bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impaired contour object perception in psychosis
Authors: Kamath Rohit S. , Weldon Kimberly B. , Moser Hannah R. , Montoya Samantha , Abdullahi Kamar S. , Burton Philip C. , Sponheim Scott R. , Olman Cheryl A. , Schallmo Michael-Paul 
Published: July 2024

AbstractContour integration, the process of joining spatially separated elements into a single unified line, has consistently been found to be impaired in schizophrenia. Recent work suggests that this deficit could be associated with psychotic symptomatology, rather than a specific diagnosis such as schizophrenia. Examining a transdiagnostic sample of participants with psychotic psychopathology, we obtained quantitative indices of contour perception in a psychophysical behavioral task. We found impaired contour discrimination performance among people with psychotic psychopathology (PwPP, n = 62) compared to healthy controls (n = 34) and biological relatives of PwPP (n = 44). Participants with schizophrenia (n = 31) showed impaired task performance compared to participants with bipolar disorder (n = 18). We also measured responses during an analogous task using ultra-high field (7T) functional MRI and found higher responses in the lateral occipital cortex of PwPP compared to controls. Using task-based functional connectivity analyses, we observed abnormal connectivity between visual brain areas during contour perception among PwPP. These connectivity differences only emerged when participants had to distinguish the contour object from background distractors, suggesting that a failure to suppress noise elements relative to contour elements may underlie impaired contour processing in PwPP. Our results are consistent with impaired contour integration in psychotic psychopathology, and especially schizophrenia, that is related to cognitive dysfunction, and may be linked to impaired functional connectivity across visual regions.
Effect of parents’ country of birth on the relationship between socioeconomic status and childhood overweight and obesity in Southwest Sydney, Australia: learnings from the Growing Healthy Kids population prevalence survey
Authors: Kovai Vilas , Chong Shanley , Tang Janice , Jalaludin Bin , Thomas Margaret , Camilleri Michelle , Williams Mandy 
Published: July 2024

AbstractBackgroundChildhood obesity is a major public health concern in Australia and the multicultural population of South-West Sydney. This study examined the influence of parents’ country of birth (COB) on the association between family socio-economic status (SES), assessed by area-level disadvantage and annual household income, and childhood obesity.MethodsThe analysis of data from the cross-sectional Growing Healthy Kids in Southwest Sydney (GHK-SWS) baseline survey of 1,815 children aged 5-16 years living in South Western Sydney, Australia employed generalised linear multinomial mixed models, with results presented as odds ratio and 95% confidence intervals.ResultsThis study found a significant relationship between SES measures and the risk of overweight and obesity in the study population. The risks of childhood obesity are greatest in lower socioeconomic groups (across both SES metrics) regardless of their parents’ COB status. However, the overweight results are inconsistent across SES metrics and COB status. The risk of being overweight was lower for Australian-born parents living in disadvantaged areas but higher for those reporting lower income; and higher for Overseas-born parents living in disadvantaged areas but lower for those reporting low household income.ConclusionParents’ SES is a consistent predictor of childhood obesity, and this relationship is not modified by parents’ COB. However, the likelihood of a child being overweight varied between the parents’ SES measures and COB. Prioritisation of the target population for area-level preventive public health interventions to modify obesogenic factors is recommended for a) obese children living in most disadvantaged areas and moderate disadvantaged areas regardless of their parents’ COB; b) overweight and obese children of moderate disadvantaged areas regardless of their parents’ COB.
“It’s his cheerfulness that gives me hope”: A Qualitative Analysis of Access to Pediatric Cancer Care in Northern Tanzania
Authors: Metcalf Madeline , Kajoka Happiness D. , Majaliwa Esther , Tupetz Anna , Staton Catherine A. , Vissoci João Ricardo , Espinoza Pamela , Cotache-Condor Cesia , Rice Henry E. , Mmbaga Blandina T. , Smith Emily R. 
Published: July 2024

