bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring machine learning to hardware implementations for large data rate x-ray instrumentation
Authors: Rahimifar Mohammad Mehdi , Wingering Quentin , Gouin-Ferland Berthié , Rahali Hamza Ezzaoui , Granger Charles-Étienne , Therrien Audrey C 
Published: November 2023

Abstract
Over the past decade, innovations in radiation and photonic detectors considerably improved their resolution, pixel density, sensitivity, and sampling rate, which all contribute to increased data generation rates. This huge data increases the amount of storage required, as well as the cabling between the source and the storage units. To overcome this problem, edge machine learning (EdgeML) proposes to move computation units near the detectors, utilizing machine learning (ML) models to emulate non-linear mathematical relationships between detector’s output data. ML algorithms can be implemented in digital circuits, such as application-specific integrated circuits and field-programmable gate arrays, which support both parallelization and pipelining. EdgeML has both the benefits of edge computing and ML models to compress data near the detectors. This paper explores the currently available tool-flows designed to translate software ML algorithms to digital circuits near the edge. The main focus is on tool-flows that provide a diverse range of supported models, optimization techniques, and compression methods. We compare their accessibility, performance, and ease of use, and compare them for two high data-rate instrumentation applications: (1) CookieBox, and (2) billion-pixel camera.
Leveraging environmental assessment and environmental justice to deliver equitable, decarbonized built infrastructure
Authors: Greer Fiona 
Published: November 2023

Abstract
Climate change is the most pressing sustainability issue of our time, with anthropogenic greenhouse gas emissions causing economic, environmental, and human health impacts. We need to achieve net-zero civil infrastructure systems to limit global temperature increases. Energy production and supply, transportation, buildings, and industry are examples of civil infrastructure systems. Examining the full scope of impacts throughout the conception, design, construction, operation, maintenance, and decommissioning of infrastructure systems will allow for improved mitigation and adaptation planning. Current planning processes and mechanisms will need to be transformed to achieve ‘climate-smart’ infrastructure that focus on thoughtful minimization of impacts, cooperation with communities, and understanding the implications of failing to act. Social equity is often left as an afterthought in environmentally conscious infrastructure planning. Life-cycle assessment (LCA) is the most complete and decision-powerful model for cataloging environmental impacts of a system. However, the methodology has limitations regarding how it might be leveraged to support multicriteria decision-making in decarbonizing our civil infrastructure systems, such as when trying to account for community preferences, an important element of a just transition. Future planning for the decarbonization of our built environment would benefit from a multi-criteria approach that encompasses elements of LCA, equity, and stakeholder collaboration, the latter two of which are key tenets for advancing environmental justice.
Integrating Data Across Multiple Sites in the Northeastern United States to Examine Associations Between a Prenatal Metal Mixture and Child Cognition
Authors: Rosa Maria José , Foppa Pedretti Nicolo , Goldson Brandon , Mathews Nicole , Merced-Nieves Francheska , Xhani Naim , Bosquet Enlow Michelle , Gershon Richard , Ho Emily , Huddleston Kathi , Wright Robert O , Wright Rosalind J , Colicino Elena 
Published: November 2023

Abstract
We applied a novel hierarchical Bayesian weighted quantile sum (HBWQS) regression to combine data across 3 study sites to examine associations between prenatal exposure to metals and cognitive functioning in childhood. Data from 326 mother-child dyads enrolled in an ongoing cohort study, the Programming of Intergenerational Stress Mechanisms (PRISM) Study, based in New York, New York (recruitment in 2013–2020) and Boston, Massachusetts (recruitment 2011–2013), and the First Thousand Days of Life (FTDL) cohort study (recruitment 2012–2019), based in northern Virginia, were used. Arsenic, cadmium, manganese, lead, and antimony were measured in urine collected during pregnancy. Cognitive functioning was assessed in children aged 3–11 years using the National Institutes of Health Toolbox Cognition Battery. The HBWQS regression showed a negative association between the urinary metal mixture and the Cognition Early Childhood Composite Score in the PRISM New York City (β = −3.67, 95% credible interval (CrI): −7.61, −0.01) and FTDL (β = −3.76, 95% CrI: −7.66, −0.24) samples, with a similar trend in the PRISM Boston sample (β = −3.24, 95% CrI: −6.77, 0.144). We did not detect these associations in traditionally pooled models. HBWQS regression allowed us to account for site heterogeneity and detect associations between prenatal metal-mixture exposure and cognitive outcomes in childhood. Given the ubiquity of metals exposure, interventions aimed at reducing prenatal exposure may improve cognitive outcomes in children.
This article is part of a Special Collection on Environmental Epidemiology.
A feedback loop between management, intraspecific trait variation and harvesting practices
Authors: Locqueville Jonathan , Violle Cyrille , McKey Doyle , Caillon Sophie , Coq Sylvain 
Published: November 2023

