bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data
Authors: Wang Xi , Lian Qiwei , Dong Haoyu , Xu Shuo , Su Yaru , Wu Xiaohui 
Published: January 2023

AbstractGene set scoring (GSS) has been routinely conducted for gene expression analysis of bulk or single-cell RNA-seq data, which helps to decipher single-cell heterogeneity and cell-type-specific variability by incorporating prior knowledge from functional gene sets. Single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) is a powerful technique for interrogating single-cell chromatin-based gene regulation, and genes or gene sets with dynamic regulatory potentials can be regarded as cell-type specific markers as if in scRNA-seq. However, there are few GSS tools specifically designed for scATAC-seq, and the applicability and performance of RNA-seq GSS tools on scATAC-seq data remain to be investigated. We systematically benchmarked ten GSS tools, including four bulk RNA-seq tools, five single-cell RNA-seq (scRNA-seq) tools, and one scATAC-seq method. First, using matched scATAC-seq and scRNA-seq datasets, we find that the performance of GSS tools on scATAC-seq data is comparable to that on scRNA-seq, suggesting their applicability to scATAC-seq. Then the performance of different GSS tools were extensively evaluated using up to ten scATAC-seq datasets. Moreover, we evaluated the impact of gene activity conversion, dropout imputation, and gene set collections on the results of GSS. Results show that dropout imputation can significantly promote the performance of almost all GSS tools, while the impact of gene activity conversion methods or gene set collections on GSS performance is more GSS tool or dataset dependent. Finally, we provided practical guidelines for choosing appropriate pre-processing methods and GSS tools in different scenarios.
Improved cognitive-motor processing speed and decreased functional connectivity after high intensity aerobic exercise in individuals with chronic stroke
Authors: Andrushko Justin W. , Rinat Shie , Greeley Brian , Larssen Beverley C. , Jones Christina B. , Rubino Cristina , Denyer Ronan , Ferris Jennifer , Campbell Kristin L. , Neva Jason L. , Boyd Lara A. 
Published: January 2023

AbstractAfter stroke, impaired motor performance is linked to an increased demand for cognitive resources. Aerobic exercise improves cognitive function in healthy populations and may be effective in altering cognitive function post-stroke. We sought to determine if high intensity aerobic exercise paired with motor training in individuals with chronic stroke alters cognitive-motor function and functional connectivity between the dorsolateral prefrontal cortex (DLPFC), a key region for cognitive-motor processes, and the sensorimotor network. Twenty-five participants with chronic stroke were randomly assigned to exercise (n = 14; 66 ± 11 years; 4 females), or control (n = 11; 68 ± 8 years; 2 females) groups. Both groups performed five-days of paretic upper limb motor training after either high intensity aerobic exercise (3 intervals of 3 minutes each, total exercise duration of 23-minutes) or watching a documentary (control). Resting-state fMRI, and TMT-A and B were recorded pre- and post-intervention. Both groups showed implicit motor sequence learning (p< .001), but there was no added benefit of exercise (p= .738). Regardless of group, the changes in task score (p= .025), and dwell time (p= .043) were correlated with a decrease in DLPFC-sensorimotor network functional connectivity (p= .024), which is thought to reflect a reduction in the cognitive demand and increased automaticity. The exercise group experienced greater overall cognitive-motor improvements measured with the trail making test part A (TMT-A: task score:p= .012; dwell time:p= .024; movement time:p= .567). Aerobic exercise may improve cognitive-motor processing speed post-stroke.Significance statementAfter stroke, impaired motor performance is linked to an increased demand for cognitive resources. In our work we show that high intensity aerobic exercise paired with an implicit motor learning task improves cognitive-motor processing speed and reduces resting-state functional connectivity between the dorsolateral prefrontal cortex and the sensorimotor network in individuals living with chronic stroke. These data likely reflect a reduction in cognitive resource dependence during a cognitive-motor task after stroke and a shift towards cognitive-motor automaticity.
Sustained Selective Attention in Adolescence: Cognitive Development and Predictors of Distractibility at School
Authors: Hobbiss Michael H. , Lavie Nilli 
Published: January 2023

