bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical encounter heterogeneity and methods for resolving in networked EHR data: A study from N3C and RECOVER programs
Authors: Leese Peter , Anand Adit , Girvin Andrew , Manna Amin , Patel Saaya , Yoo Yun Jae , Wong Rachel , Haendel Melissa , Chute Christopher G , Bennett Tellen , Hajagos Janos , Pfaff Emily , Moffitt Richard 
Published: October 2022

ABSTRACTOBJECTIVEClinical encounter data are heterogeneous and vary greatly from institution to institution. These problems of variance affect interpretability and usability of clinical encounter data for analysis. These problems are magnified when multi-site electronic health record data are networked together. This paper presents a novel, generalizable method for resolving encounter heterogeneity for analysis by combining related atomic encounters into composite ‘macrovisits.’MATERIALS AND METHODSEncounters were composed of data from 75 partner sites harmonized to a common data model as part of the NIH Researching COVID to Enhance Recovery Initiative, a project of the National Covid Cohort Collaborative. Summary statistics were computed for overall and site-level data to assess issues and identify modifications. Two algorithms were developed to refine atomic encounters into cleaner, analyzable longitudinal clinical visits.RESULTSAtomic inpatient encounters data were found to be widely disparate between sites in terms of length-of-stay and numbers of OMOP CDM measurements per encounter. After aggregating encounters to macrovisits, length-of-stay (LOS) and measurement variance decreased. A subsequent algorithm to identify hospitalized macrovisits further reduced data variability.DISCUSSIONEncounters are a complex and heterogeneous component of EHR data and native data issues are not addressed by existing methods. These types of complex and poorly studied issues contribute to the difficulty of deriving value from EHR data, and these types of foundational, large-scale explorations and developments are necessary to realize the full potential of modern real world data.CONCLUSIONThis paper presents method developments to manipulate and resolve EHR encounter data issues in a generalizable way as a foundation for future research and analysis.
Systems strengthening approach during antenatal care improves maternal nutrition and reduces childhood stunting in West Bengal, India
Authors: Mehta Kayur , Mukherjee Sreeparna Ghosh , Bhattacharjee Ipsita , Fate Kassandra , Kachwaha Shivani , Kant Aastha , Banerjee Meghendra , Shet Anita 
Published: October 2022

AbstractBackgroundEarly childhood growth failure including stunting is associated with suboptimal health and cognitive development outcomes. Despite progress, the prevalence of childhood stunting in India remains amongst the highest globally.ObjectiveWe aimed to evaluate the impact of a systems strengthening interventional package, including body-mass-index measurement at pregnancy registration, monthly weight monitoring, on-the-spot supplementary nutrition, iron-folic acid supplementation, and targeted dietary counselling provided to women during their antenatal care on childhood stunting.MethodsThis is a prospective follow-up comparison study. Women from three districts in West Bengal, India in their first trimester of pregnancy between May 2018 and May 2019 were enrolled into the study. Pregnancy, birth and infant characteristics were collected, and anthropometric indices measured. The relative risk of stunting in children in intervention and comparison groups were compared using generalized linear model to adjust for clustering effect.ResultsA total of 809 mother-child dyads (406 intervention; 403 comparison) were followed between May 2018 and May 2021. The median age of women in the intervention and comparison group was 23 (IQR 20-25) and 25 (IQR 24-27) years respectively. Median gestational weight gain was higher amongst women in the intervention group (9 vs. 8 kilograms, p=0.04). Low-birth-weight prevalence was 29.3% (119/406) and 32.0% (129/403) in the intervention and comparison group respectively. At 12-35 months of age, children born to women in the intervention group had significantly reduced risk of stunting (RR=0.58, 95% CI 0.45-0.75, p<0.001). The odds of stunting amongst children born with low birthweight to women in the comparison group were statistically significant [OR 2.44 (1.44-4.14)], unlike those amongst children born to women in the intervention group [1.19 (0.58-2.46)].ConclusionsThese results indicate that strengthening of routine antenatal care including targeted nutritional counselling to expectant mothers can have distal beneficial effects on childhood stunting beyond the immediate post-natal period.Teaser TextThis article describes the impact of a systems strengthening approach during antenatal care that improved maternal nutrition and reduced childhood stunting in West Bengal, India.
“This guideline is not practical; it might be practical to specialists like you”: Doctors’ experiences of the Global Initiative for Asthma (GINA) guideline in Nigeria; A qualitative study
Authors: Ozoh Obianuju Beatrice , Dede Sandra Kelechi , Eze Joy Nkiru , Mortimer Kevin , Chinouya Martha 
Published: October 2022

