bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a search filter to retrieve reports of interrupted time series studies from MEDLINE and PubMed
Authors: Nguyen Phi-Yen , McKenzie Joanne E. , Turner Simon L. , Page Matthew J. , McDonald Steve 
Published: September 2023

ABSTRACTBackgroundInterrupted time series (ITS) studies contribute importantly to systematic reviews of population-level interventions. However, there is no search filter designed to identify only ITS studies from bibliographic databases. We aimed to develop and validate search filters to retrieve ITS studies in MEDLINE and PubMed.MethodsA set of 1,017 known ITS studies (published 2013-2017) were analysed using text mining to generate candidate terms. A population set of 1,398 time-series studies were used to select discriminating terms. Various combinations of candidate terms were iteratively tested to generate three search filters. An independent set of 700 ITS studies were used to validate the filters’ sensitivities. The filters were test-run in Ovid MEDLINE; their retrieved records were randomly screened for ITS studies to determine their precision. Finally, all three MEDLINE filters were translated to PubMed format and their sensitivities in PubMed were estimated.ResultsThree search filters were created: aprecision-maximisingfilter with high precision (78%; 95% CI 74%-82%) but moderate sensitivity (63%; 59%-66%), useful for rapid reviews; asensitivity- and-precision-maximisingfilter with high sensitivity (81%; 77%-83%) but lower precision (32%; 28%-36%), useful when a balance of expediency and comprehensiveness is required; and a sensitivity-maximisingfilter with high sensitivity (88%; 85%-90%) but likely very low precision, useful for search strategies accompanying specific content terms.ConclusionOur filters strike different balances between comprehensiveness and screening workload and suit different research needs. To improve retrieval of ITS studies, authors need to identify ITS designs in titles more frequently.
Cooperativity and induced oligomerisation control the interaction of SARS-CoV-2 with its cellular receptor and patient-derived antibodies
Authors: Asor Roi , Olerinyova Anna , Burnap Sean A. , Kushwah Manish S. , Soltermann Fabian , Rudden Lucas Powell , Hensen Mario , Vasiljevic Snežana , Brun Juliane , Hill Michelle , Chang Liu , Dejnirattisa Wanwisa , Supasa Piyada , Mogkolsapaya Juthatip , Zhou Daming , Stuart David I. , Screaton Gavin R. , Degiacomi Matteo , Zitzmann Nicole , Benesch Justin L. P. , Struwe Weston B. , Kukura Philipp 
Published: September 2023

AbstractViral entry is mediated by oligomeric proteins on the virus and cell surfaces. The association is therefore open to multivalent interactions between these proteins, yet such recognition is typically rationalised as affinity between monomeric equivalents. As a result, assessment of the thermodynamic mechanisms that control viral entry has been limited. Here, we use mass photometry to overcome the analytical challenges consequent to multivalency. Examining the interaction between the spike protein of SARS-CoV-2 and the ACE2 receptor, we find that ACE2 induces oligomerisation of spike in a variant-dependent fashion. We also demonstrate that patient-derived antibodies use induced-oligomerisation as a primary inhibition mechanism or to enhance the effects of receptor-site blocking. Our results reveal that naive affinity measurements are poor predictors of potency, and introduce a novel antibody-based inhibition mechanism for oligomeric targets.One-Sentence SummaryMultivalent interactions between viral proteins, cell-surface receptors, and anti-viral antibodies regulate infection and inhibition.
MixOmics Integration of Biological Datasets Identifies Highly Correlated Key Variables of COVID-19 severity
Authors: Harriott Noa C. , Chimenti Michael S. , Ryan Amy L. 
Published: September 2023

