bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryo-EM structure of human PAPP-A2 and mechanism of substrate recognition
Authors: Sridar Janani , Mafi Amirhossein , Judge Russell A. , Xu Jun , Kong Kailyn A. , Wang John C. K. , Stoll Vincent S. , Koukos Georgios , Simon Reyna J. , Eaton Dan , Bratkowski Matthew , Hao Qi 
Published: October 2023

AbstractPregnancy-Associated Plasma Protein A isoforms, PAPP-A and PAPP-A2, are metalloproteases that cleave insulin-like growth factor binding proteins (IGFBPs) to modulate insulin-like growth factor signaling. The structures of homodimeric PAPP-A in complex with IGFBP5 anchor peptide, and inhibitor proteins STC2 and proMBP have been recently reported. Here, we present the single-particle cryo-EM structure of the monomeric, N-terminal LG, MP, and the M1 domains (with the exception of LNR1/2) of human PAPP-A2 to 3.13 Å resolution. Our structure together with functional studies provides insight into a previously reported patient mutation that inactivates PAPP-A2 in a distal region of the protein. Using a combinational approach, we suggest that PAPP-A2 recognizes IGFBP5 in a similar manner as PAPP-A and show that PAPP-A2 cleaves IGFBP5 less efficiently due to differences in the M2 domain. Overall, our studies characterize the cleavage mechanism of IGFBP5 by PAPP-A2 and shed light onto key differences with its paralog PAPP-A.
Blame it on my youth: the origins of attitudes towards immigration
Authors: Jeannet Anne-Marie , Dražanová Lenka 
Published: October 2023

AbstractRecent studies have demonstrated generational differences in attitudes towards immigration, however, less is known about what are the exact factors behind these differences. Our study investigates why cohorts formulate distinct patterns in attitudes towards immigration through a collective process of political socialization during their formative years. The theoretical arguments are tested using hierarchical age-period-cohort modelling across thirteen cohorts in thirteen European countries using micro attitudinal data (2002–2020) integrated with historical macro-political data. We find that contextual exposure to the principle of equality in the formative political climate is central to the formulation of a person’s attitudes towards immigration later in life. While the prevalence of the principle of equality affects immigration attitudes in adulthood positively, the principle of tradition does not. The findings imply that even subtle and cyclical shifts in national politics affect the political orientations of those undergoing the process of political socialization.
The evolution of epidemics and the publication of epidemic news in the local press: a study in the region of Braga (Northern Portugal)
Authors: Azevedo Mariana , Mourão Paulo Reis 
Published: October 2023

AbstractThe periods 1918–1920 and 2019–2021 were characterized by epidemic moments. The COVID-19 pandemic recalled the crises associated with the Spanish flu, exanthematic typhus, and smallpox of the 1920s. However, few works have focused on a comparative task of these episodes in local newspapers. Through the analysis of the daily editions of Commercio do Minho and its successor, Correio do Minho, we fill this gap with this work. It was possible to portray the socioeconomic reach of these pandemics in a community in the northern coastal region of Portugal. Using time series analysis of the number of news items as well as the number of deaths from each of the episodes in the periods 1918 and 1920 and 2020 and 2021 (namely using Autoregressive Distributed Lag models), we conclude that the COVID-19 pandemic exhibited a greater focus on the problem in the local press. Other results made it possible to view the differentiated response of the number of news items regarding each epidemic episode depending on the number of deaths in the population, both between 1918 and 1920 and between 2020 and 2021. Thus, our work came to demonstrate three pieces of evidence in the relationship between news and epidemic processes. Firstly, COVID-19, as an example of the most recent pandemic, brought a reactivity of the local press resulting in a greater number of news, even compared to the number of fatalities. Secondly, the number of news published on epidemic/pandemic issues tends to follow the evolution of the severity of the event—there is more news in the months that follow periods of greater severity of the disease. Finally, the “disappearance” of published news faster in 1918–1920 also reveals a lesser focus that newsrooms perceived on society of that time in the face of the reported pandemic (Nie et al. 2022).
Antiplatelet therapy and incident cognitive impairment or dementia—a systematic review and meta-analysis of randomised clinical trials
Authors: Kitt Kevin , Murphy Robert , Clarke Aoibhin , Reddin Catriona , Ferguson John , Bosch Jackie , Whiteley William , Canavan Michelle , Judge Conor , O’Donnell Martin 
Published: October 2023

Abstract

Objective
The benefit of antiplatelet therapy in preventing cognitive impairment or dementia is uncertain. We investigated the association between antiplatelet therapy and incident cognitive impairment or dementia in randomised clinical trials.

