bluuebunny/crossref_metadata_2025_split huggingface dataset:
Worldwide prevalence of suicidal ideation and suicide plan among people with schizophrenia: a meta-analysis and systematic review of epidemiological surveys
Authors: Bai W. , Liu Z. H. , Jiang Y. Y. , Zhang Q. E. , Rao W. W. , Cheung T. , Hall B. J. , Xiang Y. T. 
Published: October 2021

AbstractSchizophrenia is a severe psychiatric disorder with high premature mortality rates. This is a meta-analysis and systematic review of the prevalence of suicidal ideation (SI) and suicide plan (SP) among people with schizophrenia. PubMed, Web of Science, Embase, and PsycINFO were systematically searched from their respective inception to October 10, 2020. Data on prevalence of SI and/or SP were synthesized using the random effects model. Twenty-six studies covering 5079 people with schizophrenia were included for meta-analysis. The lifetime and point prevalence of SI were 34.5% (95% CI: 28.2−40.9%), and 29.9% (95% CI: 24.2−35.6%), respectively. The lifetime prevalence of SP was 44.3% and the point prevalence of SP ranged between 6.4 and 13%. Subgroup and meta-regression analyses revealed that source of patients, survey countries, and sample size were significantly associated with the point prevalence of SI, while male proportion and quality assessment scores were significantly associated with the lifetime and point prevalence of SI. Survey time and mean age were significantly associated with lifetime prevalence of SI. Both SI and SP are common in people living with schizophrenia, especially in males and inpatients. Routine screening and effective interventions for SI and SP should be implemented in this population.
Engineering of Fe-pnictide heterointerfaces by electrostatic principles
Authors: Haindl Silvia , Nikolaev Sergey , Sato Michiko , Sasase Masato , MacLaren Ian 
Published: October 2021

AbstractInterface-related phenomena have great potential to control the superconducting state in Fe-based superconductors. We propose a comprehensive classification of Fe-pnictide heterointerfaces based on electrostatic principles that allow the prediction of the interface microstructure, in particular, distinguishing between clean heterointerfaces and the formation of interfacial layers. The concept was successfully tested on a novel LnOFeAs/BaFe2As2 (Ln = La, Sm) Fe-pnictide heterostructure. With the addition of different cations/anions, it is possible to produce clean interfaces or interfacial layers. The impact of the microstructure on superconductivity in the Fe-pnictide heterostructures is discussed.
Objective comparison of methods to decode anomalous diffusion
Authors: Muñoz-Gil Gorka , Volpe Giovanni , Garcia-March Miguel Angel , Aghion Erez , Argun Aykut , Hong Chang Beom , Bland Tom , Bo Stefano , Conejero J. Alberto , Firbas Nicolás , Garibo i Orts Òscar , Gentili Alessia , Huang Zihan , Jeon Jae-Hyung , Kabbech Hélène , Kim Yeongjin , Kowalek Patrycja , Krapf Diego , Loch-Olszewska Hanna , Lomholt Michael A. , Masson Jean-Baptiste , Meyer Philipp G. , Park Seongyu , Requena Borja , Smal Ihor , Song Taegeun , Szwabiński Janusz , Thapa Samudrajit , Verdier Hippolyte , Volpe Giorgio , Widera Artur , Lewenstein Maciej , Metzler Ralf , Manzo Carlo 
Published: October 2021

AbstractDeviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this approach breaks down for cases of practical interest, e.g., short or noisy trajectories, heterogeneous behaviour, or non-ergodic processes. Recently, several new approaches have been proposed, mostly building on the ongoing machine-learning revolution. To perform an objective comparison of methods, we gathered the community and organized an open competition, the Anomalous Diffusion challenge (AnDi). Participating teams applied their algorithms to a commonly-defined dataset including diverse conditions. Although no single method performed best across all scenarios, machine-learning-based approaches achieved superior performance for all tasks. The discussion of the challenge results provides practical advice for users and a benchmark for developers.
Normal & reversed spin mobility in a diradical by electron-vibration coupling
Authors: Shen Yi , Xue Guodong , Dai Yasi , Quintero Sergio Moles , Chen Hanjiao , Wang Dongsheng , Miao Fang , Negri Fabrizia , Zheng Yonghao , Casado Juan 
Published: October 2021

