MIT laboratories.
Risk factors for positive margins after wide local excision of cutaneous squamous cell carcinoma

Abstract Background and objectives: The standard treatment for cutaneous squamous cell carcinoma (cSCC) is wide local excision (WLE). Incomplete tumor excision is associated with increased recurrence rates and mortality risk. Risk factors for positive margins after WLE of cSCC has been examined in only a few studies. We sought to assess the influence of several clinicopathological factors on margin status in the largest cSCC population to date. Methods: We performed a retrospective review of records at two skin cancer clinics identifying patients with biopsy-proven cSCC who underwent WLE. We mined clinicopathological information for eligible subjects including age, gender, lesion location, immunosuppression, previous treatment, lesion size, biopsy type, tumor subtype, tumor thickness, degree of differentiation, ulceration and perineural invasion. Results: A total of 1468 patients were eligible and 117 (8%) had positive margins after WLE. Older age at diagnosis (p = .011), lesion location on the head and neck (p < .001), previous treatment (p < .001), increased lesion diameter (p < .001), invasive subtype (p = .020) or increased tumor thickness (p < .001) were statistically significant risk factors for positive surgical margins. Conclusions: Our results present an opportunity to stratify cSCC patients into low- or high-risk for incomplete tumor clearance after WLE based on several clinicopathological factors. These findings should educate and inform the dermatologic surgeon’s choice of primary management of cSCC.
Bootstrapping domain-specific meta-languages in language workbenches

It is common practice to bootstrap compilers of programming languages. By using the compiled language to implement the compiler, compiler developers can code in their own high-level language and gain a large-scale test case. In this paper, we investigate bootstrapping of compiler-compilers as they occur in language workbenches. Language workbenches support the development of compilers through the application of multiple collaborating domain-specific meta-languages for defining a language's syntax, analysis, code generation, and editor support. We analyze the bootstrapping problem of language workbenches in detail, propose a method for sound bootstrapping based on fixpoint compilation, and show how to conduct breaking meta-language changes in a bootstrapped language workbench. We have applied sound bootstrapping to the Spoofax language workbench and report on our experience.
Genome-wide association studies in women of African ancestry identified 3q26.21 as a novel susceptibility locus for oestrogen receptor negative breast cancer.

Multiple breast cancer loci have been identified in previous genome-wide association studies, but they were mainly conducted in populations of European ancestry. Women of African ancestry are more likely to have young-onset and oestrogen receptor (ER) negative breast cancer for reasons that are unknown and understudied. To identify genetic risk factors for breast cancer in women of African descent, we conducted a meta-analysis of two genome-wide association studies of breast cancer; one study consists of 1,657 cases and 2,029 controls genotyped with Illumina’s HumanOmni2.5 BeadChip and the other study included 3,016 cases and 2,745 controls genotyped using Illumina Human1M-Duo BeadChip. The top 18,376 single nucleotide polymorphisms (SNP) from the meta-analysis were replicated in the third study that consists of 1,984 African Americans cases and 2,939 controls. We found that SNP rs13074711, 26.5 Kb upstream of TNFSF10 at 3q26.21, was significantly associated with risk of oestrogen receptor (ER)-negative breast cancer (odds ratio [OR]=1.29, 95% CI: 1.18-1.40; P = 1.8 × 10 − 8). Functional annotations suggest that the TNFSF10 gene may be involved in breast cancer aetiology, but further functional experiments are needed. In addition, we confirmed SNP rs10069690 was the best indicator for ER-negative breast cancer at 5p15.33 (OR = 1.30; P = 2.4 × 10 − 10) and identified rs12998806 as the best indicator for ER-positive breast cancer at 2q35 (OR = 1.34; P = 2.2 × 10 − 8) for women of African ancestry. These findings demonstrated additional susceptibility alleles for breast cancer can be revealed in diverse populations and have important public health implications in building race/ethnicity-specific risk prediction model for breast cancer.
FGFR2 mutations in bent bone dysplasia syndrome activate nucleolar stress and perturb cell fate determination