Abstract
Abstract. Intraspecific variation in plants is a major ecological mechanism whose local determinants are still poorly understood. In particular, the relationship between this variation and human practices may be key to understanding human–nature relationships. We argue that it is necessary to consider how human practices both influence and depend on the phenotypic variability of species of interest. Arnica montana (arnica) is a good model to study the complex interactions between human actions and plant phenotype, as (i) its ecological niche is shaped by human management actions and (ii) its variability has consequences for harvesters. Using a functional trait approach, we examined feedback loops linking management actions, plant phenotype and harvesting practices. In 27 sites in southeastern France, we measured vegetative and reproductive functional traits of arnica of interest for harvesters, and recorded management actions (grazing; mowing) and ecological variables (including height of surrounding vegetation and tree cover). We examined their effects on plant traits with linear mixed models and used path analysis to test if the effects of human management on traits are mediated by the height of surrounding vegetation. Management actions affected functional traits of arnica. Biomass removal practices (grazing, mowing) were associated with smaller plants producing smaller leaves with reduced specific leaf area. We uncovered the core role of the height of surrounding vegetation in determining this phenotype. Tree cover was associated with reduced flowering. The observed intraspecific variation in response to management actions differentially impacts the two main harvesting practices. Flower-head harvesting depends on reproductive traits that are not impacted by mowing (which is done in winter) but adversely affected by tree cover. In contrast, traits associated with large biomass under tree cover or with high surrounding vegetation are favourable for whole-plant harvesters. Our trait-based approach unveiled clear links between management actions and plant phenotype, with impacts on both vegetative and reproductive traits. These changes induced by management also affect the practices of harvesters. We thus demonstrated a feedback loop between human actions and plant phenotype and provided a novel perspective on human-related causes and consequences of plant intraspecific variability.
Cleaner fish coloration does not always reduce predation risk: testing the effect of protective mimicry in the false cleanerfish, Aspidontus taeniatus
Authors: Sato Hajime , Sakai Yoichi , Kuwamura Tetsuo 
Published: November 2023

Abstract
Cleaning symbiosis of the bluestreak cleaner wrasse, Labroides dimidiatus (Labridae), is a well-known example of mutualism in coral reefs. The cleaner wrasse is characterized by its bluish body colour with black stripes, and the false cleanerfish, Aspidontus taeniatus (Blenniidae), mimics those characteristics precisely. Cleaner fish mimicry is believed to evolve as an aggressive mimicry to bite the fins of deceived fishes; however, protective mimicry to reduce predation risk has not been examined sufficiently. Here, we tested the effect of protective mimicry through field observations and aquarium experiments. Field observations revealed that false cleanerfish were occasionally attacked by piscivorous lizardfishes (Synodontidae). In the aquarium experiments, ambushing predators, the honeycomb grouper, Epinephelus merra (Serranidae), which did not show predatory behaviour to false cleanerfish in the field, attacked the cleaner wrasse (model), the false cleanerfish (mimic), and the lance blenny, Aspidontus dussumieri (non-mimic). When a shelter was provided in the tank, the false cleanerfish and the lance blenny immediately hid inside the shelter for a considerable duration to escape from the predator. These results suggest that cleaner fish coloration does not always decrease predation risks, and our conclusions support the possibility that this mimicry evolved primarily as aggressive mimicry.
Species conservation in the era of genomic science
Authors: Cook Carly N , Redford Kent H , Schwartz Mark W 
Published: November 2023

