bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-read proteogenomics to connect disease-associated sQTLs to the protein isoform effectors of disease
Authors: Abood Abdullah , Mesner Larry D. , Jeffery Erin D. , Murali Mayank , Lehe Micah , Saquing Jamie , Farber Charles R. , Sheynkman Gloria M. 
Published: March 2023

AbstractA major fraction of loci identified by genome-wide association studies (GWASs) lead to alterations in alternative splicing, but interpretation of how such alterations impact proteins is hindered by the technical limitations of short-read RNA-seq, which cannot directly link splicing events to full-length transcript or protein isoforms. Long-read RNA-seq represents a powerful tool to define and quantify transcript isoforms, and recently, infer protein isoform existence. Here we present a novel approach that integrates information from GWAS, splicing QTL (sQTL), and PacBio long-read RNA-seq in a disease-relevant model to infer the effects of sQTLs on the ultimate protein isoform products they encode. We demonstrate the utility of our approach using bone mineral density (BMD) GWAS data. We identified 1,863 sQTLs from the Genotype-Tissue Expression (GTEx) project in 732 protein-coding genes which colocalized with BMD associations (H4PP ≥ 0.75). We generated deep coverage PacBio long-read RNA-seq data (N=∼22 million full-length reads) on human osteoblasts, identifying 68,326 protein-coding isoforms, of which 17,375 (25%) were novel. By casting the colocalized sQTLs directly onto protein isoforms, we connected 809 sQTLs to 2,029 protein isoforms from 441 genes expressed in osteoblasts. Using these data, we created one of the first proteome-scale resources defining full-length isoforms impacted by colocalized sQTLs. Overall, we found that 74 sQTLs influenced isoforms likely impacted by nonsense mediated decay (NMD) and 190 that potentially resulted in the expression of new protein isoforms. Finally, we identified colocalizing sQTLs inTPM2for splice junctions between two mutually exclusive exons, and two different transcript termination sites, making it impossible to interpret without long-read RNA-seq data. siRNA mediated knockdown in osteoblasts showed twoTPM2isoforms with opposing effects on mineralization. We expect our approach to be widely generalizable across diverse clinical traits and accelerate system-scale analyses of protein isoform activities modulated by GWAS loci.
Forest structural diversity determines tree growth synchrony in response to climate change
Authors: Astigarraga J. , Calatayud J. , Ruiz-Benito P. , Madrigal-González J. , Tijerín-Triviño J. , Zavala M. A. , Andivia E. , Herrero A. 
Published: March 2023

AbstractAfter centuries of deforestation, many industrialised countries are experiencing an increase in forest area and biomass due to changes in land- and forest-use since the mid-20thcentury. At the same time, the impacts of climate change on forests are aggravating, but the interplay between past land- and forest-use (i.e. land- and forest-use legacies) and climate change in forest functioning remains elusive. Here using network theory and linear mixed models, we quantified how land- and forest-use legacies modulate tree growth synchrony in response to climate change. We analysed tree growth data from European beech (Fagus sylvaticaL.) stands with different histories of forest management at the species’ rear edge. We found that tree growth synchrony increased following heatwaves, late spring frosts, and reduced precipitation. Interestingly, the greatest tree growth synchrony occurred in recently-established forests, while stands containing large trees and heterogeneous tree sizes showed much lower growth synchrony. Our results highlight the importance of maintaining large trees and structurally heterogeneous forests to mitigate the negative effects of climate change on forest productivity, and thereby, increase forest resilience to future forest climate risks.
PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science
Authors: Cho Min Hyung , Cho Kwang-Hwi , No Kyoung Tai 
Published: March 2023

