Miracle-dz/UniFAR-FTUs huggingface dataset:
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment

Abstract The Tumor Immune Single Cell Hub 2 (TISCH2) is a resource of single-cell RNA-seq (scRNA-seq) data from human and mouse tumors, which enables comprehensive characterization of gene expression in the tumor microenvironment (TME) across multiple cancer types. As an increasing number of datasets are generated in the public domain, in this update, TISCH2 has included 190 tumor scRNA-seq datasets covering 6 million cells in 50 cancer types, with 110 newly collected datasets and almost tripling the number of cells compared with the previous release. Furthermore, TISCH2 includes several new functions that allow users to better utilize the large-scale scRNA-seq datasets. First, in the Dataset module, TISCH2 provides the cell–cell communication results in each dataset, facilitating the analyses of interacted cell types and the discovery of significant ligand–receptor pairs between cell types. TISCH2 also includes the transcription factor analyses for each dataset and visualization of the top enriched transcription factors of each cell type. Second, in the Gene module, TISCH2 adds functions for identifying correlated genes and providing survival information for the input genes. In summary, TISCH2 is a user-friendly, up-to-date and well-maintained data resource for gene expression analyses in the TME. TISCH2 is freely available at http://tisch.comp-genomics.org/.
Utilizing the TractSeg Tool for Automatic Corticospinal Tract Segmentation in Patients With Brain Pathology

Purpose: White-matter tract segmentation in patients with brain pathology can guide surgical planning and can be used for tissue integrity assessment. Recently, TractSeg was proposed for automatic tract segmentation in healthy subjects. The aim of this study was to assess the use of TractSeg for corticospinal-tract (CST) segmentation in a large cohort of patients with brain pathology and to evaluate its consistency in repeated measurements. Methods: A total of 649 diffusion-tensor-imaging scans were included, of them: 625 patients and 24 scans from 12 healthy controls (scanned twice for consistency assessment). Manual CST labeling was performed in all cases, and by 2 raters for the healthy subjects. Segmentation results were evaluated based on the Dice score. In order to evaluate consistency in repeated measurements, volume, Fractional Anisotropy (FA), and Mean Diffusivity (MD) values were extracted and correlated for the manual versus automatic methods. Results: For the automatic CST segmentation Dice scores of 0.63 and 0.64 for the training and testing datasets were obtained. Higher consistency between measurements was detected for the automatic segmentation, with between measurements correlations of volume = 0.92/0.65, MD = 0.94/0.75 for the automatic versus manual segmentation. Conclusions: The TractSeg method enables automatic CST segmentation in patients with brain pathology. Superior measurements consistency was detected for the automatic in comparison to manual fiber segmentation, which indicates an advantage when using this method for clinical and longitudinal studies.
Genome-Wide Association Studies Identify an Association of Transferrin Binding Protein B Variation and Invasive Serogroup Y Meningococcal Disease in Older Adults

Abstract Background Neisseria meningitidis serogroup Y, especially ST-23 clonal complex (Y:cc23), represents a larger proportion of invasive meningococcal disease (IMD) in older adults compared to younger individuals. This study explored the meningococcal genetic variation underlying this association. Methods Maximum-likelihood phylogenies and the pangenome were analyzed using whole-genome sequence (WGS) data from 200 Y:cc23 isolates in the Neisseria PubMLST database. Genome-wide association studies (GWAS) were performed on WGS data from 250 Y:cc23 isolates from individuals with IMD aged ≥65 years versus < 65 years. Results Y:cc23 meningococcal variants did not cluster by age group or disease phenotype in phylogenetic analyses. Pangenome comparisons found no differences in presence or absence of genes in IMD isolates from the different age groups. GWAS identified differences in nucleotide polymorphisms within the transferrin-binding protein B (tbpB) gene in isolates from individuals ≥65 years of age. TbpB structure modelling suggests these may impact binding of human transferrin. Conclusions These data suggest differential iron scavenging capacity amongst Y:cc23 meningococci isolated from older compared to younger patients. Iron acquisition is essential for many bacterial pathogens including the meningococcus. These polymorphisms may facilitate colonization, thereby increasing the risk of disease in vulnerable older people with altered nasopharyngeal microbiomes and nutritional status.
The effects of hormonal contraceptive use on sleep in women: A systematic review and meta‐analysis

