bluuebunny/crossref_metadata_2025_split huggingface dataset:
ipd: an R package for conducting inference on predicted data
Authors: Salerno Stephen , Miao Jiacheng , Afiaz Awan , Hoffman Kentaro , Neufeld Anna , Lu Qiongshi , McCormick Tyler H , Leek Jeffrey T 
Published: February 2025

Abstract

Summary
ipd is an open-source R software package for the downstream modeling of an outcome and its associated features where a potentially sizable portion of the outcome data has been imputed by an artificial intelligence or machine learning prediction algorithm. The package implements several recent proposed methods for inference on predicted data with a single, user-friendly wrapper function, ipd. The package also provides custom print, summary, tidy, glance, and augment methods to facilitate easy model inspection. This document introduces the ipd software package and provides a demonstration of its basic usage.

Availability
ipd is freely available on CRAN or as a developer version at our GitHub page: github.com/ipd-tools/ipd. Full documentation, including detailed instructions and a usage ‘vignette’ are available at github.com/ipd-tools/ipd.
COBREXA 2: tidy and scalable construction of complex metabolic models
Authors: Kratochvíl Miroslav , Wilken St Elmo , Ebenhöh Oliver , Schneider Reinhard , Satagopam Venkata P 
Published: February 2025

Abstract

Summary
Constraint-based metabolic models offer a scalable framework to investigate biological systems using optimality principles. Construction and simulation of detailed models that utilize multiple kinds of constraint systems pose a significant coding overhead, complicating implementation of new types of analyses. We present an improved version of the constraint-based metabolic modeling package COBREXA, which utilizes a hierarchical model construction framework that decouples the implemented analysis algorithms into independent, yet re-combinable, building blocks. By removing the need to re-implement modeling components, assembly of complex metabolic models is simplified, which we demonstrate on use-cases of resource-balanced models, and enzyme-constrained flux balance models of interacting bacterial communities. Notably, these models show improved predictive capabilities in both monoculture and community settings. In perspective, the re-usable model-building components in COBREXA 2 provide a sustainable way to handle increasingly complex models in constraint-based modeling.

Availability and Implementation
COBREXA 2 is available from https://github.com/COBREXA/COBREXA.jl, and from Julia package repositories. COBREXA 2 works on all major operating systems and computer architectures. Documentation is available at https://cobrexa.github.io/COBREXA.jl/.
Humanitarianism From Below: Border Police, Professional Identities and Moral Dilemmas
Authors: Aliverti Ana , Dufraix Tapia Roberto , Ramos Rodríguez Romina , Tapia Ladino Marcela , García España Elisa 
Published: February 2025

Abstract
In this article, we empirically document the changing dynamics of border controls in the context of the COVID pandemic, and its consequences for border control workers, particularly police, border agents and the military. We focus on three areas: the Anglo-French (Dover-Calais) maritime border, the Euro-African border (Ceuta-Tetuán) and the South American border of Tarapacá-Oruro between Chile and Bolivia. We explore how sovereign strategies of containment and closure, and the diplomatic tensions that arise from them, sometimes operate uneasily with on-the-ground attempts to save lives and provide care in the most precarious situations. These competing institutional demands and moral and professional tensions and dilemmas, we argue, shape an emerging form of management of social precarity that we conceptualize as ‘humanitarianism from below’.
Leveraging genotypes and phenotypes to implement precision medicine in hidradenitis suppurativa management
Authors: Petukhova Lynn , Colvin Annelise , Koerts Nicole D K , Horváth Barbara 
Published: February 2025

Abstract
Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition with many unmet needs. It is characterized by significant clinical heterogeneity, which suggests that a diagnosis of HS captures multiple distinct disease entities and that research aimed at identifying medically relevant HS subtypes will improve its management. Precision medicine is an approach to disease management that uses information encoded in a patient’s genome, and operationalized in clinical presentations and drug responses, to identify disease subtypes. Prior research aimed at identifying HS subtypes has largely focused on phenotypic classifications derived from clinical features of cutaneous lesions. Limitations of existing HS taxonomies emphasize a need for a more nuanced understanding of disease subtypes. Evidence that has emerged from initial genetic studies of HS suggests the presence of at least three HS subtypes, each of which has different clinical implications in terms of disease risks and drug responses. These preliminary findings are instructive in terms of expanding our definitions of HS phenotypes to not only include characteristics of skin lesions, but also disease comorbidities and molecular and cellular phenotypes. Here we provide a comprehensive review of HS phenotype and genotype knowledge, and propose a strategic framework for implementing precision medicine in HS management. Future research should focus on expanding phenotype assessments to include data on multiple scales. Iterative research designs performed with phenotype and genotype data from large diverse cohorts are needed to rigorously define clinically relevant HS subtypes.
Perspectives from the frontline: Exploring the implementation of legislative change into social work practice for brothers and sisters in care in Scotland
Authors: Thomson Lizzie 
Published: February 2025

