Miracle-dz/UniFAR-FTUs huggingface dataset:
Quartz Crystal Microbalance With Dissipation Monitoring: A Versatile Tool to Monitor Phase Transitions in Biomimetic Membranes

Solid-supported lipid membranes are popular models that connect biological and artificial materials used in bio-technological applications. Controlling the lipid organization and the related functions of these model systems entails understanding and characterizing their phase behavior. Quartz crystal microbalance with dissipation (QCM-D) is an acoustic-based surface-sensitive technique which is widely used in bio-interfacial science of solid-supported lipid membranes. Its sensitivity to mass and energy dissipation changes at the solid-lipid layer-liquid interface allows the detection of phase transformations of solid-supported membrane geometries. In this perspective, we highlight this valuable feature and its related methodology, review current advances and briefly discuss future perspectives. Furthermore, a specific example on the ability of QCM D to detect lipid organization changes of cholesterol containing solid-supported lipid vesicle layers (SVLs) upon the addition of aspirin is also provided
Individual participant data meta‐analysis of continuous outcomes: A comparison of approaches for specifying and estimating one‐stage models

One‐stage individual participant data meta‐analysis models should account for within‐trial clustering, but it is currently debated how to do this. For continuous outcomes modeled using a linear regression framework, two competing approaches are a stratified intercept or a random intercept. The stratified approach involves estimating a separate intercept term for each trial, whereas the random intercept approach assumes that trial intercepts are drawn from a normal distribution. Here, through an extensive simulation study for continuous outcomes, we evaluate the impact of using the stratified and random intercept approaches on statistical properties of the summary treatment effect estimate. Further aims are to compare (i) competing estimation options for the one‐stage models, including maximum likelihood and restricted maximum likelihood, and (ii) competing options for deriving confidence intervals (CI) for the summary treatment effect, including the standard normal‐based 95% CI, and more conservative approaches of Kenward‐Roger and Satterthwaite, which inflate CIs to account for uncertainty in variance estimates. The findings reveal that, for an individual participant data meta‐analysis of randomized trials with a 1:1 treatment:control allocation ratio and heterogeneity in the treatment effect, (i) bias and coverage of the summary treatment effect estimate are very similar when using stratified or random intercept models with restricted maximum likelihood, and thus either approach could be taken in practice, (ii) CIs are generally best derived using either a Kenward‐Roger or Satterthwaite correction, although occasionally overly conservative, and (iii) if maximum likelihood is required, a random intercept performs better than a stratified intercept model. An illustrative example is provided.
Effect of optic disc–fovea distance on the normative classifications of macular inner retinal layers as assessed with OCT in healthy subjects

Purpose To determine the influence of the optic disc–fovea distance (DFD) on the normative classifications based on thickness measurements of macular inner retinal layers with spectral-domain optical coherence tomography (OCT) in healthy subjects. Methods A total of 182 eyes from 182 healthy subjects were included (mean (SD) spherical equivalent −0.8 (1.9) dioptres). We performed macula and optic disc imaging with the Topcon 3D OCT 2000. The thickness of the macular inner retinal layers (macular retinal nerve fibre layer (mRNFL), ganglion cell-inner plexiform layer (GCIPL) and both combined (ganglion cell complex; GCC)) and the corresponding classifications based on the built-in normative database were recorded. The occurrence of an abnormal normative classification (occurrence of any thickness variable below the fifth percentile) was related to the DFD and other factors (axial length/refraction, optic disc area, fovea–disc angle, age, gender, image quality, visual field mean deviation and peripapillary retinal nerve fibre layer thickness), using logistic regression. Results The mean (SD) DFD was 4.90 (0.29) mm. A greater DFD was associated with a higher percentage of abnormal normative classification in the OCT parameters describing the thickness of the mRNFL (OR (95%CI) per 0.1 mm increase in DFD: 1.30 (1.13 to 1.50), p<0.001), GCIPL (1.18 (1.02 to 1.38), p=0.023) and GCC measurement (1.29 (1.08 to 1.55), p=0.006). Conclusions Eyes with a greater DFD are prone to false-positive classifications in the thickness assessment of the macular inner retinal layers. The thicknesses should always be interpreted in the context of DFD.
Hierarchical Block Sparse Neural Networks