Hormonal contraceptives are some of the most widely used medications worldwide, but studies on their effects on sleep are contradictory, with some reporting a sleep‐promoting effect, while others a sleep‐inhibiting effect. Our objective was, therefore, to undertake a systematic review and meta‐analysis of the literature on this subject to try to clarify their effects. A search was conducted in three databases (PubMed, Scopus and Web of Science). Only studies evaluating hormonal contraception use were considered eligible, and both objective and subjective sleep‐related outcomes were considered. Individual effect size was calculated for each article, and meta‐analyses were performed using a DerSimonian and Laird random effects method. The initial search identified 2076 articles, of which 13 met the criteria for the study after full text evaluation. A total of 33 meta‐analyses were performed, three of them related to subjective measures and 30 considering data from polysomnography. The only statistically significant result between contraceptive users and non‐contraceptive users was observed in respect of wake after sleep onset, which was 7 min shorter among contraceptive users (−7.12 [−12.80; −1.44]; I2 = 65%; p = 0.01). In conclusion, hormonal contraceptives are not associated with clinically relevant changes in sleep patterns in women.
Efficacy of a Digital Personalized Elimination Diet for the Self-Management of Irritable Bowel Syndrome and Comorbid Irritable Bowel Syndrome and Inflammatory Bowel Disease

INTRODUCTION: Most patients with irritable bowel syndrome (IBS) and dual-diagnosis IBS and inflammatory bowel disease (IBD) report that symptoms originate from or are exacerbated by trigger foods. Despite patient interest and need, there is no consensus on what diet is optimal. Popular diets have notable limitations including cost, length, implementation complexity, and lack of personalization. METHODS: This pilot study evaluated the feasibility, desirability, and effect on gastrointestinal symptoms of a digitally delivered personalized elimination diet for patients with IBS and comorbid IBS/IBD, powered by machine learning. Participants were recruited online and were provided access to a digital personalized nutrition tool for 9 weeks (N = 37; IBS only = 16, Crohn's disease and IBS = 9, and ulcerative colitis and IBS = 12). RESULTS: Significant symptom improvement was seen for 81% of participants at study midpoint and persisted for 70% at end point, measured by the relevant symptom severity score (IBS symptom severity score, Patient Simple Clinical Colitis Activity Index, or Mobile Health Index for Crohn's disease). Clinically significant symptom improvement was observed in 78% of participants at midpoint and 62% at end point. Twenty-five participants (67.6%) achieved total symptomatic resolution by the end of study. Patient-reported quality of life improved for 89% of participants. Ninety-five percentage daily engagement, 95% retention, 89% adherence and 92% satisfaction with the program were reported. DISCUSSION: Dietary elimination can improve symptoms and quality of life in patients with IBS and comorbid IBS/IBD. Digital technology can personalize dietary interventions and improve adherence. Randomized controlled trials are warranted.
Photometric Redshift Calibration Requirements for WFIRST Weak-lensing Cosmology: Predictions from CANDELS

In order for the Wide-Field Infrared Survey Telescope (WFIRST) and other stage IV dark energy experiments (e.g., Large Synoptic Survey Telescope, LSST; and Euclid) to infer cosmological parameters not limited by systematic errors, accurate redshift measurements are needed. This accuracy can be met by using spectroscopic subsamples to calibrate the photometric redshifts for the full sample. In this work, we find the minimal number of spectra required for the WFIRST weak-lensing redshift calibration by employing the Self-Organizing Map (SOM) spectroscopic sampling technique. We use galaxies from the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) to build the LSST+WFIRST lensing analog sample of ∼36,000 objects and to train the LSST+WFIRST SOM. We find that 26% of the WFIRST lensing sample consists of sources fainter than the Euclid depth in the optical, 91% of which live in color cells already occupied by brighter galaxies. We demonstrate the similarity between faint and bright galaxies as well as the feasibility of redshift measurements at different brightness levels. Our results suggest that the spectroscopic sample acquired for calibration to the Euclid depth is sufficient for calibrating the majority of the WFIRST color space. For the spectroscopic sample to fully represent the synthetic color space of WFIRST, we recommend obtaining additional spectroscopy of ∼0.2–1.2k new sources in cells occupied by mostly faint galaxies. We argue that either the small area of the CANDELS fields and the small overall sample size or the large photometric errors might be the reason for no/fewer bright galaxies mapped to these cells. Acquiring the spectra of these sources will confirm the above findings and will enable the comprehensive calibration of the WFIRST color–redshift relation.
RISE FOR HEALTH: Rationale and protocol for a prospective cohort study of bladder health in women

