bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncoupling protein 1-driven Cre (Ucp1-Cre) is expressed in the epithelial cells of mammary glands and various non-adipose tissues
Authors: Kim Kyungchan , Wann Jamie , Kim Hyeong-Geug , So Jisun , Rosen Evan D. , Roh Hyun Cheol 
Published: October 2023

ABSTRACTObjectiveUncoupling protein 1 (UCP1), a mitochondrial protein responsible for nonshivering thermogenesis in adipose tissue, serves as a distinct marker for thermogenic brown and beige adipocytes.Ucp1-Cremice are thus widely used to genetically manipulate these thermogenic adipocytes. However, evidence suggests that UCP1 may also be expressed in non-adipocyte cell types. In this study, we investigated the presence of UCP1 expression in different mouse tissues that have not been previously reported.MethodsWe employedUcp1-Cremice crossed with Cre-inducible transgenic reporter Nuclear tagging and Translating Ribosome Affinity Purification (NuTRAP) mice, to investigateUcp1-Creexpression in various tissues of adult female mice and developing embryos. Tamoxifen-inducibleUcp1-CreERT2mice crossed with NuTRAP mice were used to assess active UCP1 expression. Immunostaining, RNA analysis, and single-cell/nucleus RNA-seq (sc/snRNA-seq) data analysis were performed to determine the expression of endogenous UCP1 andUcp1-Cre-driven reporter expression. We also investigated the impact of UCP1 deficiency on mammary gland development and function usingUcp1-knockout (KO) mice.ResultsUcp1-Creexpression was observed in the mammary glands within the inguinal white adipose tissue of femaleUcp1-Cre; NuTRAP mice. However, endogenousUcp1was not actively expressed asUcp1-CreERT2failed to induce the reporter expression in the mammary glands.Ucp1-Crewas activated during embryonic development in various tissues, including mammary glands, as well as in the brain, kidneys, eyes, and ears, specifically in epithelial cells in these organs. While sc/snRNA-seq data suggest potential expression of UCP1 in mammary epithelial cells in adult mice and humans,Ucp1-KO female mice displayed normal mammary gland development and function.ConclusionsOur findings reveal widespreadUcp1-Creexpression in various non-adipose tissue types, starting during early development. These results highlight the importance of exercising caution when interpreting data and devising experiments involvingUcp1-Cremice.
Directional predictions of HIV transmission with optimised genomics in cohorts of serodiscordant couples
Authors: Zhao Lele , Hall Matthew , Wymant Chris , Abeler-Dörner Lucie , Otecko Newton , MacIntyre-Cockett George , Chaudron Sandra E. , Thomson Laura , Golubchik Tanya , Lingappa Jairam , Ferretti Luca , Lythgoe Katrina , Fraser Christophe , Herbeck Joshua , Bonsall David ,   the PANGEA consortium
Published: October 2023

AbstractViral genetic information from people living with HIV can deepen our understanding of the infection’s epidemiology at many scales. To better understand the potentials and limits of tools that utilise such information, we show the performance of two representative tools (HIV-TRACEandphyloscanner) in describing HIV transmission dynamics, with different types of genetic data, and compare with previous findings. The samples were collected from three cohort studies in Sub-Saharan Africa and were deep sequenced to produce both short Illumina reads and long PacBio reads. By comparingphyloscanner’s performance with short and long reads, we show that long reads provide improved phylogenetic resolution for the classic transmission topology in joint within-host trees. Our pipeline accurately predicted the direction of transmission 88%-92% of the time. We also show that the timing of sample collection plays an important role in the reconstruction of directionality using deep sequencing data. Consensus sequences were also generated and used asHIV-TRACEinput to show different patterns of clustering sensitivity and specificity for data from different genomic regions or the entire genome. Finally, we discuss adjusting expectations about sensitivity and specificity of different types of sequence data, considering rapid pathogen evolution, and highlight the potentials of high within-host phylogenetic resolution in HIV. In conclusion, viral genetic data collected and presented differently could greatly influence our ability to describe the underlying dynamics. Methods for source attribution analysis have reached levels of superior accuracy. However, residual uncertainty emphasizes sequence analysis alone cannot conclusively prove linkage at the individual level.ImportanceUnderstanding HIV transmission dynamics is key to designing effective HIV testing and prevention strategies. By using different sequencing techniques on well-characterised cohorts, we were able to evaluate the effect of genetic data resolution on the accuracy of identifying likely transmission pairs and the direction of transmission within pairs. We find that the longer reads generated by PacBio sequencing are more suitable for transmission analyses.
Bilateral Intracortical Inhibition during Unilateral Motor Preparation and Sequence Learning
Authors: Hamel R. , Waltzing B. M. , Hinder M.R. , McAllister C. , Jenkinson N. , Galea J.M 
Published: October 2023

