bluuebunny/crossref_metadata_2025_split huggingface dataset:
CITEdb: a manually curated database of cell–cell interactions in human
Authors: Shan Nayang , Lu Yao , Guo Hao , Li Dongyu , Jiang Jitong , Yan Linlin , Gao Jiudong , Ren Yong , Zhao Xingming , Hou Lin 
Published: September 2022

Abstract

Motivation
The interactions among various types of cells play critical roles in cell functions and the maintenance of the entire organism. While cell–cell interactions are traditionally revealed from experimental studies, recent developments in single-cell technologies combined with data mining methods have enabled computational prediction of cell–cell interactions, which have broadened our understanding of how cells work together, and have important implications in therapeutic interventions targeting cell–cell interactions for cancers and other diseases. Despite the importance, to our knowledge, there is no database for systematic documentation of high-quality cell–cell interactions at the cell type level, which hinders the development of computational approaches to identify cell–cell interactions.

Results
We develop a publicly accessible database, CITEdb (Cell–cell InTEraction database, https://citedb.cn/), which not only facilitates interactive exploration of cell–cell interactions in specific physiological contexts (e.g. a disease or an organ) but also provides a benchmark dataset to interpret and evaluate computationally derived cell–cell interactions from different tools. CITEdb contains 728 pairs of cell–cell interactions in human that are manually curated. Each interaction is equipped with structured annotations including the physiological context, the ligand–receptor pairs that mediate the interaction, etc. Our database provides a web interface to search, visualize and download cell–cell interactions. Users can search for cell–cell interactions by selecting the physiological context of interest or specific cell types involved. CITEdb is the first attempt to catalogue cell–cell interactions at the cell type level, which is beneficial to both experimental, computational and clinical studies of cell–cell interactions.

Availability and implementation
CITEdb is freely available at https://citedb.cn/ and the R package implementing benchmark is available at https://github.com/shanny01/benchmark.

Supplementary information
Supplementary data are available at Bioinformatics online.
Integrating phylogenetic and functional data in microbiome studies
Authors: Douglas Gavin M , Hayes Molly G , Langille Morgan G I , Borenstein Elhanan 
Published: September 2022

Abstract

Motivation
Microbiome functional data are frequently analyzed to identify associations between microbial functions (e.g. genes) and sample groups of interest. However, it is challenging to distinguish between different possible explanations for variation in community-wide functional profiles by considering functions alone. To help address this problem, we have developed POMS, a package that implements multiple phylogeny-aware frameworks to more robustly identify enriched functions.

Results
The key contribution is an extended balance-tree workflow that incorporates functional and taxonomic information to identify functions that are consistently enriched in sample groups across independent taxonomic lineages. Our package also includes a workflow for running phylogenetic regression. Based on simulated data we demonstrate that these approaches more accurately identify gene families that confer a selective advantage compared with commonly used tools. We also show that POMS in particular can identify enriched functions in real-world metagenomics datasets that are potential targets of strong selection on multiple members of the microbiome.

Availability and implementation
These workflows are freely available in the POMS R package at https://github.com/gavinmdouglas/POMS.

Supplementary information
Supplementary data are available at Bioinformatics online.
WMSA: a novel method for multiple sequence alignment of DNA sequences
Authors: Wei Yanming , Zou Quan , Tang Furong , Yu Liang 
Published: September 2022

Abstract

Motivation
Multiple sequence alignment (MSA) is a fundamental problem in bioinformatics. The quality of alignment will affect downstream analysis. MAFFT has adopted the Fast Fourier Transform method for searching the homologous segments and using them as anchors to divide the sequences, then making alignment only on segments, which can save time and memory without overly reducing the sequence alignment quality. MAFFT becomes slow when the dataset is large.

Results
We made a software, WMSA, which uses the divide-and-conquer method to split the sequences into clusters, aligns those clusters into profiles with the center star strategy and then makes a progressive profile–profile alignment. The alignment is conducted by the compiled algorithms of MAFFT, K-Band with multithread parallelism. Our method can balance time, space and quality and performs better than MAFFT in test experiments on highly conserved datasets.