Abstract
The exponential increase in the availability of genomic data, derived from sequencing thousands of loci or whole genomes, provides exciting new insights into the diversity of life. However, it can also challenge established species concepts and existing management regimes derived from these concepts. Genomic data can help inform decisions about how to manage genetic diversity, but policies that protect identified taxonomic entities can generate conflicting recommendations that create challenges for practitioners. We outline three dimensions of management concern that arise when facing new and potentially conflicting interpretations of genomic data: defining conservation entities, deciding how to manage diversity, and evaluating the risks and benefits of management actions. We highlight the often-underappreciated role of values in influencing management choices made by individuals, scientists, practitioners, the public, and other stakeholders. Such values influence choices through mechanisms such as the Rashomon effect, whereby management decisions are complicated by conflicting perceptions of the causes and consequences of the conservation problem. To illustrate how this might operate, we offer a hypothetical example of this effect for the interpretation of genomic data and its implications for conservation management. Such value-based decisions can be challenged by the rigidity of existing management regimes, making it difficult to achieve the necessary flexibility to match the changing biological understanding. We finish by recommending that both conservation geneticists and practitioners reflect on their respective values, responsibilities, and roles in building a more robust system of species management. This includes embracing the inclusion of stakeholders in decision-making because, as in many cases, there are not objectively defensible right or wrong decisions.
Building distributive populism: basic income and political alternatives to ethno-nationalism
Authors: Doussard Marc 
Published: November 2023

Abstract
Left-behind places face linked economic and political problems that must be resolved jointly. This paper examines the potential contribution of basic income programs to that goal. Consisting of regular, no-strings-attached payments to citizens, basic income programs ensure resources and stability for poor and economically precarious households who comprise a significant share of left-behind places’ populations. Advocacy for basic income emphasizes social and ethical commitment to individuals who have paid the price for economic decline. Thus, even though the goal of national and universal basic income remains distant in the UK, activism for basic income has succeeded in creating alternative paths for populist sentiments originating in the decline of left-behind places. Drawing on extensive fieldwork and interviews with advocates in the UK and elsewhere, I demonstrate that activism for basic income diverts potential support for ethno-nationalism and European withdrawal to alternate, place-contingent and variegated regional political paths.
An online database for einkorn wheat to aid in gene discovery and functional genomics studies
Authors: Sharma Parva Kumar , Ahmed Hanin Ibrahim , Heuberger Matthias , Koo Dal-Hoe , Quiroz-Chavez Jesus , Adhikari Laxman , Raupp John , Cauet Stéphane , Rodde Nathalie , Cravero Charlotte , Callot Caroline , Yadav Inderjit Singh , Kathiresan Nagarajan , Athiyannan Naveenkumar , Ramirez-Gonzalez Ricardo H , Uauy Cristobal , Wicker Thomas , Abrouk Michael , Gu Yong Q , Poland Jesse , Krattinger Simon G , Lazo Gerard R , Tiwari Vijay K 
Published: November 2023

Abstract
Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding.
Database URL https://wheat.pw.usda.gov/GG3/pangenome
Sex- and gender-specific differences in symptoms and health-related quality of life among patients with gastroesophageal reflux disease
Authors: Pelzner Kim , Fuchs Claudia , Petersen Matti , Maus Martin , Bruns Christiane J , Leers Jessica M 
Published: November 2023