ABSTRACTMotor sequence learning gradually quickens reaction time, suggesting that sequence learning alters motor preparation processes. Interestingly, evidence has shown that preparing sequence movements decreases short intracortical inhibition (SICI) in the contralateral motor cortex (M1), but also that sequence learning alters motor preparation processes in both the contralateral and ipsilateral M1s. Therefore, one possibility is that sequence learning alters the SICI decreases occurring during motor preparation in bilateral M1s. To examine this, two novel hypotheses were tested: unilateral sequence preparation would decrease SICI in bilateral M1s, and sequence learning would alter such bilateral SICI responses. Paired-pulse transcranial magnetic stimulation was delivered over the contralateral and ipsilateral M1s to assess SICI in an index finger muscle during the preparation of sequences initiated by either the right index or little finger. In the absence of sequence learning, SICI decreased in both the contralateral and ipsilateral M1s during the preparation of sequences initiated by the right index finger, suggesting that SICI decreases in bilateral M1s during unilateral motor preparation. As sequence learning progressed, SICI decreased in the contralateral M1 whilst it increased in the ipsilateral M1. Moreover, these bilateral SICI responses were observed at the onset of motor preparation, suggesting that sequence learning altered baseline SICI levels rather than the SICI decreases occurring during motor preparationper se. Altogether, these results suggest that SICI responses in bilateral M1s reflect two motor processes: an acute decrease of inhibition during motor preparation, and a cooperative but bidirectional shift of baseline inhibition levels as sequence learning progresses.
Load modulation affects pediatric lower limb joint moments during a step-up task
Authors: Goyal Vatsala , Gordon Keith E. , Sukal-Moulton Theresa 
Published: October 2023

AbstractPerformance in a single step has been suggested to be sensitive measure of movement quality in pediatric clinical populations. Although there is less information available in children with typical development, researchers have postulated the importance of analyzing the effect of body weight modulation on the initiation of stair ascent, especially during single limb stance where upright stability is most critical. The purpose of this study was to investigate the effect of load modulation from -20% to +15% of body weight on typical pediatric lower limb joint moments during a step-up task. Fourteen participants between 5-21 years with no known history of neurological or musculoskeletal concerns were recruited to perform multiple step-up trials. Peak extensor support and hip abduction moments were identified during the push-off and pull-up stance phases. Linear regressions were used to determine the relationship between peak moments and load. Mixed effects models were used to estimate the effect of load on hip, knee, and ankle percent contributions to peak support moments. There was a positive linear relationship between peak support moments and load in both stance phases, where these moments scaled with load. There was no relationship between peak hip abduction moments and load. While the ankle and knee were the primary contributors to the support moments, the hip contributed more than expected in the pull-up phase. Clinicians can use these results to contextualize movement differences in pediatric clinical populations including cerebral palsy and highlight potential target areas for rehabilitation for populations such as adolescent athletes.
Perceptions and responses to COVID-19 through wastewater surveillance information and online search behavior: A randomized controlled trial
Authors: Murakami Michio , Nomura Shuhei , Ando Hiroki , Kitajima Masaaki 
Published: October 2023

