bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations of proton pump inhibitors with susceptibility to influenza, pneumonia, and COVID-19: Evidence from a large population based cohort study
Authors: Zeng Ruijie , Ma Yuying , Zhang Lijun , Luo Dongling , Jiang Rui , Wu Huihuan , Zhuo Zewei , Yang Qi , Li Jingwei , Leung Felix W , Duan Chongyang , Sha Weihong , Chen Hao 
Published: August 2022

AbstractAdverse effects of proton pump inhibitors (PPIs) have raised wide concerns. The association of PPIs with influenza is unexplored, while that with pneumonia or COVID-19 remains controversial. Our study aims to evaluate whether PPI use increases the risks of these respiratory infections. The current study included 160,923 eligible participants at baseline who completed questionnaires on medication use, which included PPI or histamine-2 receptor antagonist (H2RA), from the UK Biobank. Cox proportional hazards regression and propensity score-matching analyses were used to estimate the hazard ratios (HRs) and 95% confidence intervals (CIs). Comparisons with H2RA users were tested. PPI use was associated with increased risks of developing influenza (HR 1.32, 95%CI 1.12-1.56) and pneumonia (hazard ratio [HR] 1.42, 95% confidence interval [CI] 1.26-1.59). In contrast, the risk of COVID-19 infection was not significant with regular PPI use (HR 1.08, 95%CI 0.99-1.17), while the risks of severe COVID-19 (HR 1.19. 95%CI 1.11-1.27) and mortality (HR 1.37. 95%CI 1.29-1.46) were increased. However, when compared with H2RA users, PPI users were associated with a higher risk of influenza (HR 1.74, 95%CI 1.19-2.54), but the risks with pneumonia or COVID-19-related outcomes were not evident. In conclusion, PPI users are associated with increased risks of influenza, pneumonia, as well as COVID-19 severity and mortality compared to non-users, while the effects on pneumonia or COVID-19-related outcomes under PPI use were attenuated when compared to the use of H2RAs. Appropriate use of PPIs based on comprehensive evaluation is required.
Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages
Authors: Domazet-Lošo Mirjana , Široki Tin , Domazet-Lošo Tomislav 
Published: August 2022

AbstractThe recent analyses in animals show that gene gain and loss fluctuate during evolutionary time. However, these studies lack the full profile of macroevolutionary trajectories as they do not consider other eukaryotic lineages and deeper evolutionary periods that go back to the origin of cellular organisms. To give a more inclusive view on the macroevolutionary patterns of genome complexity across the tree of life, we here recovered the evolutionary dynamics of gene family gain and loss ranging from the ancestor of cellular organisms to four focal species that represent animal, plant, and fungal diversity. We show that in all considered lineages the gene family content follows a common evolutionary pattern, where the number of gene families reaches the highest value at a major evolutionary and ecological transition, and then gradually decreases towards extant organisms. This pattern suggests that the genome complexity, approximated by the number of residing gene families, does not continuously increase through evolutionary time. We conclude that simplification by gene family loss is a dominant force in Phanerozoic genomes of various lineages, probably underpinned by intense ecological specializations and functional outsourcing. These findings support current theoretical predictions on the macroevolutionary change in genome complexity.
Model based control can give rise to devaluation insensitive choice
Authors: Garrett Neil , Allan Sean , Daw Nathaniel D. 
Published: August 2022

AbstractInfluential recent work aims to ground psychiatric dysfunction in the brain’s basic computational mechanisms. For instance, compulsive symptoms as in drug abuse have been argued to arise from imbalance between multiple systems for instrumental learning. Computational models suggest that such multiplicity arises because the brain adaptively simplifies laborious “model-based” deliberation by sometimes relying on a cheaper, more habitual “model-free” shortcut. Support for this account comes in part from failures to appropriately change behavior in light of new events. Notably, instrumental responding can, in some circumstances, persist despite reinforcer devaluation, perhaps reflecting control by model-free mechanisms that are driven by past reinforcement rather than knowledge of the (now devalued) outcome. However, another important line of theory – heretofore mostly studied in Pavlovian conditioning – posits a different mechanism that can also modulate behavioral change. It concerns how animals identify different rules or contingencies that may apply in different circumstances, by covertly clustering experiences into distinct groups identified with different “latent causes” or contexts. Such clustering has been used to explain the return of Pavlovian responding following extinction.Here we combine both lines of theory to investigate the consequences of latent cause inference on instrumental sensitivity to reinforcer devaluation. We show that because segregating events into different latent clusters prevents generalization between them, instrumental insensitivity to reinforcer devaluation can arise in this theory even using only model-based planning, and does not require or imply any habitual, model-free component. In simulations, these ersatz habits (like laboratory ones) emerge after overtraining, interact with contextual cues, and show preserved sensitivity to reinforcer devaluation on a separate consumption test, a standard control. While these results do not rule out a contribution of model-free learning per se, they point to a subtle and important role of state inference in instrumental learning and highlight the need for caution in using reinforcer devaluation procedures to rule in (or out) the contribution of different learning mechanisms. They also offer a new perspective on the neurocomputational substrates of drug abuse and the relevance of laboratory reinforcer devaluation procedures to this phenomenon.
Human neurogenesis is altered via glucocorticoid-mediated regulation ofZBTB16expression
Authors: Krontira Anthi C. , Cruceanu Cristiana , Dony Leander , Kyrousi Christina , Link Marie-Helen , Kappelmann Nils , Pöhlchen Dorothee , Raimundo Catarina , Goeke Signe-Penner , Schowe Alicia , Czamara Darina , Lahti-Pulkkinen Marius , Sammallahti Sara , Wolford Elina , Heinonen Kati , Roeh Simone , Sportelli Vincenza , Wölfel Barbara , Ködel Maik , Sauer Susann , Rex-Haffner Monika , Räikkönen Katri , Labeur Marta , Cappello Silvia , Binder Elisabeth B. 
Published: August 2022