Methods
We searched PubMed, EMBASE and CENTRAL for randomised clinical trials published from database inception through 1 February 2023. Trials that evaluated the association of antiplatelet therapy with incident cognitive impairment or dementia were included. For single-agent antiplatelet, the control group was placebo. For dual agent antiplatelet therapy, the control group was single-agent monotherapy. A random-effects meta-analysis model was used to report pooled treatment effects and 95% confidence intervals (CIs). The primary outcome was incident cognitive impairment or dementia. Secondary outcomes included change in cognitive test scores.

Results
A total of 11 randomised clinical trials were included (109,860 participants). All reported the incidence of cognitive impairment or dementia on follow-up. The mean (SD) age of trial participants was 66.2 (7.9) years. Antiplatelet therapy was not significantly associated with a reduced risk of cognitive impairment or dementia (11 trials; 109,860 participants) (3.49% versus 4.18% of patients over a mean trial follow-up of 5.8 years; odds ratio [OR], 0.94 [95% CI, 0.88–1.00]; absolute risk reduction, 0.2% [95% CI, −0.4% to 0.009%]; I2 = 0.0%). Antiplatelet therapy was not significantly associated with mean change in cognitive test scores.

Conclusion
In this meta-analysis, antiplatelet therapy was not significantly associated with a lower risk of incident cognitive impairment or dementia, but the CIs around this outcome do not exclude a modest preventative effect.
Individual survival is dictated by group personality in a marsh ecosystem predator–prey interaction
Authors: Salerno Christina M , Williams Regan C , Kamel Stephanie J 
Published: October 2023

Abstract
Predator–prey interactions structure ecological communities, and personality can significantly mediate these interactions. Personality expression is often contingent on social context, suggesting that group personality may be key in determining the outcomes of predator encounters. Here, we test the influence of individual personality and group composition on survival of the marsh periwinkle, Littoraria irrorata, when exposed to its main predator, the blue crab, Callinectes sapidus, both integral players in mediating the productivity and health of salt marsh ecosystems. Snails were categorized as having bold or shy personality types, which were unrelated to shell length, though neither trait influenced survival when individual snails were exposed to a predator. However, when snails were partitioned into groups differing in personality composition, snails in groups with bold individuals had higher survival than those in groups with none. While group type did not influence the survival of bold snails, shy snails performed better in mixed groups: the presence of a few bold individuals emerged as especially effective in decreasing mortality of shy snails. The effect of personality on predator escape is thus conditional on group personality composition, indicating that social context can directly impact the survival and success of its individual members, with broad implications for community dynamics.
Single-cell RNA-sequencing data clustering using variational graph attention auto-encoder with self-supervised leaning
Authors: Li Bo , Peng Chen , You Zeran , Zhang Xiaolong , Zhang Shihua 
Published: October 2023

Abstract
The emergence of single-cell RNA-seq (scRNA-seq) technology makes it possible to capture their differences at the cellular level, which contributes to studying cell heterogeneity. By extracting, amplifying and sequencing the genome at the individual cell level, scRNA-seq can be used to identify unknown or rare cell types as well as genes differentially expressed in specific cell types under different conditions using clustering for downstream analysis of scRNA-seq. Many clustering algorithms have been developed with much progress. However, scRNA-seq often appears with characteristics of high dimensions, sparsity and even the case of dropout events’, which make the performance of scRNA-seq data clustering unsatisfactory. To circumvent the problem, a new deep learning framework, termed variational graph attention auto-encoder (VGAAE), is constructed for scRNA-seq data clustering. In the proposed VGAAE, a multi-head attention mechanism is introduced to learn more robust low-dimensional representations for the original scRNA-seq data and then self-supervised learning is also recommended to refine the clusters, whose number can be automatically determined using Jaccard index. Experiments have been conducted on different datasets and results show that VGAAE outperforms some other state-of-the-art clustering methods.
Analyzing microbial evolution through gene and genome phylogenies
Authors: Teichman Sarah , Lee Michael D , Willis Amy D 
Published: October 2023

Abstract
Microbiome scientists critically need modern tools to explore and analyze microbial evolution. Often this involves studying the evolution of microbial genomes as a whole. However, different genes in a single genome can be subject to different evolutionary pressures, which can result in distinct gene-level evolutionary histories. To address this challenge, we propose to treat estimated gene-level phylogenies as data objects, and present an interactive method for the analysis of a collection of gene phylogenies. We use a local linear approximation of phylogenetic tree space to visualize estimated gene trees as points in low-dimensional Euclidean space, and address important practical limitations of existing related approaches, allowing an intuitive visualization of complex data objects. We demonstrate the utility of our proposed approach through microbial data analyses, including by identifying outlying gene histories in strains of Prevotella, and by contrasting Streptococcus phylogenies estimated using different gene sets. Our method is available as an open-source R package, and assists with estimating, visualizing, and interacting with a collection of bacterial gene phylogenies.
In utero or early-in-life exposure to antibiotics and the risk of childhood atopic dermatitis, a population-based cohort study
Authors: Fuxench Zelma Chiesa , Mitra Nandita , Del Pozo Domenica , Hoffstad Ole , Shin Daniel B , Langan Sinéad M , Petersen Irene , Bhate Ketaki , Margolis David J 
Published: October 2023

Abstract

Background
Atopic dermatitis (AD) is a common inflammatory disease of the skin that begins early in life and can be lifelong. The purpose of our study was to evaluate whether fetal exposure and/or early-life exposure of a child to antibiotics increases the risk of early-onset AD.