AbstractWastewater surveillance is anticipated to be a representative and timely method to assess infectious disease status; however, its influence on public perception and behavior remains unclear. Therefore, in this study, we used a randomized controlled trial to analyze the influence of wastewater surveillance-based information on understanding of, interest in, relief regarding, preventive behavioral intention against, and subsequent online search behavior related to coronavirus disease 2019 (COVID-19). Valid responses were obtained from 1,000 individuals in both control and intervention groups from Yahoo crowdsourcing users aged ≥18 years in Japan. This survey was conducted from August 4 to August 7, 2023, just before the common Japanese tradition of returning to hometowns. The questionnaire not only collected personal attributes but also gauged responses to COVID-19 information. This information highlighted the early detection capabilities and representativeness of wastewater surveillance compared with sentinel surveillance at medical institutions. At one-week post-survey, we obtained the survey participants’ online search history for key words such as “bullet train,” “highway,” “airplane,” and “wastewater.” The findings showed no significant differences between the two groups in terms of COVID-19 interest or preventive behavior before information provision, verifying the effectiveness of participant randomization. Wastewater surveillance-based information did not notably elevate understanding or specific intentions regarding COVID-19, such as wearing masks and receiving vaccination. However, it significantly increased interest in, relief concerning the infection status, and general preventive behavioral intentions. Heightened interest and general preventive intentions did not depend on prior interest or behavior. However, those who previously engaged in preventive behavior or who were less interested in COVID-19 exhibited more relief after exposure to wastewater surveillance-based information. Furthermore, this information could slightly influence online searches related to return travel modes, such as highways. In conclusion, information from wastewater surveillance effectively shapes individual perceptions of and responses to infections.
Changing patterns of cigarette and ENDS transitions in the USA: a multistate transition analysis of adults in the PATH Study in 2017–2019 vs 2019–2021
Authors: Brouwer Andrew F. , Jeon Jihyoun , Jimenez-Mendoza Evelyn , Land Stephanie R. , Holford Theodore R. , Friedman Abigail S. , Tam Jamie , Mistry Ritesh , Levy David T. , Meza Rafael 
Published: October 2023

AbstractIntroductionThe use of cigarettes and electronic nicotine delivery system (ENDS) has likely changed since 2019 with the rise of pods and disposables, the outbreak of lung injuries related to vaping THC, flavor bans, and the COVID pandemic. We analyzed patterns of initiation, cessation, and transitions between cigarettes, ENDS, and dual use before and after 2019.MethodsUsing the Population Assessment of Tobacco and Health (PATH) Study, we applied a multistate transition model to 28,061 adults in Waves 4–5 (2017–19) and 24,751 adults in Waves 5–6 (2019–21), estimating transition rates for initiation, cessation, and switching products for each period overall and by age group.ResultsCigarette initiation among adults who never used either product decreased from 2017–19 to 2019–21, but ENDS initiation did not significantly change. Persistence of ENDS-only use remained high, with 75–80% still using ENDS only after 1 year. Cigarette-only use transitions remained similar, with about 88% remaining, 7% transitioning to non-current use, and 5% transitioning to dual or ENDS-only use. In contrast, dual use to ENDS-only transitions increased from 9.5% (95%CI: 7.3–11.7%) to 20.1% (95%CI: 17.5–22.7%) per year from 2017–19 to 2019–21, decreasing the persistence of dual use. The dual use to cigarette-only transition remained at about 25%. These changes were qualitatively similar across adult age groups, though adults ages 18–24 years exhibited the highest probability of switching from cigarette-only use to dual use and from dual use to ENDS-only use.ConclusionsPersistence of ENDS use among adults remained high in 2019–21, but a larger fraction of dual users transitioned to ENDS-only use compared to 2017–19. Because the fraction of cigarette-only users switching to dual use remained low, the public health implications of the increased dual use to ENDS-only transition are minimal.
How does the proportion of never treatment influence the success of mass drug administration programmes for the elimination of lymphatic filariasis?
Authors: Kura Klodeta , Stolk Wilma A. , Basáñez Maria-Gloria , Collyer Benjamin S. , de Vlas Sake J. , Diggle Peter J , Gass Katherine , Graham Matthew , Hollingsworth T. Déirdre , King Jonathan D. , Krentel Alison , Anderson Roy M. , Coffeng Luc E. 
Published: October 2023