SummaryGlucocorticoids are important for proper organ maturation and their levels are tightly regulated during development. Here we use human cerebral organoids and mice to study cell-type specific effects of glucocorticoids on neurogenesis. We show that glucocorticoids increase a specific type of basal progenitors (co-expressingPAX6andEOMES) that has been shown to drive cortical expansion in gyrified species. This effect is mediated via the transcription factorZBTB16and leads to increased production of neurons. A phenome-wide mendelian randomization analysis of an enhancer variant that moderates glucocorticoid-inducedZBTB16levels, reveals causal relationships with higher educational attainment and altered brain structure. The relationship with postnatal cognition is supported by data from a prospective pregnancy cohort. This study provides a novel cellular and molecular pathway for the effects of glucocorticoids on human neurogenesis that relates to lasting postnatal phenotypes.
Dicamba drift alters patterns of chewing herbivory in three common agricultural weeds
Authors: Johnson Nia , Zhang Grace , Soble Anah , Baucom Regina S 
Published: August 2022

ABSTRACTHow agricultural regimes, such as novel herbicide exposure, may influence plant-herbivore interactions and specifically patterns of plant herbivory has come under increased interest in recent years due to rapidly changing herbicide use in agroecosystems. This paper examines patterns of plant herbivory using three common agricultural weeds exposed to low doses of dicamba, a synthetic auxin herbicide that is exponentially increasing in use given the adoption of dicamba tolerant crops. We used a replicated field study to examine how the amount and type of chewing herbivory may be altered in Ipomoea purpurea (common morning glory, Convolvulaceae), Datura stramonium (jimsonweed, Solanaceae), and Abutilon theophrasti (velvetleaf, Malvaceae) exposed to dicamba drift (i.e., 1% of the field dose). We found an increase in chewing herbivory damage when plants were exposed to dicamba and changes in the type of herbivory following exposure. Chewing herbivory differed among species in the presence of dicamba drift: A. theophrasti and D. stramonium showed more total leaf-chewing herbivory than controls, but I. purpurea showed no difference in the overall amount of herbivory. We also found that the type of herbivory was significantly altered in drift. A. theophrasti and I. purpurea both exhibited declines in hole feeding but increases in margin feeding, whereas D. stramonium showed no such changes. Overall, our results show that herbicide drift can induce shifts in plant-herbivore interactions, highlighting the need for mechanistic studies to uncover the cause underlying the shifts and comparative studies on weed communities to understand long-term consequences.
The Ecosystem Integrity Index: a novel measure of terrestrial ecosystem integrity
Authors: Hill S.L.L. , Harrison M.L.K , Maney C. , Fajardo J. , Harris M. , Ash N. , Bedford J. , Danks F.S. , Guaras D. , Hughes J. , Jones M. , Mason T. , Burgess N. 
Published: August 2022