AbstractDespite much research into the development of attention in adolescence, mixed results and between-task differences have precluded clear conclusions regarding the relative early- or late-maturation of attention abilities. Moreover, although adolescents constantly face the need to pay attention to their lessons at school, it remains unclear whether laboratory measures of attention can predict their ability to sustain attention focus during school lessons. Here we therefore devised a task that was sensitive to measure both sustained and selective attention and tested whether any of our task measures can predict adolescents’ levels of inattention during their school lessons. 166 adolescents (aged 12-17) and 50 adults performed in our sustained-selective attention task, searching for letter targets, while ignoring salient yet-entirely-irrelevant distractor faces, under different levels of perceptual load-an established determinant of attention in adults. Inattention levels during a just-preceding classroom lesson were measured using our novel self-report classroom-distractibility checklist. The results established that sustained attention (measured with response variability) continued to develop throughout adolescence, across perceptual load levels. In contrast there was an earlier maturation of the effect of perceptual load on selective attention: load modulation of distractor interference was larger in the early adolescence compared to later periods. Both distractor interference and response variability were significant unique predictors of distractibility in the classroom, including when interest in the lesson and cognitive aptitude were controlled for. Overall, the results demonstrate divergence of development of sustained and selective attention in adolescence, and establish both as significant predictors of attention in the important educational setting of school lessons.
Multiple conformational states assembly of multidomain proteins using evolutionary algorithm based on structural analogues and sequential homologues
Authors: Peng Chunxiang , Zhou Xiaogen , Liu Jun , Hou Minghua , Li Stan Z. , Zhang Guijun 
Published: January 2023

AbstractWith the breakthrough of AlphaFold2, nearly all single-domain protein structures can be built at experimental resolution. However, accurate modelling of full-chain structures of multidomain proteins, particularly all relevant conformations for those with multiple states remain challenging. In this study, we develop a multidomain protein assembly method, M-SADA, for assembling multiple conformational states. In M-SADA, a multiple population-based evolutionary algorithm is proposed to sample multiple conformational states under the guidance of multiple energy functions constructed by combining homologous and analogous templates with inter-domain distances predicted by deep learning. On a developed benchmark dataset containing 72 multidomain proteins with multiple conformational states, the performance of M-SADA is significantly better than that of AlphaFold2 on multiple conformational states modelling, where 29/72 (40.3%) of proteins can be assembled with a TM-score >0.90 for highly distinct conformational states with M-SADA while AlphaFold2 does so in only 2/72 (2.8%) of proteins. Furthermore, M-SADA is tested on a developed benchmark dataset containing 296 multidomain proteins with single conformational state, and results show that the average TM-score of M-SADA on the best models is 0.913, which is 5.2% higher than that of AlphaFold2 models (0.868).
Pilot Analysis of Genetic Effects on Personality Test Scores with AI: ABO Blood Type in Japan
Authors: Kanazawa Masayuki 
Published: January 2023

AbstractIt is estimated that genetic factors are responsible for approximately 30-60% of an individual’s personality. However, statistical analyses have yet to demonstrate a significant and consistent relationship between personality tests and genetic factors. Conversely, a significant portion of individuals in Japan, South Korea, and Taiwan believe that there is a linkage between ABO blood type, which is determined genetically, and personality. This pilot study analyzed data from a large-scale survey (N=2,887) using a combination of traditional statistical methods and AI to examine this relationship. The results indicated the relationship between ABO blood type and self-reported personality traits on several single-question items, in accordance with expected outcomes. These findings suggest that this relationship may extend beyond ABO blood type and personality to encompass other inherited characteristics. The influence of the level of interest on personality and was also discussed.
Dissecting the Functional Organization of theC. elegansSerotonergic System at Whole-Brain Scale
Authors: Dag Ugur , Nwabudike Ijeoma , Kang Di , Gomes Matthew A. , Kim Jungsoo , Atanas Adam A. , Bueno Eric , Estrem Cassi , Pugliese Sarah , Wang Ziyu , Towlson Emma , Flavell Steven W. 
Published: January 2023