Abstract
Legislative changes aiming to protect and support relationships between brothers and sisters in Scotland’s care system came into force in July 2021. These changes strengthened existing duties on local authorities to ensure siblings live together if they are in care, and to support them to keep in touch if they cannot live together. Drawing on literature and theory concerning policy implementation in a social work practice context, particularly the concept of ‘street-level bureaucracy’, this small-scale qualitative study used focus groups with social workers (n = 7) from three Scottish local authority areas one year after the enactment of the legislative changes, and thematic analysis of the findings, to explore the implementation of legislative change into practice. The findings highlight a range of factors facilitating implementation, including increased momentum from broader care system reform in Scotland and enhanced focus on sibling relationships in care planning and review processes. Limited resources were seen to constrain implementation, particularly a lack of suitable placement options for larger sibling groups and limited time for social workers to spend supporting children to have contact with their siblings. The findings inform recommendations in relation to resources, training and learning, and assessment and planning, necessary to facilitate successful implementation efforts.
Efficacy and Drug Survival of Tralokinumab in Severe Atopic Dermatitis: An 18-Month Multicenter Experience
Authors: Barei Francesca , Calzari Paolo , Pezzolo Elena , Napolitano Maddalena , Rossi Mariateresa , Guanti Mario Bruno , Caroppo Francesca , Belloni Fortina Anna , Patruno Cataldo , Campanati Anna , Bianchelli Tommaso , D’Agostino Giovanni Marco , Nettis Eustachio , Pugliese Francesco , Picone Vincenzo , Trave Ilaria , Cozzani Emanuele , Stingeni Luca , Hansel Katharina , Dall'Olio Matilde , Galli Benedetta , Coppola Rosa , Panasiti Vincenzo , Maurelli Martina , Girolomoni Giampiero , Ortoncelli Michela , Ribero Simone , Marzano Angelo V , Ferrucci Silvia 
Published: February 2025

Abstract

Background
Tralokinumab has demonstrated efficacy in the treatment atopic dermatitis (AD) in both clinical trials and real-world settings. However, limited data exists on the long-term use of tralokinumab in real-world settings.

Objective
A multicentric Italian study, evaluating tralokinumab's drug survival (DS) and efficacy up to 18 months of treatment among 471 patients with severe AD was conducted.

Methods
EASI (Eczema Area and Severity Index), P-NRS (Pruritus Numerical Rating Scale), SD-NRS (Sleep Disturbance NRS), DLQI (Dermatology Life Quality Index) and ADCT (Atopic Dermatitis Control Tool) were recorded up to 18 months of treatment. DS was analyzed using Kaplan-Meier methodic.

Results
Overall DS rate was 81.5% at 12 months. A significant higher DS was found for females (p&lt;0.001, log-rank=11.90), patients with negative family history (FH) of AD (p=0.015, log-rank=5.96) and patients ≥60-year-old (p=0.018; log-rank=5.6) when considering DS due to inefficacy. The study demonstrates a significant reduction in the clinical scores evaluated, with patients naïve to biologics or Janus kinase inhibitors (JAKi) showing a faster improvement. In the univariate regression analysis, females (p=0.038, OR=1.613; C.I. 1.026-2.534), having no atopic comorbidity (p=0.039; OR=1.692; C.I. 1.027-2.783), negative FH of AD (p=0.031; OR=1.665; C.I. 1.047-2.649) and not using concomitant systemic treatment in the previous months (p=0.003; OR=22.065; C.I. 2.803-173.691) were associated with an increased likelihood of reaching EASI-75. In the multivariate analysis, only the latter variable remained significant (p=0.004, OR=23.037, C.I. 2.793-190.052).