Objectives
We hypothesize that antibiotic exposure in utero or early in life (e.g. first 90 days) increases the likelihood that children develop AD.

Methods
Utilizing a large, prospectively collected electronic medical records database, we studied the association of antibiotic exposure received in utero or very early in life and the relative risk of onset of AD in a population-based cohort study. Associations were estimated using proportional hazards models as hazard ratios (HRs) with 95% confidence intervals (CIs).

Results
The risk of AD in childhood was increased after in utero or early-life antibiotic exposure. For any in utero antibiotic exposure the HR (CI) was 1.38 (1.36–1.39). However, penicillin demonstrated the strongest association with AD for both in utero exposure [1.43 (1.41–1.44)] and for childhood exposure [1.81 (1.79–1.82)]. HRs were higher in children born to mothers without AD than in those with AD pointing to effect modification by maternal AD status.

Conclusions
Children born to mothers exposed to antibiotics while in utero had, depending on the mother’s history of AD, approximately a 20–40% increased risk of developing AD. Depending on the antibiotic, children who received antibiotics early in life had a 40–80% increased risk of developing AD. Our study supports and refines the association between incident AD and antibiotic administration. It also adds population-based support to therapeutic attempts to treat AD by modifying the skin microbiome.
Cardiology professionals’ views of social robots in augmenting heart failure patient care
Authors: Bouchard Karen , Liu Peter P , Dautenhahn Kerstin , Fiedorowicz Jess G , Afrin Jenifar , Dans Michael , McGuinty Caroline , Tulloch Heather 
Published: October 2023

Abstract

Aims
Social robots are arriving to the modern healthcare system. Whether patients with heart failure, a prevalent chronic disease with high health and human costs would derive benefit from a social robot intervention has not been investigated empirically. Diverse healthcare provider’s perspectives are needed to develop an acceptable and feasible social robot intervention to be adopted for the clinical benefit of patients with heart failure. Using a qualitative research design, this study investigated healthcare providers’ perspectives of social robot use in heart failure patient care.

Methods and results
Interdisciplinary healthcare providers from a tertiary care cardiac hospital completed a structured individual interview and a supplemental questionnaire. The framework method was used to analyse the qualitative data. Respondents (n = 22; saturation was reached with this sample; 77% female; 52% physicians) were open to using social robots to augment their practice, particularly with collecting pertinent data and providing patient and family education and self-management prompts, but with limited responsibility for direct patient care. Prior to implementation, providers required robust evidence of: value-added beyond current remote patient monitoring devices, patient and healthcare provider partnerships, streamlined integration into existing practice, and capability of supporting precision medicine goals. Respondents were concerned that social robots did not address and masked broader systemic issues of healthcare access and equity.

Conclusion
The adoption of social robots is a viable option to assist in the care of patients with heart failure, albeit in a restricted capacity. The results inform the development of a social robotic intervention for patients with heart failure, including improving social robot efficiencies and increasing their uptake, while protecting patients’ and providers’ best interest.
Macroevolution of floral scent chemistry across radiations of male euglossine bee-pollinated plants
Authors: Liu Jasen W , Milet-Pinheiro Paulo , Gerlach Günter , Ayasse Manfred , Nunes Carlos Eduardo Pereira , Alves-dos-Santos Isabel , Ramírez Santiago R 
Published: October 2023

Abstract
Floral volatiles play key roles as signaling agents that mediate interactions between plants and animals. Despite their importance, few studies have investigated broad patterns of volatile variation across groups of plants that share pollinators, particularly in a phylogenetic context. The “perfume flowers,” Neotropical plant species exhibiting exclusive pollination by male euglossine bees in search of chemical rewards, present an intriguing system to investigate these patterns due to the unique function of their chemical phenotypes as both signaling agents and rewards. We leverage recently developed phylogenies and knowledge of biosynthesis, along with decades of chemical ecology research, to characterize axes of variation in the chemistry of perfume flowers, as well as understand their evolution at finer taxonomic scales. We detect pervasive chemical convergence, with many species across families exhibiting similar volatile phenotypes. Scent profiles of most species are dominated by compounds of either the phenylpropanoid or terpenoid biosynthesis pathways, while terpenoid compounds drive more subtle axes of variation. We find recapitulation of these patterns within two independent radiations of perfume flower orchids, in which we further detect evidence for the rapid evolution of divergent floral chemistries, consistent with the putative importance of scent in the process of adaptation and speciation.
Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis
Authors: Dai Xiaokang , Xiang Songzhu , Zhang Yulin , Yang Siting , Hu Qianqian , Wu Zhihao , Zhou Tingting , Xiang Jingsong , Chen Gongyou , Tan Xiaohua , Wang Jing , Ding Jihua 
Published: October 2023