AbstractWhile the importance of ecosystem integrity has long been recognised (Leopold, 1949), conservation science has tended to focus on measuring and monitoring species and habitats, avoiding the complexities of working at the ecosystem level. Ecosystems are highly dynamic, defined by both living and non-living components as well as their interactions (CBD, 1992), making it difficult to assess baseline levels of integrity. We present a novel index that represents the integrity of all terrestrial ecosystems globally at 1km2resolution: the Ecosystem Integrity Index (EII). The index provides a simple, yet scientifically robust, way of measuring, monitoring and reporting on ecosystem integrity. It is formed of three components; structural, compositional and functional integrity, and measured against a natural (current potential) baseline on a scale of 0 to 1. We find that ecosystem integrity is severely impacted in terrestrial areas across the globe with approximately one fifth of all ecosystems and one quarter of all ecoregions having lost, on average, over half of their ecosystem integrity. At a national scale, we estimate similar challenges with 115 nations or territories having lost, on average, over half of their ecosystem integrity. This presents a significant threat for humanity as such levels of degradation are likely to be linked to substantial declines in the ecosystem services on which humanity is reliant. The EII has been developed principally to help national governments measure and report on Goal A of the Kunming-Montreal Global Biodiversity Framework (GBF) (CBD, 2022a), for which it has been listed as a Component Indicator. The EII will also be useful in helping non-state actors measure and report their contributions to the GBF and is listed as an indicator by both the Taskforce for Nature-Related Financial Disclosures (TNFD) (TNFD, 2023) and the Science Based Targets Network (SBTN) (SBTN, 2023). The EII aims to enable these actors to make informed decisions on the conservation, restoration and sustainable use of ecosystems for which they are wholly or partly responsible. We propose that with sufficient effort, ecosystem integrity can be restored and contribute towards the GBF’s vision of living in harmony with nature, resulting in the safeguarding of the ecosystem services on which humanity depends.
“Correcting” gene trees to be more like species trees increases topological error when incomplete lineage sorting is high
Authors: Yan Zhi , Ogilvie Huw A. , Nakhleh Luay 
Published: August 2022

AbstractThe evolutionary histories of individual loci in a genome can be estimated independently, but this approach is error-prone due to the limited amount of sequence data available for each gene, which has led to the development of a diverse array of gene tree error correction methods which reduce distance to the species tree. We investigate the performance of two representatives of these methods: TRACTION and TreeFix, in the case where incomplete lineage sorting is high. We found that gene tree error correction only increases the level of error in gene tree topologies by “correcting” them to be closer to the species tree, even when the true gene and species trees are discordant. We confirm that full Bayesian inference of the gene trees under the multispecies coalescent model is more accurate than independent inference. Gene tree correction must be considered a multi-locus task where the gene tree distribution is taken into account, rather than treating gene trees independently.Significance statementGene tree information is essential for studying elucidating gene, genome, species, and phenotypic evolution, and a wide array of phylogenetic methods have been developed for gene tree estimation. Given that gene tree estimates are often inaccurate, several methods for “correcting” gene tree estimates have been devised. Here we show that correction methods that neglect the distribution of gene trees that is induced by the species phylogeny could produce poor results, calling for the development of species phylogeny-aware gene tree correction.
Recent Trends in Aspirin Use for Cardiovascular Disease Prevention in the United States - 2015-2023
Authors: Murugiah Karthik , See Claudia , Huang Chenxi 
Published: August 2022

ABSTRACTBACKGROUNDRecent trials show a lack of benefit of routine aspirin use for primary prevention. We assessed recent trends in aspirin use for both primary and secondary prevention in the United States population.METHODSWe used National Health Interview Survey (NHIS) data from 2015-2023 and reported the annual weighted proportion of aspirin use among participants ≥40 years without a self-reported history of angina, coronary heart disease, myocardial infarction, or stroke (primary prevention cohort) and those with (secondary prevention cohort), overall and by subgroups. Statistical comparisons were made only between 2019 and 2023 due to an NHIS study redesign in 2019.RESULTSFrom 2019 to 2023 overall aspirin use for primary prevention decreased from 20.6% to 15.7%. It declined in all subgroups, including among individuals ≥70 years from 38.7% to 30.7%, and those age <60 years but with ≥3 CVD risk factors (29.1% to 19.7%). Overall aspirin use for secondary prevention also declined, but to a lesser extent from 65.7% to 61.9%. (all P <0.001)CONCLUSIONIn response to recent data there has been a significant reduction in aspirin use for primary prevention, appropriately among older participants, but also among younger participants with multiple cardiovascular risk factors. There was also a minor decrease in its use for secondary prevention which warrants further study.
Coding nucleic acid sequences with graph convolutional network
Authors: Wang Ruo Han , Ng Yen Kaow , Zhang Xianglilan , Wang Jianping , Li Shuai Cheng 
Published: August 2022