Conclusion
A significant improvement in clinical scores was observed, with patients naïve to biologics or JAKi experiencing faster progress. Female sex, absence of atopic comorbidities, and a negative FH of AD were linked to a higher likelihood of achieving EASI-75 in the univariate analysis but lost significance in the multivariate analysis. For discontinuation due to inefficacy, patients aged 60 and older, females, and those with a negative FH of AD had significantly better survival rates.
Electrophysiological activity underlying motor inhibition facilitated by touch
Authors: Tang Yuting , Zhang Xiaotong , Wang Houmin , Gao Yuxin , Ou Jianlin , Chen Zhuoming , Long Jinyi 
Published: February 2025

Abstract
Tactile sensory information obtained from oneself or others may provide a calming effect and has been shown to enhance participants’ motor control. The extent to which these touch activities may support motor inhibition and the related electrophysiological mechanisms remain unknown. Here, we investigated these effects in twenty healthy volunteers via electroencephalography under 3 touching conditions (self-touch, other-touch, and no-touch) during a stop-signal task. We found that both the self-touch and other-touch conditions resulted in better stopping accuracy and lower stop-signal reaction times than the no-touch condition. Additionally, these 2 touch conditions elicited larger N2 and P3 responses during successful inhibition of planned finger movements. Time-varying network analysis based on electroencephalography was further used to explore the differences in brain networks during conflict monitoring substages under different touch conditions. A top–down projection from the frontal cortex (Fz) to the parietal and occipital cortices was observed along with increased functional connectivity efficiency under touch conditions. These results indicate that tactile information may enhance neural processing efficiency in the human brain by eliciting larger event-related potential components and promoting information processing in the brain network during conflict monitoring processes, thereby contributing to the reactive inhibitory component of motor inhibition.
Anti-SARS-CoV-2 IgG Antibody Titers in Cotemporary lots of Intravenous Immune Globulin and Fresh Frozen Plasma Compared to COVID Convalescent Plasma
Authors: Smith Ethan A , Javier Ginny M , Multani Ashrit , Beaird Omer Eugene , Gaynor Pryce , Yanagimoto-Ogawa Lauren , Schaenman Joanna , Allyn Paul , Alfarhat George , Vijayan Tara , Ziman Alyssa , Garner Omai 
Published: February 2025

Abstract
Given declining COVID convalescent plasma (CCP) collection and increasing scarcity, we compared anti-SARS-CoV-2 IgG antibody titers between CCP, intravenous immunoglobulin (IVIG) and fresh frozen plasma (FFP). Herein, we report comparative anti-SARS-CoV-2 IgG antibody titers between five lots of each blood product, using the DiaSorin Liaison® SARS-CoV-2 TrimericS IgG assay.
Feather Evolution Following Flight Loss In Crown Group Birds: Relaxed Selection And Developmental Constraints
Authors: Saitta Evan T , Carden Lilja , Mitchell Jonathan S , Makovicky Peter J 
Published: February 2025

Abstract
Feathers are complex structures exhibiting structural/functional disparity across species and plumage. Flight was lost in &gt;30 extant lineages from ~79.58 Ma–15 Ka. Effects of flight loss on senses, neuroanatomy, and skeletomusculature are known. To study how flightlessness affects feathers, we measured 11 feather metrics across the plumage of 30 flightless taxa and their phylogenetically closest volant taxa, with broader sampling of primaries across all orders of crown birds. Our sample includes 27 independent flight losses, representing nearly half of extant flightless species. Feather asymmetry measured by barb angle differences between trailing and leading vanes decreases in flightless lineages, most prominently in flight feathers and weakest in contour feathers. Greatest changes in feather anatomy occur in older flightless lineages (penguins, ratites). Comparative methods show some microscopic feather traits are not dramatically modified after flightlessness compared to body mass increase and relative wing and tail fan reduction, but changes toward greater symmetry are stronger. Relaxing selection for flight does not rapidly modify feather flight adaptations, apart from asymmetry. Feathers of recently flightless lineages resemble their volant relatives. Developmental constraints and relaxed selection for novel feather morphologies may explain some observed changes. Macroscopic changes to flight apparati (skeletomusculature, airfoil size) are more evident in recently flightless taxa and could more reliably detect flightlessness in fossils, with increased feather symmetry as a potential microscopic signal. We observed apical modification in later stages of feather development (asymmetric displacement of barb loci), while morphologies arising during early developmental stages are only altered after millions of years of flightlessness.
Quantitative differences in rumen epithelium proteins and detection of lysine acetylation in lambs fed a low or high metabolizable energy diet
Authors: Bond Judith J , Hudson Nicholas J , Kamath Karthik S , Wheeler David , Woodgate Serey , Oddy Victor H 
Published: February 2025