ABSTRACTBackgroundPediatric cancer is a significant and growing burden in low- and middle-income countries. The objective of this project was to describe the factors influencing access to pediatric cancer care in Northern Tanzania using the Three Delays Model.MethodsThis was a cross-sectional qualitative study conducted between June and September 2023 at Kilimanjaro Christian Medical Centre (KCMC). Parents and caregivers of children obtaining pediatric cancer care at KCMC were approached for participation in in-depth interviews (IDIs) and a demographic survey. All IDIs were facilitated in Swahili by a bilingual research coordinator. Thirteen IDIs and surveys were completed during the study period. Analysis utilized inductive and deductive coding approaches to identify dominant themes and sub-themes impacting access to pediatric oncology care.ResultsParticipants reported significant financial barriers to accessing pediatric cancer care along the entire care continuum. Early delays were impacted by waiting for symptoms to resolve or worsen. The most substantial delays resulted from health infrastructure at mid-level health facilities, misdiagnoses, and delayed referral to KCMC for treatment. Participants did not describe delays after arrival to KCMC and rather offered perspective on their child’s cancer diagnosis, their concerns while obtaining care, and their hopes for the future. Financial support provided by the Tanzanian government was the only facilitator noted by participants.ConclusionsWe suggest targeted interventions including 1) empowerment of CHWs and local traditional healers to advocate for earlier care seeking behavior, 2) implementation of clinical structures and training at intermediary medical centers aimed at earlier referral to a treatment facility, 3) incorporation of support and education initiatives for families of children with a cancer diagnosis. Lastly, we suggest that national health plans include pediatric cancer care.
Effect of children’s BMI on the association between parents’ socio-demographic and economic characteristics, and Parental perceptions of their child’s weight status in South-western Sydney: The Growing Healthy Kids Survey, Australia
Authors: Kovai Vilas , Chong Shanley , Jalaludin Bin , Tang Janice , Camilleri Michelle , Thomas Margaret , Fox Francis , Williams Mandy 
Published: July 2024

AbstractBackgroundParents’ perception of children’s weight status has been recognised as one of the influencing factors when planning childhood overweight and obesity prevention programs. We aimed to examine whether children’s BMI modified the association between parents’ socio-demographic and economic characteristics and their perceptions of their children’s weight status in South Western Sydney Local Health District.MethodsWe analysed 1,353 parents’ perceptions of their child’s weight status using the ‘Growing Healthy Kids-Population Health Survey’ baseline data. Generalised linear multinomial mixed models were used to determine the associations. Results are presented as odds ratio and associated 95% confidence intervals by BMI.ResultsThis study found that the weight status of about 23% of healthy-weight children, 65% of overweight children and 55% of obese children was incorrectly perceived by parents. Father as the primary parent and parents who completed ≤12 years of school education were less likely to perceive their overweight or obese children as overweight. Parents who lived in more disadvantaged areas were more likely to perceive their obese children as overweight. Parents who lived in moderate disadvantaged areas were less likely to perceive their overweight children as overweight. Parents who had reported an annual household income between $52,000-$103,999 were more likely to perceive their overweight children as of healthy weight and parents who reported an annual household income below $103,999 were twice as likely to perceive their obese children as having a healthy weight.ConclusionThe findings suggest that there may be benefit in designing interventions that focus on improving parents’ misperception of children’s weight status. The groups of parents who should be prioritised for preventive public health interventions to modify the parental misperceptions of their child’s weight status include a) fathers, b) parents who completed ≤12 years of school education and parents who had Trade, TAFE or Diploma as educational qualification, c) parents living in moderately disadvantaged areas and d) parents with low and high household-income.
Tissue expression in surgically retrieved cam deformity and capsule from patient hips with Cam-type Femoroacetabular Impingement Syndrome
Authors: Yuh Catherine , Malloy Philip , Mell Steven P , Khan Zeeshan , Nho Shane J. , Pourzal Robin , Chahla Jorge , Hall Deborah J 
Published: July 2024