The spectrum of bladder health and the factors that promote bladder health and prevent lower urinary tract symptoms (LUTS) among women are not well understood. This manuscript describes the rationale, aims, study design, sampling strategy, and data collection for the RISE FOR HEALTH (RISE) study, a novel study of bladder health in women conducted by the Prevention of Lower Urinary Tract Symptom (PLUS) Research Consortium.
A Novel Clustering Algorithm with Map Energy Minimization

Cluster analysisisthe fundamentalmethod for DNA microarray gene classi cation[1], structure activ-ity relationship [2] and any kind of correlation matrix analyses. The hierarchical clustering analysis isthe most widely used method providing us clear-separated clusters, however, often distributes closelyrelated clusters into apart positions because the direction of branches at each node is arbitrary. Thislimitation often makes the correlation matrix look like checkered pattern.In this work, we propose a new clustering method to overcome this problem. Our new methodsearches a set of row and column orders in which any pair of the highly coherent rows (or columns)are placed adjacently in the correlation matrix map. The nal map is no longer expected to havecheckered pattern. We assumed that it could perform this process to minimize the energy of thecorrelation map pattern. We named our new method \Map Energy Minimization Clustering (Meminclustering)".
Giving volume to the elephant in the imaging room

Rudolf Virchow, the founder of cellular pathology, held that even when physical or chemical investigations yield the laws of physiology or medicine, the anatomist can still proudly state: This is the structure in which the law becomes manifest. In his words, “physiology presupposes anatomy. ” Pathological anatomy studies, at usual microstructural scales (approximately 1–100 μm), via light microscopic 2D histology, provided many insights into structure–function relationships of health and disease. For example, such studies established the progression of granulomas, bronchial erosions, microcavities, and destructive lung disease in tuberculosis. While histologic studies remain the cornerstone of such efforts, the advent of nano or micro‐X‐ray computed tomography (n/μCT) has now made it additionally possible to obtain 3D visualizations of soft and hard tissues, while preserving the tissue for additional investigations. This has applications for old as well as new diseases (Katsamenis et al, 2019; Tanabe & Hirai, 2021).
Clinical utility of cerebrospinal fluid biomarkers measured by LUMIPULSE® system

Cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD) are well‐established in research settings, but their use in routine clinical practice remains a largely unexploited potential. Here, we examined the relationship between CSF biomarkers, measured by a fully automated immunoassay platform, and brain β‐amyloid (Aβ) deposition status confirmed by amyloid positron emission tomography (PET).
Machine learning methods for nanolaser characterization

Nanocavity lasers, which are an integral part of an on-chip integrated photonic network, are setting stringent requirements on the sensitivity of the techniques used to characterize the laser performance. Current characterization tools cannot provide detailed knowledge about nanolaser noise and dynamics. In this progress article, we will present tools and concepts from the Bayesian machine learning and digital coherent detection that offer novel approaches for highly-sensitive laser noise characterization and inference of laser dynamics. The goal of the paper is to trigger new research directions that combine the fields of machine learning and nanophotonics for characterizing nanolasers and eventually integrated photonic networks
Strong Lottery Ticket Hypothesis with ε-perturbation