AbstractBackgroundDespite several years since the COVID-19 pandemic was declared, challenges remain in understanding the factors that can predict the severity of COVID-19 disease and complications of SARS-CoV-2 infection. While many large-scale Multiomic datasets have been published, integration of these datasets has the potential to substantially increase the biological insight gained allowing a more complex comprehension of the disease pathogenesis. Such insight may improve our ability to predict disease progression, detect severe cases more rapidly and develop effective therapeutics.MethodsIn this study we have applied an innovative machine learning algorithm to delineate COVID-severity based on integration of paired samples of proteomic and transcriptomic data from a small cohort of patients testing positive for SARS-CoV-2 infection with differential disease severity. Targeted plasma proteomics and an onco-immune targeted transcriptomic panel was performed on sequential samples from a cohort of 23 severe, 21 moderate and 10 mild COVID-19 patients. We applied DIABLO, a new integrative method, to identify multi-omics biomarker panels that can discriminate between multiple phenotypic groups, such as the varied severity of disease in COVID-19 patients.ResultsAs COVID-19 severity is known among our sample group, we can train models using this as the outcome variable and calculate features that are important predictors of severe disease. In this study, we detect highly correlated key variables of severe COVID-19 using transcriptomic discriminant analysis and multi-omics integration methods.ConclusionsThis approach highlights the power of data integration from a small cohort of patients offering a better biological understanding of the molecular mechanisms driving COVID-19 severity and an opportunity to improve prediction of disease trajectories and targeted therapeutics.
Two disparity channels in human visual cortex with different contrast and blur sensitivity
Authors: Kaestner Milena , Chen Yulan D. , Clement Caroline , Hodges Alex , Norcia Anthony M. 
Published: September 2023

ABSTRACTPurposeOur goal is to describe the contrast and blur sensitivity of multiple horizontal disparity sub-systems and to relate them to the contrast and spatial sensitivities of their monocular inputs.MethodsSteady-State Visual Evoked Potentials (SSVEPs) amplitudes were recorded in response to Dynamic Random Dot Stereograms (DRDS) alternating at 2 Hz between zero disparity and varying magnitudes of crossed disparity for disparity plane and disparity grating stimuli. Half-image contrasts ranged between 2.5 and 80% and over a range of Gaussian blurs from 1.4 to 12 arcmin. Separate experiments measured contrast and blur sensitivity for the monocular half-images.ResultsThe first and second harmonics disparity responses were maximal for disparity gratings and for the disparity plane condition, respectively. The first harmonic of the disparity grating response was more affected by both contrast and blur than was the second harmonic of the disparity plane response which had higher contrast sensitivity than the first harmonic.ConclusionThe corrugation frequency, contrast and blur tuning of the first harmonic suggest that it reflects activity of neurons tuned to higher luminance spatial frequencies that are selective for relative disparity, whereas the second harmonic reflects the activity of neurons sensitive to absolute disparity that are driven by low monocular spatial spatial frequencies.Translational RelevanceSSVEPs to DRDS provide two objective neural measures of disparity processing, the first harmonic – whose stimulus preferences are similar to those of behavioral stereoacuity – and the second harmonic that represents an independent disparity-specific, but not necessarily stereoscopic mechanism.
Towards a mechanistic understanding of the role of error monitoring and memory in social anxiety
Authors: Hosseini Kianoosh , Pettit Jeremy W. , Soto Fabian A. , Mattfeld Aaron T. , Buzzell George A. 
Published: September 2023

AbstractCognitive models state social anxiety (SA) involves biased cognitive processing that impacts what is learned and remembered within social situations, leading to the maintenance of SA. Neuroscience work links SA to enhanced error monitoring, reflected in error-related neural responses arising from mediofrontal cortex (MFC). Yet, the role of error monitoring in SA remains unclear, as it is unknown whether error monitoring can drive changes in memory, biasing what is learned or remembered about social situations. Thus, we developed a novel paradigm to investigate the role of error-related MFC theta oscillations (associated with error monitoring) and memory biases in SA. EEG was collected while participants completed a novel Face-Flanker task, involving presentation of task-unrelated, trial-unique faces behind target/flanker arrows on each trial. A subsequent incidental memory assessment evaluated memory biases for error events. Severity of SA symptoms were associated with greater error-related theta synchrony over MFC, as well as between MFC and sensory cortex. SA was positively associated with memory biases for error events. Consistent with a mechanistic role in biased cognitive processing, greater error-related MFC-sensory theta synchrony during the Face-Flanker predicted subsequent memory biases for error events. Our findings suggest high SA individuals exhibit memory biases for error events, and that this behavioral phenomenon may be driven by error-related MFC-sensory theta synchrony associated with error monitoring. Moreover, results demonstrate the potential of a novel paradigm to elucidate mechanisms underlying relations between error monitoring and SA.
Developmental Mouse Brain Common Coordinate Framework
Authors: Kronman Fae A. , Liwang Josephine K. , Betty Rebecca , Vanselow Daniel J. , Wu Yuan-Ting , Tustison Nicholas J. , Bhandiwad Ashwin , Manjila Steffy B. , Minteer Jennifer A. , Shin Donghui , Lee Choong Heon , Patil Rohan , Duda Jeffrey T. , Puelles Luis , Gee James C. , Zhang Jiangyang , Ng Lydia , Kim Yongsoo 
Published: September 2023