ABSTRACTGenome sequencing technologies reveal a huge amount of genomic sequences. Neural network-based methods can be prime candidates for retrieving insights from these sequences because of their applicability to large and diverse datasets.However, the highly variable lengths of nucleic acid sequences severely impair the presentation of sequences as input to the neural network. Genetic variations further complicate tasks that involve sequence comparison or alignment. Here, we propose a graph representation of nucleic acid sequences calledgapped pattern graphs. These graphs can be transformed through a Graph Convolutional Network to form lower-dimensional embeddings for downstream tasks. On the basis of the gapped pattern graphs, we implemented a neural network model and demonstrated its performance in studying phage sequences. We compared our model with equivalent models based on other forms of input in performing four tasks related to nucleic acid sequences—phage and ICE discrimination, phage integration site prediction, lifestyle prediction, and host prediction. Other state-of-the-art tools were also compared, where available. Our method consistently outperformed all the other methods in various metrics on all four tasks. In addition, our model was able to identify distinct gapped pattern signatures from the sequences.
Cortical Betz cells analogue in songbirds utilizes Kv3.1 to generate ultranarrow spikes
Authors: Zemel Benjamin M. , Nevue Alexander A. , Tavares Leonardo E. , Dagostin Andre , Lovell Peter V. , Jin Dezhe Z. , Mello Claudio V. , von Gersdorff Henrique 
Published: August 2022

AbstractComplex motor skills in vertebrates require specialized upper motor neurons with precise action potential (AP) firing. To examine how diverse populations of upper motor neurons subserve distinct functions and the specific repertoire of ion channels involved, we conducted a thorough study of the excitability of upper motor neurons controlling somatic motor function in the zebra finch. We found that robustus arcopallialis projection neurons (RAPNs), key command neurons for song production, exhibit ultranarrow spikes and higher firing rates compared to neurons controlling non-vocal somatic motor functions (AId neurons). This striking difference was primarily due to the expression of a high threshold, fast-activating voltage-gated K+ channel, Kv3.1 (KCNC1). RAPN properties thus mirror those of the sparse, specialized Betz cells in the motor cortex of humans and other primates, which also fire ultranarrow spikes enabled by Kv3.1 expression. These large layer 5 pyramidal neurons are involved in fine digit control and are notably absent in rodents. Our study thus provides evidence that songbird RAPNs and primate Betz cells have convergently evolved the use of Kv3.1 to ensure precise, rapid AP firing required for fast and complex motor skills.
Strategies used by students with autism when solving multiplicative problems: an exploratory study
Authors: Goñi-Cervera Juncal , Martínez Romillo María Cristina , Polo-Blanco Irene 
Published: August 2022

Purpose
This paper aims to study the strategies used by ten students diagnosed with autism when solving multiplication and division problems because these operations are rarely studied in students with this condition.

Design/methodology/approach
This study conducted an exploratory study with ten students diagnosed with autism to explore and describe the strategies used in solving equal group problems. The authors also describe in detail the case of a student whom the authors deem to be representative because of the reasoning the student employed.

Findings
The informal strategies that they used are described, as well as the difficulties observed in the various problems, depending on the operation required to solve them. The strategies used include direct modeling with counting and others that relied on incorrect additive relationships, with strategies based on multiplication and division operations being scarce. Difficulties were observed in several problems, with measurement division being particularly challenging for the study participants.

Practical implications
The detailed description of the strategies used by the students revealed the meanings that they associate with the operations they are executing and brought to light potential difficulties, which can help teachers plan their instruction.

Originality/value
This research supplements other studies focusing on mathematical problem-solving with autistic students.
Effect of cluster initiatives and natural clusters on business performance
Authors: Zizka Miroslav , Stichhauerova Eva 
Published: August 2022

Purpose
This study aims to determine how much company participation in a type of cluster affects its economic performance.

Design/methodology/approach
This study includes companies operating in seven industries (automotive, engineering, textiles, information technology (IT) services, furniture, packaging and nanotechnology) in the Czech Republic. The companies are divided into three groups: members of institutionalized cluster, operating in the same region (natural clusters) and operating in other regions. Data envelopment window analysis is used to measure their performance for 2009–2019.

Findings
Results show that the effect of clustering differs among industries. Companies in three industries (automotive, engineering, nanotechnology) reveal a positive impact of the cluster initiative on performance growth. Two industries (textile, packaging) with companies operating in a natural cluster show better performance than those in an institutionalized cluster. Moreover, the IT services and the furniture industries show no positive effect of clustering on corporate performance.

Research limitations/implications
This research includes 686 companies from seven industries and monitored for 11 years. On the one hand, the sample includes a relatively high number of companies overall; but on the other hand, the sample is relatively small, especially for nonclustered companies. The reason is the lack of available financial statements for small companies.

Practical implications
From the perspective of practical cluster policy, the authors can recommend that monitoring the performance of member companies in clusters must be one of the criteria for evaluating the success of a cluster, such as cluster initiatives.

Originality/value
This study distinguishes between long-standing natural clusters in a given industry and institutionalized ones that have emerged because of a top-down initiative. An original database is created for clustered and nonclustered companies in seven industries, covering the entire Czech Republic.