AbstractSummaryThe nature of taxonomic science and the scientific nomenclature system makes it difficult to use scientific names as identifiers without running into complications. To facilitate high-throughput analysis of biological data involving scientific names, we designed PhyloSophos, a Python package that takes into account the properties of scientific names and taxonomic systems to map name inputs to the entries within the reference database of choice. We would like to present three case-studies which demonstrates how our implementations, including rule-based pre-processing and recursive mapping could improve mapping performance and information availability. We expect PhyloSophos to help with the systematic processing of poorly digitized and curated biological data, such as biodiversity information and ethnopharmacological resources, thus enabling full-scale bioinformatics analysis using these data.Availability and implementationPhyloSophos is available at GitHubhttps://github.com/mhcho4096/phylosophos.Supplementary informationSupplementary data are available at Bioinformatics online.
A new species ofLethrinops(Cichliformes: Cichlidae) from a Lake Malawi satellite lake, believed to be extinct in the wild
Authors: Turner George F. , Crampton Denise A. , Genner Martin J. 
Published: March 2023

AbstractA new species of cichlid fish,Lethrinops chilingaliis described from specimens collected from Lake Chilingali, near Nkhotakota, Malawi. It is assigned to the genusLethrinopsbased on the form of the lower jaw dental arcade and by the absence of traits diagnostic of the phenotypically similarCtenopharynx, TaeniolethrinopsandTramitichromis. It also lacks the enlarged cephalic lateral line canal pores found in species ofAlticorpusandAulonocara. The presence of a broken horizontal stripe on the flanks of females and immature/non-territorial males ofLethrinops chilingalidistinguishes them from all congeners, includingLethrinops lethrinus, in which the stripe is typically continuous.Lethrinops chilingalialso has a relatively shorter snout, shorter lachrymal bone and less ventrally positioned mouth thanLethrinops lethrinus. It appears likely thatLethrinops chilingaliis now extinct in the wild, as this narrow endemic species has not been positively recorded in the natural environment since 2009. Breeding populations remain in captivity.
Relationship Between Obesity and Balance in Parachinar, District Kurram, Kpk-An Analytical Cross-Sectional Study
Authors: Hussain Sayed Sajid 
Published: March 2023

ABSTRACTOBJECTIVETo find out the effects of BMI on BBS and to determines the risk of falls due to impaired balance in Parachinar, District KurramMETHODSAn analytical cross-section study was carried out to determine the effects of BMI on BBS; the study included 269 individuals who are classified based on their body mass index. There were 157 males and 112 female. The clinical evaluation instruments Berg balance scale and Time Up and Go test (TUG) were used to collect the data and investigate the relationship between body mass index-based obesity and balance. Data was collected in Parachinar District Kurram from individuals have BMI 22.5kg/m2 or greater and age 20-50 years.RESULTSThe BBS and TUG scores revealed that obese people had poor balance due to their body weight, as well as a decline in body balance and stability performance. There were 71.4% individuals who had BMI of 27.5-32.5kg/m2(class 1 obesity) and 10% individuals had severed obesity (class 3). 66.9% individuals had low risk of fall, 20% had medium risk of fall, and 12.3% had high risk of fall.CONCLUSIONThis study concluded that obesity has effects on balance and obese individuals have poor balance performance. According to this study individuals with greater BMI have poor balance performance and have high risk of falls. The results of this study illustrates that there is an association of BMI and BBS because the P-value is <0.05 and concluded that obesity cause impaired balance and which leads to increase a risk of falls.
Relationship between neural activity and neuronal cell fate in regeneratingHydrarevealed by cell-type specific imaging
Authors: Escobar Alondra , Kim Soonyoung , Primack Abby S. , Duret Guillaume , Juliano Celina E. , Robinson Jacob T. 
Published: March 2023