Sparse deep neural networks(DNNs) are efficient in both memory and compute when compared to dense DNNs. But due to irregularity in computation of sparse DNNs, their efficiencies are much lower than that of dense DNNs on regular parallel hardware such as TPU. This inefficiency leads to poor/no performance benefits for sparse DNNs. Performance issue for sparse DNNs can be alleviated by bringing structure to the sparsity and leveraging it for improving runtime efficiency. But such structural constraints often lead to suboptimal accuracies. In this work, we jointly address both accuracy and performance of sparse DNNs using our proposed class of sparse neural networks called HBsNN (Hierarchical Block sparse Neural Networks). For a given sparsity, HBsNN models achieve better runtime performance than unstructured sparse models and better accuracy than highly structured sparse models.
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes

Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics (SMD) to assess the strength of protein-peptide interactions. The idea behind using SMD simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity. However, mechanical stability defined as a peak in force-extension profile depends on the choice of the pulling direction. Here we propose an uncommon choice of the pulling direction along resultant dipole moment (RDM) vector, which has not been explored in SMD simulations so far. Using explicit solvent all-atom MD simulations, we apply SMD technique to probe mechanical resistance of ligand-receptor system pulled along two different vectors. A novel pulling direction—when ligand unbinds along the RDM vector—results in stronger forces compared to commonly used ligand unbinding along center of masses vector. Our observation that RDM is one of the factors influencing the mechanical stability of protein-peptide complex can be used to improve the ranking of binding affinities by using mechanical stability as an effective scoring function.
Neutrophilic Asthma Is Associated with Increased Airway Bacterial Burden and Disordered Community Composition

Neutrophilic asthma (NA) is an important asthma inflammatory phenotype associated with disease severity, airflow limitation, and steroid resistance, and its mechanism is still uncertain. Evidences suggest a potential role for bacteria in its pathogenesis, but, so far, this remains poorly understood. We sought to investigate airway bacterial burden, community composition, and inflammatory response in NA. Fifty-four stable asthmatics without infection were enrolled and separated into either NA group (n = 20) or non-NA group (n = 34). Subject demographics, Asthma Control Test (ACT) scores, medications, and pulmonary functions were documented. Sputum cytology, airway bacterial burden, microbial community composition, and inflammatory cytokines were assessed. The total airway bacterial burden was significantly increased in subjects with NA versus non-NA and was positively correlated with the sputum neutrophil percentage. Airway neutrophilia was associated with less airway bacterial community richness and diversity, along with a distinct community composition. In patients with NA, bacteria in phylum Proteobacteria, especially Haemophilus spp. and Moraxella spp. , showed significant increases in both actual loads and relative abundances, while bacteria in phyla Firmicutes, Actinobacteria, and Saccharibacteria showed decreased relative abundances compared with non-NA. Patients with NA demonstrated higher levels of interleukin-1β (IL-1β), IL-6, IL-8, IL-12, IL-17A, and tumor necrosis factor-α (TNF-α) in sputum samples compared with non-NA. Increased bacterial burden and distinct microbiota composition were the key characters of neutrophilic phenotype in asthma, accompanied by excessive airway inflammation. Understanding the relationship between airway microbiota and neutrophilic inflammation may help in treatment and management of asthma, such as targeting airway microbiota.
Lingke: a Fine-grained Multi-turn Chatbot for Customer Service

