bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Deep Learning Models to Improve Ulcerative Colitis Endoscopic Disease Activity Scoring Under Multiple Scoring Systems
Authors: Byrne Michael F , Panaccione Remo , East James E , Iacucci Marietta , Parsa Nasim , Kalapala Rakesh , Reddy Duvvur N , Ramesh Rughwani Hardik , Singh Aniruddha P , Berry Sameer K , Monsurate Ryan , Soudan Florian , Laage Greta , Cremonese Enrico D , St-Denis Ludovic , Lemaître Paul , Nikfal Shima , Asselin Jerome , Henkel Milagros L , Travis Simon P 
Published: October 2022

Abstract

Background and Aims
Lack of clinical validation and inter-observer variability are two limitations of endoscopic assessment and scoring of disease severity in patients with ulcerative colitis [UC]. We developed a deep learning [DL] model to improve, accelerate and automate UC detection, and predict the Mayo Endoscopic Subscore [MES] and the Ulcerative Colitis Endoscopic Index of Severity [UCEIS].

Methods
A total of 134 prospective videos [1550 030 frames] were collected and those with poor quality were excluded. The frames were labelled by experts based on MES and UCEIS scores. The scored frames were used to create a preprocessing pipeline and train multiple convolutional neural networks [CNNs] with proprietary algorithms in order to filter, detect and assess all frames. These frames served as the input for the DL model, with the output being continuous scores for MES and UCEIS [and its components]. A graphical user interface was developed to support both labelling video sections and displaying the predicted disease severity assessment by the artificial intelligence from endoscopic recordings.

Results
Mean absolute error [MAE] and mean bias were used to evaluate the distance of the continuous model’s predictions from ground truth, and its possible tendency to over/under-predict were excellent for MES and UCEIS. The quadratic weighted kappa used to compare the inter-rater agreement between experts’ labels and the model’s predictions showed strong agreement [0.87, 0.88 at frame-level, 0.88, 0.90 at section-level and 0.90, 0.78 at video-level, for MES and UCEIS, respectively].

Conclusions
We present the first fully automated tool that improves the accuracy of the MES and UCEIS, reduces the time between video collection and review, and improves subsequent quality assurance and scoring.
Ethnic enclaves, early school leaving, and adolescent crime among immigrant youth
Authors: Hermansen Are Skeie 
Published: October 2022

Abstract
Spatial concentration of immigrant minorities raises concerns about the intergenerational consequences of place-based ethnic inequalities. This study asks how socioeconomic properties of the ethnic neighbourhood environment during adolescence predict future criminal behaviour and early school leaving among immigrant youth using administrative data from Norway. The results show that immigrant youth’s adolescent exposure to better-educated immigrant neighbours from the same origin country is related to lower risks of criminal engagement and higher likelihoods of completing upper-secondary education, while growing up in areas with less-educated coethnics is associated with adverse outcomes. Although effect sizes are modest, these relationships are robust to adjustment for a broad set of background characteristics and fixed effects at the level of neighbourhoods and national-origin groups. Coethnic neighbours’ educational resources are more strongly associated with adolescent crime and early school leaving among immigrant youth from disadvantaged family backgrounds. Overall, these findings support the predictions of influential theories of assimilation which emphasize that access to social capital and socioeconomic resources found within local ethnic enclaves shape the future life chances of immigrant youth.
Gut microbial ecology of Philippine gekkonids: ecoevolutionary effects on microbiome compositions
Authors: Eliades Samuel J , Colston Timothy J , Siler Cameron D 
Published: October 2022