Availability and implementation
Source code is freely available at https://github.com/malabz/WMSA/, which is implemented in C/C++ and supported on Linux, and datasets are available at https://github.com/malabz/WMSA-dataset.

Supplementary information
Supplementary data are available at Bioinformatics online.
The influence of COVID-19 infection-associated immune response on the female reproductive system
Authors: Saadedine Mariam , El Sabeh Malak , Borahay Mostafa A , Daoud Georges 
Published: September 2022

AbstractCoronavirus disease 2019 (COVID-19) is a multi-system disease that has led to a pandemic with unprecedented ramifications. The pandemic has challenged scientists for the past 2 years and brought back previously abandoned research topics. COVID-19 infection causes a myriad of symptoms ranging from mild flu-like symptoms to severe illness requiring hospitalization. Case reports showed multiple systemic effects of COVID-19 infection, including acute respiratory distress syndrome, fibrosis, colitis, thyroiditis, demyelinating syndromes, and mania, indicating that COVID-19 can affect most human body systems. Unsurprisingly, a major concern for women all over the globe is whether a COVID-19 infection has any long-term effects on their menstrual cycle, fertility, or pregnancy. Published data have suggested an effect on the reproductive health, and we hypothesize that the reported reproductive adverse effects are due to the robust immune reaction against COVID-19 and the associated cytokine storm. While the COVID-19 receptor (angiotensin converting enzyme, ACE2) is expressed in the ovaries, uterus, vagina, and placenta, we hypothesize that it plays a less important role in the adverse effects on the reproductive system. Cytokines and glucocorticoids act on the hypothalamo–pituitary gonadal axis, arachidonic acid pathways, and the uterus, which leads to menstrual disturbances and pregnancy-related adverse events such as preterm labor and miscarriages. This hypothesis is further supported by the apparent lack of long-term effects on the reproductive health in females, indicating that when the cytokine storm and its effects are dampened, the reproductive health of women is no longer affected.
Functional linear regression for discretely observed data: from ideal to reality
Authors: Zhou Hang , Yao Fang , Zhang Huiming 
Published: September 2022

Summary
Despite extensive studies on functional linear regression, there exists a fundamental gap in theory between the ideal estimation from fully observed covariate functions and the reality that one can only observe functional covariates discretely with noise. The challenge arises when deriving a sharp perturbation bound for the estimated eigenfunctions in the latter case, which renders existing techniques for functional linear regression not applicable. We use a pooling method to attain the estimated eigenfunctions and propose a sample-splitting strategy to estimate the principal component scores, which facilitates the theoretical treatment for discretely observed data. The slope function is estimated by approximated least squares, and we show that the resulting estimator attains the optimal convergence rates for both estimation and prediction when the number of measurements per subject reaches a certain magnitude of the sample size. This phase transition phenomenon differs from the known results for the pooled mean and covariance estimation, and reveals the elevated difficulty in estimating the regression function. Numerical experiments, using simulated and real data examples, yield favourable results when compared with existing methods.
Propensity scores in the design of observational studies for causal effects
Authors: Rosenbaum P R , Rubin D B 
Published: September 2022