The strong Lottery Ticket Hypothesis (LTH) claims the existence of a subnetwork in a sufficiently large, randomly initialized neural network that approximates some target neural network without the need of training. We extend the theoretical guarantee of the strong LTH literature to a scenario more similar to the original LTH, by generalizing the weight change in the pre-training step to some perturbation around initialization. In particular, we focus on the following open questions: By allowing an $\varepsilon$-scale perturbation on the random initial weights, can we reduce the over-parameterization requirement for the candidate network in the strong LTH? Furthermore, does the weight change by SGD coincide with a good set of such perturbation? We answer the first question by first extending the theoretical result on subset sum to allow perturbation on the candidates. Applying this result to the neural network setting, we show that such $\varepsilon$-perturbation reduces the over-parameterization requirement of the strong LTH. To answer the second question, we show via experiments that the perturbed weight achieved by the projected SGD shows better performance under the strong LTH pruning.
Applications of Bayesian Confirmatory Factor Analysis in Behavioral Measurement: Strong Convergence of a Bayesian Parameter Estimator

ABSTRACT This article is concerned with the large-sample parameter estimatorbehavior in applications of Bayesian confirmatory factor analysis in behavioral measurement. The property of strong convergence of the popular Bayesian posterior median estimator is discussed, which states numerical convergence with probability 1 of the resulting estimates to the population parameter value as sample size increases without bound. This property is stronger than the consistency and convergence in distribution of that estimator, which have been commonly referred to in the literature. A numerical example is utilized to illustrate this almost sure convergence of a Bayesian latent correlation estimator. The paper contributes to the body of research on optimal statistical features of Bayesian estimates and concludes with a discussion of the implications of this large-sample property of the Bayesian median estimator for empirical measurement studies.
Implementing blockchain in information systems: a review

ABSTRACT Blockchain, as a distributed ledger and decentralized database, has the potential to form a secured system of value exchange. Due to its attractive features, blockchain has drawn a lot of attention. As the pioneer of blockchain, Bitcoin has been implemented for more than a decade, and it reflects high levels of stability and reliability. It is foreseeable that blockchain will be implemented and applied to daily activities among institutions, businesses, and personnel. We conduct a study consisting of operating mechanisms, core technologies, research directions, applications, and drawbacks. This paper links that research to blockchain-based information systems.
Be discs in coplanar circular binaries: Phase-locked variations of emission lines

The first results of radiative transfer calculations on decretion discs of binary Be stars are presented. A smoothed particle hydrodynamics code computes the structure of Be discs in coplanar circular binary systems for a range of orbital and disc parameters. The resulting disc configuration consists of two spiral arms, and can be given as input into a Monte Carlo code, which calculates the radiative transfer along the line of sight for various observational coordinates. Making use of the property of steady disc structure in coplanar circular binaries, observables are computed as functions of the orbital phase. Orbital-phase series of line profiles are given for selected parameter sets under various viewing angles, to allow comparison with observations. Flat-topped profiles with and without superimposed multiple structures are reproduced, showing, for example, that triple-peaked profiles do not have to be necessarily associated with warped discs and misaligned binaries. It is demonstrated that binary tidal effects give rise to phase-locked variability of the violet-to-red (V/R) ratio of hydrogen emission lines. The V/R ratio exhibits two maxima per cycle; in certain cases those maxima are equal, leading to a clear new V/R cycle every half orbital period. This study opens a way in identifying binaries and in constraining the parameters of binary systems that exhibit phase-locked variations induced by tidal interaction with a companion star.
Physical Stability and Antioxidant of Peel-Off Gel Mask Ethanol Extract of Buas-buas Leaf (Premna serratifolia L.)