Fibroblast Growth Factor (FGF) signaling promotes self-renewal in progenitor cells by encouraging proliferation and inhibiting cellular senescence. Yet, these beneficial effects can be hijacked by disease-causing mutations in FGF receptor (FGFR) during embryogenesis. By studying dominant FGFR2 mutations that are germline in bent bone dysplasia syndrome (BBDS), we reveal a mechanistic connection between FGFR2, ribosome biogenesis, and cellular stress that links cell fate determination to disease pathology. We previously showed that FGFR2 mutations in BBDS, which amplify nucleolar targeting of FGFR2, activate ribosomal DNA (rDNA) transcription and delay differentiation in osteoprogenitor cells and patient-derived bone. Here we find that the BBDS mutations augment the ability of FGFR2 to recruit histone-remodeling factors that epigenetically activate transcriptionally silent rDNA. Nucleolar morphology is controlled by chromatin structure, and the high levels of euchromatic rDNA induced by the BBDS mutations direct nucleolar disorganization, alter ribosome biogenesis, and activate the Rpl11-Mdm2-p53 nucleolar stress response pathway. Inhibition of p53 in cells expressing the FGFR2 mutations in BBDS rescues delayed osteoblast differentiation, suggesting that p53 activation is an essential pathogenic factor in, and potential therapeutic target for, BBDS. This work establishes rDNA as developmentally regulated loci that receive direct input from FGF signaling to balance self-renewal and cell fate determination.
Luminescence and Scintillation Response of Ce3+-Doped Oxide Glasses with High Gd2O3 Content

This report presents the luminescence and scintillation response of Ce3+-doped oxide glasses with high Gd2O3 (30 mol%) content. The characteristic emission of Ce3+ 5d → 4f transition peaking around 380 nm was observed in its luminescence spectra under UV and X-ray excitation. Photoluminescence decay kinetics was governed by a few tens of nanoseconds decay time. The integral scintillation efficiency of about 22% of that of the Bi4Ge3O12 scintillator was obtained under X-ray irradiation. The light yield and its dependence on the integration time were measured and compared with that of the Bi4Ge3O12 crystal. The total mass attenuation coefficient at 662 keV γ-rays was also determined and compared with the theoretical one calculated using the WinXCom program.
Accurate Imputation-Based Screening of Gln368Ter Myocilin Variant in Primary Open-Angle Glaucoma.

PURPOSE Myocilin (MYOC) is a well-established primary open-angle glaucoma (POAG) risk gene, with rare variants known to have high penetrance. The most common clinically relevant risk variant, Gln368Ter, has an allele frequency of 0.1% to 0.3% in populations of European ancestry. Detection of rare MYOC variants has traditionally been conducted using Sanger sequencing. Here we report the use of genotyping arrays and imputation to assess whether rare variants including Gln368Ter can be reliably detected. METHODS A total of 1155 cases with advanced POAG and 1992 unscreened controls genotyped on common variant arrays participated in this study. Accuracy of imputation of Gln368Ter variants was compared with direct sequencing. A genome-wide association study was performed using additive model adjusted for sex and the first six principal components. RESULTS We found that although the arrays we used were designed to tag common variants, we could reliably impute the Gln368Ter variant (rs74315329). When tested in 1155 POAG cases and 1992 controls, rs74315329 was strongly associated with risk (odds ratio = 15.53, P = 1.07 × 10-9). All POAG samples underwent full sequencing of the MYOC gene, and we found a sensitivity of 100%, specificity of 99.91%, positive predictive value of 95.65%, and negative predictive value of 100% between imputation and sequencing. Gln368Ter was also accurately imputed in a further set of 1801 individuals without POAG. Among the total set of 3793 (1992 + 1801) individuals without POAG, six were predicted (probability > 95%) to carry the risk variant. CONCLUSIONS We demonstrate that some clinically important rare variants can be reliably detected using arrays and imputation. These results have important implications for the detection of clinically relevant incidental findings in ongoing and future studies using arrays.
Large Scale Environmental Sound Classification Based on Efficient Feature Extraction

In recent years, plenty of studies endeavor to analyze the life auditory scenarios via mining non-speech sounds. Conventional audio recognition schemes clearly bound the feature extraction and recognition stages, such as in speech recognition. However, such separation leads to inconsistency in the purposes at each stage. The recognition stage contributes to portray the global data distribution focusing on "relationship" between signal samples. However, such consideration can hardly be embedded into feature extraction process which centered on the local structure, thus, the prominent "relation" information is destroyed. In this paper, we propose a unified acoustic recognition framework taking advantage of primitive feature input without injuring discriminant information and adopting effective classification scheme accordingly. We formulate the sound into subspace representation and initially adopt Grassmannian distance to classify the subspace-indexed non-speech sounds. To validate the proposed framework, we conducted experiments using RWCP Sound Scene Database. The experimental results demonstrated the proposed framework achieved fine recognition performance with high efficiency.