Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of lithium and cancer risk in patients with bipolar disorder: population-based cohort study

Background Lithium inhibits glycogen synthase kinase-3, which is an enzyme involved in the pathogenesis of cancer. Aims To investigate the association between lithium and cancer risk in patients with bipolar disorder. Method A retrospective cohort study was designed using the National Health Insurance Research Database (NHIRD) in Taiwan. Patients using lithium comprised the index drug group and patients using anticonvulsants only comprised the control group. Time-dependent Cox regression was used to evaluate the hazard ratios (HRs) for risk of cancer. Results Compared with anticonvulsant-only exposure, lithium exposure was associated with significantly lower cancer risk (HR = 0.735, 95% CI 0.554–0.974). The hazard ratios for the first, second and third tertiles of the cumulative defined daily dose were 0.762 (95% CI 0.516–1.125), 0.919 (95% CI 0.640–1.318) and 0.552 (95% CI 0.367–0.831), respectively. Conclusions Lithium is associated with reduced overall cancer risk in patients with bipolar disorder. A dose–response relationship for cancer risk reduction was observed.
Family History of Cancer and Risk of Biliary Tract Cancers: Results from the Biliary Tract Cancers Pooling Project

Background: Although some familial cancer syndromes include biliary tract cancers (BTCs; cancers of the gallbladder, intrahepatic and extrahepatic bile ducts, and ampulla of Vater), the few studies that have examined the relationships between family history of cancer (FHC) and BTCs have reported inconclusive findings. The objective of this study was to investigate the associations of FHC with risk of BTC in the Biliary Tract Cancers Pooling Project (BiTCaPP). Methods: We used Cox proportional hazards regressions models to estimate HRs and 95% confidence intervals for associations between FHC (any, first-degree, in female relative, in male relative, relative with gastrointestinal cancer, and relative with hormonally related cancer) and BTC risk by anatomic site within the biliary tract, adjusting for sex and race/ethnicity. Sensitivity analyses were conducted that restricted to studies reporting cholecystectomy data and to people without a history of cholecystectomy. Results: Data on FHC were available from 12 prospective studies within BiTCaPP, which collectively contributed 2,246 cases (729 gallbladder, 345 intrahepatic and 615 extrahepatic bile duct, and 385 ampulla of Vater cancers) with 21,706,107 person-years of follow-up. A marginal, inverse association between FHC and gallbladder cancer was driven to the null when analysis was restricted to studies reporting cholecystectomy data and to people without a history of cholecystectomy. FHC was not associated with risk of BTC at the other anatomic sites. Conclusions: These findings do not support an association between FHC and BTCs. Impact: In a study of 1.5 million people, FHC is not a risk factor for BTCs. Cancer Epidemiol Biomarkers Prev; 27(3); 348–51. ©2018 AACR.
Influence of the Vaginal Microbiota on Toxic Shock Syndrome Toxin 1 Production by Staphylococcus aureus

ABSTRACT Menstrual toxic shock syndrome (TSS) is a serious illness that afflicts women of premenopausal age worldwide and arises from vaginal infection by Staphylococcus aureus and concurrent production of toxic shock syndrome toxin-1 (TSST-1). Studies have illustrated the capacity of lactobacilli to reduce S. aureus virulence, including the capacity to suppress TSST-1. We hypothesized that an aberrant microbiota characteristic of pathogenic bacteria would induce the increased production of TSST-1 and that this might represent a risk factor for the development of TSS. A S. aureus TSST-1 reporter strain was grown in the presence of vaginal swab contents collected from women with a clinically healthy vaginal status, women with an intermediate status, and those diagnosed with bacterial vaginosis (BV). Bacterial supernatant challenge assays were also performed to test the effects of aerobic vaginitis (AV)-associated pathogens toward TSST-1 production. While clinical samples from healthy and BV women suppressed toxin production, in vitro studies demonstrated that Streptococcus agalactiae and Enterococcus spp. significantly induced TSST-1 production, while some Lactobacillus spp. suppressed it. The findings suggest that women colonized by S. aureus and with AV, but not BV, may be more susceptible to menstrual TSS and would most benefit from prophylactic treatment.
Divide, Denoise, and Defend against Adversarial Attacks