SUMMARYSerotonin controls many aspects of animal behavior and cognition. But how serotonin acts on its diverse receptor types in neurons across the brain to modulate global activity and behavior is unknown. Here, we examine how serotonin release from a feeding-responsive neuron inC. elegansalters brain-wide activity to induce foraging behaviors, like slow locomotion and increased feeding. A comprehensive genetic analysis identifies three core serotonin receptors that collectively induce slow locomotion upon serotonin release and three others that interact with them to further modulate this behavior. The core receptors have different functional roles: some induce behavioral responses to sudden increases in serotonin release, whereas others induce responses to persistent release. Whole-brain calcium imaging reveals widespread serotonin-associated brain dynamics, impacting different behavioral networks in different ways. We map out all sites of serotonin receptor expression in the connectome, which, together with synaptic connectivity, helps predict serotonin-associated brain-wide activity changes. These results provide a global view of how serotonin acts at defined sites across a connectome to modulate brain-wide activity and behavior.
A scoping review of trauma informed approaches in acute, crisis, emergency and residential mental health care
Authors: Saunders Katherine R. K. , McGuinness Elizabeth , Barnett Phoebe , Foye Una , Sears Jessica , Carlisle Sophie , Allman Felicity , Tzouvara Vasiliki , Schlief Merle , San Juan Norha Vera , Stuart Ruth , Griffiths Jessica , Appleton Rebecca , McCrone Paul , Olive Rachel Rowan , Nyikavaranda Patrick , Jeynes Tamar , Mitchell Lizzie , Simpson Alan , Johnson Sonia , Trevillion Kylee 
Published: January 2023

AbstractExperiences of trauma in childhood and adulthood are highly prevalent among service users accessing acute, crisis, emergency, and residential mental health services. These settings, and restraint and seclusion practices used, can be extremely traumatic, leading to a growing awareness for the need for trauma informed care (TIC). The aim of TIC is to acknowledge the prevalence and impact of trauma and create a safe environment to prevent re-traumatisation. This scoping review maps the TIC approaches delivered in these settings and reports related service user and staff experiences and attitudes, staff wellbeing, and service use outcomes.We searched seven databases (EMBASE; PsycINFO; MEDLINE; Web of Science; Social Policy and Practice; Maternity and Infant Care Database; Cochrane Library Trials Register) between 24/02/2022-10/03/2022, used backwards and forwards citation tracking, and consulted academic and lived experience experts, identifying 4244 potentially relevant studies. Thirty-one studies were included.Most studies (n=23) were conducted in the USA and were based in acute mental health services (n=16). We identified few trials, limiting inferences that can be drawn from the findings. The Six Core Strategies (n=7) and the Sanctuary Model (n=6) were the most commonly reported approaches. Rates of restraint and seclusion reportedly decreased. Some service users reported feeling trusted and cared for, while staff reported feeling empathy for service users and having a greater understanding of trauma. Staff reported needing training to deliver TIC effectively.TIC principles should be at the core of all mental health service delivery. Implementing TIC approaches may integrate best practice into mental health care, although significant time and financial resources are required to implement organisational change at scale. Most evidence is preliminary in nature, and confined to acute and residential services, with little evidence on community crisis or emergency services. Clinical and research developments should prioritise lived experience expertise in addressing these gaps.
The central nervous system’s proteogenomic and spatial imprint upon systemic viral infections with SARS-CoV-2
Authors: Radke Josefine , Meinhardt Jenny , Aschman Tom , Chua Robert Lorenz , Farztdinov Vadim , Lukkassen Sören , Ten Foo Wei , Friebel Ekaterina , Ishaque Naveed , Franz Jonas , Huhle Valerie Helena , Mothes Ronja , Peters Kristin , Thomas Carolina , Streit Simon , Manitius Regina von , Körtvélyessy Péter , Vielhaber Stefan , Reinhold Dirk , Hauser Anja , Osterloh Anja , Enghard Philipp , Ihlow Jana , Elezkurtaj Sefer , Horst David , Kurth Florian , Müller Marcel A. , Gassen Nils C. , Schneider Julia , Jechow Katharina , Timmermann Bernd , Fernandez-Zapata Camila , Böttcher Chotima , Stenzel Werner , Wyler Emanuel , Corman Victor , Stadelmann-Nessler Christine , Ralser Markus , Eils Roland , Heppner Frank L. , Mülleder Michael , Conrad Christian , Radbruch Helena 
Published: January 2023

