bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting Biological Pathways of Psychopathology using Cognitive Genomics
Authors: Lam Max , Chen Chia-Yen , Hill W. David , Xia Charley , Tian Ruoyu , Levey Daniel F. , Gelernter Joel , Stein Murray B. , team Biogen Biobank , Hatoum Alexander S. , Huang Hailiang , Malhotra Anil K. , Runz Heiko , Ge Tian , Lencz Todd 
Published: July 2021

AbstractCognitive deficits are known to be related to most forms of psychopathology. Here, we perform local genetic correlation analysis as a means of identifying independent segments of the genome that show biologically interpretable pleiotropic associations between cognitive dimensions and psychopathology. We identified collective segments of the genome, which we call “meta-loci”, that showed differential pleiotropic patterns for psychopathology relative to either General Cognitive Ability (GCA) or Non-Cognitive Skills (NCS). We observed that neurodevelopmental gene sets expressed during the prenatal-early childhood predominated in GCA-relevant meta-loci, while post-natal synaptic gene sets were more involved in NCS-relevant meta-loci. Notably, we found that GABA-ergic, cholinergic, and glutamatergic genes drove pleiotropic relationships within dissociable NCS meta-loci.
Will a natural collective immunity of Ukrainians restrain new COVID-19 waves?
Authors: Nesteruk Igor 
Published: July 2021

ABSTRACTThe visible and real sizes the COVID-19 epidemic in Ukraine were estimated with the use of the number of laboratory-confirmed cases (accumulated in May and June 2021), the generalized SIR-model and the parameter identification procedure taking into account the difference between registered and real number of cases. The calculated optimal value of the visibility coefficient shows that most Ukrainians have already been infected with the coronavirus, and some more than once, i.e., Ukrainians have probably achieved a natural collective immunity. Nevertheless, a large number of new strains and short-lived antibodies can cause new pandemic waves. In particular, the beginning of such a wave, we probably see in Ukraine in mid-July 2021. The further dynamics of the epidemic and its comparison with the results of mathematical modeling will be able to answer many important questions about the natural immunity and effectiveness of vaccines.
The role of IT ambidexterity, digital dynamic capability and knowledge processes as enablers of patient agility: an empirical study
Authors: van de Wetering Rogier , Versendaal Johan 
Published: July 2021

AbstractThere is a limited understanding of IT’s role as a crucial enabler of patient agility and the department’s ability to respond to patient’s needs and wishes adequately. This study’s objective is to contribute to the insights of the validity of the hypothesized relationship between IT resources, practices and capabilities, and hospital departments’ knowledge processes and the department’s ability to adequately sense and respond to patient needs and wishes, i.e., patient agility. This study conveniently sampled data from 107 clinical hospital departments in the Netherlands and uses structural equation modeling for model assessment. IT ambidexterity positively enhances the development of a digital dynamic capability. Likewise, IT ambidexterity also positively impacts the hospital department’s knowledge processes. Both digital dynamic capability and knowledge processes positively influence patient agility. IT ambidexterity promotes taking advantage of IT resources and experiments to reshape patient services and enhance patient agility.
The impact of premature extrauterine exposure on infants’ stimulus-evoked brain activity across multiple sensory systems
Authors: Mellado Gabriela Schmidt , Pillay Kirubin , Adams Eleri , Alarcon Ana , Andritsou Foteini , Cobo Maria M , Fry Ria Evans , Fitzgibbon Sean , Moultrie Fiona , Baxter Luke , Slater Rebeccah 
Published: July 2021