AbstractGiven the rapidly changing landscapes of habitats across the globe, a sound understanding of host-associated microbial communities and the ecoevolutionary forces that shape them is needed to assess general organismal adaptability. Knowledge of the symbiotic endogenous microbiomes of most reptilian species worldwide remains limited. We sampled gut microbiomes of geckos spanning nine species and four genera in the Philippines to (i) provide baseline data on gut microbiota in these host species, (ii) test for significant associations between host phylogenetic relationships and observed microbial assemblages, potentially indicative of phylosymbiosis, and (iii) identify correlations between multiple ecoevolutionary factors (e.g. species identity, habitat tendencies, range extents, and maximum body sizes) and gut microbiomes in Philippine gekkonids. We recovered no significant association between interspecific host genetic distances and observed gut microbiomes, providing limited evidence for phylosymbiosis in this group. Philippine gekkonid microbiomes were associated most heavily with host species identity, though marked variation among conspecifics at distinct sampling sites indicates that host locality influences gut microbiomes as well. Interestingly, individuals grouped as widespread and microendemic regardless of host species identity displayed significant differences in alpha and beta diversity metrics examined, likely driven by differences in rare OTU presence between groups. These results provide much needed insight in host-associated microbiomes in wild reptiles and the ecoevolutionary forces that structure such communities.
Accurate modeling of replication rates in genome-wide association studies by accounting for Winner’s Curse and study-specific heterogeneity
Authors: Zou Jennifer , Zhou Jinjing , Faller Sarah , Brown Robert P , Sankararaman Sriram S , Eskin Eleazar 
Published: October 2022

AbstractGenome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex human traits, but only a fraction of variants identified in discovery studies achieve significance in replication studies. Replication in genome-wide association studies has been well-studied in the context of Winner’s Curse, which is the inflation of effect size estimates for significant variants due to statistical chance. However, Winner’s Curse is often not sufficient to explain lack of replication. Another reason why studies fail to replicate is that there are fundamental differences between the discovery and replication studies. A confounding factor can create the appearance of a significant finding while actually being an artifact that will not replicate in future studies. We propose a statistical framework that utilizes genome-wide association studies and replication studies to jointly model Winner’s Curse and study-specific heterogeneity due to confounding factors. We apply this framework to 100 genome-wide association studies from the Human Genome-Wide Association Studies Catalog and observe that there is a large range in the level of estimated confounding. We demonstrate how this framework can be used to distinguish when studies fail to replicate due to statistical noise and when they fail due to confounding.
Spindly is a nucleocytosolic O-fucosyltransferase in Dictyostelium and related proteins are widespread in protists and bacteria
Authors: van der Wel Hanke , Garcia Ana Maria , Gas-Pascual Elisabet , Willis Macy M , Kim Hyun W , Bandini Giulia , Gaye Maissa Mareme , Costello Catherine E , Samuelson John , West Christopher M 
Published: October 2022

Abstract
O-GlcNAcylation is a prominent modification of nuclear and cytoplasmic proteins in animals and plants and is mediated by a single O-GlcNAc transferase (OGT). Spindly (Spy), a paralog of OGT first discovered in higher plants, has an ortholog in the apicomplexan parasite Toxoplasma gondii, and both enzymes are now recognized as O-fucosyltransferases (OFTs). Here we investigate the evolution of spy-like genes and experimentally confirm OFT activity in the social amoeba Dictyostelium—a protist that is more related to fungi and metazoa. Immunofluorescence probing with the fucose-specific Aleuria aurantia lectin (AAL) and biochemical cell fractionation combined with western blotting suggested the occurrence of nucleocytoplasmic fucosylation. The absence of reactivity in mutants deleted in spy or gmd (unable to synthesize GDP-Fuc) suggested monofucosylation mediated by Spy. Genetic ablation of the modE locus, previously predicted to encode a GDP-fucose transporter, confirmed its necessity for fucosylation in the secretory pathway but not for the nucleocytoplasmic proteins. Affinity capture of these proteins combined with mass spectrometry confirmed monofucosylation of Ser and Thr residues of several known nucleocytoplasmic proteins. As in Toxoplasma, the Spy OFT was required for optimal proliferation of Dictyostelium under laboratory conditions. These findings support a new phylogenetic analysis of OGT and OFT evolution that indicates their occurrence in the last eukaryotic common ancestor but mostly complementary presence in its eukaryotic descendants with the notable exception that both occur in red algae and plants. Their generally exclusive expression, high degree of conservation, and shared monoglycosylation targets suggest overlapping roles in physiological regulation.
FGF20andPGM2variants are associated with childhood asthma in family-based whole-genome sequencing studies
Authors: Hecker Julian , Chun Sung , Samiei Ahmad , Liu Cuining , Laurie Cecelia , Kachroo Priyadarshini , Lutz Sharon M , Lee Sanghun , Smith Albert V , Lasky-Su Jessica , Cho Michael H , Sharma Sunita , Soto Quirós Manuel Enrique , Avila Lydiana , Celedón Juan C , Raby Benjamin , Zhou Xiaobo , Silverman Edwin K , DeMeo Dawn L ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Lange Christoph , Weiss Scott T 
Published: October 2022