AbstractBackgroundMass drug administration (MDA) is the cornerstone for the elimination of lymphatic filariasis (LF). The proportion of the population that is never treated (NT) is a crucial determinant of whether this goal is achieved within reasonable timeframes.MethodsUsing two individual-based stochastic LF transmission models, we assess the maximum permissible level of NT for which the 1% mf prevalence threshold can be achieved (with 90% probability) within 10 years under different scenarios of annual MDA coverage, drug combination and transmission setting.ResultsForAnopheles-transmission settings, we find that treating 80% of the eligible population annually with ivermectin+albendazole (IA) can achieve the 1% mf prevalence threshold within 10 years of annual treatment when baseline mf prevalence is 10%, as long as NT <10%. Higher proportions of NT are acceptable when more efficacious treatment regimens are used. ForCulex-transmission settings with a low (5%) baseline mf prevalence and Diethylcarbamazine+Albendazole (DA) or Ivermectin+Diethylcarbamazine+Albendazole (IDA) treatment, elimination can be reached if treatment coverage among eligibles is 80% or higher. For 10% baseline mf prevalence, the target can be achieved when the annual coverage is 80% and NT ≤15%. Higher infection prevalence or levels of NT would make achieving the target more difficult.ConclusionsThe proportion of people never treated in MDA programmes for LF can strongly influence the achievement of elimination and the impact of NT is greater in high transmission areas. This study provides a starting point for further development of criteria for the evaluation of NT.
Sex differences in ADHD diagnosis and clinical care: A national study of population healthcare records in Wales
Authors: Martin Joanna , Langley Kate , Cooper Miriam , Rouquette Olivier Y. , John Ann , Sayal Kapil , Ford Tamsin , Thapar Anita 
Published: October 2023

AbstractBackgroundPopulation-based studies have observed sex biases in the diagnosis and treatment of attention deficit hyperactivity disorder (ADHD). Females are less likely to be diagnosed or prescribed ADHD medication. This study uses national healthcare records, to investigate sex differences in diagnosis and clinical care in young people with ADHD, particularly regarding recognition and treatment of other mental health conditions.MethodThe cohort included individuals diagnosed with ADHD, born between 1989 and 2013 and living in Wales between 2000 and 2019. Routine primary and secondary healthcare record data were used to derive diagnoses of ADHD and other neurodevelopmental and mental health conditions, as well as ADHD and antidepressant medications. Demographic variables included ethnicity, socioeconomic deprivation, and contact with social services.ResultsThere were 16,458 individuals diagnosed with ADHD (20.3% females, ages 3–30 years), with a male-to-female ratio of 3.9:1. Higher ratios (4.8:1) were seen in individuals diagnosed younger (<12 years), with the lowest ratio (1.9:1) in those diagnosed as adults (>18). Males were younger at first recorded ADHD diagnosis (mean=10.9 vs 12.6 years), more likely to be prescribed ADHD medication, and younger at diagnosis of co-occurring neurodevelopmental conditions. In contrast, females were more likely to receive a diagnosis of anxiety, depression, or another mental health condition and to be prescribed antidepressant medications, prior to ADHD diagnosis. These sex differences were largely stable across demographic groups.ConclusionThis study adds to the evidence base that females with ADHD are experiencing later recognition and treatment of ADHD. The results indicate that this may be partly because of diagnostic over-shadowing from other mental health conditions, such as anxiety and depression, or initial misdiagnosis. Further research and dissemination of findings to the public are needed to improve awareness, timely diagnosis, and treatment of ADHD in females.
Postacute Sequelae SARS-CoV-2 Infection by Vaccination Status: A Six-Month Latent Class Analysis
Authors: Sun Xiaowu , DeShazo Jonathan P. , Anatale-Tardiff Laura , Fusco Manuela Di , Allen Kristen E. , Porter Thomas M. , Coetzer Henriette , Lopez Santiago M.C , Puzniak Laura , Cappelleri Joseph C. 
Published: October 2023