AbstractPrematurity can result in widespread neurodevelopmental impairment, with the impact of premature extrauterine exposure on brain function detectable in infancy. A range of neurodynamic and haemodynamic functional brain measures have previously been employed to study the neurodevelopmental impact of prematurity, with methodological and analytical heterogeneity across studies obscuring how multiple sensory systems are affected. Here, we outline a standardised template analysis approach to measure the evoked response magnitudes for visual, tactile, and noxious stimulation within individual infants (n=15) using EEG. By studying a cohort of very preterm infants longitudinally (n=10), we observe that the evoked response template magnitudes are significantly associated with age-related maturation. In a subsequent cross-sectional study, we observe significant differences in visual and tactile response template magnitudes between infants born in the very preterm and late preterm periods (n=10 and 8), age-matched at study. These findings demonstrate the significant impact of premature extrauterine exposure on brain function and suggest that prematurity can accelerate maturation of the visual and tactile sensory system in infants born very prematurely. This study highlights the value of using a standardised multi-modal evoked-activity analysis approach to assess premature neurodevelopment, and will likely complement resting-state EEG and behavioural assessments in the study of the functional impact of developmental care interventions.HighlightsMulti-modal sensory stimulation is used to assess premature infant brain functionA template analysis approach is outlined for multi-modal stimulus-evoked EEG activityStimulus-evoked template magnitudes change with agePrematurity results in accelerated maturation of visual and tactile sensory systems
Evaluation of a city-wide school-located influenza vaccination program in Oakland, California with respect to race and ethnicity: a matched cohort study
Authors: Nguyen Anna , Arnold Benjamin F. , Kennedy Chris J. , Mishra Kunal , Pokpongkiat Nolan , Seth Anmol , Djajadi Stephanie , Holbrook Kate , Pan Erica , Kirley Pam D. , Libby Tanya , Hubbard Alan E. , Reingold Arthur , Colford John M. , Benjamin-Chung Jade 
Published: July 2021

AbstractObjectivesTo evaluate the effectiveness of city-wide school-located influenza vaccination by race/ethnicity from 2014-2018.MethodsWe used multivariate matching to pair schools in the intervention district in Oakland, CA with schools in West Contra Costa County, CA, a comparison district. We estimated difference-in-differences (DIDs) in caregiver-reported influenza vaccination coverage and laboratory-confirmed influenza hospitalization incidence.ResultsDifferences in influenza vaccination coverage in the intervention vs. comparison site were larger among White and Latino students than Asian/Pacific Islander (API), Black, and multiracial students. Concerns about vaccine effectiveness or safety were more common among Black and multiracial caregivers; logistical barriers to vaccination were more common among White, API, and Latinos. In both sites, hospitalization in 2017-18 was higher in Blacks vs. other races/ethnicities. All-age influenza hospitalization incidence was lower in the intervention site vs. comparison site among White/API individuals in 2016-17 and 2017-18 and Black older adults in 2017-18, but not in other groups.ConclusionsSLIV was associated with higher vaccination coverage and lower influenza hospitalization, but associations varied by race/ethnicity. SLIV alone may be insufficient to ensure equitable health outcomes for influenza.
An Explainable Artificial Intelligence Approach for Predicting Cardiovascular Outcomes using Electronic Health Records
Authors: Wesołowski Sergiusz , Lemmon Gordon , Hernandez Edgar J. , Henrie Alex , Miller Thomas A. , Weyhrauch Derek , Puchalski Michael D. , Bray Bruce E. , Shah Rashmee U. , Deshmukh Vikrant G. , Delaney Rebecca , Yost H. Joseph , Eilbeck Karen , Tristani-Firouzi Martin , Yandell Mark 
Published: July 2021

AbstractUnderstanding the conditionally-dependent clinical variables that drive cardiovascular health outcomes is a major challenge for precision medicine. Here, we deploy a recently developed massively scalable comorbidity discovery method called Poisson Binomial based Comorbidity discovery (PBC), to analyze Electronic Health Records (EHRs) from the University of Utah and Primary Children’s Hospital (over 1.6 million patients and 77 million visits) for comorbid diagnoses, procedures, and medications. Using explainable Artificial Intelligence (AI) methodologies, we then tease apart the intertwined, conditionally-dependent impacts of comorbid conditions and demography upon cardiovascular health, focusing on the key areas of heart transplant, sinoatrial node dysfunction and various forms of congenital heart disease. The resulting multimorbidity networks make possible wide-ranging explorations of the comorbid and demographic landscapes surrounding these cardiovascular outcomes, and can be distributed as web-based tools for further community-based outcomes research. The ability to transform enormous collections of EHRs into compact, portable tools devoid of Protected Health Information solves many of the legal, technological, and data-scientific challenges associated with large-scale EHR analyzes.
Early, intensive rehabilitation improves gross motor function after perinatal stroke: results of a randomized controlled trial
Authors: Hurd Caitlin , Livingstone Donna , Brunton Kelly , Smith Allison , Gorassini Monica , Watt Man-Joe , Andersen John , Kirton Adam , Yang Jaynie F. 
Published: July 2021