Traditional chatbots usually need a mass of human dialogue data, especially when using supervised machine learning method. Though they can easily deal with single-turn question answering, for multi-turn the performance is usually unsatisfactory. In this paper, we present Lingke, an information retrieval augmented chatbot which is able to answer questions based on given product introduction document and deal with multi-turn conversations. We will introduce a fine-grained pipeline processing to distill responses based on unstructured documents, and attentive sequential context-response matching for multi-turn conversations.
Cancer and suicidal ideation and behaviours: protocol for a systematic review and meta-analysis

Introduction Prevalence of suicidal ideation (SI) and behaviours are higher among patients with cancer than general population. No systematic review/meta-analysis investigated this topic; therefore, our aim will be to assess the relationship between cancer and SI and behaviours. Methods We will search PubMed/MEDLINE, EMBASE, SCOPUS, Web of Science, PsycINFO and Cochrane Library databases from their inception until 30 June 2018. Case–control and cohort studies focused on the association between cancer (any type) and suicidal outcomes (suicide, suicide attempt and SI) will be included. Two team members will independently: (A) perform the selection of the included studies and data extraction, with the supervision of a third member in case of discrepancies and (B) assess each study with: (1) Newcastle-Ottawa Scale (NOS); (2) Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement; (3) Grading of Recommendations Assessment, Development and Evaluation (GRADE). We will conduct a random-effects meta-analysis. Individual and pooled ORs and associated 95% CIs will be calculated as well as between-study heterogeneity. We will examine the potential for publication bias. If possible, we will explore reasons for potential between-study heterogeneity. Ethics and dissemination This study does not require ethical approval. The study will be submitted to a peer-reviewed journal, will be publicly disseminated and will be the topic of research presentations. PROSPERO registration number CRD42017072482.
Coeliac disease

ABSTRACT Coeliac disease (CD) develops in genetically susceptible individuals who, in response to unclear environmental triggers, develop an immune response triggered by gluten ingestion. It is now recognised as a global disease affecting about 0.7% of the world’s population. The clinical presentation ranges from malabsorption to asymptomatic individuals diagnosed by screening high-risk groups. Diagnosis requires the demonstration of small intestinal villous atrophy in the presence of circulating coeliac auto-antibodies and/or an unequivocal response to a gluten-free diet (GFD). Recent guidelines suggest that, in a subset of children, duodenal biopsies can be avoided in the presence of strict symptomatic and serological criteria. While the majority of patients respond to a GFD, up to 20% of patients with CD have persistent or recurrent symptoms. There are several aetiologies for residual or new symptoms in a patient with CD on a GFD, with inadvertent exposure to gluten being the most common. Following a GFD can be challenging for patients with CD and understanding the barriers/challenges faced by patients in maintaining a GFD is crucial for compliance. Abbreviations: AGA: anti-gliadin antibodies; Anti-DGP-ab: anti-deamidated gliadin peptide antibodies; Anti-tTG-ab: anti-tissue transglutaminase antibodies; ATD: auto-immune thyroid disorders; BMD: bone mineral density; CD: coeliac disease; DH: dermatitis herpetiformis; EMA: anti-endomysial antibodies; FDR: first-degree relatives; GFD: gluten-free diet; HbA1c: haemoglobin A1c; HLA: human leucocyte antigen; IBS: irritable bowel syndrome; LMIC: low- and middle-income countries; NPV: negative predictive value; NRCD: non-responsive coeliac disease; POCT: point-of-care tests; SDR: second-degree relatives; SIBO: small intestinal bacterial overgrowth; T1DM: type 1 diabetes mellitus; ULN: upper limit of normal.
Transfer RNA function and evolution

Department of Biochemistry, The University of Western Ontario, London, ON, Canada; Department of Chemistry, The University of Western Ontario, London, ON, Canada; Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Chemistry, Yale University, New Haven, CT, USA
Multi-stage SVM approach for cardiac arrhythmias detection in short single-lead ECG recorded by a wearable device