This study aims to determine the physical stability and antioxidant activity of peel-off gel mask ethanol extract of buas-buas leaf ( Premna serratifolia L.). The ethanol extract of buas-buas leaves was obtained by maceration using 70% ethanol solvent, then concentrated using a rotary evaporator to get a thick extract. Formulation EEDB into a peel-off gel mask with a concentration of each EEDB (FI: 1%, FII: 2%, FIII : 3%). The EEDB peel-off gel mask formula was tested for physical stability by cycling test method using a climatic chamber at a temperature of 40°C ± 2°C and 4°C ± 2°C for six cycles. The tests included organoleptic, homogeneity, viscosity, pH, spreadability, and drying time. An antioxidant test was carried out using the DPPH method. The results of the physical stability test on the three EEDB peel-off gel mask formulas (FI: 1%, FII: 2%, FIII: 3%) showed good physical stability because there was no significant difference during six storage cycles (P>0.05) with the results of the preparation have a characteristic aroma of oleum citri, brownish-green in color, have a thick, homogeneous texture, meet the requirements of pH, viscosity, spreadability, and drying time. The stability test results of the antioxidant activity of the peel-off gel mask EEDB in the three formulas showed no significant change (P>0.05). The antioxidant activity during six storage cycles with the highest average percent inhibition before and after the cycling test, namely in Formula III, was 77.20 ± 0.28%.
The Healthy Context Paradox: When Reducing Bullying comes at a Cost to Certain Victims

Abstract Bullying remains one of the most serious problems affecting school systems around the world. The negative consequences of bullying in the short and long term have been widely documented, showing that victimized students are at greater risk of suffering psychosocial distress. In this paper, we first summarize the current situation of bullying prevention, adopting a contextual perspective, and briefly highlighting the characteristics of the most effective prevention programs. Secondly, we address a disturbing phenomenon detected in classrooms where bullying has been reduced through interventions and which has been termed “the healthy context paradox”. In these healthier contexts, students who remain in a situation of victimization have been found to present poorer psychological adjustment after the intervention. Understanding the causes of this phenomenon may offer clues for the prevention of bullying. In this regard, we present three hypotheses recently proposed to explain the phenomenon. Finally, we offer some implications for the study and prevention of bullying derived from “the healthy context paradox”.
A computational examination of large-scale pool fires: variations in crosswind velocity and pool shape

Abstract A high-fidelity large-eddy simulation and unsteady flamelet combustion model construct is deployed to numerically investigate the effects of crosswind magnitude and pool fire shape on large-scale pool fire attributes. These include general flame dynamics, flame shape and radiative flux magnitude in and around the fire. Three pool fire shapes at a nominal length scale of 10 m are subjected to four crosswind magnitudes between 0 and 20 m s$^{-1}$. The pool shapes studied are circular, square and rectangular. The study includes the sensitivity of parameters to mesh and time step refinement. Results demonstrate that the rectangular shape, under crosswind, has low-levels of vertical velocity induction, resulting in a plume that is closer to the ground. In the quiescent regime, under-resolved meshes provide a higher radiative heat flux prediction compared with the most refined mesh. However, as crosswind increases, low mesh resolutions underpredicted radiative flux. This is due to the coarse mesh resolution not capturing small-scale vortical features that increased mixing and combustion efficiency. A transition of peak radiative flux with respect to crosswind occurs from the leeward- to windward-side of the pool, while sharp pool features result in larger radiative heat fluxes concentrated in regions of high scalar dissipation rate.
Optimal design of two-dimensional riser fairings for vortex-induced vibration suppression based on genetic algorithm

Vortex-induced vibration (VIV) manifests its destructiveness on marine risers in deep-water oil and gas development. Many types of riser fairings are employed in the practical applications of ocean engineering due to their effectiveness in suppressing VIV. However, few reports have been found on the optimal design of the fairing profile. In this study, we conduct shape optimization by integrating computational fluid dynamics and genetic algorithm at a low Reynolds number. The fairing profile is parameterized by B\'ezier curves with control points adopted as design variables, and lift coefficient is selected as the objective function to obtain optimal fairing. The optimal solution shows that the water-drop-shaped fairing presents a high performance in the condition of two degrees of freedom (DOFs), whereas the caudal fin-like-shaped fairing has good stability in 3-DOF condition. Optimization results indicate that the water-drop-shaped fairing suppresses amplitude up to 99% and reduces drag coefficient by almost 51% at Ur=5.0 for the 2-DOF condition. For the 3-DOF condition, the formation of two symmetric vorticities with opposite directions generated at the bilateral of the optimal fairing leads to fairing stability in flow.