AbstractBackgroundAsthma is a heterogeneous common respiratory disease that remains poorly understood. The established genetic associations fail to explain the high estimated heritability, and the prevalence of asthma differs between populations and geographic regions. Robust association analyses incorporating different genetic ancestries and whole-genome sequencing data may identify novel genetic associations.MethodsWe performed family-based genome-wide association analyses of childhood-onset asthma based on whole-genome sequencing (WGS) data for the ‘The Genetic Epidemiology of Asthma in Costa Rica’ study (GACRS) and the Childhood Asthma Management Program (CAMP). Based on parent–child trios with children diagnosed with asthma, we performed a single variant analysis using an additive and a recessive genetic model and a region-based association analysis of low-frequency and rare variants.ResultsBased on 1180 asthmatic trios (894 GACRS trios and 286 CAMP trios, a total of 3540 samples with WGS data), we identified three novel genetic loci associated with childhood-onset asthma: rs4832738 on 4p14 ($P=1.72\ast{10}^{-9}$, recessive model), rs1581479 on 8p22 ($P=1.47\ast{10}^{-8}$, additive model) and rs73367537 on 10q26 ($P=1.21\ast{10}^{-8}$, additive model in GACRS only). Integrative analyses suggested potential novel candidate genes underlying these associations: PGM2 on 4p14 and FGF20 on 8p22.ConclusionOur family-based whole-genome sequencing analysis identified three novel genetic loci for childhood-onset asthma. Gene expression data and integrative analyses point to PGM2 on 4p14 and FGF20 on 8p22 as linked genes. Furthermore, region-based analyses suggest independent potential low-frequency/rare variant associations on 8p22. Follow-up analyses are needed to understand the functional mechanisms and generalizability of these associations.
Exposure of commercially exploited shellfish to changing pH levels: how to scale-up experimental evidence to regional impacts
Authors: Townhill B L , Artioli Y , Pinnegar J K , Birchenough S N R 
Published: October 2022

Abstract
Ocean acidification has become one of the most intensively studied climate change topics and it is expected to have both direct and indirect impacts on species, ecosystems, and economies. Experiments have been performed on different taxa, life stages, and at different pH levels. Despite this wealth of information, several key challenges remain, including (1) uncertainty about how to incorporate current pH ranges and variability experienced by organisms into experiments, and (2) how to bring this information together to support analysis and assessments at the broader ecosystem level. Sophisticated modelling tools are needed to ‘scale-up’ from experimental results to regional-scale insights. This paper highlights the challenges of combining information to determine how commercially exploited species may be affected under future pH levels, and how modelling and experimental results might be better aligned, using northwest Europe and the waters around the British Isles as an example. We argue that in most cases the current evidence does not offer sufficient information into impacts at projected pH levels, and that future experiments should be designed to consider the pH levels actually experienced by organisms, as well as variability in pH. These types of study are key in safeguarding commercially exploited shellfish stocks.
Chaos synchronization in the presence of external disturbances with a novel layered control strategy
Authors: Shafei H R , Shafei A M , Momeni A 
Published: October 2022