SummaryThe design of any study, whether experimental or observational, that is intended to estimate the causal effects of a treatment condition relative to a control condition refers to those activities that precede any examination of outcome variables. As defined in our 1983 article (Rosenbaum & Rubin, 1983), the propensity score is the unit-level conditional probability of assignment to treatment versus control given the observed covariates; so the propensity score explicitly does not involve any outcome variables, in contrast to other summaries of variables sometimes used in observational studies. Balancing the distributions of covariates in the treatment and control groups by matching or balancing on the propensity score is therefore an aspect of the design of the observational study. In this invited comment on our 1983 article, we review the situation in the early 1980s and recall some apparent paradoxes that propensity scores helped to resolve. We demonstrate that it is possible to balance an enormous number of low-dimensional summaries of a high-dimensional covariate, even though it is generally impossible to match individuals closely for all the components of a high-dimensional covariate. In a sense, there is only one crucial observed covariate, the propensity score, and there is one crucial unobserved covariate, the principal unobserved covariate. The propensity score and the principal unobserved covariate are equal when treatment assignment is strongly ignorable, that is, unconfounded. Controlling for observed covariates is a prelude to the crucial step from association to causation, the step that addresses potential biases from unmeasured covariates. The design of an observational study also prepares for the step to causation: by selecting comparisons to increase the design sensitivity, by seeking opportunities to detect bias, by seeking mutually supportive evidence affected by different biases, by incorporating quasi-experimental devices such as multiple control groups, and by including the economist’s instruments. All of these considerations reflect the formal development of sensitivity analyses that were largely informal prior to the 1980s.
Bioactive glass-based fibrous wound dressings
Authors: Homaeigohar Shahin , Li Meng , Boccaccini Aldo R 
Published: September 2022

AbstractSince the discovery of silicate bioactive glass (BG) by Larry Hench in 1969, different classes of BGs have been researched over decades mainly for bone regeneration. More recently, validating the beneficial influence of BGs with tailored compositions on angiogenesis, immunogenicity and bacterial infection, the applicability of BGs has been extended to soft tissue repair and wound healing. Particularly, fibrous wound dressings comprising BG particle reinforced polymer nanofibers and cotton-candy-like BG fibers have been proven to be successful for wound healing applications. Such fibrous dressing materials imitate the physical structure of skin’s extracellular matrix and release biologically active ions e.g. regenerative, pro-angiogenic and antibacterial ions, e.g. borate, copper, zinc, etc., that can provoke cellular activities to regenerate the lost skin tissue and to induce new vessels formation, while keeping an anti-infection environment. In the current review, we discuss different BG fibrous materials meant for wound healing applications and cover the relevant literature in the past decade. The production methods for BG-containing fibers are explained and as fibrous wound dressing materials, their wound healing and bactericidal mechanisms, depending on the ions they release, are discussed. The present gaps in this research area are highlighted and new strategies to address them are suggested.
Japanese Encephalitis Emergence in Australia: The Potential Population at Risk
Authors: Yakob Laith , Hu Wenbiao , Frentiu Francesca D , Gyawali Narayan , Hugo Leon E , Johnson Brian , Lau Colleen , Furuya-Kanamori Luis , Magalhaes Ricardo Soares , Devine Gregor 
Published: September 2022

Abstract
In Australia, Japanese encephalitis virus circulated in tropical north Queensland between 1995 and 2005. In 2022, a dramatic range expansion across the southern states has resulted in 30 confirmed human cases and 6 deaths. We discuss the outbreak drivers and estimate the potential size of the human population at risk.
Neutral-Coating Capillary Electrophoresis Coupled with High-Resolution Mass Spectrometry for Top-Down Identification of Hemoglobin Variants
Authors: Luo Ruben Yiqi , Wong Carolyn , Xia James Qiangwei , Glader Bertil E , Shi Run-Zhang , Zehnder James L 
Published: September 2022

Abstract

Background
Identification of hemoglobin (Hb) variants is of significant value in the clinical diagnosis of hemoglobinopathy. However, conventional methods for identification of Hb variants in clinical laboratories can be inadequate due to the lack of structural characterization. We describe the use of neutral-coating capillary electrophoresis coupled with high-resolution mass spectrometry (CE-HR-MS) to achieve high-performance top-down identification of Hb variants.

Methods
An Orbitrap Q-Exactive Plus mass spectrometer was coupled with an ECE-001 capillary electrophoresis (CE) unit through an EMASS-II ion source. A PS1 neutral-coating capillary was used for CE. Samples of red blood cells were lysed in water and diluted in 10 mM ammonium formate buffer for analysis. Deconvolution of raw mass spectrometry data was carried out to merge multiple charge states and isotopic peaks of an analyte to obtain its monoisotopic mass.