Objective: Use of wearable ECG devices for arrhythmia screening is limited due to poor signal quality, small number of leads and short records, leading to incorrect recognition of pathological events. This paper introduces a novel approach to classification (normal/‘N’, atrial fibrillation/‘A’, other/‘O’, and noisy/‘P’) of short single-lead ECGs recorded by wearable devices. Approach: Various rhythm and morphology features are derived from the separate beats (‘local’ features) as well as the entire ECGs (‘global’ features) to represent short-term events and general trends respectively. Various types of atrial and ventricular activity, heart beats and, finally, ECG records are then recognised by a multi-level approach combining a support vector machine (SVM), decision tree and threshold-based rules. Main results: The proposed features are suitable for the recognition of ‘A’. The method is robust due to the noise estimation involved. A combination of radial and linear SVMs ensures both high predictive performance and effective generalisation. Cost-sensitive learning, genetic algorithm feature selection and thresholding improve overall performance. The generalisation ability and reliability of this approach are high, as verified by cross-validation on a training set and by blind testing, with only a slight decrease of overall F1-measure, from 0.84 on training to 0.81 on the tested dataset. ‘O’ recognition seems to be the most difficult (test F1-measures: 0.90/‘N’, 0.81/‘A’ and 0.72/‘O’) due to high inter-patient variability and similarity with ‘N’. Significance: These study results contribute to multidisciplinary areas, focusing on creation of robust and reliable cardiac monitoring systems in order to improve diagnosis, reduce unnecessary time-consuming expert ECG scoring and, consequently, ensure timely and effective treatment.
Trajectories of body fatness from age 5 to 60 y and plasma biomarker concentrations of the insulin-insulin-like growth factor system.

Background A major pathway through which obesity increases the risk of cardiometabolic diseases and cancer is by inducing hormonal and metabolic abnormalities, including hyperinsulinemia and altered insulin-like growth factor (IGF) signaling. However, little is known about the influence of lifetime adiposity on the relevant biomarkers. Objective The aim of this study was to examine associations of trajectories of body fatness with plasma biomarker concentrations of the insulin-IGF system in 2 large prospective cohorts of US men and women. Design Associations between trajectories of body fatness and concentrations of plasma C-peptide, IGF-I, IGF-binding protein (IGFBP) 1, IGFBP-3, and the IGF-I-to-IGFBP-3 molar ratio was examined in 9386 women of the Nurses' Health Study and 3941 men of the Health Professionals Follow-Up Study. Group-based trajectory modeling was used to create trajectory groups on the basis of self-reported somatotype data at ages 5, 10, 20, 30, and 40 y and body mass index (BMI) at ages 45, 50, 55, and 60 y. We used multivariate linear regression models to examine the associations of trajectories with biomarker concentrations. Results Five trajectories of body fatness were identified: "lean-stable," "lean-moderate increase," "lean-marked increase," "medium-stable/increase," and "medium-marked increase. " Compared with the lean-stable group, the lean-marked increase and medium-marked increase groups had significantly higher concentrations of C-peptide (percentage difference-women: 44% and 73%; men: 27% and 51%) and lower concentrations of IGFBP-1 (women: -61% and -78%; men: -47% and -65%). Adjustment for current BMI attenuated the association to null for the medium-marked increase group, but the lean-marked increase group still had modestly higher concentrations of C-peptide (women: 10%; men: 6%) and lower concentrations of IGFBP-1 (women: -18%; men: -21%) than the lean-stable group. Conclusions Adiposity across the life span was associated with higher C-peptide and lower IGFBP-1 concentrations in adulthood. The associations were largely driven by attained adiposity and, to a lesser extent, weight gain in early-middle adulthood. This trial was registered at www.clinicaltrials. gov as NCT03419455.
Changing Employers’ Implicit Attitudes About the Competence of People Who Are Blind