Abstract3D standard reference brains serve as key resources to understand the spatial organization of the brain and promote interoperability across different studies. However, unlike the adult mouse brain, the lack of standard 3D reference atlases for developing mouse brains has hindered advancement of our understanding of brain development. Here, we present a multimodal 3D developmental common coordinate framework (DevCCF) spanning mouse embryonic day (E) 11.5, E13.5, E15.5, E18.5, and postnatal day (P) 4, P14, and P56 with anatomical segmentations defined by a developmental ontology. At each age, the DevCCF features undistorted morphologically averaged atlas templates created from Magnetic Resonance Imaging and co-registered high-resolution templates from light sheet fluorescence microscopy. Expert-curated 3D anatomical segmentations at each age adhere to an updated prosomeric model and can be explored via an interactive 3D web-visualizer. As a use case, we employed the DevCCF to unveil the emergence of GABAergic neurons in embryonic brains. Moreover, we integrated the Allen CCFv3 into the P56 template with stereotaxic coordinates and mapped spatial transcriptome cell-type data with the developmental ontology. In summary, the DevCCF is an openly accessible resource that can be used for large-scale data integration to gain a comprehensive understanding of brain development.
Distributions of Recorded Pain in Mental Health Records: A Natural Language Processing Based Study
Authors: Chaturvedi Jaya , Stewart Robert , Ashworth Mark , Roberts Angus 
Published: September 2023

AbstractObjectiveThe objective of this study is to determine demographic and diagnostic distributions of physical pain recorded in the clinical notes of a mental health electronic health records database by utilising natural language processing and to examine the level of overlap in recorded physical pain between primary and secondary care.Design, Setting and ParticipantsThe data were extracted from an anonymised version of the electronic health records from a large mental community and secondary healthcare provider serving a catchment of 1.3M residents in south London. These included patients under active referral and aged 18+ at the index date of July 1, 2018, and had at least one clinical document (>=30 characters) associated with their record between July 1, 2017 and July 1, 2019. This cohort was compared to linked primary care records from one of the four catchment boroughs.OutcomeThe primary outcome of interest was the presence or absence of recorded physical pain within the clinical notes of the patients. This does not include mental, psychological or metaphorical pain.ResultsA total of 27,211 patients were retrieved based on the extraction criteria. Of these, 52% (14,202) had narrative text containing relevant mentions of physical pain. Patients who were older (OR 1.17, 95% CI 1.15-1.19), female (OR 1.42, 95% CI 1.35-1.49), of Asian (OR 1.30, 95% CI 1.16-1.45) or Black (OR 1.49, 95% CI 1.40-1.59) ethnicities, and living in deprived neighbourhoods (OR 1.64, 95% CI 1.55-1.73) showed higher odds of recorded pain. Patients with an SMI diagnosis were found to be less likely to report pain (OR 0.43, 95% CI 0.41-0.46, p<0.001). When comparing the overlap between primary and secondary care, 17% of the CRIS cohort also had records within LDN, and 31% of these had recorded pain in both records.ConclusionThe findings of this study show the sociodemographic and diagnostic differences in recorded pain, and have significant implications for the assessment and management of physical pain in patients with mental health disorders.Strengths and Limitations of this studyThis study utilises natural language processing on clinical notes to access a large sample with information about pain.This is the first cross-sectional study to summarise and describe the distribution of recorded pain within the clinical notes of mental health records.The recorded mentions of pain within clinical notes clearly depend on the patient sharing and the clinician recording their experiences.The findings are not generalisable to the general population since this study only looks at patients receiving mental healthcare within a specific geographic catchment.
Development and Performance Assessment of a Novel Plasma p-Tau181 Assay Reflecting Tau Tangle Pathology in Alzheimer’s Disease
Authors: Tagai Kenji , Tatebe Harutsugu , Matsuura Sayo , Hong Zhang , Kokubo Naomi , Matsuoka Kiwamu , Endo Hironobu , Oyama Asaka , Hirata Kosei , Shinotoh Hitoshi , Kataoka Yuko , Matsumoto Hideki , Oya Masaki , Kurose Shin , Takahata Keisuke , Ichihashi Masanori , Kubota Manabu , Seki Chie , Shimada Hitoshi , Takado Yuhei , Kawamura Kazunori , Zhang Ming-Rong , Soeda Yoshiyuki , Takashima Akihiko , Higuchi Makoto , Tokuda Takahiko 
Published: September 2023