AbstractBackgroundPerinatal stroke injures motor regions of the brain, compromising movement for life. Early, intensive, active interventions for the upper extremity are efficacious, but interventions for the lower extremity (LE) remain infrequent and understudied.ObjectiveTo determine the efficacy of ELEVATE – Engaging the Lower Extremity Via Active Therapy Early - on gross motor function, as compared to usual care.MethodWe conducted a single-blind, two-arm, randomized controlled trial (RCT), with the Immediate Group receiving the intervention while the Delay Group served as a three-month waitlist-control. A separate cohort living beyond commuting distance was trained by their parents with guidance from physical therapists. Participants were 8 months to 3 years old, with MRI-confirmed perinatal ischemic stroke and early signs of hemiparesis. The intervention was play-based, focused on weight-bearing, balance and walking for 1 hour/day, 4 days/week for 12 weeks. The primary outcome was the Gross Motor Function Measure-66 (GMFM-66). Secondary outcomes included steps and gait analyses. Final follow-up occurred at age four.ResultsThirty-four children participated (25 RCT, 9 Parent-trained). The improvement in GMFM-66 over 12 weeks was greater for the Immediate than the Delay Group (average change 3.4 units higher) and greater in younger children. Average step counts reached 1370–3750 steps/session in the last week of training for all children. Parent-trained children also improved but with greater variability.ConclusionsEarly, activity-intensive LE therapy for young children with perinatal stroke is feasible and improves gross motor function in the short term. Longer term improvement may require additional bouts of intervention.Clinical trial registratioThis study was registered at ClinicalTrials.gov (NCT01773369).
Waiting times, patient flow, and occupancy density in South African primary health care clinics: implications for infection prevention and control
Authors: Karat Aaron S , McCreesh Nicky , Baisley Kathy , Govender Indira , Kallon Idriss I , Kielmann Karina , MacGregor Hayley , Vassall Anna , Yates Tom A , Grant Alison D 
Published: July 2021

AbstractBackgroundTransmission of respiratory pathogens, such asMycobacterium tuberculosisand severe acute respiratory syndrome coronavirus 2, is more likely during close, prolonged contact and when sharing a poorly ventilated space. In clinics in KwaZulu-Natal (KZN) and Western Cape (WC), South Africa, we estimated clinic visit duration, time spent indoors and outdoors, and occupancy density of waiting rooms.MethodsWe used unique barcodes to track attendees’ movements in 11 clinics in two provinces, multiple imputation to estimate missing arrival and departure times, and mixed-effects linear regression to examine associations with visit duration.Results2,903 attendees were included. Median visit duration was 2 hours 36 minutes (interquartile range [IQR] 01:36–3:43). Longer mean visit times were associated with being female (13.5 minutes longer than males; p<0.001) and attending with a baby (18.8 minutes longer than those without; p<0.01), and shorter mean times with later arrival (14.9 minutes shorter per hour after 0700; p<0.001) and attendance for tuberculosis or ante/postnatal care (24.8 and 32.6 minutes shorter, respectively, than HIV/acute care; p<0.01).Overall, attendees spent more of their time indoors (median 95.6% [IQR 46–100]) than outdoors (2.5% [IQR 0–35]). Attendees at clinics with outdoor waiting areas spent a greater proportion (median 13.7% [IQR 1– 75]) of their time outdoors.In two clinics in KZN (no appointment system), occupancy densities of ∼2.0 persons/m2were observed in smaller waiting rooms during busy periods. In one clinic in WC (appointment system), occupancy density did not exceed 1.0 persons/m2despite higher overall attendance.ConclusionsLonger waiting times were associated with early arrival, being female, and attending with a young child. Attendees generally waited where they were asked to. Regular estimation of occupancy density (as patient flow proxy) may help staff assess for risk of infection transmission and guide intervention to reduce time spent in risky spaces.
Nutritional risk assessment using Malnutrition Universal Screening Tool (MUST) in COVID-19 patients: An observational study in a tertiary care hospital in Eastern India
Authors: Nag Sudeshna Maitra , Bhowmick Subhrojyoti , Bhowmick Sayantani , Deb Uttiya , Kundu Debarati , Ray Krishnangshu , Purkayastha Sujit Kar 
Published: July 2021