AbstractUnderstanding how neural circuits are regenerated following injury is a fundamental question in neuroscience.Hydrais a powerful model for studying this process because it has significant and reproducible regenerative abilities, a simple and transparent body that allows for whole nervous system imaging, and established methods for creating transgenics with cell-type-specific expression. In addition, cnidarians such asHydrasplit from bilaterians (the group that encompasses most model organisms used in neuroscience) over 500 million years ago, so similarities with other models likely indicates deeply conserved biological processes.Hydrais a long-standing regeneration model and is an emerging model for neuroscience; however, relatively little is known regarding the restoration of neural activity and behavior following significant injury. In this study, we ask if regenerating neurons reach a terminal cell fate and then reform functional neural circuits, or if neural circuits regenerate first and then guide the constituent cells toward their terminal fate. To address this question, we developed a dual-expression transgenicHydraline that expresses a cell-type-specific red fluorescent protein (tdTomato) in ec5 peduncle neurons, and a calcium indicator (GCaMP7s) in all neurons. This transgenic line allowed us to monitor neural activity while we simultaneously track the reappearance of terminally differentiated ec5 neurons as determined by the expression of tdTomato. Using SCAPE (Swept Confocally Aligned Planar Excitation) microscopy, we tracked both calcium activity and expression of tdTomato-positive neurons in 3D with single-cell resolution during regeneration ofHydra’saboral end. We observed tdTomato expression in ec5 neurons approximately four hours before the neural activity begins to display synchronized patterns associated with a regenerated neural circuit. These data suggest that regenerating neurons undergo terminal differentiation prior to re-establishing their functional role in the nervous system. The combination of dynamic imaging of neural activity and gene expression during regeneration makeHydraa powerful model system for understanding the key molecular and functional processes involved in neuro-regeneration following injury.
Flexible and site-specific manipulation of histones in live animals
Authors: Finkin-Groner Efrat , Al-Kachak Amni , Agustinus Albert , Bastle Ryan , Lepack Ashley , Lyu Yang , Maze Ian , David Yael 
Published: March 2023

AbstractRecent advances in protein engineering have provided a wealth of methods that allow for the site-specific manipulation of proteinsin vitroand in cells. However, the efforts to expand these toolkits for use in live animals has been limited. Here, we report a new method for the semi-synthesis of site-specifically modified and chemically defined proteins in live animals. Importantly, we illustrate the usefulness of this methodology in the context of a challenging, chromatin bound N-terminal histone tail within rodent postmitotic neurons located in ventral striatum (Nucleus Accumbens/NAc). This approach provides the field with a precise and broadly applicable methodology for manipulating histonesin vivo, thereby serving as a unique template towards examining chromatin phenomena that may mediate transcriptomic and physiological plasticity within mammals.
Time-resolved cryo-EM of G protein activation by a GPCR
Authors: Papasergi-Scott Makaía M. , Pérez-Hernández Guillermo , Batebi Hossein , Gao Yang , Eskici Gözde , Seven Alpay B. , Panova Ouliana , Hilger Daniel , Casiraghi Marina , He Feng , Maul Luis , Gmeiner Peter , Kobilka Brian K. , Hildebrand Peter W. , Skiniotis Georgios 
Published: March 2023

SummaryG protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating the exchange of guanine nucleotide in the Gα subunit. To visualize this mechanism, we developed a time-resolved cryo-EM approach that examines the progression of ensembles of pre-steady-state intermediates of a GPCR-G protein complex. Using variability analysis to monitor the transitions of the stimulatory Gs protein in complex with the β2-adrenergic receptor (β2AR) at short sequential time points after GTP addition, we identified the conformational trajectory underlying G protein activation and functional dissociation from the receptor. Twenty transition structures generated from sequential overlapping particle subsets along this trajectory, compared to control structures, provide a high-resolution description of the order of events driving G protein activation upon GTP binding. Structural changes propagate from the nucleotide-binding pocket and extend through the GTPase domain, enacting alterations to Gα Switch regions and the α5 helix that weaken the G protein-receptor interface. Molecular dynamics (MD) simulations with late structures in the cryo-EM trajectory support that enhanced ordering of GTP upon closure of the alpha-helical domain (AHD) against the nucleotide-bound Ras-homology domain (RHD) correlates with irreversible α5 helix destabilization and eventual dissociation of the G protein from the GPCR. These findings also highlight the potential of time-resolved cryo-EM as a tool for mechanistic dissection of GPCR signaling events.
Positive selection of somatically mutated clones identifies adaptive pathways in metabolic liver disease
Authors: Wang Zixi , Zhu Shijia , Jia Yuemeng , Wang Yunguan , Kubota Naoto , Fujiwara Naoto , Gordillo Ruth , Lewis Cheryl , Zhu Min , Sharma Tripti , Li Lin , Zeng Qiyu , Lin Yu-Hsuan , Hsieh Meng-Hsiung , Gopal Purva , Wang Tao , Hoare Matt , Campbell Peter , Hoshida Yujin , Zhu Hao 
Published: March 2023