AbstractBackgroundThe Global Initiative for Asthma (GINA) report sets out updated evidence-based strategy for asthma management. Little is known about how this report is perceived and implemented in low-income and middle-income countries (LMICs) like Nigeria. We explored the experiences of asthma management as informed by the current GINA guideline among doctors in Lagos, Nigeria.MethodsUsing a qualitative research approach, in-depth interviews were conducted among doctors in Lagos, Nigeria to explore their experiences of asthma management in the context of the current GINA report. The thematic framework approach was used for data analysis.ResultsEleven doctors (five general practitioners (GPs) and six Family Physicians (FPs) took part. Four overarching themes were identified:Knowledge of, and attitude towards the GINA strategy: Whilst most doctors were aware of the existence of the GINA report, there was limited knowledge about its content including current recommendations for mild asthma treatment.Asthma diagnosis and treatment: There was limited access to lung function testing facilities and its role in asthma diagnosis was underappreciated.Barriers to managing asthma according to GINA recommendations: These included complexity of the GINA report, unavailability and unaffordability of asthma medicines and poor patient adherence to medications, driven by socio-cultural factors.Enablers of GINA-recommended asthma management: Improvement in asthma education for doctors and the general population and better access to diagnostic tests and medicines.ConclusionWhilst there was awareness of the existence of the GINA report, there was limited knowledge about its content and several barriers to its implementation were reported. Education about the GINA report, investment in diagnostic and treatment services and simplification of recommendations were identified as possible solutions.
A Scoping Review Protocol on Integration of mobile-linked POC diagnostics in community-based healthcare: User Experience
Authors: Nxele Siphesihle R. , Moetlhoa Boitumelo , Kgarosi Kabelo , Mashamba-Thompson Tivani 
Published: October 2022

AbstractBackgroundMobile-linked point-of-care diagnostics forms an integral part of diagnostic health services for efficient communication between patients and healthcare professionals despite geographical location and time of diagnosis. The efficiency of this technology lies in the user experience which means that the interaction of the user with the implemented technology needs to be simple, convenient, and consistent. Having a well-structured user experience of these devices in community-based healthcare will aid in sustainable implementation. Herein, we propose to conduct a literature search to systematically map out evidence based on mobile-linked POC diagnostics user experience at a community level in resource-limited settings.MethodologyThe proposed scoping review will be guided by the advanced Arksey and O’Malley methodological framework and further advanced by Levacet al. A comprehensive search will be conducted to find relevant published literature from the following electronic databases: Scopus, Web of Science, EBSCOhost (Medline, CINAHL, Africa-wide, Academic Search Complete). Grey literature will also be searched, including reports from government and international organizations such as World Health Organization (WHO), Foundation for Innovative New Diagnostics (FIND), and the Food and Drug Administration (FDA). Two independent reviewers will screen the relevant studies and the degree of the agreement will be determined by calculating Cohen’s kappa statistic. The quality of eligible data will also be appraised using the mixed method appraisal tool version 2018.DiscussionWe anticipate that the planned scoping review will present useful evidence to inform stakeholders on the integration of mobile-linked diagnostic devices in community-based healthcare which will guide further research on the subject.
Neural signatures of second language proficiency in narrative processing
Authors: Zhang Ruiqing , Wang Jing , Lin Hui , Turk-Browne Nicholas B. , Cai Qing 
Published: October 2022

AbstractMaking sense of speech in a second language relies on multiple abilities. Differences in brain activity related to proficiency in language tasks have often been attributed to processing demands. However, during naturalistic narrative comprehension, listeners at different proficiency levels may form different representations of the same speech. We hypothesized that the synchronization of these representations across people could thus be used to measure second-language proficiency. Using a searchlight shared response model, we found that highly proficient participants showed synchronization in regions similar to those of native speakers, including in the default mode network and in the lateral prefrontal cortex. In contrast, participants with low proficiency showed more synchronization in auditory cortex and word-level semantic processing areas in the temporal lobe. Moderate proficiency showed the greatest neural diversity, suggesting lower consistency in the source of this partial proficiency. Based on these synchronization differences, we were able to reliably classify the proficiency level or predict behavioral performance on an independent English test in held-out participants, suggesting the identified neural systems represented proficiency-sensitive information that was generalizable to other individuals. These findings suggest higher second-language proficiency leads to a more native-like neural processing of naturalistic language, including in systems beyond the cognitive control network or the core language network.HighlightsNeural synchronization in second-language speech processing reflects proficiency.High-proficiency individuals neurally resemble native speakers.Low-proficiency individuals are synchronized in perceptual and word semantics areas.Proficiency level can be predicted using neural synchronization signatures.
Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes
Authors: Zhang Xixi , Li Zimu , Zhang Yanjun , Liu Yutong , Wang Jingjing , Liu Banghui , Chen Qiuluan , Wang Qian , Fu Lutang , Wang Peiyi , Zhong Xiaolin , Jin Liang , Chen Ling , He Jun , Zhao Jincun , Xiong Xiaoli 
Published: October 2022

AbstractSARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed and open. The locked conformations feature tightly packed trimers with structural elements incompatible with RBD in “up” position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably due to their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. Intriguingly, locked conformations were the only conformations captured for S proteins of bat and pangolin origin SARS-related coronaviruses. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures to other available spike structures of Sarbecoviruses to identify conserved features and discuss their possible functions.
Music and Speech Elicit Similar Subcortical Responses in Human Listeners
Authors: Shan Tong , Cappelloni Madeline S. , Maddox Ross K. 
Published: October 2022

AbstractMusic and speech are two sounds that are unique to human beings and encountered in daily life. Both are transformed by the auditory pathway from an initial acoustical encoding to higher level cognition. Most studies of speech and music processing are focused on the cortex, and the subcortical response to natural, polyphonic music is essentially unstudied. This study was aimed to compare the subcortical encoding of music and speech using the auditory brainstem response (ABR). While several methods have recently been developed to derive the ABR to continuous speech, they are either not applicable to music or give poor results. In this study, we explored deriving the ABR through deconvolution using three regressors: 1) the half-wave rectified stimulus waveform, 2) the modeled inner hair cell potential, and 3) the auditory nerve model firing rate (ANM), where the latter two were generated from a computational auditory periphery model. We found the ANM regressor yields robust and interpretable ABR waveforms to diverse genres of music and multiple types of speech. We then used the ANM-derived ABRs to compare the subcortical responses to music and speech and found that they are highly similar in morphology. We further investigated cortical responses using the same deconvolution method, and found the responses there were also quite similar, which was unexpected based on previous studies. We conclude that when using our proposed deconvolution regressor that accounts for acoustical differences’ nonlinear effects on peripheral encoding, the derived brainstem and cortical responses to music and speech are highly correlated.
SARS-CoV-2 multi-antigen protein microarray for detailed characterization of antibody responses in COVID-19 patients
Authors: Celikgil Alev , Massimi Aldo B. , Nakouzi Antonio , Herrera Natalia G. , Morano Nicholas C. , Lee James H. , Yoon Hyun ah , Garforth Scott J. , Almo Steven C. 
Published: October 2022

AbstractAntibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target multiple epitopes on different domains of the spike protein, and other SARS-CoV-2 proteins. We developed a SARS-CoV-2 multi-antigen protein microarray with the nucleocapsid, spike and its domains (S1, S2), and variants with single (D614G, E484K, N501Y) or double substitutions (N501Y/Deletion69/70), allowing a more detailed high-throughput analysis of the antibody repertoire following infection. The assay was demonstrated to be reliable and comparable to ELISA. We analyzed antibodies from 18 COVID-19 patients and 12 recovered convalescent donors. S IgG level was higher than N IgG in most of the COVID-19 patients, receptor-binding domain of S1 showed high reactivity, but no antibodies were detected against heptad repeat domain 2 of S2. Furthermore, antibodies were detected against S variants with single and double substitutions in COVID-19 patients who were infected with SARS-CoV-2 early in the pandemic. Here we demonstrated that SARS-CoV-2 multi-antigen protein microarray is a powerful tool for detailed characterization of antibody responses, with potential utility in understanding the disease progress and assessing current vaccines and therapies against evolving SARS-CoV-2.
Intuitive movement-based prosthesis control enables arm amputees to reach naturally in virtual reality
Authors: Segas Effie , Mick Sébastien , Leconte Vincent , Dubois Océane , Klotz Rémi , Cattaert Daniel , de Rugy Aymar 
Published: October 2022