AbstractAimsTo diagnose malnutrition, the nutritional status of each infected patient should be evaluated before starting general treatment. The role of Malnutrition Universal Screening Tool (MUST) in evaluating nutritional status of COVID-19 patients is still unknown. The aim of this study was to evaluate the use of MUST in assessment of nutritional status of COVID-19 patients.MethodsWe retrospectively analyzed the data of hospitalized COVID-19 patients above 18 years of age from July 25th to September 25th, 2020. All COVID-19 patients with a length of hospital stay greater than 24 hours underwent malnutrition screening and nutritional assessment based upon MUST. Demographic data, laboratory parameters and MUST score were retrieved from case files.ResultsOut of 106 COVID-19 patients included in the study, 68 (64%) were male and 38 (36%) were female. Number of deaths due to COVID-19 was 17 (16.03%). A total of 22 (20.75%) patients had MUST score of 2 and above. Analysis between MUST score and age group showed statistically significant result (p=0.012). MUST score according to clinical outcome at the end of hospitalization was also statistically significant (p<0.001).ConclusionOur results highlight a possible role of MUST as screening tool for malnutrition in COVID-19 patients.
Laboratory study to investigate the sensitivity and specificity of a diagnostic dressing to detect burn wound infection
Authors: Thet N.T. , Jenkins A.T.A. , Mercer-Chalmers J.D. , Coy K. , Booth S. , Collins D. , Bremner S. , Spickett-Jones F. , Greenwood R. , Young A.E. 
Published: July 2021

AbstractBurn Wound Infection (BWI) is difficult to define and detect before it manifests with clear clinical symptoms. In this paper, an ex vivo study of a prototype BWI detecting wound dressing is reported. Consenting patients with burns were recruited from four burns services in the United Kingdom, their burn infection state recorded at time of recruitment and retrospectively following treatment. Their wound dressings were used as a source of inoculating bacteria to create an ex vivo biofilm model in the laboratory with reasonable fidelity to the original microbial state of their wound. The prototype infection detecting wound dressing, which responds to cytolytic toxins secreted by bacteria, was placed on the ex vivo biofilm and the response of the dressing correlated with the clinical decision on the patient’s wound infection state. The study illustrated a number of broader issues with clinical BWI diagnosis, notably the absence of objective diagnostic criteria: a ‘reference standard’ for BWI. The absence of such a reference standard made analysis of the relationship between the dressing response and BWI diagnosis challenging, however a point estimate of 68% sensitivity from the study suggests the potential future utility of using a sensor which detects secreted bacterial virulence factors to assist in BWI diagnosis.
Gastrodia-Uncaria Water Extract Inhibits Endoplasmic Reticulum Stress and Matrix Metalloproteinase in Protecting against Cerebral Ischemia
Authors: Yiu-Ting Choi Angus , Wen Xian Jia , Yi MA Sum , Zhixiu Lin , Wai Chan Chun 
Published: July 2021

