bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pangenome reconstruction ofLactobacillaceaemetabolism predicts species-specific metabolic traits
Authors: Ardalani Omid , Phaneuf Patrick , Mohite Omkar S. , Nielsen Lars K. , Palsson Bernhard O. 
Published: September 2023

AbstractStrains across theLactobacillaceaefamily form the basis for a trillion-dollar industry. Our understanding of the genomic basis for their key traits is fragmented, however, including the metabolism that is foundational to their industrial uses. Pangenome analysis of publicly availableLactobacillaceaegenomes allowed us to generate genome-scale metabolic network reconstructions for 26 species of industrial importance. Their manual curation led to more than 75,000 gene-protein-reaction associations that were deployed to generate 2,446 genome-scale metabolic models. Cross-referencing genomes and known metabolic traits allowed for manual metabolic network curation and validation of the metabolic models. As a result, we provide the first pangenomic basis for metabolism in theLactobacillaceaefamily and a collection of predictive computational metabolic models that enable a variety of practical uses.
Mental health-related hospitalisations among adolescents with previous child protection contact from birth to age 11
Authors: Judd Jessica , Pilkington Rhiannon , Malvaso Catia , Procter Alexandra , Montgomerie Alicia , Anderson Jemma , Jureidini Jon , Petersen Julie , Lynch John , Chittleborough Catherine 
Published: September 2023

AbstractObjectivesTo examine the burden of mental health-related hospitalisations among adolescents by levels of previous child protection contact.Design, setting and participantsWhole-of-population study of children born in South Australia, 1991-1999 (n=175,115), using de-identified linked administrative data from the Better Evidence Better Outcomes Linked Data (BEBOLD) platform.Main outcome measuresAdolescents: proportion of adolescents aged 12-17 years with mental health hospitalisations; Hospitalisations: proportion of all adolescent mental health hospitalisations according to the level of child protection contact from 0-11 years.ResultsOverall, 15.5% (27,203/175,115 children) of adolescents had a history of child protection contact between ages 0-11 years, and 3.2% (5,646/175,115; 95% CI, 3.1 – 3.3) had a mental health-related hospitalisation between ages 12-17 years. Of the 10,633 mental health-related hospitalisations, 44.9% (95% CI, 44.0 – 45.9) were among adolescents with previous child protection contact even though they comprised only 15.5% of the study population. Of 5,646 adolescents with at least one mental health-related hospitalisation, 40.4% (95% CI, 39.1 – 41.7) had previous child protection contact. Among the population who experienced out-of-home care, 17.5% (209/1,191; 95% CI, 15.5 – 19.8) had experienced a mental health-related hospitalisation during adolescence, compared to 2.3% (3,366/147,912; 95% CI, 2.2 – 2.4) of adolescents with no prior child protection contact.ConclusionAlmost 45% of mental health hospitalisations for 12-17-year-olds occurred among children who had child protection contact, despite that group comprising only 15.5% of the study population. Potential trauma sequelae associated with child protection history is important to consider in the response to adolescents hospitalised due to mental health challenges.Significance of StudyThe knownAdolescent mental health is an important public health issue and those in child protection are at higher risk of experiencing mental health challenges.The newWe have quantified the burden of adolescent mental health hospitalisations attributable to the population with prior child protection system contact. For adolescents aged 12-17 years, those with a child protection history accounted for 44.9% of all adolescent mental health hospitalisations.The implicationsPotential trauma sequelae associated with child protection history are important to consider in the response to adolescents hospitalised due to mental health challenges.
Malaria species positivity rates among symptomatic individuals across regions of differing transmission intensities in Mainland Tanzania
Authors: Popkin Hall Zachary R. , Seth Misago D. , Madebe Rashid A. , Budodo Rule , Bakari Catherine , Francis Filbert , Pereus Dativa , Giesbrecht David J. , Mandara Celine I. , Mbwambo Daniel , Aaron Sijenunu , Lazaro Samwel , Bailey Jeffrey A. , Juliano Jonathan J. , Ishengoma Deus S. 
Published: September 2023