Abstract
In this study, a novel layered control system is designed to manage chaotic systems in the presence of external uncertainties and external disturbances. An optimal-robust control system with updated gains through an adaptive rule has been designed to deal with uncertainties in chaotic systems. An optimal control law based on the control Lyapunov function is integrated with an adaptive non-singular terminal sliding mode control law to robustly manage uncertain chaotic systems. The Lyapunov theory is also utilized to illustrate the asymptotic stability of the mentioned layered control strategy. In order to show the effectiveness of the proposed control scheme over the adaptive sliding mode control method, the chaos synchronization problem of two different chaotic systems has been conducted with this approach. The simulation results show that the presented scheme can manage chaotic systems against uncertainties and external disturbances robustly with less control effort as compared with the other method.
A Result on Parabolic Gradient Regularity in Orlicz Spaces and Application to Absorption-Induced Blow-Up Prevention in a Keller–Segel-Type Cross-Diffusion System
Authors: Winkler Michael 
Published: October 2022

Abstract
The Neumann problem for (0.1)$$ \begin{align}& V_t = \Delta V-aV+f(x,t) \end{align}$$is considered in bounded domains $\Omega \subset {\mathbb {R}}^n$ with smooth boundary, where $n\ge 1$ and $a\in {\mathbb {R}}$. By means of a variational approach, a statement on boundedness of the quantities $$ \begin{eqnarray*} \sup_{t\in (0,T)} \int_\Omega \big|\nabla V(\cdot,t)\big|^p L^{\frac{n+p}{n+2}} \Big( \big|\nabla V(\cdot,t)\big| \Big) \end{eqnarray*}$$in dependence on the expressions (0.2)$$ \begin{align}& \sup_{t\in (0,T-\tau)} \int_t^{t+\tau} \int_\Omega |f|^{\frac{(n+2)p}{n+p}} L\big( |f|\big) \end{align}$$is derived for $p\ge 2$, $\tau&gt;0$, and $T\ge 2\tau $, provided that $L\in C^0([0,\infty ))$ is positive, strictly increasing, unbounded, and slowly growing in the sense that $\limsup _{s\to \infty } \frac {L(s^{\lambda _0})}{L(s)} &lt;\infty $ for some $\lambda _0&gt;1$. In the particular case when $p=n\ge 2$, an additional condition on growth of $L$, particularly satisfied by $L(\xi ):=\ln ^\alpha (\xi +b)$ whenever $b&gt;0$ and $\alpha&gt;\frac {(n+2)(n-1)}{2n}$, is identified as sufficient to ensure that as a consequence of the above, bounds for theintegrals in (0.2) even imply estimates for the spatio-temporal modulus of continuity of solutions to (0.1). A subsequent application to the Keller–Segel system $$ \begin{eqnarray*} \left\{ \begin{array}{l} u_t = \nabla \cdot \big( D(v)\nabla u\big) - \nabla \cdot \big( uS(v)\nabla v\big) + ru - \mu u^2, \\[1mm] v_t = \Delta v-v+u, \end{array} \right. \end{eqnarray*}$$shows that when $n=2$, $r\in {\mathbb {R}}$, $0&lt;D\in C^2([0,\infty ))$, and $S\in C^2([0,\infty )) \cap W^{1,\infty }((0,\infty ))$ and thus especially in the presence of arbitrarily strong diffusion degeneracies implied by rapid decay of $D$, any choice of $\mu&gt;0$ excludes blowup in the sense that for all suitably regular nonnegative initial data, an associated initial-boundary value problem admits a global bounded classical solution.
It Just Feels Right. Visuality and Emotion Norms in Right-Wing Populist Storytelling
Authors: Katja Freistein , Frank Gadinger , Christine Unrau 
Published: October 2022

Abstract
This paper contributes to debates on the growing appeal of right-wing populism by combining a focus on visuality, narratives, and emotions. We argue that right-wing populists’ claims extend to establishing alternative emotion norms that collectivize feelings and their expression, and are conveyed in visual narratives. The emotional range covered by these norms transcends emotions usually associated with right-wing populism such as fear or humiliation. By employing seemingly inoffensive modes of presentation, emotional responses including indignation, compassion, and schadenfreude can be used as narrative bait for hitherto uninterested audiences. Following from that, emotion norms, such as exclusive forms of sympathy and humor, can be established. We illustrate our argument in three short case studies from Austria, France, and Italy. The conceptual and methodological insights are particularly relevant for those interested in the power of emotions, different modes of visual storytelling in world politics, and the performative effects of right-wing populist practices and narratives in politics.
Overly broad-spectrum antibiotic treatment of wild-type Pseudomonas aeruginosa infections in relation to the EUCAST new definition of susceptibility testing categories, a retrospective multicentre cohort study
Authors: Ourghanlian Clément , Fihman Vincent , Morel Antoine , Lafont Charlotte , Galy Adrien , Calimouttoupoulle Eimma , Woerther Paul-Louis , Lepeule Raphaël 
Published: October 2022