AbstractSeveral blood-based assays for phosphorylated tau (p-tau) have been developed to detect brain tau pathologies in Alzheimer’s disease (AD). However, plasma p-tau measured by currently available assays is influenced by brain amyloid and, therefore, could not accurately reflect brain tau deposits. Here, we devised a novel immunoassay that can quantify N- and C-terminally truncated p-tau fragments (mid-p-tau181) in human plasma. We measured plasma p-tau181 levels in 164 participants who underwent both amyloid and tau positron emission tomography (PET) scans using mid-p-tau181 and conventional p-tau181 assays. The mid-p-tau181 assay displayed stronger correlations with tau PET accumulation than the conventional assay in the AD continuum and accurately distinguished between tau PET-positive and -negative cases. Furthermore, the mid-p-tau181 assay demonstrated a trajectory similar to tau PET alongside cognitive decline. Consequently, our mid-p-tau181 assay could be useful in evaluating the extent of brain tau burden in AD.
Refining COVID-19 retrospective diagnosis with continuous serological tests: a Bayesian mixture model
Authors: Glemain Benjamin , de Lamballerie Xavier , Zins Marie , Severi Gianluca , Touvier Mathilde , Deleuze Jean-François ,   SAPRIS-SERO study group, Lapidus Nathanaël , Carrat Fabrice 
Published: September 2023

AbstractCOVID-19 serological tests with a “positive”, “intermediate” or “negative” result according to predefined thresholds cannot be directly interpreted as a probability of having been infected with SARS-CoV-2. Based on 81,797 continuous anti-spike tests collected in France after the first wave, a Bayesian mixture model was developed to provide a tailored infection probability for each participant. Depending on the serological value and the context (age and administrative region), a negative or a positive test could correspond to a probability of infection as high as 61.9% or as low as 68.0%, respectively. In infected individuals, the model estimated a proportion of “non-responders” of 14.5% (95% CI, 11.2-18.1%), corresponding to a sub-group of persons who exhibited a weaker serological response to SARS-CoV-2. This model allows for an individual interpretation of serological results as a probability of infection, depending on the context and without any notion of threshold.
Predictors of COVID-19 Vaccine Acceptability Among Refugees and Other Migrant Populations: A Systematic Scoping Review
Authors: Yazdani Yasaman , Pai Poojitha , Sayfi Shahab , Mohammadi Arash , Perdes Saber , Spitzer Denise , Fabreau Gabriel E. , Pottie Kevin 
Published: September 2023

AbstractObjectiveThis study aimed to map the existing literature to identify predictors of COVID-19 vaccine acceptability among refugees, immigrants, and other migrant populations.MethodsA systematic search of Medline, Embase, APA PsycInfo and Cumulative Index of Nursing and Allied Health Literature (CINAHL) was conducted up to 31 January 2023 to identify the relevant English peer-reviewed observational studies. Two independent reviewers screened, selected studies, and extracted data.ResultsWe identified 34 cross-sectional studies, primarily conducted in high income countries (76%). Lower vaccine acceptance was associated with mistrust in the host countries’ government and healthcare system, concerns about the safety and effectiveness of COVID-19 vaccines, limited knowledge of COVID-19 infection and vaccines, lower COVID-19 risk perception, and lower integration level in the host country. Female gender, younger age, lower education level, and being single were associated with lower vaccine acceptance in most studies. Additionally, sources of information about COVID-19 and vaccines and previous history of COVID-19 infection, also influence vaccine acceptance. Vaccine acceptability towards COVID-19 booster doses and various vaccine brands were not adequately studied.ConclusionsVaccine hesitancy and lack of trust in COVID-19 vaccines became significant public health concerns within migrant populations. These findings may help in providing information for current and future vaccine outreach strategies among migrant populations.
Epidemiology and clinical profile of sports injuries treated in the Douala General Hospital and the Douala Laquintinie Hospital
Authors: Tanko Tankeng Leonard , William Ngatchou Djomo , Nana Theophile Chunteng , Bill-Erich Mbianyor , Gilbert Akwa , Kange Lifafa Kinge , Bonny Aimé 
Published: September 2023