ABSTRACTIntroductionCam-type femoroacetabular impingement syndrome (FAIS) is a pre-arthritic hip condition, defined as a bony growth on the proximal femur that causes abnormal joint contact. The tissue presentation of the cam deformity and capsule in FAIS remains understudied. The purpose of this study was to 1) evaluate histopathological features in cam deformity and capsule from FAIS patients, 2) assess the extent of local inflammation within the capsule, and 3) determine relationships between cam deformity tissue composition versus α angle and patient factors.MethodsCam deformity and capsular tissues were collected from FAIS patients undergoing arthroscopic surgery. Samples were histologically processed, imaged using light and polarized light microscopy, and assessed with point counting. Correlation-based statistics were performed to identify features correlated with α angle and patient factors.ResultsAcross 21 cam deformity samples assessed, a total of 16,259 points were counted. The tissue within the cam deformity was observed to be heterogeneous between specimens, comprised of 16 distinct structures spanning different states of viability. In samples with articular cartilage, the tissue was highly disrupted and/or calcified. The presence of fibrocartilage, necrotic cartilage, and vasculature had significant low-moderate correlations with α angle. During assessment of capsular tissue quality, synovitis was observed in most samples.ConclusionThe cam deformity is complex and heterogeneous, both within individual cam deformities and between individuals with FAIS. Several cam deformity tissue features were correlated with α angle, age, sex, and BMI. The heterogeneity observed in these samples indicates that tissue properties within the cam deformity varies between patients with FAIS, which may contribute to outcomes of hip arthroscopic surgery and a patient’s level of risk for the subsequent development of osteoarthritis. Our findings suggest distinct tissue phenotypes of FAIS exist, which may be an important consideration for FAIS treatment strategies.
Exploring Comorbidity Networks in Mild Traumatic Brain Injury Subjects through Graph Theory: A Traumatic Brain Injury Model Systems Study
Authors: Mehta Kaustav , Sudhakar Shyam Kumar 
Published: July 2024

AbstractTraumatic brain injuries (TBIs) are characterized by myriad comorbidities that affect the functioning of the affected individuals. The comorbidities that TBI subjects experience span a wide range, ranging from psychiatric diseases to those that affect the various systems of the body. This is compounded by the fact that the problems that TBI subjects face could span over an extended period post-primary injury. Further, no drug exists to prevent the spread of secondary injuries after a primary impact. In this study, we employed graph theory to understand the patterns of comorbidities after mild TBIs. Upon application of network analysis and a novel clustering algorithm, we discovered interesting associations between comorbidities in young and old subjects with the condition. Specifically, bipolar disorder was seen as related to cardiovascular comorbidities, a pattern that was observed only in the young subjects. Similar associations between obsessive-compulsive disorder and rheumatoid arthritis were observed in young subjects. Psychiatric comorbidities exhibited differential associations with non-psychiatric comorbidities depending on the age of the cohort. The study results might have implications for effective surveillance and the management of comorbidities post mild TBIs.
A VgrG2b fragment cleaved by caspase-11/4 promotesPseudomonas aeruginosainfection through suppressing the NLRP3 inflammasome
Authors: Qian Yan , Liu Qiannv , Cheng Xiangyun , Wang Chunlei , Kong Chun , Li Mengqian , Ren Chao , Jiang Dong , Wang Shuo , Xia Pengyan 
Published: July 2024

AbstractThe T6SS ofPseudomonas aeruginosaplays an essential role in the establishment of chronic infections. Inflammatory cytokines mediated by inflammasomes are crucial for the body to resist bacterial infections. Here we found that during the infection ofP. aeruginosa, non-canonical inflammasome was activated in macrophages, but the activation of downstream NLRP3 inflammasome was inhibited. The VgrG2b ofP. aeruginosais recognized and cleaved by caspase-11, generating a free C-terminal fragment. The VgrG2b C-terminus can bind to NLRP3, inhibiting the activation of the NLRP3 inflammasome by rejecting NEK7 binding to NLRP3. Administrating a specific peptide that inhibits the cleavage of VgrG2b by caspase-11 to mice can significantly improve their survival rate during infection. Our discovery elucidates a mechanism by whichP. aeruginosainhibits host immune response, providing a new approach for the future clinical treatment ofP. aeruginosainfections.
BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization
Authors: Tahmid Md Toki , Shahgir Haz Sameen , Mahbub Sazan , Dong Yue , Bayzid Md. Shamsuzzoha 
Published: July 2024