Abstract

Objectives
EUCAST changed the definition of the ‘intermediate’ (I) category in 2019, now defined as ‘susceptible, increased exposure’. This new definition could lead to an increased prescription of antibiotics still reported as ‘S’, compared with those now reported as ‘I’. The objective of this study was to evaluate the influence of this definition on the use of overly broad-spectrum antibiotics for the treatment of infections caused by WT Pseudomonas aeruginosa.

Methods
A retrospective observational multicentre study was conducted, involving five hospitals. Two 15 month study periods were defined, before and after the implementation of the new definition. All patients with an infection caused by WT P. aeruginosa treated by β-lactams were included. The main endpoint was the proportion of patients treated by an overly broad-spectrum antibiotic treatment by meropenem or ceftolozane/tazobactam.

Results
Two hundred and ninety-one patients were included. No difference between groups was found, in terms of infection, microbiology or demographic characteristics. Two overly broad-spectrum antibiotic treatments by meropenem or ceftolozane/tazobactam were observed in Period 1 (1.2%), versus 13 in Period 2 (10.8%; P &lt; 0.001). No overly broad-spectrum treatment was observed when the antimicrobial stewardship team had given advice.

Conclusions
This new definition can cause a negative impact on the use of overly broad-spectrum antibiotic treatment due to misunderstanding by clinicians. Its successful implementation requires adaptation of software for reporting antibiotic susceptibility, a sustained strong information campaign by microbiologists and support by an antimicrobial stewardship team.
Clinical and temporal characterization of COVID-19 subgroups using patient vector embeddings of electronic health records
Authors: Ta Casey N , Zucker Jason E , Chiu Po-Hsiang , Fang Yilu , Natarajan Karthik , Weng Chunhua 
Published: October 2022

Abstract

Objective
To identify and characterize clinical subgroups of hospitalized Coronavirus Disease 2019 (COVID-19) patients.

Materials and Methods
Electronic health records of hospitalized COVID-19 patients at NewYork-Presbyterian/Columbia University Irving Medical Center were temporally sequenced and transformed into patient vector representations using Paragraph Vector models. K-means clustering was performed to identify subgroups.

Results
A diverse cohort of 11 313 patients with COVID-19 and hospitalizations between March 2, 2020 and December 1, 2021 were identified; median [IQR] age: 61.2 [40.3–74.3]; 51.5% female. Twenty subgroups of hospitalized COVID-19 patients, labeled by increasing severity, were characterized by their demographics, conditions, outcomes, and severity (mild-moderate/severe/critical). Subgroup temporal patterns were characterized by the durations in each subgroup, transitions between subgroups, and the complete paths throughout the course of hospitalization.

Discussion
Several subgroups had mild-moderate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections but were hospitalized for underlying conditions (pregnancy, cardiovascular disease [CVD], etc.). Subgroup 7 included solid organ transplant recipients who mostly developed mild-moderate or severe disease. Subgroup 9 had a history of type-2 diabetes, kidney and CVD, and suffered the highest rates of heart failure (45.2%) and end-stage renal disease (80.6%). Subgroup 13 was the oldest (median: 82.7 years) and had mixed severity but high mortality (33.3%). Subgroup 17 had critical disease and the highest mortality (64.6%), with age (median: 68.1 years) being the only notable risk factor. Subgroups 18–20 had critical disease with high complication rates and long hospitalizations (median: 40+ days). All subgroups are detailed in the full text. A chord diagram depicts the most common transitions, and paths with the highest prevalence, longest hospitalizations, lowest and highest mortalities are presented. Understanding these subgroups and their pathways may aid clinicians in their decisions for better management and earlier intervention for patients.