Introduction: Long-held societal beliefs about the incompetence and dependence of people who are blind are thought to contribute to their low employment rates. This experimental study examined the impact of a meeting between a vocational rehabilitation (VR) professional and a hiring manager on these beliefs, or implicit attitudes, about the competence of people who are blind. Method: Participants were 57 hiring managers working for a financial services company in the southern United States who participated in a one-hour meeting with a VR professional. Two VR professionals, one sighted and one blind, conducted the meetings, utilizing one of two approaches, resulting in a 4 (group) × 3 (time) experimental design. Implicit attitudes were measured with the Implicit Association Test-Blind & Visually Impaired (IAT-BVI) at pre-test, post-test, and a 4-month follow-up and data were analyzed using repeated-measures ANOVA. Results: IAT-BVI scores decreased significantly following the meeting, though the size of the change was small. Type of approach and the interaction between approach and the VR professional’s vision status were not significantly associated with IAT-BVI change. Although vision status was not significantly associated with IAT-BVI change, follow-up analyses documented that participants who met with the blind VR professional had a significant decrease in IAT-BVI scores. Discussion: Hiring managers’ implicit attitudes significantly improved following a meeting with a VR professional, providing evidence that a brief interaction can decrease employers’ implicit bias regarding the competence of blind people. In addition, hiring managers who met with the blind VR professional showed significant improvement in their implicit attitudes after the meeting, with a medium-to-large effect. Implications for Practice: VR professionals should communicate with employers as much as possible about the work capabilities of individuals who are blind to help improve their implicit attitudes, and be aware that incorporating exposure to a competent blind person may result in a greater impact.
Rumination, Brooding, and Reflection: Prospective Associations with Suicide Ideation and Suicide Attempts.

OBJECTIVE Rumination is often cited as a risk factor for suicide, yet few studies of rumination have utilized clinical samples, and no studies have examined its prospective association with suicide attempts. The purpose of this study was to examine concurrent and prospective associations of brooding and reflection (the two components of rumination) with suicide ideation and suicide attempts among a high-risk clinical sample. METHOD Participants were 286 adolescents and young adults (77% Caucasian, 59% female) aged 13-25 seeking psychiatric emergency services. A majority (71%) were presenting with a primary complaint of suicide ideation or recent suicide attempt. Participants completed a baseline assessment at the index visit; 226 participants (79%) completed a 4-month follow-up assessment of suicidal thoughts and behaviors. RESULTS Brooding was associated with lifetime history of one or more suicide attempts, but not concurrent suicide ideation. Reflection was not associated with lifetime suicide attempts or concurrent suicide ideation. Furthermore, prospective associations of brooding and reflection with suicide ideation and suicide attempts were weak-to-small in magnitude and statistically nonsignificant. CONCLUSIONS Rumination appears to have a limited association with suicide-related outcomes within a high-risk clinical sample. Additional longitudinal studies utilizing clinical samples are critically needed to better understand these associations.
Development of a western blot method for detection of fish ectoparasite Argulus siamensis antigens

ABSTRACT A study was undertaken to develop a western blot method for detection of immunogenic proteins of fish ectoparasite, Argulus siamensis for its further use as potential vaccine candidates. Argulus antigens were prepared by homogenization and injected to rohu (Labeo rohita) juveniles for development of immune serum. The serum was used to immunostain the antigens in western blot. The other reagents added in sequence were rabbit anti-rohu serum, goat anti-rabbit ALP conjugate and substrate (BCIP-NBT). However, similar banding patterns were observed with both control and immunized rohu serum. Hence, a possible cross-reaction was suspected and verified in number of western blot experiments. A typical cross-reaction observed was of rabbit serum reacting directly with Argulus antigens. Hence, the rabbit anti-rohu serum was replaced with guinea pig anti-rohu serum. Another cross-reaction of goat anti-guinea pig ALP conjugate with rohu serum was eliminated by using goat anti-rabbit ALP conjugate with guinea pig serum. Thus, the final western blot method consisting of Argulus antigens → rohu serum → guinea pig anti-rohu serum → goat anti-rabbit ALP conjugate → substrate, yielded distinguishing results between control and Argulus-immunized rohu serum samples. The developed test has tremendous downstream applications, particularly in immunoproteomic studies of Argulus antigens.