Deep neural networks, although shown to be a successful class of machine learning algorithms, are known to be extremely unstable to adversarial perturbations. Improving the robustness of neural networks against these attacks is important, especially for security-critical applications. To defend against such attacks, we propose dividing the input image into multiple patches, denoising each patch independently, and reconstructing the image, without losing significant image content. This proposed defense mechanism is non-differentiable which makes it non-trivial for an adversary to apply gradient-based attacks. Moreover, we do not fine-tune the network with adversarial examples, making it more robust against unknown attacks. We present a thorough analysis of the tradeoff between accuracy and robustness against adversarial attacks. We evaluate our method under black-box, grey-box, and white-box settings. The proposed method outperforms the state-of-the-art by a significant margin on the ImageNet dataset under grey-box attacks while maintaining good accuracy on clean images. We also establish a strong baseline for a novel white-box attack.
Effects of lipopolysaccharide on maturation of bovine oocyte in vitro and its possible mechanisms

Lipopolysaccharide disturbs the secretion of gonadotropin, endometrial function and implantation efficiency. However, there is little information regarding the effects of lipopolysaccharide on cyclic ovary activity, especially oocyte maturation. Therefore, we aimed to investigate the effects of lipopolysaccharide on the maturation potential of bovine oocytes. We found that lipopolysaccharide exposure significantly decreased the first polar body extrusion rate and delayed the cell cycle progression. The abnormal spindle rate was significantly increased in lipopolysaccharide treatment group, accompanied by disrupted localization and level of phosphorylated mitogen-activated protein kinase (p-MAPK). Moreover, lipopolysaccharide treatment significantly increased intracellular reactive oxygen species (ROS) levels and the early apoptotic rate in oocytes. The pro-apoptotic caspase-3 and Bax mRNA levels and caspase-3 protein level were significantly increased, whereas the anti-apoptotic Bcl-2 and XIAP transcript abundance were significantly decreased in lipopolysaccharide exposure group. Furthermore, the dimethyl-histone H3 lysine 4 (H3K4me2) level was significantly increased, while the DNA methylation (5-mC) and dimethyl-histone H3 lysine 9 (H3K9me2) levels were markedly decreased in oocytes treated with lipopolysaccharide. In conclusion, lipopolysaccharide exposure inhibits the maturation potential of bovine oocytes by affecting cell cycle, cytoskeletal dynamics, oxidative stress, and epigenetic modifications.
ProPPA

Formal languages like process algebras have been shown to be effective tools in modelling a wide range of dynamic systems, providing a high-level description that is readily transformed into an executable model. However, their application is sometimes hampered because the quantitative details of many real-world systems of interest are not fully known. In contrast, in machine learning, there has been work to develop probabilistic programming languages, which provide system descriptions that incorporate uncertainty and leverage advanced statistical techniques to infer unknown parameters from observed data. Unfortunately, current probabilistic programming languages are typically too low-level to be suitable for complex modelling. In this article, we present a Probabilistic Programming Process Algebra (ProPPA), the first instance of the probabilistic programming paradigm being applied to a high-level, formal language, and its supporting tool suite. We explain the semantics of the language in terms of a quantitative generalisation of Constraint Markov Chains and describe the implementation of the language, discussing in some detail the different inference algorithms available and their domain of applicability. We conclude by illustrating the use of the language on simple but non-trivial case studies: here, ProPPA is shown to combine the elegance and simplicity of high-level formal modelling languages with an effective way of incorporating data, making it a promising tool for modelling studies.
A Theoretical and Empirical Linkage between Road Accidents and Binge Eating Behaviors in Adolescence