Results
The neutral-coating CE could baseline separate individual Hb subunits dissociated from intact Hb forms, and the HR-MS could achieve both intact-protein analysis and top-down analysis of analytes. A number of patient samples that contain Hb subunit variants were analyzed, and the variants were successfully identified using the CE-HR-MS method.

Conclusions
The CE-HR-MS method has been demonstrated as a useful tool for top-down identification of Hb variants. With the ability to characterize the primary structures of Hb subunits, the CE-HR-MS method has significant advantages to complement or partially replace the conventional methods for the identification of Hb variants.
Case report on ambulatory pulmonary pressure monitoring: an attempt to reduce readmissions for heart failure with preserved ejection fraction
Authors: Angullo-Gómez María , Robles-Mezcua Ainhoa , Becerra-Muñoz Víctor Manuel , García-Pinilla José Manuel 
Published: September 2022

Abstract

Background
Despite many recent advances in heart failure (HF) therapies, there remains an unmet need in patients with HF with preserved ejection fraction (HFpEF) for adequate treatment and follow-up, with the potential to reduce associated mortality and morbidity. Increased intracardiac and intrapulmonary pressures have been shown to precede the onset of symptoms of decompensated HF by several days or even weeks, so there have been several attempts to influence the prognosis of HF by monitoring through various methods. One of these is ambulatory pulmonary pressure monitoring to guide treatment in anticipation of decompensation.

Case summary
We present the case of a 65-year-old woman with rheumatic valve disease and mechanical aortic and mitral prosthesis since 2003 and pacemaker since 2014, with development of severe tricuspid regurgitation in 2018 and with new valve implantation and multiple decompensations of HFpEF despite optimal medical treatment. Under follow-up in the Heart Failure Unit and after multiple unsuccessful treatment adjustments, it was decided to implant a pulmonary artery pressure monitoring device—CardioMEMS®—in order to optimize patient follow-up and treatment. The procedure was carried out without complications and early optimization of treatment was possible, resulting in a significant reduction in decompensations and admissions for HF.

Discussion
Ambulatory pulmonary pressure monitoring is shown to be a safe and effective option to anticipate treatment of heart failure decompensation even with preserved left ventricular ejection fraction, with a significantly positive impact on hospital readmissions and consequent benefit on morbidity and mortality.
Effect of resected lung lobe on the prediction of postoperative pulmonary function
Authors: Shibazaki Takamasa , Mori Shohei , Noda Yuki , Tsukamoto Yo , Kato Daiki , Nakada Takeo , Yabe Mitsuo , Matsudaira Hideki , Hirano Jun , Ohtsuka Takashi 
Published: September 2022

Abstract

OBJECTIVES
This study examined whether a resected lung lobe can affect the accuracy of postoperative forced expiratory volume in 1 s (FEV1) predicted using the subsegment counting method and three-dimensional computed tomography (3D-CT) volumetry.

METHODS
Overall, 125 patients who underwent lobectomy through video-assisted thoracic surgery were enrolled in this retrospective study. Pulmonary function tests were performed preoperatively and postoperatively at 3 months. We defined the accuracy index as the ratio of predicted postoperative FEV1 to measured postoperative FEV1 and compared the accuracy index of the subsegment counting method and 3D-CT volumetry. Factors affecting the accuracy index were also examined.

RESULTS
The accuracy index of the subsegment counting method was 0.94 ± 0.12, versus 0.93 ± 0.11 for 3D-CT volumetry (P = 0.539). There was a significant difference among the resected lobes in the accuracy index of the subsegment counting method (P &lt; 0.001) but not in that of 3D-CT volumetry (P = 0.370). The resected lobe, the number of staples used for interlobar dissection and interstitial pneumonia were significantly associated with the accuracy index of the subsegment counting method (all P &lt; 0.001). The number of staples and interstitial pneumonia were significantly associated with the accuracy index of 3D-CT volumetry (P &lt; 0.001, respectively), whereas the resected lobe was not a significant factor (P = 0.240).