Abstract
Thirty-six Merino wethers (10-month-old) were fed ad libitum for 30 days two diets;1) low metabolizable energy diet (LME; 30% lucerne: 70% cereal chaff) and 2) high ME diet (HME; 40% rolled barley grain: 50% lucerne: 10% cereal chaff). Effects of diet on dry matter intake (DMI), metabolizable energy intake (MEI), liveweight (LWT), average daily gain (ADG), carcass lean or fat gain, liver and empty rumen weight and plasma metabolites were analysed. A membrane enriched protein fraction of rumen epithelium isolated enzymatically from whole depth rumen wall was quantified for each sheep using tandem mass tag mass spectrometry (TMT-MS). The presence or absence of acetylation of lysine residues on identified proteins was counted and the position of the lysine acetylation recorded. In lambs fed the HME diet, DMI (P&lt;0.001), MEI (P&lt;0.001), ADG (P&lt;0.001), fat (P&lt;0.001) and lean gain (P&lt;0.001), as well as liver (P&lt;0.001) and empty rumen (P&lt;0.009) weight were greater than those fed the LME diet. Plasma glucose (P&lt;0.001) and β hydroxybutyrate (P&lt;0.001) at 3 and 5 h after feeding was greater in HME diet than in the LME fed lambs. Changes in rumen epithelium protein abundance in the LME versus HME fed lambs were associated with metabolism in the peroxisome, protein processing in the endoplasmic reticulum (ER), valine, leucine and isoleucine degradation and carbon metabolism. Acetylation of lysine was detected in enzymes involved in glycolysis, tricarboxylic acid (TCA) cycle and fatty acid (FA) metabolism. Quantitative differences in the abundance of rumen epithelium proteins that carry out intracellular processes of energy expenditure were associated with the concentration of ME (MJ/ kg DM) in the diet of growing lambs. The detection of lysine acetylation sites suggests a difference in the ME of the diet regulates enzymatic activity in central metabolic pathways in the rumen epithelium cells.
Factors associated with longitudinal progression of the cumulative burden of morbidity and overall mortality after cisplatin-based chemotherapy for testicular cancer
Authors: Kerns Sarah L , Dinh Paul C , Monahan Patrick O , Stump Timothy , Fung Chunkit , Sesso Howard D , Feldman Darren R , Hamilton Robert J , Vaughn David J , Huddart Robert , Kollmannsberger Christian , Martin Neil E , Nevel Kathryn , Kincaid John , Einhorn Lawrence H , Travis Lois B 
Published: February 2025

Abstract

Background
To comprehensively evaluate the longitudinal progression of cumulative burden of morbidity (CBM) in testicular cancer survivors (TCS) following standard-dose cisplatin-chemotherapy and the impact of modifiable risk factors on morbidity and early-mortality.

Methods
Participants completed first-line chemotherapy ≥6 months before baseline assessments with comprehensive questionnaires and physical-examinations. Based on follow-up assessments (median: 7 years later), longitudinal progression of adverse health outcomes (AHOs) and CBM score (encompassing AHO number and severity) was examined. Baseline health behaviors and AHOs were evaluated for associations with mortality using mixed-effects parametric proportional-hazards regression to identify modifiable risk factors.

Results
Among 616 TCS longitudinally assessed, 23% experienced worsening CBM post-chemotherapy (median: 11 years [IQR = 7-15]). Declines were driven by worsening treatment-related AHOs: tinnitus (29.7%), hearing loss (24.4%), Raynaud’s (22.6%), neuropathy (18.5%), and neuropathic-pain (10.7%). Baseline factors associated with worsening neuropathy included lack of aerobic physical-activity (OR = 1.98, 95%CI = 1.06-3.72) and obesity (OR = 1.85, 95%CI = 1.17-2.92). These were also related to worsening neuropathic-pain (OR = 2.82, p = .009; and OR = 2.29; p = .023). Twenty-nine deaths occurred among 1,830 five-year TCS (4.2% cumulative hazard) (median age: 48-years [range = 22-74]). Participants reporting neuropathic-pain (HR = 3.64, 95%CI = 1.45-9.10), no aerobic (HR = 6.56, 95%CI = 2.73-15.8), or no low-impact physical-activity (HR = 3.96, 95%CI = 1.40-11.2) had significantly higher mortality, as did TCS indicating fair (HR = 9.23, 95%CI = 3.08-27.8) or poor (HR = 18.5, 95%CI = 3.30-103) health. Relationships between pain and mortality were mediated through lowered physical-activity (p = .036).