AbstractRecent data indicate that non-Plasmodium falciparumspecies may be more prevalent than previously realized in sub-Saharan Africa, the region where 95% of the world’s malaria cases occur. AlthoughPlasmodium malariae, Plasmodium ovalespp., andPlasmodium vivaxare generally less severe thanP. falciparum, treatment and control are more challenging, and their geographic distributions are not well characterized. In order to characterize the distribution of malaria species in Mainland Tanzania (which has a high burden and geographically heterogeneous transmission levels), we randomly selected 3,284 samples from 12,845 samples to determine presence and parasitemia of different malaria species. The samples were collected from cross-sectional surveys in 100 health facilities across ten regions and analyzed via quantitative real-time PCR to characterize regional positivity rates for each species.P. falciparumwas most prevalent, butP. malariaeandP. ovalewere found in all regions except Dar es Salaam, with high levels (>5%) ofP. ovalein seven regions (70%). The highest positivity rate ofP. malariaewas 4.5% in Mara region and eight regions (80%) had positivity rates ≥1%. We also detected threeP. vivaxinfections in the very low-transmission Kilimanjaro region. While most samples that tested positive for non-falciparum malaria were co-infected withP. falciparum, 23.6% (n = 13/55) ofP. malariaeand 14.7% (n = 24/163) ofP. ovalespp. samples were mono-infections.P. falciparumremains by far the largest threat, but our data indicate that malaria elimination efforts in Tanzania will require increased surveillance and improved understanding of the biology of non-falciparum species.
Sensitivity of dual-task motor performance to varying levels of cognitive impairment: a systematic review and quality assessment
Authors: Kos Maciej , Pavel Misha , Jimison Holly B. , Saczynski Jane S. 
Published: September 2023

Summary/AbstractDementia is one of the key public challenges of this century, with the number of persons with dementia worldwide projected to reach 115 million by 2050. This review aimed to answer whether monitoring of motor performance alone and during a cognitively taxing task (dual-task) is sufficiently sensitive to distinguish between levels of cognitive function (normal function, mild cognitive impairment, dementia) and, thus, appropriate for dementia screening. In the reviewed 15 studies, cognitively healthy controls had a higher dual-task gait speed than persons with impaired cognition (9/12 studies). The difference between dual- and single-task gait speeds (dual-task cost) was lower in healthy controls (7/8 studies). Such differences were not detected between patients with mild cognitive impairment and Alzheimer’s disease.These results suggest that monitoring of dual-task performance may be used in early dementia screening. Diversity in research designs, lack of established statistical and reporting standards prevent meta-analysis of data.
Larval thermosensitivity shapes adult population dynamics inAnophelesmosquitoes
Authors: Estupiñán Juan , Weyrich Anna M. , Schlösser Paula , Naujoks Charlene , Gilden-hard Markus , Diarra Assetou , Diallo Mouctar , Sangare Djibril , Telschow Arndt , Hsieh Chih-hao , Levashina Elena A. , Carrillo-Bustamante Paola 
Published: September 2023

AbstractMosquitoes are vectors of human life-threatening pathogens, posing a significant global health threat. While the influence of temperature on mosquito life-history traits has been extensively studied in laboratory settings, the ecological factors shaping mosquito development and population dynamics in natural environments remain poorly understood. Here, we used a multi-disciplinary approach, integrating field data from Mali, laboratory experiments, and mathematical modeling, to investigate the causal relationships between climate variables and the abundance ofAnopheles gambiae s.l. mosquitoes. Using convergent-cross mapping analyses an adult abundance in the Nanguilabou village, we observed that the dynamics of adult mosquito populations was driven by larval thermosensitivity. To elucidate the underlying mechanisms, we conducted experimental studies that revealed a density-dependent larval thermal response. Through mathematical modeling, we quantified the complex interplay between temperature and larval density, demonstrating that temperature and density have independent, non-synergistic effects on larval developmental speed, mortality, and pupation rates. Our findings provide a mechanistic understanding of how larval development shapes adult mosquito populations, highlighting the significance of multidisciplinary approaches in studying climate-driven mosquito population dynamics.
A Humanized Yeast System for Evaluating the Protein Prenylation of a Wide Range of Human and Viral CaaX Sequences
Authors: Hildebrandt Emily R. , Sarkar Anushka , Ravishankar Rajani , Kim June H. , Schmidt Walter K. 
Published: September 2023