Abstract
Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.
Crowdsourcing routines: the behavioral and motivational underpinnings of expert participation
Authors: Bagherzadeh Mehdi , Gurca Andrei , Velayati Rezvan 
Published: October 2023

Abstract
As different crowdsourcing routines (metaphorically labeled as “fishing” and “hunting” in this study) are available to address highly technical problems, solution-seeking organizations need to mindfully design, select, and deploy crowdsourcing routines that account for the behavior and motivation of experts. Drawing on a survey involving 260 experts in science, technology, engineering, and math fields, we found that elite experts (individuals with seniority, aged over 40, and a proven track record in the field with numerous publications and patents) are generally less inclined to search for crowdsourcing open calls and prefer to be contacted by solution seekers. In contrast, non-elite experts (early career experts, aged under 40, and with fewer patents and publications) actively search to find open calls. Regarding their motivational underpinnings, our findings suggest that elite experts are motivated more by non-financial incentives than non-elite experts. Furthermore, as the frequency with which they are contacted increases, non-elite experts tend to prefer more non-financial over financial incentives. These results indicate that the fishing crowdsourcing routine generally elicits solutions from unproven, non-elite experts who demand more financial rewards. However, the hunting routine taps a pool of elite experts with proven capabilities who are less financially oriented and thus may provide better, yet less expensive solutions.
The ‘Domino Effect’ of Ongoing Violence on Transitional Justice: The Case of Colombia’s Special Jurisdiction for Peace
Authors: Figari Layus Rosario , Vargas Trujillo Juliette 
Published: October 2023

ABSTRACT∞
This article examines the tangible consequences of ongoing armed violence for the implementation of Colombia’s innovative transitional court, the Special Jurisdiction for Peace (Jurisdicción Especial para la Paz, JEP). Establishing transitional justice mechanisms in contexts of persistent armed violence poses significant challenges and the implementation process is likely to seem flawed or lacking to those actors involved. These complex scenarios raise critical questions for the field of transitional justice, notably regarding the expectations of victims and the feasibility of providing truth, justice and reparation in hostile settings. Based on the case of the Colombia’s northwestern Urabá region, this article argues that contexts of ongoing violence have a direct adverse effect on the possibility of the meaningful and effective participation of victims, perpetrators and other key actors in transitional justice processes. Consequently, this restricted participation initiates a ‘domino effect,’ which negatively impacts other transitional goals, including, in the specific case of the JEP, its restorative aims.
Swedish multicentre study of target attainments with β-lactams in the ICU: which MIC parameter should be used?
Authors: Smekal Anna-Karin , Furebring Mia , Lipcsey Miklos , Giske Christian G 
Published: October 2023

Abstract

Background
Therapeutic drug monitoring (TDM) has been suggested to optimize antimicrobial target attainment, typically using 100%T&gt;MIC, in β-lactam treatment in the ICU. The MIC parameter used in this equation is mostly the worst case scenario MIC (MICWCS)—the highest MIC the empirical treatment should cover. However, the impact of the MIC parameter used in pharmacokinetic/pharmacodynamic calculations has been poorly investigated.

Objectives
To assess the influence of target attainment rates for two different MIC parameters using actual MICs of the causative pathogens as the primary reference.

Methods
In a Swedish multicentre study of target attainment for 138 ICU patients treated with β-lactams, the causative pathogen was isolated and subjected to reference MIC testing. Whenever the strain belonged to the WT distribution, we assigned it to the category MICECOFF (epidemiological cut-off value). In the calculations we compared the MICECOFF and the MICWCS.

Results
The proportion of patients with target attainment failure for all antibiotics using 100%T&gt;MIC was 45% (95% CI, 37%–53%) for MICWCS and 23% (95% CI, 16%–31%) for MICECOFF. When the target 50%T&gt;4×MIC was used, corresponding attainment failures were 57% (95% CI, 49%–66%) and 25% (95% CI, 17%–32%) for MICWCS and MICECOFF, respectively.

Conclusions
MICWCS can overestimate target attainment failure. The use of MICWCS could be one reason for the difficulties in establishing a relationship between target failure and mortality in other studies. Based on findings herein, the MICECOFF, which is based on the MIC of the causative pathogen, should be considered a more suitable alternative. When no pathogen is detected, the MICECOFF of likely pathogens according to infection type should be used.