AbstractBackgroundA sport injury is any body tissue damage that results from the practice of sports or exercise. Despite the number of cases treated at hospitals, very little is reported. Regarding the rising participation in sports and as a consequence sports injuries, this study aimed to present the epidemiology and clinical profile of sport injuries treated at two tertiary hospitals in Douala Cameroon.MethodsThis was a hospital based cross sectional descriptive study during nine months, carried out in the Douala General hospital and the Douala Laquintinie Hospital. Medical records of patients who were treated for sports injuries from January 2012 to April 2022 were included in the study. Severe injury was considered to be an injury score of greater than or equal to three according to the abbreviated injury scale of the injured body region.ResultsAmong 72 consecutive eligible records, there was a male predominance (86.1%) with a 6.2 M:F sex ratio. The mean age 24.97±13.8 years and the modal age range was 11-21 years. The prevalence of sports injuries was 1.12% amongst all trauma cases. 48.6% of injured persons were students, 36.1 % employed, 8.3% athletes and 6.9% unemployed. 59.7% of injuries occurred during recreational sports while 22.2% occurred during physical education, 11.1% during trainings and 6.9% during competitions. Football accounted for 66.7% injuries, running 13.9% and 12.5% in jumping. 59.7% of injuries were fractures, 6.9% dislocations, 27.7% soft tissue injuries and 5.6% head injuries. 47.2% of injuries occurred on the lower extremities, 29.2% on the upper extremities, 6.9% on the face, 5.6% abdominopelvic, 4.2% on the thorax, 5.6% head injuries and 1.4% on the neck. Overall 73.7% of sports injuries were severe injuries.ConclusionSports injuries treated in hospitals are severe injuries. The majority of sports injuries treated in hospitals are fractures. Most sports injuries occur in the lower extremity. Football records the highest number of injuries.
Epidemiological findings and estimates of the instantaneous reproduction number and control strategies of the first Mpox outbreak in Latin America
Authors: Díaz-Brochero Cándida , Cucunubá Zulma M. 
Published: September 2023

AbstractBackground and objectivesince 2022, the world has experienced the largest Mpox outbreak in history. The region of the Americas has been especially affected, accounting for 67% of the cumulative cases worldwide. Key epidemiological characteristics of the outbreak for the Latin American region remain understudied. Here we provide estimations of R(t) and describe the key epidemiological trends, and vaccination strategies of the Mpox outbreak in six Latin American countries.Materials and methodswe investigated the public health response to the Mpox outbreak in six Latin American countries from official sources. The surveillance data were obtained from the official Mpox report of the Pan American Health Organization. We calculated cumulative and incident confirmed cases according to the report date for each country and represented these findings in epidemic curves. The R(t) was estimated on weekly sliding windows for each country.ResultsThe maximum means of R(t) ranged from 2.28 to 3.15 from May to July 2022. At epidemiological week 42, the R(t) estimates were as follows: Argentina: 0.94 (95% Credible interval -CrI-0.77 to 1.12), Chile: 0.83 (95% CrI: 0.64 to 1.05), Colombia: 0.60 (95% CrI: 0.52 to 0.69), Mexico: 0.75 (95% CrI: 0.67 to 0.84). For Peru and Brazil, R(t) decreased to less than 1 in weeks 32 and 33, with estimates between 0.89 (95% CrI: 0.82 to 0.96) and 0.94 (95% CrI: 0.89 to 0.98), respectively.Conclusionour results provide relevant information about current trends and future scenarios of the Mpox outbreak in Latin America. From late August to early September 2022, R(t) started to decrease to values less than 1, despite the limited delivery of vaccination programs implemented across the region. However, a large population remains at risk, and there is a possibility of new waves of the disease as the epidemic continues its course.