Summary
Gastroesophageal Reflux Disease (GERD) is a common chronic gastrointestinal disorder affecting both men and women. Nonerosive reflux disease generally affects more women, whereas GERD complications such as Barrett’s esophagus (BE) or esophageal cancer affect more men. The aim of this study was to evaluate sex- and gender-specific symptoms and health-related quality of life (HRQoL) among men and women with GERD. Patients with clinical signs of reflux and completion of 24-hour pH-Impedance testing at the University Hospital Cologne were included into the study. Evaluation of symptoms and HRQoL included the following validated questionnaires: GERD-Health-Related Quality of Life (GERD HRQL), Gastrointestinal Quality of Life Index (GIQLI), and Hospital Anxiety and Depression Scale (HADS). In all, 509 women and 355 men with GERD were included. Men had a significantly higher DeMeester score (60.2 ± 62.6 vs. 43 ± 49.3, P &lt; 0.001) and a higher incidence of BE (18.6 vs. 11.2%, P = 0.006). Women demonstrated significantly higher levels of anxiety (30.9 vs. 14.5%, P = 0.001), more severely impacting symptoms (45.3 ± 11.3 vs. 49.9 ± 12.3, P &lt; 0.001), as well as physical (14.2 ± 5.7 vs. 16.7 ± 5.6, P &lt; 0.001) and social dysfunction (13.3 ± 4.8 vs. 14.8 ± 4.3, P = 0.002). Women further reported a lower HRQoL (85.3 ± 22.7 vs. 92.9 ± 20.8, P &lt; 0.001). Men and women differ on biological, psychological, and sociocultural levels.
Treatment of Antibiotic Refractory Chronic Pouchitis With JAK Inhibitors and S1P Receptor Modulators: An ECCO CONFER Multicentre Case Series
Authors: Ribaldone Davide Giuseppe , Testa Giulia , Verstockt Bram , Molnar Tamas , Savarino Edoardo , Schmidt Carsten , Vieujean Sophie , Teich Niels , Meianu Corina , Juillerat Pascal , Grellier Nathan , Lobaton Triana 
Published: November 2023

Abstract

Background and Aims
Data regarding the effectiveness and safety of Janus kinase [JAK] inhibitors and sphingosine-1-phosphate [S1P] receptor modulators in antibiotic refractory chronic pouchitis [CARP] are lacking.

Methods
This ECCO-CONFER project retrospectively collected data for JAK inhibitor or S1P receptor modulator treatments for CARP with at least 3 months of follow-up. The outcomes included corticosteroid- and antibiotic-free clinical response and remission at 3 and 12 months, and trends in modified pouchitis disease activity index [mPDAI], endoscopic PDAI, C-reactive protein, and calprotectin.

Results
Seventeen treatments in 15 patients were evaluated. Previous pouchitis treatments included infliximab [5/15], adalimumab [4/15], vedolizumab [9/15], and ustekinumab [5/15]. Pooling data on JAK inhibitors [eight tofacitinib, one filgotinib, and six upadacitinib] after 3 months [T3], steroid- and antibiotic-free clinical response was achieved in 53.3% [8/15], and steroid- and antibiotic-free clinical remission was achieved in 40% [6/15]. Of the patients with at least 12 months of follow-up, steroid- and antibiotic-free clinical response was achieved in 50% [3/6] and remission in one patient [16.7%], endoscopic response in 50% [3/6], and endoscopic remission in 50% [3/6]. Of the two ozanimod treatments at T3, steroid- and antibiotic-free clinical response was achieved in one patient, without remission; both discontinued ozanimod before T12. No side effects were reported.

Conclusions
Small molecules may represent a suitable option for CARP refractory to multiple biologics, deserving further investigation.
Long-term outcome of bicuspid aortic valve disease
Authors: Aschauer Julia , Zilberszac Robert , Gleiss Andreas , Colizzi Christian , Binder Thomas , Bruno Piergiorgio , Laufer Günther , Massetti Massimo , Gabriel Harald , Rosenhek Raphael 
Published: November 2023

Abstract

Aims
Bicuspid aortic valve (BAV) is a common congenital condition that is frequently associated with aortic stenosis (AS) and aortic regurgitation (AR), as well as aortic aneurysms, but specific outcome data are scarce. The present study sought to assess outcomes in a large cohort of consecutive patients with BAV.

Methods and results
A total of 581 consecutive patients (median age 29 years, 157 female) with BAV were included in the study and followed prospectively in a heart valve clinic follow-up programme. The overall survival rate after 10 years was 94.5%. During follow-up, 158 patients developed an indication for surgery. Event-free survival rates were 97%, 94%, 87%, and 73% at 1, 2, 5, and 10 years, respectively. In the multivariable analysis, event rates were independently predicted by AS [subdistribution hazard ratio (SHR) 2.3 per degree of severity], AR (SHR 1.5 per degree of severity), baseline aortic dilatation ≥ 40 mm (SHR 1.9), and age (SHR 1.3) (P &lt; 0.001).