ABSTRACTSomatic mutations in non-malignant tissues accumulate with age and insult, but whether these mutations are adaptive on the cellular or organismal levels is unclear. To interrogate mutations found in human metabolic disease, we performed lineage tracing in mice harboring somatic mosaicism subjected to non-alcoholic steatohepatitis (NASH). Proof-of-concept studies with mosaic loss ofMboat7, a membrane lipid acyltransferase, showed that increased steatosis accelerated clonal disappearance. Next, we induced pooled mosaicism in 63 known NASH genes, allowing us to trace mutant clones side-by-side. Thisin vivotracing platform, which we coined MOSAICS, selected for mutations that ameliorate lipotoxicity, including mutant genes identified in human NASH. To prioritize new genes, additional screening of 472 candidates identified 23 somatic perturbations that promoted clonal expansion. In validation studies, liver-wide deletion ofBcl6, Tbx3,orSmyd2resulted in protection against NASH. Selection for clonal fitness in mouse and human livers identifies pathways that regulate metabolic disease.Highlights:MosaicMboat7mutations that increase lipotoxicity lead to clonal disappearance in NASH.In vivo screening can identify genes that alter hepatocyte fitness in NASH.MosaicGpammutations are positively selected due to reduced lipogenesis.In vivo screening of transcription factors and epifactors identified new therapeutic targets in NASH.
Automation in architecture, engineering and construction: a scientometric analysis and implications for management
Authors: Klarin Anton , Xiao Qijie 
Published: March 2023

PurposeMany economic, political and socio-cultural events in the 2020s have been strong headwinds for architecture, engineering and construction (AEC). Nevertheless, technological advancements (e.g. artificial intelligence (AI), big data and robotics) provide promising avenues for the development of AEC. This study aims to map the state of the literature on automation in AEC and thereby be of value not only to those researching automation and its composition of a variety of distinct technological and system classes within AEC, but also to practitioners and policymakers in shaping the future of AEC.Design/methodology/approachThis review adopts scientometric methods, which have been effective in the research of large intra and interdisciplinary domains in the past decades. The full dataset consists of 1,871 articles on automation in AEC.FindingsThis overarching scientometric review offers three interdisciplinary streams of research: technological frontiers, project monitoring and applied research in AEC. To support the scientometric analysis, the authors offer a critical integrative review of the literature to proffer a multilevel, multistage framework of automation in AEC, which demonstrates an abundance of technological paradigm discussions and the inherent need for a holistic managerial approach to automation in AEC.Originality/valueThe authors underline employee well-being, business sustainability and social growth outcomes of automation and provide several managerial implications, such as the strategic management approach, ethical management view and human resource management perspective. In doing so, the authors seek to respond to the Sustainable Development Goals proposed by the United Nations as this becomes more prevalent for the industry and all levels of society in general.
Are financially illiterate individuals all the same? A study on incorrect and “do not know” answers to financial knowledge questions
Authors: Cucinelli Doriana , Soana Maria Gaia 
Published: March 2023