AbstractSymptoms post-SARS-CoV-2 infection may persist for months and cause significant impairment and impact to quality of life. Acute symptoms of SARS-CoV-2 infection are well studied, yet data on clusters of symptoms over time, or postacute sequelae of SARS-CoV-2 infection (PASC), are limited. We aim to characterize PASC phenotypes by identifying symptom clusters over a six-month period following infection in individuals vaccinated (boosted and not) and those unvaccinated.Subjects with ≥1 self-reported symptom and positive RT-PCR for SARS-CoV-2 at CVS Health US test sites were recruited between January and April 2022. Patient-reported outcomes symptoms, heath-related quality of life (QoL), work productivity and activity impairment (WPAI) were captured at 1 month, 3 months, and 6 months post-acute infection.Logistic regression and latent class analysis (LCA) were performed on 20 symptoms using baseline socio-demographic, clinical characteristics, and vaccination status as well as EQ-5and WPAI results as covariables. Subjects with more symptoms were associated with lower health-related quality of life, and worse WPAI scores.LCA identified three phenotypes that are primarily differentiated by number of symptoms. These three phenotypes remained consistent across time periods. Vaccinated individuals were more likely to be in the low symptom burden latent classes at all time points compared to unvaccinated individuals.
Spatial mapping of rheumatoid arthritis synovial niches reveals specific macrophage networks associated with response to therapy
Authors: De Lima Julien , Boutet Marie-Astrid , Bortolotti Olivier , Chépeaux Laure-Agnès , Glasson Yaël , Dumé Anne-Sophie , Le Pluart Adrien , Nerviani Alessandra , Fossati-Jimack Liliane , Michaud Henri-Alexandre , Guicheux Jérôme , Goff Benoit Le , Pitzalis Costantino , Courties Gabriel , Apparailly Florence , Blanchard Frederic 
Published: October 2023

AbstractRheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease affecting peripheral joints and for which approximately 40% of the patients respond insufficiently to the available synthetic or biologic disease modifying anti-rheumatic drugs (DMARDs). The infiltration of the synovial membrane by lymphocytes and monocytes profoundly alters its homeostatic functions, leading to chronic joint inflammation and bone destruction. A better understanding of how DMARDs impact the complex synovial cell social network in relationship to response/ non-response remains an unmet need to design more targeted and active therapeutic strategies. Here, we used imaging mass cytometry (IMC) to comparatively profile more than 115,000 cells in the synovial tissue of healthy, low inflammatory osteoarthritis and matched active early treatment-naïve RA patients at baseline and at 6 months after starting DMARDs treatment. We notably highlighted that tissue resident macrophages (LYVE1+CD206+) in perivascular synovial niches encompassing specific subsets of vascular cells, fibroblasts and immune cells vanished in active RA but were recovered in response to DMARDs treatment. Combined ligand-receptor analysis of single-cell RNA sequencing datasets identified that IL10, C-type lectin or TAM (TYRO3, AXL and MERTK) receptors were particularly involved in the restoration of these spatial cell interactions in the context of clinical remission. In addition to providing an unprecedented synovial spatial mapping, our work uncovered novel potential cellular and molecular targets for the development of therapies for RA.One Sentence SummarySingle-cell spatial profiling of rheumatoid arthritis synovium identifies specific cell states linked to treatment response
Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence
Authors: Ferguson Scott , Jones Ashley , Murray Kevin , Andrew Rose L. , Bothwell Helen , Schwessinger Benjamin , Borevitz Justin 
Published: October 2023

AbstractStructural variants (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely relatedEucalyptusspecies to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences, or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals ofE. melliodoraandE. sideroxylon, along with recent high quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads, inE. melliodoraandE. sideroxylonrespectively. Focusing on inversions and translocations, symmetric SVs which are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.