CONCLUSIONS
The resected lobe affected the accuracy of the subsegment counting method but not that of 3D-CT volumetry. Furthermore, 3D-CT volumetry predicted postoperative FEV1 independent of the resected lobe.
Left main coronary disease: evolving management concepts
Authors: Armstrong Paul W , Bates Eric R , Gaudino Mario 
Published: September 2022

Abstract
Remarkable advances in the management of coronary artery disease have enhanced our approach to left main coronary artery (LMCA) disease. The traditional role of coronary artery bypass graft surgery has been challenged by the less invasive percutaneous coronary interventional approach. Additionally, major strides in optimal medical therapy now provide a rich menu of treatment choices in selected circumstances. Although a LMCA stenosis &gt;70% is an acceptable threshold for revascularization, those patients with a LMCA narrowing between 40 and 69% present a more complex scenario. This review examines the relative merits of the different treatment options, addresses key diagnostic and therapeutic unknowns, and identifies future work likely to advance progress.
Parental alcohol and drug abuse and offspring mortality by age 10: a population-based register study
Authors: Berg Venla , Kuja-Halkola Ralf , Khemiri Lotfi , Larsson Henrik , Lichtenstein Paul , Latvala Antti 
Published: September 2022

Abstract

Background
Parental substance abuse (SA) of alcohol and drugs is associated with offspring mortality, including sudden infant death syndrome (SIDS), in infancy, but research on cause-specific mortality and mortality in later childhood is scarce.

Methods
Using population-based register data on all births in Sweden in 1973–2013 (N = 4.2 million) and Cox regressions, we examined the associations of mother’s and father’s SA registered between 2 years before and 12 years after the child birth with offspring all-cause and cause-specific mortality in infancy and childhood.

Results
Parental SA was associated with increased offspring all-cause and natural-cause mortality in infancy, but not in the neonatal period, and with external-cause mortality in ages 1–9. Risk of SIDS was 130–280% higher in infants with parental SA compared to infants with no parental SA. Adjusting for parental socioeconomic and immigrant status and severe psychiatric disorders, paternal SA was associated with 66% higher mortality due to communicable diseases and infections in infancy, and both maternal and paternal SA were associated with 40–174% higher mortality due to accidents in infancy and in ages 1–9. The associations between parental SA and offspring mortality were similar for male and female offspring.

Conclusions
Child mortality is rare in contemporary Sweden, and parental SA has variable associations with elevated offspring mortality throughout the first 10 years of life, excluding the neonatal period, which is indicative of insufficient recognition of children at risk. Preventive measures should be long-term and targeted to both parental and offspring behaviour.
Demes: a standard format for demographic models
Authors: Gower Graham , Ragsdale Aaron P , Bisschop Gertjan , Gutenkunst Ryan N , Hartfield Matthew , Noskova Ekaterina , Schiffels Stephan , Struck Travis J , Kelleher Jerome , Thornton Kevin R 
Published: September 2022

Abstract
Understanding the demographic history of populations is a key goal in population genetics, and with improving methods and data, ever more complex models are being proposed and tested. Demographic models of current interest typically consist of a set of discrete populations, their sizes and growth rates, and continuous and pulse migrations between those populations over a number of epochs, which can require dozens of parameters to fully describe. There is currently no standard format to define such models, significantly hampering progress in the field. In particular, the important task of translating the model descriptions in published work into input suitable for population genetic simulators is labor intensive and error prone. We propose the Demes data model and file format, built on widely used technologies, to alleviate these issues. Demes provide a well-defined and unambiguous model of populations and their properties that is straightforward to implement in software, and a text file format that is designed for simplicity and clarity. We provide thoroughly tested implementations of Demes parsers in multiple languages including Python and C, and showcase initial support in several simulators and inference methods. An introduction to the file format and a detailed specification are available at https://popsim-consortium.github.io/demes-spec-docs/.