Abstractπ−conjugated radicals have great promise for use in organic spintronics, however, the mechanisms of spin relaxation and mobility related to radical structural flexibility remain unexplored. Here, we describe a dumbbell shape azobenzene diradical and correlate its solid-state flexibility with spin relaxation and mobility. We employ a combination of X-ray diffraction and Raman spectroscopy to determine the molecular changes with temperature. Heating leads to: i) a modulation of the spin distribution; and ii) a “normal” quinoidal → aromatic transformation at low temperatures driven by the intramolecular rotational vibrations of the azobenzene core and a “reversed” aromatic → quinoidal change at high temperatures activated by an azobenzene bicycle pedal motion amplified by anisotropic intermolecular interactions. Thermal excitation of these vibrational states modulates the diradical electronic and spin structures featuring vibronic coupling mechanisms that might be relevant for future design of high spin organic molecules with tunable magnetic properties for solid state spintronics.
Anti-spike antibody response to natural SARS-CoV-2 infection in the general population
Authors: Wei Jia , Matthews Philippa C. , Stoesser Nicole , Maddox Thomas , Lorenzi Luke , Studley Ruth , Bell John I. , Newton John N. , Farrar Jeremy , Diamond Ian , Rourke Emma , Howarth Alison , Marsden Brian D. , Hoosdally Sarah , Jones E. Yvonne , Stuart David I. , Crook Derrick W. , Peto Tim E. A. , Pouwels Koen B. , Walker A. Sarah , Eyre David W. ,   the COVID-19 Infection Survey team, Thomas Tina , Cook Duncan , Ayoubkhani Daniel , Black Russell , Felton Antonio , Crees Megan , Jones Joel , Lloyd Lina , Sutherland Esther , Pritchard Emma , Vihta Karina-Doris , Doherty George , Kavanagh James , Chau Kevin K. , Hatch Stephanie B. , Ebner Daniel , Ferreira Lucas Martins , Christott Thomas , Dejnirattisai Wanwisa , Mongkolsapaya Juthathip , Cameron Sarah , Tamblin-Hopper Phoebe , Wolna Magda , Brown Rachael , Cornall Richard , Screaton Gavin , Lythgoe Katrina , Bonsall David , Golubchik Tanya , Fryer Helen , Cox Stuart , Paddon Kevin , James Tim , House Thomas , Robotham Julie , Birrell Paul , Jordan Helena , Sheppard Tim , Athey Graham , Moody Dan , Curry Leigh , Brereton Pamela , Jarvis Ian , Godsmark Anna , Morris George , Mallick Bobby , Eeles Phil , Hay Jodie , VanSteenhouse Harper , Lee Jessica , White Sean , Evans Tim , Bloemberg Lisa , Allison Katie , Pandya Anouska , Davis Sophie , Conway David I. , MacLeod Margaret , Cunningham Chris 
Published: October 2021

AbstractUnderstanding the trajectory, duration, and determinants of antibody responses after SARS-CoV-2 infection can inform subsequent protection and risk of reinfection, however large-scale representative studies are limited. Here we estimated antibody response after SARS-CoV-2 infection in the general population using representative data from 7,256 United Kingdom COVID-19 infection survey participants who had positive swab SARS-CoV-2 PCR tests from 26-April-2020 to 14-June-2021. A latent class model classified 24% of participants as ‘non-responders’ not developing anti-spike antibodies, who were older, had higher SARS-CoV-2 cycle threshold values during infection (i.e. lower viral burden), and less frequently reported any symptoms. Among those who seroconverted, using Bayesian linear mixed models, the estimated anti-spike IgG peak level was 7.3-fold higher than the level previously associated with 50% protection against reinfection, with higher peak levels in older participants and those of non-white ethnicity. The estimated anti-spike IgG half-life was 184 days, being longer in females and those of white ethnicity. We estimated antibody levels associated with protection against reinfection likely last 1.5-2 years on average, with levels associated with protection from severe infection present for several years. These estimates could inform planning for vaccination booster strategies.
The membrane associated accessory protein is an adeno-associated viral egress factor
Authors: Elmore Zachary C. , Patrick Havlik L. , Oh Daniel K. , Anderson Leif , Daaboul George , Devlin Garth W. , Vincent Heather A. , Asokan Aravind 
Published: October 2021