Conclusion
BAV disease is associated with a high rate of cardiac events, but state-of-the-art care results in good survival with low rates of infective endocarditis, aortic dissection, and sudden death. Incremental degrees of AS and regurgitation, the presence of aortic dilatation, and age are predictive of cardiac events.
Update on long-term cardiovascular risk after pre-eclampsia: a systematic review and meta-analysis
Authors: Inversetti Annalisa , Pivato Carlo Andrea , Cristodoro Martina , Latini Alessia Chiara , Condorelli Gianluigi , Di Simone Nicoletta , Stefanini Giulio 
Published: November 2023

Abstract

Background/introduction
There is a need for further studies on the cardiovascular risk of women experiencing pre-eclampsia (PE).

Purpose
To update the literature regarding the association between a history of PE and subsequent cardiovascular diseases, including cardiovascular death, coronary heart diseases, heart failure, and stroke, focusing on the trend in the effect size (ES) estimates over time.

Methods and results
Following PRISMA guidelines, from inception to May 2023, we performed a systematic review of PubMed, MEDLINE, Scopus, and EMBASE. Randomized, cohort, or case-control studies in English were included if fulfiling the following criteria:(i) The association between PE and subsequent cardiovascular disease was adjusted for clinically relevant variables, (ii) the presence of a control group, and (iii) at least 1 year of follow-up. Pooled adjusted ESs and 95% confidence intervals (CIs) were used as effect estimates and calculated with a random-effect model. Twenty-two studies met the inclusion criteria. PE was associated with a higher risk of cardiovascular death (ES 2.08, 95% CI 1.70–2.54, I2 56%, P &lt; 0.00001), coronary artery diseases (ES 2.04, 95% CI 1.76–2.38, I2 87%, P &lt; 0.00001), heart failure (ES 2.47, 95% CI 1.89–3.22, I2 83%, P &lt; 0.00001), and stroke (ES 1.75, 95% CI 1.52–2.02, I2 72%, P &lt; 0.00001) after adjusting for potential confounders. This risk is evident in the first 1-to-3 years of follow-up and remains significant until 39 years of follow-up.

Conclusions
Compared to women who experienced a normal pregnancy, those suffering from PE have about double the risk of lifetime cardiovascular disease.
Modeling the effects of consanguinity on autosomal and X-chromosomal runs of homozygosity and identity-by-descent sharing
Authors: Cotter Daniel J , Severson Alissa L , Kang Jonathan T L , Godrej Hormazd N , Carmi Shai , Rosenberg Noah A 
Published: November 2023

Abstract
Runs of homozygosity (ROH) and identity-by-descent (IBD) sharing can be studied in diploid coalescent models by noting that ROH and IBD-sharing at a genomic site are predicted to be inversely related to coalescence times—which in turn can be mathematically obtained in terms of parameters describing consanguinity rates. Comparing autosomal and X-chromosomal coalescent models, we consider ROH and IBD-sharing in relation to consanguinity that proceeds via multiple forms of first-cousin mating. We predict that across populations with different levels of consanguinity, (1) in a manner that is qualitatively parallel to the increase of autosomal IBD-sharing with autosomal ROH, X-chromosomal IBD-sharing increases with X-chromosomal ROH, owing to the dependence of both quantities on consanguinity levels; (2) even in the absence of consanguinity, X-chromosomal ROH and IBD-sharing levels exceed corresponding values for the autosomes, owing to the smaller population size and lower coalescence time for the X chromosome than for autosomes; (3) with matrilateral consanguinity, the relative increase in ROH and IBD-sharing on the X chromosome compared to the autosomes is greater than in the absence of consanguinity. Examining genome-wide SNPs in human populations for which consanguinity levels have been estimated, we find that autosomal and X-chromosomal ROH and IBD-sharing levels generally accord with the predictions. We find that each 1% increase in autosomal ROH is associated with an increase of 2.1% in X-chromosomal ROH, and each 1% increase in autosomal IBD-sharing is associated with an increase of 1.6% in X-chromosomal IBD-sharing. For each calculation, particularly for ROH, the estimate is reasonably close to the increase of 2% predicted by the population-size difference between autosomes and X chromosomes. The results support the utility of coalescent models for understanding patterns of genomic sharing and their dependence on sex-biased processes.