AbstractIn COVID-19 neurological alterations are noticed during the systemic viral infection. Various pathophysiological mechanisms on the central nervous system (CNS) have been suggested in the past two years, including the viral neurotropism hypothesis. Nevertheless, neurological complications can also occur independent of neurotropism and at different stages of the disease and may be persistent.Previous autopsy studies of the CNS from patients with severe COVID-19 show infiltration of macrophages and T lymphocytes, especially in the perivascular regions as well as pronounced microglial activation, but without signs of viral encephalitis.However, there is an ongoing debate about long-term changes and cytotoxic effects in the CNS due to the systemic inflammation.Here, we show the brain-specific host response during and after COVID-19. We profile single-nucleus transcriptomes and proteomes of brainstem tissue from deceased COVID-19 patients who underwent rapid autopsy. We detect a disease phase-dependent inflammatory type-I interferon response in acute COVID-19 cases. Integrating single-nucleus RNA sequencing and spatial transcriptomics, we could localize two patterns of reaction to severe systemic inflammation. One neuronal with direct focus on cranial nerve nuclei and one diffusely affecting the whole brainstem, the latter reflecting a bystander effect that spreads throughout the vascular unit and alters the transcriptional state of oligodendrocytes, microglia and astrocytes.Our results indicate that even without persistence of SARS-CoV-2 in the CNS, the tissue activates highly protective mechanisms, which also cause functional disturbances that may explain the neurological symptoms of COVID-19, triggered by strong systemic type-I IFN signatures in the periphery.
Patterns of infection among travellers to Singapore arriving from mainland China
Authors: Pung Rachael , Kucharski Adam J. , Marc Ho Zheng Jie , Lee Vernon J. 
Published: January 2023

AbstractIn light of the rapid growth of COVID-19 in mainland China, countries and regions outside of China have implemented travel restrictions of varying intensity. Using surveillance data of symptomatic travellers arriving from mainland China and detected in Singapore, this provides a proxy on the COVID-19 in mainland China. Furthermore, this allows us to ensure that travel-related restrictions commensurate with the current epidemiological situation and risk.
High risk injection drug use and uptake of HIV prevention and treatment services among people who inject drugs in KwaZulu-Natal, South Africa
Authors: Zanoni Brian C. , Milford Cecilia , Sithole Kedibone , Mosery Nzwakie , Wilson Michael , Bosman Shannon , Smit Jennifer 
Published: January 2023

AbstractThe use of injection drugs in South Africa is increasing. HIV prevention, treatment and addiction services for people who inject drugs (PWID) in South Africa are not well documented. We conducted a mixed-methods study to understand current drug use practices and access to HIV prevention and treatment services for PWID in KwaZulu-Natal, South Africa. We used respondent-driven sampling to recruit 45 people who reported injecting opiates within the past 6 months from Durban, KwaZulu-Natal, South Africa. We found high rates of practices that increase HIV/viral hepatitis risk including the use of shared needles (43%) and direct blood injections (bluetoothing) (18%). Despite 35% of participants living with HIV, only 40% accessed antiretroviral therapy within the past year, and one accessed PrEP. None of the participants reported ever testing for Hepatitis C.
Listract test: a Standardized Assessment Method for Isolated Lisfranc Instability in Cadaver Models
Authors: Mathur Vasundhara , Osei-Hwedieh David O. , Sayyed Hosseinian Sayyed Hadi , Raduan Fernando , Kaiser Philip , Ghaednia Hamid , Waryasz Gregory , Bejarano-Pineda Lorena , Kwon John , Ashkani-Esfahani Soheil 
Published: January 2023