AbstractThe C-terminal CaaX sequence (cysteine-aliphatic-aliphatic-any of several amino acids) is subject to isoprenylation on the conserved cysteine and is estimated to occur in 1-2% of proteins within yeast and human proteomes. Recently, non-canonical CaaX sequences in addition to shorter and longer length CaX and CaaaX sequences have been identified that can be prenylated. Much of the characterization of prenyltransferases has relied on the yeast system because of its genetic tractability and availability of reporter proteins, such as thea-factor mating pheromone, Ras GTPase, and Ydj1 Hsp40 chaperone. To compare the properties of yeast and human prenyltransferases, including the recently expanded target specificity of yeast farnesyltransferase, we have developed yeast strains that express human farnesyltransferase or geranylgeranyltransferase-I in lieu of their yeast counterparts. The humanized yeast strains display robust prenyltransferase activity that functionally replaces yeast prenyltransferase activity in a wide array of tests, including the prenylation of a wide variety of canonical and non-canonical human CaaX sequences, virus encoded CaaX sequences, non-canonical length sequences, and heterologously expressed human proteins HRas and DNAJA2. These results reveal highly overlapping substrate specificity for yeast and human farnesyltransferase, and mostly overlapping substrate specificity for GGTase-I. This yeast system is a valuable tool for further defining the prenylome of humans and other organisms, identifying proteins for which prenylation status has not yet been determined.Summary StatementWe report yeast engineered to express human prenylation enzymes with which prenylation can be investigated for established and novel CaaX sequences associated with proteins involved in human disease.
A flexible, modular and versatile functional part assembly toolkit for gene cluster engineering inStreptomyces
Authors: Zhao Xuejin , Zong Yeqing , Lou Qiuli , Qin Chenrui , Lou Chunbo 
Published: September 2023

ABSTRACTStreptomyceshas enormous potential to produce novel natural products (NPs) as it harbors a huge reservoir of uncharacterized and silent natural product biosynthetic gene clusters (BGCs). However, the lack of efficient gene cluster engineering strategies has hampered the pace of new drug discovery. Here, we developed an easy-to-use, highly flexible DNA assembly toolkit for gene cluster engineering. The DNA assembly toolkit are compatible with various DNA assembling approaches including Biobrick, Golden Gate, CATCH, yeast homologous recombination-based DNA assembly and homing endonuclease-mediated assembly. This compatibility offers great flexibility in handling multiple genetic parts or refactoring large gene clusters. To demonstrate the utility of this toolkit, we quantified a library of modular regulatory parts, and engineered a gene cluster (act) using characterized promoters that led to increased production. Overall, this work provides a powerful part assembly toolkit that can be used for natural product discovery and optimization inStreptomyces.
Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species
Authors: Mich John K. , Sunil Smrithi , Johansen Nelson , Martinez Refugio A. , Leytze Mckaila , Gore Bryan B. , Mahoney Joseph T. , Ben-Simon Yoav , Bishaw Yemeserach , Brouner Krissy , Campos Jazmin , Canfield Ryan , Casper Tamara , Dee Nick , Egdorf Tom , Gary Amanda , Gibson Shane , Goldy Jeff , Groce Erin L. , Hirschstein Daniel , Loftus Luke , Lusk Nick , Malone Jocelin , Martin Naomi X. , Monet Deja , Omstead Victoria , Opitz-Araya Ximena , Oster Aaron , Pom Christina A. , Potekhina Lydia , Reding Melissa , Rimorin Christine , Ruiz Augustin , Sedeño-Cortés Adriana E. , Shapovalova Nadiya V. , Taormina Michael , Taskin Naz , Tieu Michael , Valera Cuevas Nasmil J. , Weed Natalie , Way Sharon , Yao Zizhen , McMillen Delissa A. , Kunst Michael , McGraw Medea , Thyagarajan Bargavi , Waters Jack , Bakken Trygve E. , Yao Shenqin , Smith Kimberly A. , Svoboda Karel , Podgorski Kaspar , Kojima Yoshiko , Horwitz Greg D. , Zeng Hongkui , Daigle Tanya L. , Lein Ed S. , Tasic Bosiljka , Ting Jonathan T. , Levi Boaz P. 
Published: September 2023