ABSTRACTStroke is the second leading cause of death in worldwide, in which cerebral ischemia accounts for 87% of all cases. The building up of endoplasmic reticulum stress in cerebral ischemia contributes to the disruption of blood brain barrier and neuronal cell death. The only FDA-approved drug, recombinant tissue plasminogen activator, is still of limited use due to the narrow window period and lack of neuroprotective effect. Therefore, it is necessary to explore alternative treatment on cerebral ischemia. Tianma-Gouteng decoction is a traditional Chinese Medicine prescription used to treat brain diseases in China. In this study, we investigated the neuroprotective effect of a water extract consisting of Gastrodia elata and Uncaria rhynchophylla, which are the two main herbs in the decoction. Cerebral ischemia was induced in rats using middle cerebral artery occlusion. GUW-treated rats have significantly reduced infarction volume and recovered neurological functions. The number of protein aggregates and caspase-12 positive cells were significantly inhibited. In vitro oxygen-glucose deprivation / reoxygenation stroke model demonstrated that the unfolded protein response proteins GRP78 and PDI were upregulated by GUW. Less ubiquitin puncta and normalized ubiquitin distribution indicated the reduction in endoplasmic reticulum stress. Furthermore, a lower Evan blue signal and MMPsense signal was observed, suggesting that GUW may preserve the blood brain barrier integrity through inhibiting MMP activity. Taken together, this suggested that GUW protected ischemic neurons and the blood brain barrier through inhibiting endoplasmic reticulum stress.
Herbarium specimens reveal herbivory patterns across the genus Cucurbita
Authors: Jenny Laura A. , Shapiro Lori R. , Davis Charles C. , Davies T. Jonathan , Pierce Naomi E. , Meineke Emily 
Published: July 2021

AbstractPREMISEQuantifying how closely related plant species differ in susceptibility to insect herbivory is important for our understanding of variation in plant-insect ecological interactions and evolutionary pressures on plant functional traits. However, empirically measuring in situ variation in herbivory over the entire geographic range where a plant-insect complex occurs is logistically difficult. Recently, new methods have been developed to use herbarium specimens to investigate patterns in plant-insect interactions across geographic areas, and during periods of accelerating anthropogenic change. Such investigations can provide insights into changes in herbivory intensity and phenology in plants that are of ecological and agricultural importance.METHODSHere, we analyze 274 pressed herbarium samples from all 14 species in the economically important plant genus Cucurbita (Cucurbitaceae) to investigate variation in herbivory damage. This collection is comprised of specimens of wild, undomesticated Cucurbita that were collected from across their native range in the Neotropics and subtropics, and Cucurbita cultivars that were collected from both within their native range and from locations where they have been introduced for agriculture in temperate Eastern North America.RESULTSWe find that herbivory is common on individuals of all Cucurbita species collected from throughout their geographic ranges; however, estimates of herbivory varied considerably among individuals, with greater damage observed in specimens collected from unmanaged habitat. We also find evidence that mesophytic species accrue more insect damage than xerophytic species.CONCLUSIONSOur study demonstrates that herbarium specimens are a useful resource for understanding ecological interactions between domesticated crop plants and co-evolved insect herbivores.
Deep embeddings to comprehend and visualize microbiome protein space
Authors: Odrzywolek Krzysztof , Karwowska Zuzanna , Majta Jan , Byrski Aleksander , Milanowska-Zabel Kaja , Kosciolek Tomasz 
Published: July 2021

AbstractUnderstanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the possibility of predicting their function through conventional homology-based approaches is limited. Here, we leverage a deep-learning-based representation of proteins to assess its utility in alignment-free analysis of microbial proteins. We trained a language model on the Unified Human Gastrointestinal Protein catalogue and validated the resulting protein representation on the bacterial part of the SwissProt database. Finally, we present a use case on proteins involved in SCFA metabolism. Results indicate that the deep learning model manages to accurately represent features related to protein structure and function, allowing for alignment-free protein analyses. Technologies that contextualize metagenomic data are a promising direction to deeply understand the microbiome.