AbstractRecent advancements in Transformer-based models have spurred interest in their use for biological sequence analysis. However, adapting models like BERT is challenging due to sequence length, often requiring truncation for proteomics and genomics tasks. Additionally, advanced tokenization and relative positional encoding techniques for long contexts in NLP are often not directly transferable to DNA/RNA sequences, which require nucleotide or character-level encodings for tasks such as 3D torsion angle prediction. To tackle these challenges, we propose an adaptive dual tokenization scheme for bioinformatics that utilizes both nucleotide-level (NUC) and efficient BPE tokenizations. Building on the dual tokenization, we introduce BiRNA-BERT, a 117M parameter Transformer encoder pretrained with our proposed tokenization on 28 billion nucleotides across 36 million coding and non-coding RNA sequences. The learned representation by BiRNA-BERT generalizes across a range of applications and achieves state-of-the-art results in long-sequence downstream tasks and achieves a performance comparable to 6× larger models in short-sequence tasks with 27×less pre-training compute. BiRNA-BERT can dynamically adjust its tokenization strategy based on sequence lengths, utilizing NUC for shorter sequences and switching to BPE for longer ones, thereby offering, for the first time, the capability to efficiently handle arbitrarily long DNA/RNA sequences.1
Genomic Signatures of Domestication in a Fungus Obligately Farmed by Leafcutter Ants
Authors: Leal-Dutra Caio A. , Vizueta Joel , Baril Tobias , Kooij Pepijn W. , Rødsgaard-Jørgensen Asta , Schantz-Conlon Benjamin H. , Croll Daniel , Shik Jonathan Z. 
Published: July 2024

AbstractThe naturally selected fungal crop (Leucoagaricus gongylophorus) farmed by leafcutter ants shows striking parallels with artificially selected plant crops domesticated by humans (e.g., polyploidy, engorged nutritional rewards, dependence on cultivation). To date, poorly resolvedL. gongylophorusgenomes based on short-read sequencing have constrained hypotheses about how millions of years under cultivation by ants shaped the fungal crop genome and potentially drove domestication. We use PacBio HiFi sequencing ofL. gongylophorusfrom the leafcutter antAtta colombicato identify 18 putatively novel biosynthetic gene clusters that likely cemented life as a cultivar (e.g., plant fragment degradation, ant-farmer communication, antimicrobial defense). Comparative analyses with cultivated and free-living fungi showed genomic signatures of stepwise domestication transitions: 1) free-living to ant-cultivated: loss of genes conferring stress response and detoxification, 2) hyphal food to engorged nutritional rewards: expansions of genes governing cellular homeostasis, carbohydrate metabolism, and siderophore biosynthesis, and 3) detrital provisioning to freshly cut plant fragments: gene expansions promoting cell wall biosynthesis, fatty acid metabolism, and DNA repair. Comparisons acrossL. gongylophorusfungi farmed by three leafcutter ant species highlight genomic signatures of exclusively vertical clonal propagation and widespread transposable element activity. These results show how natural selection can shape domesticated cultivar genomes towards long-term ecological resilience of farming systems that have thrived across millennia.
Allopatric speciation in cattails: Genomic landscapes of divergence acrossTyphaspp. suggest balancing selection, introgressions, and the absence of adaptive divergence
Authors: Aleman Alberto , Freeland Joanna R. , Shafer Aaron B. A. , Dorken Marcel E. 
Published: July 2024