AbstractProper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have revealed substantial diversity of glial cells, particularly astrocytes. To better understand glial cell types and their roles in neurobiology, we built a new suite of adeno-associated viral (AAV)-based genetic tools to enable genetic access to astrocytes and oligodendrocytes. These oligodendrocyte and astrocyte enhancer-AAVs are highly specific (usually > 95% cell type specificity) with variable expression levels, and our astrocyte enhancer-AAVs show multiple distinct expression patterns reflecting the spatial distribution of astrocyte cell types. To provide the best glial-specific functional tools, several enhancer-AAVs were: optimized for higher expression levels, shown to be functional and specific in rat and macaque, shown to maintain specific activity in epilepsy where traditional promoters changed activity, and used to drive functional transgenes in astrocytes including Cre recombinase and acetylcholine-responsive sensor iAChSnFR. The astrocyte-specific iAChSnFR revealed a clear reward-dependent acetylcholine response in astrocytes of the nucleus accumbens during reinforcement learning. Together, this collection of glial enhancer-AAVs will enable characterization of astrocyte and oligodendrocyte populations and their roles across species, disease states, and behavioral epochs.
Cytogenetic resource enables mechanistic resolution of changing trends in human pluripotent stem cell aberrations linked to feeder-free culture
Authors: Stavish Dylan , Price Christopher J. , Gelezauskaite Gabriele , Leonhard Kimberly A. , Taapken Seth M. , McIntire Erik M. , Laing Owen , James Bethany M. , Riley Jack J. , Zerbib Johanna , Baker Duncan , Harding Amy L. , Jestice Lydia H. , Eleveld Thomas F. , Gillis Ad J.M. , Hillenius Sanne , Looijenga Leendert H.J. , Gokhale Paul J. , Ben-David Uri , Ludwig Tenneille E. , Barbaric Ivana 
Published: September 2023

SummarySince the first derivation of human pluripotent stem cells (hPSCs), the number of culture conditions has steadily increased, making hPSC culture more facile. Nonetheless, there remains the persistent issue of culture-acquired genetic changes, hampering the reproducibility of hPSC research and jeopardising their clinical use. Here, we utilised comprehensive karyotyping datasets from over 20,000 hPSC cultures sampled under different conditions to ascertain association of genetic changes with specific culture regimens. We found condition-dependent patterns of aberrations, with higher prevalence of chromosome 1q gains in recent years, associated with increased use of contemporary, feeder-free cultures. Mechanistically, we show the context-dependent selection of 1q variants is mainly driven byMDM4, a gene amplified in many cancers, located on chromosome 1q. To facilitate reproducibility of hPSC research and their safe clinical utility, we provide a unique hPSC karyotype resource for informing the risk assessment of genetic aberrations and developing strategies to suppress their occurrence.
FUKG: answering flexible queries over knowledge graphs
Authors: Yagüe José Félix , Huitzil Ignacio , Bobed Carlos , Bobillo Fernando 
Published: September 2023

Purpose
There is an increasing interest in the use of knowledge graphs to represent real-world knowledge and a common need to manage imprecise knowledge in many real-world applications. This paper aims to study approaches to solve flexible queries over knowledge graphs.

Design/methodology/approach
By introducing fuzzy logic in the query answering process, the authors are able to obtain a novel algorithm to solve flexible queries over knowledge graphs. This approach is implemented in the FUzzy Knowledge Graphs system, a software tool with an intuitive user-graphical interface.

Findings
This approach makes it possible to reuse semantic web standards (RDF, SPARQL and OWL 2) and builds a fuzzy layer on top of them. The application to a use case shows that the system can aggregate information in different ways by selecting different fusion operators and adapting to different user needs.

Originality/value
This approach is more general than similar previous works in the literature and provides a specific way to represent the flexible restrictions (using fuzzy OWL 2 datatypes).
Understanding tourists' environmentally responsible behaviour: environmental citizenship behaviour as an antecedent and trust in destination's local government as a moderator
Authors: Candan Buket , Dölarslan Emre Şahin 
Published: September 2023