AbstractAdeno-associated viruses (AAV) rely on helper viruses to transition from latency to lytic infection. Some AAV serotypes are secreted in a pre-lytic manner as free or extracellular vesicle (EV)-associated particles, although mechanisms underlying such are unknown. Here, we discover that the membrane-associated accessory protein (MAAP), expressed from a frameshifted open reading frame in the AAV cap gene, is a novel viral egress factor. MAAP contains a highly conserved, cationic amphipathic domain critical for AAV secretion. Wild type or recombinant AAV with a mutated MAAP start site (MAAPΔ) show markedly attenuated secretion and correspondingly, increased intracellular retention. Trans-complementation with MAAP restored secretion of multiple AAV/MAAPΔ serotypes. Further, multiple processing and analytical methods corroborate that one plausible mechanism by which MAAP promotes viral egress is through AAV/EV association. In addition to characterizing a novel viral egress factor, we highlight a prospective engineering platform to modulate secretion of AAV vectors or other EV-associated cargo.
The serine proteases dipeptidyl-peptidase 4 and urokinase are key molecules in human and mouse scar formation
Authors: Vorstandlechner Vera , Laggner Maria , Copic Dragan , Klas Katharina , Direder Martin , Chen Yiyan , Golabi Bahar , Haslik Werner , Radtke Christine , Tschachler Erwin , Hötzenecker Konrad , Ankersmit Hendrik Jan , Mildner Michael 
Published: October 2021

AbstractDespite recent advances in understanding skin scarring, mechanisms triggering hypertrophic scar formation are still poorly understood. In the present study, we investigate mature human hypertrophic scars and developing scars in mice at single cell resolution. Compared to normal skin, we find significant differences in gene expression in most cell types present in scar tissue. Fibroblasts show the most prominent alterations in gene expression, displaying a distinct fibrotic signature. By comparing genes upregulated in murine fibroblasts during scar development with genes highly expressed in mature human hypertrophic scars, we identify a group of serine proteases, tentatively involved in scar formation. Two of them, dipeptidyl-peptidase 4 (DPP4) and urokinase (PLAU), are further analyzed in functional assays, revealing a role in TGFβ1-mediated myofibroblast differentiation and over-production of components of the extracellular matrix in vitro. Topical treatment with inhibitors of DPP4 and PLAU during scar formation in vivo shows anti-fibrotic activity and improvement of scar quality, most prominently after application of the PLAU inhibitor BC-11. In this study, we delineate the genetic landscape of hypertrophic scars and present insights into mechanisms involved in hypertrophic scar formation. Our data suggest the use of serine protease inhibitors for the treatment of skin fibrosis.
Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
Authors: Lloréns-Rico Verónica , Gregory Ann C. , Van Weyenbergh Johan , Jansen Sander , Van Buyten Tina , Qian Junbin , Braz Marcos , Menezes Soraya Maria , Van Mol Pierre , Vanderbeke Lore , Dooms Christophe , Gunst Jan , Hermans Greet , Meersseman Philippe ,   CONTAGIOUS collaborators, Van Herck Yannick , Wilmer Alexander , Casaer Michael , Rex Stephen , Lorent Nathalie , Yserbyt Jonas , Testelmans Dries , Thevissen Karin , Wauters Els , Neyts Johan , Lambrechts Diether , Wauters Joost , Raes Jeroen 
Published: October 2021

AbstractUnderstanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome studies by analyzing the upper (n = 58) and lower (n = 35) respiratory tract microbiome in well-phenotyped COVID-19 patients and controls combining microbiome sequencing, viral load determination, and immunoprofiling. We find that time in the intensive care unit and type of oxygen support, as well as associated treatments such as antibiotic usage, explain the most variation within the upper respiratory tract microbiome, while SARS-CoV-2 viral load has a reduced impact. Specifically, mechanical ventilation is linked to altered community structure and significant shifts in oral taxa previously associated with COVID-19. Single-cell transcriptomics of the lower respiratory tract of COVID-19 patients identifies specific oral bacteria in physical association with proinflammatory immune cells, which show higher levels of inflammatory markers. Overall, our findings suggest confounders are driving contradictory results in current COVID-19 microbiome studies and careful attention needs to be paid to ICU stay and type of oxygen support, as bacteria favored in these conditions may contribute to the inflammatory phenotypes observed in severe COVID-19 patients.
Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0
Authors: Yuan Kai , Ni Xumin , Liu Chang , Pan Yuwen , Deng Lian , Zhang Rui , Gao Yang , Ge Xueling , Liu Jiaojiao , Ma Xixian , Lou Haiyi , Wu Taoyang , Xu Shuhua 
Published: October 2021