AbstractBackgroundThe gold standard for diagnosis of Lisfranc instability is direct visualization in the operation room while the examination techniques is still unstandardized and non-reproducible. We aimed to introduce a novel reproducible intraoperative mechanical testing method (Listract test) for intraoperative isolated Lisfranc instability assessment.MethodsThe Lisfranc ligament between the first cuneiform (C1) and second metatarsus (M2) in eight lower leg cadaveric specimens were dissected to replicate C1-M2 Lisfranc instability by eight foot and ankle surgeons. The 50N distraction force was applied in the direction of the C1-M2 ligament. Three methods of fixation - flexible fixation, metal screw, and bio-absorbable screw- were used to fix the injury, and Listract test was applied again after fixation. Besides intraoperative assessment, C1-M2 diastasis and area were measured using radiographs for assessment of Lisfranc instability.ResultsThe sensitivity and specificity of the Listract test for detection of C1-M2 instability were 100% and 100% intraoperatively, 33.3% and 95.2% using radiographic diastasis measurement, and 63.2% and 38% using area measurement, respectively. The Listract test had a specificity and sensitivity of 100% and 96% for intraoperative assessment, 87.5% and 64.3 for radiographic C1-M2 diastasis, and 48% and 50% for radiographic area.ConclusionThe Listract test is a simple, reproducible, and replicable intraoperative method for evaluating the Lisfranc joint for instability. Developing a device with this mechanism can help clinicians confirm the diagnosis and provide appropriate treatment particularly for equivocal diagnoses.Authors’ contributionsSAE: Conception, design, and conducting the study, analysis, drafting the manuscript; VM, DOH, SHSH, FR: conducting the study, analysis, preparing the manuscript draft; LBP, JK, GW, PK: conducting the study, manuscript preparation, discussion.
Ontogenesis of the molecular response to sleep loss
Authors: Muheim Christine M. , Ford Kaitlyn , Medina Elizabeth , Singletary Kristan , Peixoto Lucia , Frank Marcos G. 
Published: January 2023

AbstractSleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages in adults. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
Experimental Tests of the Virtual Circular Genome Model for Non-enzymatic RNA Replication
Authors: Ding Dian , Zhou Lijun , Mittal Shriyaa , Szostak Jack W. 
Published: January 2023

ABSTRACTThe virtual circular genome (VCG) model was proposed as a means of going beyond template copying to indefinite cycles of nonenzymatic RNA replication during the origin of life. In the VCG model the protocellular genome is a collection of short oligonucleotides that map to both strands of a virtual circular sequence. Replication is driven by templated nonenzymatic primer extension on a subset of kinetically trapped partially base-paired configurations, followed by shuffling of these configurations to enable continued oligonucleotide elongation. Here we describe initial experimental studies of the feasibility of the VCG model for replication. We designed a small 12-nucleotide model VCG and synthesized all 247 oligonucleotides of length 2 to 12 corresponding to this genome. We experimentally monitored the fate of individual labeled primers in the pool of VCG oligonucleotides following the addition of activated nucleotides, and investigated factors such as oligonucleotide length, concentration, composition, and temperature on the extent of primer extension. We observe a surprisingly prolonged equilibration process in the VCG system that enables a considerable extent of reaction. We find that environmental fluctuations would be essential for continuous templated extension of the entire VCG system, since the shortest oligonucleotides can only bind to templates at low temperatures, while the longest oligonucleotides require high temperature spikes to escape from inactive configurations. Finally, we demonstrate that primer extension is significantly enhanced when the mix of VCG oligonucleotides is pre-activated. We discuss the necessity of ongoingin-situactivation chemistry for continuous and accurate VCG replication.