This study aimed at identifying specific clusters of maladaptive emotional–behavioral symptoms in adolescent victims of motorbike collisions considering their scores on alexithymia and impulsivity in addition to examining the prevalence of clinical binge eating behaviors (respectively through the Youth Self-Report (YSR), Toronto Alexithymia Scale-20 (TAS-20), Barratt Impulsiveness Scale-11 (BIS-11), and Binge Eating Scale (BES)). Emotional–behavioral profiles, difficulties in identifying and describing feelings, impulsivity, and binge eating behaviors have been assessed in 159 adolescents addressing emergency departments following motorbike collisions. Our results showed a cluster of adolescents with clinical binge eating behaviors, high rates of motorbike accidents, and high levels of internalizing and externalizing problems, alexithymia, and impulsivity (23.3% of the sample); a second cluster of adolescents with clinical binge eating behaviors, a moderate number of collisions, and moderate levels of emotional and behavioral problems on the above four dimensions (25.8% of the sample); and a third cluster of youth without clinical binge eating behaviors, with a moderate number of accidents, and with low scores on the four dimensions (50.9% of the sample). Adolescents of Cluster 1 showed a higher likelihood to be involved in motorbike collisions than the youth in Clusters 2 and 3 (p < 0.0001). We suggest that adolescents’ motor collisions could be associated with their difficulties in emotion regulation and with their impaired psychological profiles, which could also underpin their disordered eating. The identification of specific clusters of psychopathological symptoms among this population could be useful for the construction of prevention and intervention programs aimed at reducing motor collision recidivism and alleviating co-occurring psychopathologies.
CMDR based differential evolution identifies the epistatic interaction in genome‐wide association studies

Motivation: Detecting epistatic interactions in genome‐wide association studies (GWAS) is a computational challenge. Such huge numbers of single‐nucleotide polymorphism (SNP) combinations limit the some of the powerful algorithms to be applied to detect the potential epistasis in large‐scale SNP datasets. Approach: We propose a new algorithm which combines the differential evolution (DE) algorithm with a classification based multifactor‐dimensionality reduction (CMDR), termed DECMDR. DECMDR uses the CMDR as a fitness measure to evaluate values of solutions in DE process for scanning the potential statistical epistasis in GWAS. Results: The results indicated that DECMDR outperforms the existing algorithms in terms of detection success rate by the large simulation and real data obtained from the Wellcome Trust Case Control Consortium. For running time comparison, DECMDR can efficient to apply the CMDR to detect the significant association between cases and controls amongst all possible SNP combinations in GWAS. Availability and Implementation: DECMDR is freely available at https://goo.gl/p9sLuJ. Contact: chuang@isu.edu. tw or e0955767257@yahoo.com. tw Supplementary information: Supplementary data are available at Bioinformatics online.
Does early-onset chronic or recurrent major depression impact outcomes with antidepressant medications? A CO-MED Trial Report

Background Prior studies have suggested that major depressive disorder (MDD) with pre-adult onset represents a distinct subtype with greater symptom severity and higher rates of suicidal ideation. Whether these patients have poorer response to various types of antidepressant treatment than those with adult-onset MDD is unclear. Method A total of 665 psychiatric and primary care out-patients (aged 18–75 years) with non-psychotic chronic or recurrent MDD participated in a single-blind, randomized trial that compared the efficacy of escitalopram plus placebo, bupropion sustained-release plus escitalopram, or venlafaxine extended-release plus mirtazapine. We compared participants who self-reported MDD onset (before age 18) to those with a later onset (adult onset) with respect to baseline characteristics and treatment/outcome variables at 12 and 28 weeks. Results Early-onset chronic/recurrent MDD was associated with a distinct set of sociodemographic (female, younger age) and clinical correlates (longer duration of illness, greater number of prior episodes, greater likelihood of atypical features, higher rates of suicidality and psychiatric co-morbidity, fewer medical problems, poorer quality of life, greater history of child abuse/neglect). However, results from unadjusted and adjusted analyses showed no significant differences in response, remission, tolerability of medications, quality of life, or retention at 12 or 28 weeks. Conclusions Although early-onset chronic/recurrent MDD is associated with a more severe clinical picture, it does not seem to be useful for predicting differential treatment response to antidepressant medication. Clinicians should remain alert to an increased risk of suicidality in this population.
Efficient content-based retrieval of motion capture data