AbstractDetermining the evolutionary forces which result in the accumulation of genetic divergence between closely related species can yield important insights into speciation. Genetic divergence can be understood by two broad non-mutually exclusive frameworks: genetic drift under allopatry and natural selection under ecological divergence. Genetic regions that are highly differentiated or conserved between closely related species can be used to infer the types of selection driving speciation. We tested the role of selection in promoting species divergence inTypha, an old, widespread plant genus characterised by high levels of intra- and interspecific gene flow. Using genome-wide data, we scanned the genomes of multiple individuals from fiveTyphaspecies to identify how selection influenced their levels of genetic divergence. We also tested whether past admixture or contemporary introgression events have contributed to the genetic variation within and among species. The genomic landscapes of divergence were predominantly neutral, including regions of exceptional differentiation, and we observed contemporary genetic introgressions with no evidence of historical hybridisation. The absence of adaptive divergence and historical hybridisation are consistent with patterns expected under allopatric speciation and genetic divergence driven primarily by drift, followed by range expansion and secondary contact leading to contemporary hybridisation and recent genetic introgressions. For all species pairs, most genomic regions associated with adaptive divergence were valleys of balancing selection, in which the maintenance of ancestral polymorphisms causes reduced levels of divergence. Reproductive isolation among multipleTyphaspecies remains incomplete, and balancing selection and recent introgressions have contributed to their standing genetic variation.
Transcriptional landscape of a hypoxia response identifies cell-specific pathways for adaptation
Authors: Kong Ji Na , Dipon Ghosh D. , Savvidis Achilleus , Sando Steve R. , Droste Rita , Robert Horvitz H. 
Published: July 2024

AbstractHow the HIF-1 (Hypoxia-Inducible) transcription factor drives and coordinates distinct responses to low oxygen across diverse cell types is poorly understood. We present a multi-tissue single-cell gene-expression atlas of the hypoxia response of the nematodeCaenorhabditis elegans. This atlas highlights how cell-type-specific HIF-1 responses overlap and diverge among and within neuronal, intestinal, and muscle tissues. Using the atlas to guide functional analyses of candidate muscle-specific HIF-1 effectors, we discovered that HIF-1 activation drives downregulation of thetspo-1(TSPO,Translocator Protein) gene in vulval muscle cells to modulate a hypoxia-driven change in locomotion caused by contraction of body-wall muscle cells. We further showed that in human cardiomyocytes HIF-1 activation decreases levels of TSPO and thereby alters intracellular cholesterol transport and the mitochondrial network. We suggest that TSPO-1 is an evolutionarily conserved mediator of HIF-1-dependent modulation of muscle and conclude that our gene-expression atlas can help reveal how HIF-1 drives cell-specific adaptations to hypoxia.
TDP43 autoregulation gives rise to shortened isoforms that are tightly controlled by both transcriptional and post-translational mechanisms
Authors: Dykstra Megan M. , Weskamp Kaitlin , Gómez Nicolás B. , Waksmacki Jacob , Tank Elizabeth , Glineburg M. Rebecca , Snyder Allison , Pinarbasi Emile , Bekier Michael , Li Xingli , Bai Jen , Shahzad Shameena , Nedumaran Juno , Wieland Clare , Stewart Corey , Willey Sydney , Grotewold Nikolas , McBride Jonathon , Moran John J. , Suryakumar Aditya V. , Lucas Michael , Tessier Peter , Ward Michael , Todd Peter , Barmada Sami J. 
Published: July 2024

AbstractThe nuclear RNA-binding protein TDP43 is integrally involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previous studies uncovered N-terminal TDP43 isoforms that are predominantly cytosolic in localization, highly prone to aggregation, and enriched in susceptible spinal motor neurons. In healthy cells, however, these shortened (s)TDP43 isoforms are difficult to detect in comparison to full-length (fl)TDP43, raising questions regarding their origin and selective regulation. Here, we show that sTDP43 is created as a byproduct of TDP43 autoregulation and cleared by nonsense mediated RNA decay (NMD). The sTDP43-encoding transcripts that escape NMD can lead to toxicity but are rapidly degraded post-translationally. Circumventing these regulatory mechanisms by overexpressing sTDP43 results in neurodegenerationin vitroandin vivovia N-terminal oligomerization and impairment of flTDP43 splicing activity, in addition to RNA binding-dependent gain-of-function toxicity. Collectively, these studies highlight endogenous mechanisms that tightly regulate sTDP43 expression and provide insight into the consequences of aberrant sTDP43 accumulation in disease.