PurposeTourists' environmentally responsible behaviour (ERB) is very important for the environmental sustainability of popular tourist destinations. The main purpose of this research paper is to explore the relationship between environmental citizenship behaviour (ECB) and trust in local government with ERB.Design/methodology/approachA theoretical model was proposed and tested. Data were collected from domestic tourists (n = 555) visiting Antalya, on the Mediterranean coast of Turkey.FindingsThe results show that all dimensions of ECB (helping, engagement and initiatives) have a positive effect on the formation of ERB among domestic tourists. The results also show that trust in the local government of the destination has a moderating effect on the relationship between the two dimensions of ECB (engagement and initiatives) and ERB. The helping dimension of ECB has the highest positive impact factor on ERB. The results provide a comprehensive framework for further research. The proposed model is strongly supported by the findings.Practical implicationsLocal policy makers can focus on how to increase the environmental motivation of domestic tourists. Environmentally friendly projects can be developed to attract their attention. This will ensure that they take more responsibility for the environment at the destination.Originality/valueUnderstanding the potential impact of local government on tourist behaviour is crucial for sustainability. However, there are few studies that directly examine the moderating effect of trust in local government on the relationship between ECB and ERB. This study addresses this gap and makes novel contributions to the relevant literature.
Revisiting the impact of geopolitical risk on Sukuk, stocks, oil and gold markets during the crises period: fresh evidence from wavelet-based approach
Authors: Raza Rabbani Mustafa , Hassan M. Kabir , Jamil Syed Ahsan , Sahabuddin Mohammad , Shaik Muneer 
Published: September 2023

Purpose In this study, the authors analyze the impact of geopolitics risk on Sukuk, Islamic and composite stocks, oil and gold markets and portfolio diversification implications during the COVID-19 pandemic and Russia–Ukraine conflict period.Design/methodology/approachThe study used a mix of wavelet-based approaches, including continuous wavelet transformation and discrete wavelet transformation. The analysis used data from the Geopolitical Risk index (GP{R), Dow Jones Sukuk index (SUKUK), Dow Jones Islamic index (DJII), Dow Jones composite index (DJCI), one of the top crude oil benchmarks which is based on the Europe (BRENT) (oil fields in the North Sea between the Shetland Island and Norway), and Global Gold Price Index (gold) from May 31, 2012, to June 13, 2022.Findings The results of the study indicate that during the COVID-19 and Russia–Ukraine conflict period geopolitical risk (GPR) was in the leading position, where BRENT confirmed the lagging relationship. On the other hand, during the COVID-19 pandemic period, SUKUK, DJII and DJCI are in the leading position, where GPR confirms the lagging position.Originality/value The present study is unique in three respects. First, the authors revisit the influence of GPR on global asset markets such as Islamic stocks, Islamic bonds, conventional stocks, oil and gold. Second, the authors use the wavelet power spectrum and coherence analysis to determine the level of reliance based on time and frequency features. Third, the authors conduct an empirical study that includes recent endogenous shocks generated by health crises such as the COVID-19 epidemic, as well as shocks caused by the geopolitical danger of a war between Russia and Ukraine.Highlights We analyze the impact of geopolitics risk on Sukuk, Islamic and composite stocks, oil and gold markets and portfolio diversification implications during the COVID-19 pandemic and Russia–Ukraine conflict period.The results of the wavelet-based approach show that Dow Jones composite and Islamic indexes have observed the highest mean return during the study period.GPR and BRENT are estimated to have the highest amount of risk throughout the observation period.Dow Jones Sukuk, Islamic and composite stock show similar trend of volatility during the COVID-19 pandemic period and comparatively gold observes lower variance during the COVID-19 pandemic and Russia–Ukraine conflict.
Surgery after sonidegib treatment achieves complete response in locally advanced basal cell carcinoma of the face
Authors: Paradisi A. , Piccerillo A. , Bocchino E. , Cappilli S. , Ricci C. , Di Stefani A. , Peris K. 
Published: September 2023

AbstractBasal cell carcinoma accounts for 75% of skin cancers worldwide and is the most common malignancy in Caucasians. Since chronic ultraviolet exposure is the major risk factor for its development, sun‐exposed areas such as the face are frequently affected. The gold‐standard treatment is surgical excision. Radiotherapy may be considered in selected cases such as unresectable primary tumors. In some patients, when the risk of a significant functional/cosmetic deficit advises against both surgery and radiotherapy, target therapy (hedgehog pathway inhibitors) can be administered alone or in a neoadjuvant setting, to reduce the tumor size and make it eligible for surgery. Vismodegib as a neoadjuvant treatment before surgery has been investigated in a single, multicentre, open‐label, phase II trial (VISMONEO); however, sonidegib has not yet been evaluated in this setting. We report the cases of two patients with locally advanced basal cell carcinoma of the face who achieved complete remission with sonidegib followed by a more limited surgical excision than would have been needed without target therapy.