PurposeAre financially illiterate individuals all the same? This study aims to answer this question. Specifically, the authors investigate whether people answering incorrectly and “do not know” to the big five questions about financial knowledge (FK), all identified by previous literature as financially illiterate, are two sides of the same coin, or rather individuals with different socio-economic and demographic characteristics, and whether this leads to different levels of risk of falling victim to financial fraud.Design/methodology/approachUsing a large and representative sample of Italian adults, the authors run both ordered probit and probit regressions to test the determinants of financially illiterate individuals, distinguishing between those answering FK questions incorrectly and those answering “do not know”. The authors also measure the probability of falling victim to financial fraud for the two groups. To check the robustness of our results, the authors run a multinomial regression, a structural equation model and an instrumental variable regression model.FindingsThe authors demonstrate that the socio-demographic and socio-economic characteristics of individuals selecting incorrect responses to FK questions are different from those of individuals selecting the “do not know” option. Moreover, the results show that the former are more likely to be victims of financial frauds.Practical implicationsThe “one-size-fits-all” approach is not suitable for financial education. It is important to consider socio-demographic and socio-economic characteristics of individuals in order to identify specific targets of education programmes aiming to reduce insecurity and excessive self-confidence as well as to increase objective FK. The study’s findings also identify vulnerable groups to which financial fraud prevention schemes should be targeted.Originality/valueTo date, financial illiteracy has been measured as the sum of incorrect and “do not know” responses given to FK questions. This approach does not allow to observe the socio-demographic and socio-economic differences between people choosing the “do not know” option and those answering incorrectly. The paper aims to overcome this limit by investigating the socio-demographic and socio-economic characteristics of individuals selecting “do not know” and incorrect responses, respectively. The authors also investigate whether the two groups have different probabilities of being victims of financial fraud.
An overview of research trends on sustainability in higher education – an exploratory study
Authors: Leal Filho Walter , Frankenberger Silva Fernanda , Salvia Amanda , Shiel Chris , Paço Arminda , Price Elizabeth , Brandli Luciana Londero , Rampasso Izabela Simon , Anholon Rosley , Quelhas Osvaldo Luiz Gonçalves , Pretorius Rudi Wessel 
Published: March 2023

Purpose
This study aims to investigate the main areas in which researchers are focusing their efforts in terms of sustainability in higher education (curriculum, campus greening, research, governance or outreach), the format in which this research is performed (in terms of individual or combined efforts) and the primary research focus (in terms of local or global issues).

Design/methodology/approach
Trends on sustainability research were investigated by means of an online survey – the World Survey on Sustainability Publishing and Research in Higher Education, which was disseminated among members of the European School of Sustainability Science and Research and the Inter-University Sustainable Development Research Programme.

Findings
The survey collected responses from 103 researchers across over 40 countries. Three trends emerged: in spite of the intrinsic value of sustainability research in higher education, this area is not as mature as one could expect; the range of themes covered is wide and addresses a variety of areas; and individuals working alone is the most common means of doing research, whereas research at the university, department and faculty level appears to be less common.

Originality/value
The paper outlines some measures via which higher education institutions may be able to take more advantage of the many opportunities sustainability research offers to them.
Reproductive phenology of critical native plant species for mineland restoration in the eastern Amazon
Authors: da Costa Ana Carolina Galindo , Vasconcelos Liziane Vilela , de Lima Carla Teixeira , Caldeira Cecílio Frois , Zappi Daniela Cristina , Giulietti Ana Maria , Watanabe Maurício Takashi Coutinho 
Published: March 2023

AbstractAmazon ironstone outcrops vegetation, or canga, is a remarkable environment in which the plants are adapted to peculiar circumstances. Knowledge regarding different aspects of this ecosystem remains modest, including necessary insights for its conservation and recovery, such as the reproductive phenology of priority species that form the plant community. This study aimed to monitor the reproductive phenology of critical native species that are categorized as rare, endemic, and/or threatened in the canga of the Amazon Rainforest, in Pará, Brazil. During February 2016 and May 2017, eleven species were evaluated regarding the presence or absence of flowering and fruiting phenophases, and these were associated with environmental variables. Phenological data were evaluated through circular statistical analysis. All studied species flowered and produced fruit during the monitoring period. The evaluated species have an annual reproductive cycle marked by seasonality and flowering peaks between March and April, during the wet season, and fruiting peaks during May, at the beginning of the dry season. The best period for collecting ripe seeds, a primary tool for the restoration of degraded areas, is June. Water availability may be essential for the establishment of annual plants and to induce flowering in both annual and perennial species. The reproductive phenophases of the studied species are concentrated within a short period and are synchronized, which may increase the possibility of cross‐pollination and minimize flower and seed predation. We discuss the challenges in including annual plants and the importance of having them and perennial species in conservation and restoration of degraded areas projects.