The reuse of human motion capture data to create new, realistic motions by applying morphing and blending techniques has become an important issue in computer animation. This requires the identification and extraction of logically related motions scattered within some data set. Such content-based retrieval of motion capture data, which is the topic of this paper, constitutes a difficult and time-consuming problem due to significant spatio-temporal variations between logically related motions. In our approach, we introduce various kinds of qualitative features describing geometric relations between specified body points of a pose and show how these features induce a time segmentation of motion capture data streams. By incorporating spatio-temporal invariance into the geometric features and adaptive segments, we are able to adopt efficient indexing methods allowing for flexible and efficient content-based retrieval and browsing in huge motion capture databases. Furthermore, we obtain an efficient preprocessing method substantially accelerating the cost-intensive classical dynamic time warping techniques for the time alignment of logically similar motion data streams. We present experimental results on a test data set of more than one million frames, corresponding to 180 minutes of motion. The linearity of our indexing algorithms guarantees the scalability of our results to much larger data sets.
Personality Traits Below Facets: The Consensual Validity, Longitudinal Stability, Heritability, and Utility of Personality Nuances

It has been argued that facets do not represent the bottom of the personality hierarchy—even more specific personality characteristics, nuances, could be useful for describing and understanding individuals and their differences. Combining 2 samples of German twins, we assessed the consensual validity (correlations across different observers), rank-order stability, and heritability of nuances. Personality nuances were operationalized as the 240 items of the Revised NEO Personality Inventory (NEO-PI-R). Their attributes were examined by analyzing item residuals, controlling for the variance of the facet the item had been assigned to and all other facets. Most nuances demonstrated significant (p < .0002) cross-method agreement and rank-order stability. A substantial proportion of them (48% in self-reports, 20% in informant ratings, and 50% in combined ratings) demonstrated a significant (p < .0002) component of additive genetic variance, whereas evidence for environmental influences shared by twins was modest. Applying a procedure to estimate stability and heritability of true scores of item residuals yielded estimates comparable with those of higher-order personality traits, with median estimates of rank-order stability and heritability being . 77 and . 52, respectively. Few nuances demonstrated robust associations with age and gender, but many showed incremental, conceptually meaningful, and replicable (across methods and/or samples) predictive validity for a range of interest domains and body mass index. We argue that these narrow personality characteristics constitute a valid level of the personality hierarchy. They may be especially useful for providing a deep and contextualized description of the individual, but also for the prediction of specific outcomes.
Effectiveness of timed and non-timed second appointments in improving uptake in breast cancer screening

Objectives To estimate the effect on breast screening uptake of delayed, targeted, second timed appointments in women who did not take up an initial breast cancer screening appointment offer. Methods Non-attending women received a four-month delayed second timed appointment following non-response to the initial invitation and the normal open invitation sent to non-attenders. A comparison group was sent a four-month delayed additional open invitation. Results Response to the second timed appointments (percentage of re-invited women eventually attending in this episode) was 20%, corresponding to an estimated increase on total uptake of 6%. Response was highest in women who had previously attended screens. Response in the women offered an additional delayed open invitation was 7.5%, corresponding to an estimated 2.3% increase in overall uptake. Conclusions Second timed appointments were almost three times as effective as additional open invitation. They should be targeted at women most likely to attend. A randomized study of second timed appointments versus open invitations should be conducted.
Immunogenicity and Protective Efficacy of a Fusion Protein Tuberculosis Vaccine Combining Five Esx Family Proteins