AbstractWe developed a method,ArchaicSeeker 2.0, to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us to discern two waves of introgression from both Denisovan-like and Neanderthal-like hominins in present-day Eurasian populations and an ancient Siberian individual. We estimated that an early Denisovan-like introgression occurred in Eurasia around 118.8–94.0 thousand years ago (kya). In contrast, we detected only one single episode of Denisovan-like admixture in indigenous peoples eastern to the Wallace-Line. Modeling ancient admixtures suggested an early dispersal of modern humans throughout Asia before the Toba volcanic super-eruption 74 kya, predating the initial peopling of Asia as proposed by the traditional Out-of-Africa model. Survived archaic sequences are involved in various phenotypes including immune and body mass (e.g.,ZNF169), cardiovascular and lung function (e.g.,HHAT), UV response and carbohydrate metabolism (e.g.,HYAL1/HYAL2/HYAL3), while “archaic deserts” are enriched with genes associated with skin development and keratinization.
Structural basis of terephthalate recognition by solute binding protein TphC
Authors: Gautom Trishnamoni , Dheeman Dharmendra , Levy Colin , Butterfield Thomas , Alvarez Gonzalez Guadalupe , Le Roy Philip , Caiger Lewis , Fisher Karl , Johannissen Linus , Dixon Neil 
Published: October 2021

AbstractBiological degradation of Polyethylene terephthalate (PET) plastic and assimilation of the corresponding monomers ethylene glycol and terephthalate (TPA) into central metabolism offers an attractive route for bio-based molecular recycling and bioremediation applications. A key step is the cellular uptake of the non-permeable TPA into bacterial cells which has been shown to be dependent upon the presence of the key tphC gene. However, little is known from a biochemical and structural perspective about the encoded solute binding protein, TphC. Here, we report the biochemical and structural characterisation of TphC in both open and TPA-bound closed conformations. This analysis demonstrates the narrow ligand specificity of TphC towards aromatic para-substituted dicarboxylates, such as TPA and closely related analogues. Further phylogenetic and genomic context analysis of the tph genes reveals homologous operons as a genetic resource for future biotechnological and metabolic engineering efforts towards circular plastic bio-economy solutions.
Resolvin-D2 targets myogenic cells and improves muscle regeneration in Duchenne muscular dystrophy
Authors: Dort Junio , Orfi Zakaria , Fabre Paul , Molina Thomas , Conte Talita C. , Greffard Karine , Pellerito Ornella , Bilodeau Jean-François , Dumont Nicolas A. 
Published: October 2021

AbstractLack of dystrophin causes muscle degeneration, which is exacerbated by chronic inflammation and reduced regenerative capacity of muscle stem cells in Duchenne Muscular Dystrophy (DMD). To date, glucocorticoids remain the gold standard for the treatment of DMD. These drugs are able to slow down the progression of the disease and increase lifespan by dampening the chronic and excessive inflammatory process; however, they also have numerous harmful side effects that hamper their therapeutic potential. Here, we investigated Resolvin-D2 as a new therapeutic alternative having the potential to target multiple key features contributing to the disease progression. Our in vitro findings showed that Resolvin-D2 promotes the switch of macrophages toward their anti-inflammatory phenotype and increases their secretion of pro-myogenic factors. Moreover, Resolvin-D2 directly targets myogenic cells and promotes their differentiation and the expansion of the pool of myogenic progenitor cells leading to increased myogenesis. These effects are ablated when the receptor Gpr18 is knocked-out, knocked-down, or blocked by the pharmacological antagonist O-1918. Using different mouse models of DMD, we showed that Resolvin-D2 targets both inflammation and myogenesis leading to enhanced muscle function compared to glucocorticoids. Overall, this preclinical study has identified a new therapeutic approach that is more potent than the gold-standard treatment for DMD.
PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes
Authors: Mokhtar Morad M. , El Allali Achraf , Hegazy Mohamed-Elamir F. , Atia Mohamed A. M. 
Published: October 2021