Conclusions
Clinically-actionable factors associated with early mortality identify high-risk TCS in need of closer monitoring and targeted interventions. The significant relationship between neuropathic-pain and mortality, mediated by low physical-activity, is the first to our knowledge in TCS.
Alcohol consumption, polygenic risk score and the risk of colorectal neoplasia
Authors: Fu Ruojin , Chen Xuechen , Seum Teresa , Hoffmeister Michael , Brenner Hermann 
Published: February 2025

Abstract

Introduction
Excess alcohol consumption is associated with increased risk of colorectal cancer (CRC), but the evidence on the individual and joint effects of alcohol consumption and genetic risk on the occurrence of various stages of colorectal carcinogenesis is limited.

Methods
We evaluated the associations of alcohol consumption and a polygenic risk score (PRS) based on 140 CRC-related loci with findings of colorectal neoplasia among 4,662 participants in the German screening colonoscopy program. Analyses were conducted by multiple logistic regression. We determined genetic risk equivalents (GREs) to quantify the effect of alcohol consumption in terms of the difference in PRS conveying equivalent risk.

Results
Moderate and high (12-&lt;25 and ≥25 g/day) alcohol consumption was associated with increased risk of advanced colorectal neoplasia (aOR [95% CI]: 1.28 [1.03-1.58] and 1.44 [1.14-1.81], respectively), while associations with any colorectal neoplasia were weaker. No significant interactions between alcohol consumption and PRS were observed. Participants with high alcohol consumption in the highest PRS tertile had a 3.4-fold increased risk of advanced neoplasia compared to those with low or no alcohol consumption in the lowest PRS tertile. The estimated impact of high alcohol consumption on the risk of advanced neoplasia was equivalent to the risk increase by a 26 percentiles higher PRS (GRE 26, 95% CI 9-44).

Conclusion
High alcohol consumption and PRS both have a major impact on the risk of advanced colorectal neoplasia. The estimated preventive impact of avoiding high alcohol consumption is as strong as the impact of having a substantially lower polygenic risk.
Impact of m6A Modification and Transcript Quantity on mRNA Composition in Plant Stress Granules
Authors: Kubiak Dawid Jakub , Szczesniak Michal Wojciech , Ostrowska Karolina , Bielewicz Dawid , Bhat Susheel Sagar , Niedojadlo Katarzyna , Szweykowska-Kulinska Zofia , Jarmolowski Artur , Fray Rupert George , Niedojadlo Janusz 
Published: February 2025

Abstract
Stress granules (SGs) are cytoplasmic structures that emerge in response to unfavorable environmental conditions. The mechanisms governing the accumulation of transcripts in SGs are only partially understood. Despite the recognized role of N6-methyladenosine (m6A) in plant transcriptome regulation, its impact on SGs' composition and assembly remains elusive. In Lupinus angustifolius, SGs display a distinctive bi-zonal structure comprising of a ring and a central area with differences in ultrastructure and composition. Subsequent to the transcriptome analysis, specific mRNA were chosen to investigate their localization within SGs and assess m6A levels. Transcripts of hypoxia-responsive genes (ADH1 and HUP7) showed significantly lower levels of m6A compared to housekeeping genes, but only ADH1 was absent in SGs. HUP7 mRNA, characterized by a low quantity of m6A, is present both in the SGs and cytoplasm, probably due to extremely high expression level. The m6A was observed only during the assembly of SGs. In mutants of Arabidopsis thaliana with reduced levels of m6A, ECT2 (reader of m6A) was not observed in SGs, and poly(A) RNA levels and the number of SGs were reduced. In summary, our findings demonstrate a limited impact of m6A modification on SGs assembly. However, the interplay between m6A modification and the overall transcript quantity in the cytoplasm appears to play a regulatory role in mRNA partitioning and assembly of SGs.
Atlas of Fourier Transforms
Authors: Shah Miti , Millsaps William , Sung Suk Hyun , Hovden Robert 
Published: February 2025

Abstract
The book Atlas of Fourier Transforms caters to enthusiasts of all proficiency levels. Here, the reader embarks into the world of Fourier transforms through carefully curated images of over 650 Fourier pairs. As the atlas unfurls, it includes concepts of symmetry, rotation, translation, addition, multiplication, and interference. For those well-versed in the art of Fourier analysis, the Atlas of Fourier Transforms offers an unparalleled dictionary of structures and their corresponding Fourier counterparts.