One strategy to develop the next generation of tuberculosis vaccines is to construct subunit vaccines based on T cell antigens. In this study, we have evaluated the vaccine potential of a fusion protein combining EsxB, EsxD, EsxG, EsxU, and EsxM of Mycobacterium tuberculosis (M. tb). This recombinant protein, named BM, was expressed in and purified from Escherichia coli. Immunization of C57BL/6 mice with purified BM protein formulated in Freund's incomplete adjuvant induced the production of Th1 cytokines (IFN-γ, TNF, and IL-2) and multifunctional CD4+ T cells. Vaccination of BALB/c mice with BM protein followed by intravenous challenge with Mycobacterium bovis BCG resulted in better levels of protection than the two leading antigens, Ag85A and PPE18. Taken together, these results indicate that BM is a protective antigen. Future studies to combine BM with other antigens and evaluate its effectiveness as a booster of BCG or as a therapeutic vaccine are warranted.
Building Efficient ConvNets using Redundant Feature Pruning

This paper presents an efficient technique to prune deep and/or wide convolutional neural network models by eliminating redundant features (or filters). Previous studies have shown that over-sized deep neural network models tend to produce a lot of redundant features that are either shifted version of one another or are very similar and show little or no variations; thus resulting in filtering redundancy. We propose to prune these redundant features along with their connecting feature maps according to their differentiation and based on their relative cosine distances in the feature space, thus yielding smaller network size with reduced inference costs and competitive performance. We empirically show on select models and CIFAR-10 dataset that inference costs can be reduced by 40% for VGG-16, 27% for ResNet-56, and 39% for ResNet-110.
Development of a New Mold Oscillation Mode for High-speed Continuous Casting of Steel Slabs

High-speed continuous casting is a prerequisite for the successful operation of hot direct rolling (HDR). However, as casting speed increases, breakout caused by solidified shell sticking tends to occur. It is therefore necessary to reduce the frictional force between the mold and the solidified shell in order to prevent shell sticking in high-speed casting.The lubrication mechanism in the mold was analyzed, and the results led to the establishment of a new modl oscillation mode which reduces frictional force. This offers an oscillation movement where the time of upward motion of the mold is longer than that of downward motion in a single oscillating cycle. The effect of this new mode on the reduction of the frictional force was ascertained by casting tests using an experimental continuous caster.On the basis of fundamental studies the new mold oscillation mode has been utilized in the No. 5 slab caster at NKK Fukuyama Works. Plant tests confirmed that the new mode is more effective in reducing frictional force than the sinusoidal mode. A high-speed casting of 3.0 m/min has been successfully achieved with this new mold oscillation mode. No difference in the surface quality of slabs could be observed between casting with the sinusoidal mold oscillation and this new mode.
Immunopathology and Infectious Diseases Endogenous Galectin-1 and Acute Inflammation Emerging Notion of a Galectin-9 Pro-Resolving Effect

The role of endogenous galectin-1 (Gal-1) in acute inflammation has been poorly investigated. We therefore performed the carrageenan-induced paw edema model in wild-type and Gal-1 / mice. On subplantar injection of carrageenan, Gal-1 / mice displayed a similar first phase of edema (<24 hours) to wild-type mice; however, a much less pronounced second phase (48 to 96 hours) was evident in this genotype. This reduced inflammation was associated with lower paw expression of inflammatory genes and cell infiltrates. Analysis of galectin protein and mRNA expression revealed high expression of Gal-1 in wild-type paws during resolution (>48 hours), with some expression of galectin-9 (Gal-9). Administration of stable Gal-1 to wild-type mice completely ablated the first phase of edema but was ineffective when administered therapeutically at the 24-hour time point. Conversely, Gal-9 administration did not alter the first phase of edema but significantly reduced the second phase when administered therapeutically. This suggests anti-inflammatory actions for both proteins in this model albeit at different phases of the inflammatory response. Collectively, these data indicate that the absence of endogenous Gal-1 results in an abrogated response during the second phase of the edema reaction. (Am J Pathol 2011, 178:1201–1209; DOI: 10.1016/j.ajpath.2010.11.073)