A﻿bstractOver the past decade, the problem of finding an efficient gene-targeting marker set or signature for plant trait characterization has remained challenging. Many databases focusing on pathway mining have been released with one major deficiency, as they lack to develop marker sets that target only genes controlling a specific pathway or certain biological process. Herein, we present the PlantPathMarks database (PPMdb) as a comprehensive, web-based, user-friendly, and interactive hub for pathway-based markers in plant genomes. Based on our newly developed pathway gene set mining approach, two novel pathway-based marker systems called pathway gene-targeted markers (PGTMs) and pathway microsatellite-targeted markers (PMTMs) were developed as a novel class of annotation-based markers. In the PPMdb database, 2,690,742 pathway-based markers reflecting 9,894 marker panels were developed across 82 plant genomes. The markers include 691,555 PGTMs and 1,999,187 PMTMs. Across these genomes, 165,378 enzyme-coding genes were mapped against 126 KEGG reference pathway maps. PPMdb is furnished with three interactive visualization tools (Map Browse, JBrowse and Species Comparison) to visualize, map, and compare the developed markers over their KEGG reference pathway maps. All the stored marker panels can be freely downloaded. PPMdb promises to create a radical shift in the paradigm of the area of molecular marker research. The use of PPMdb as a mega-tool represents an impediment for non-bioinformatician plant scientists and breeders. PPMdb is freely available at http://ppmdb.easyomics.org.
Comparing left atrial indices by CMR in association with left ventricular diastolic dysfunction and adverse clinical outcomes
Authors: Nguyen James , Weber Jonathan , Hsu Brittany , Mulyala Rajasekhar R. , Wang Lin , Cao J. Jane 
Published: October 2021

AbstractLeft atrial (LA) features are altered when diastolic dysfunction (DD) is present. The relations of LA features to the DD severity and to adverse outcomes remain unclear using CMR images. We sought to compare LA features including volumes, emptying fraction, and strains as predictors of left ventricular (LV) DD and adverse outcomes. We compared four groups including normal controls (n = 32), grade I DD (n = 69), grade II DD (n = 42), and grade III DD (n = 21). DD was graded by echocardiography following the current ASE guidelines. Maximum LA volume (LAVmax), minimum LA volume (LAVmin), and LA emptying fraction (LAEF) were assessed using CMR cine images. Phasic LA strains including reservoir, conduit, and booster pump strain were assessed by feature tracking. The outcome was a composite of hospital admissions for heart failure and all-cause mortality analyzed using Cox proportional hazard models. LAVmax and LAVmin were progressively larger while LAEF and LA strain measures were lower with worsening degree of DD (all p < 0.001). Among 132 patients with DD, 61 reached the composite outcome after on average 36-months of follow-up. Each of the LA parameters except for LA conduit strain was an independent predictor of the outcome in the adjusted Cox proportional hazard models (all p < 0.001). They remained significant outcome predictors after the model additionally adjusted for LV longitudinal strain. The AUC of outcome prediction was highest by LAEF (0.760) followed by LA reservoir strain (0.733) and LAVmin (0.725). Among all the LA features, increased LA volumes, reduced LAEF, reduced LA reservoir and booster pump strains were all associated with DD and DD severity. While LA strains are valuable, conventional parameters such as LAEF and LAVmin remain to be highly effective in outcome prediction with comparable performance.
Contribution of on-road transportation to PM2.5
Authors: Li Chao , Managi Shunsuke 
Published: October 2021

AbstractFine particulate matter (PM2.5) mainly originates from combustion emissions. On-road transportation is considered one of the primary sources of PM2.5 emission. The relationship between on-road transportation and PM2.5 concentration varies temporally and spatially, and the estimation for this variation is important for policymaking. Here, we reveal the quantitative association of PM2.5 concentration with on-road transportation by the spatial panel Durbin model and the geographical and temporal weighted regression. We find that 6.17 billion kilometres (km) per km2 on-road transportation increase is associated with a 1-μg/m3 county-level PM2.5 concentration increase in the contiguous United States. On-road transportation marginally contributes to PM2.5, only 1.09% on average. Approximately 3605 premature deaths are attributed to PM2.5 from on-road transportation in 2010, and about a total of 50,223 premature deaths ascribe to PM2.5 taking 6.49% from 2003 to 2016. Our findings shed light on the necessity of the county-level policies considering the temporal and spatial variability of the relationship to further mitigate PM2.5 from on-road transportation.