AbstractImpressive progress is being made in bionic limbs design and control. Yet, controlling the numerous joints of a prosthetic arm necessary to place the hand at a correct position and orientation to grasp objects remains challenging. Here, we designed an intuitive, movement-based prosthesis control that leverages natural arm coordination to predict distal joints missing to people with transhumeral limb loss based on proximal residual limb motion and knowledge of the movement goal. This control was validated on 29 participants, including 7 with above-elbow limb loss, who picked and placed bottles in a wide range of locations in virtual reality, with median success rates over 99% and movement times identical to those of natural movements. This control also enabled 15 participants, including 3 with limb difference, to reach and grasp real objects with a robotic arm operated according to the same principle. Remarkably, this was achieved without any prior training, indicating that this control is intuitive and instantaneously usable. It could be used for phantom limb pain management in virtual reality, or to augment reaching capabilities of invasive neural interfaces usually more focused on hand and grasp control.
Mito-SiPE: A sequence-independent, PCR-free mitochondrial DNA enrichment method for ultra-deep sequencing that minimises amplification and alignment artefacts for the analysis of mitochondrial heteroplasmy/variation
Authors: Walsh Darren J , Bernard David J , Pangilinan Faith , Esposito Madison , Harold Denise , Parle-McDermott Anne , Brody Lawrence C 
Published: October 2022

AbstractBackgroundDeep sequencing is often used to measure somatic variation in the mitochondrial genome. Selective enrichment methods, such as PCR amplification or probe hybridization/capture are commonly used. These methods can introduce bias and are prone to contamination by nuclear-mitochondrial sequences (NUMTs); elements that can introduce artefacts into analyses such as an assessment of mitochondrial heteroplasmy.ResultsHere, we demonstrate a method to obtain ultra-deep (>80,000X) sequencing coverage of the mitochondrial genome by selectively purifying the intact organelle itself using differential centrifugation and alkaline lysis. We applied this approach to seven different mouse tissues. Isolation of mitochondria yields a preparation of highly enriched mtDNA. We compared this method to the commonly used PCR-based method. Mito-SiPE avoids false-heteroplasmy calls that occur when long-range PCR amplification is used for mtDNA enrichment.DiscussionWe have described a modified version of a long-established protocol for purifying mtDNA and have quantified the increased level of mitochondrial DNA post-enrichment in 7 different mouse tissues. This method will enable researchers to identify changes in low-frequency heteroplasmy without introducing PCR biases or NUMT contamination that are falsely identified as heteroplasmy when long-range PCR is used.
Probing the diabetes and colorectal cancer relationship using gene – environment interaction analyses
Authors: Dimou Niki , Kim Andre E. , Flanagan Orlagh , Murphy Neil , Diez-Obrero Virginia , Shcherbina Anna , Aglago Elom K , Bouras Emmanouil , Campbell Peter T , Casey Graham , Gallinger Steven , Gruber Stephen B , Jenkins Mark A , Lin Yi , Moreno Victor , Ruiz-Narvaez Edward , Stern Mariana C , Tian Yu , Tsilidis Kostas K , Arndt Volker , Barry Elizabeth L , Baurley James W , Berndt Sonja I , Bézieau Stéphane , Bien Stephanie A , Bishop D Timothy , Brenner Hermann , Budiarto Arif , Carreras-Torres Robert , Cenggoro Tjeng Wawan , Chan Andrew T , Chang-Claude Jenny , Chanock Stephen J , Chen Xuechen , Conti David V , Dampier Christopher H , Devall Matthew , Drew David , Figueiredo Jane C , Giles Graham G , Gsur Andrea , Harrison Tabitha A , Hidaka Akihisa , Hoffmeister Michael , Huyghe Jeroen R , Jordahl Kristina , Kawaguchi Eric , Keku Temitope O , Larsson Susanna C , Marchand Loic Le , Lewinger Juan Pablo , Li Li , Mahesworo Bharuno , Morrison John , Newcomb Polly A , Newton Christina C , Obon-Santacana Mireia , Ose Jennifer , Pai Rish K , Palmer Julie R , Papadimitrou Nick , Pardamean Bens , Peoples Anita R , Pharoah Paul D P , Platz Elizabeth A , Potter John D , Rennert Gad , Scacheri Peter C , Schoen Robert E , Su Yu-Ru , Tangen Catherine M , Thibodeau Stephen N , Thomas Duncan C , Ulrich Cornelia , Um Caroline Y , van Duijnhoven Franzel JB , Visvanathan Kala , Vodicka Pavel , Vodickova Ludmila , White Emily , Wolk Alicja , Woods Michael O , Qu Conghui , Kundaje Anshul , Hsu Li , Gauderman W. James , Gunter Marc J , Peters Ulrike 
Published: October 2022

AbstractDiabetes is an established risk factor for colorectal cancer; however, the mechanisms underlying this relationship are not fully understood and the role of genetic variation is unclear. We used data from 3 genetic consortia (CCFR, CORECT, GECCO; 31,318 colorectal cancer cases/41,499 controls) and undertook genome-wide gene-environment interaction analyses with colorectal cancer risk, including interaction tests of genetics(G)xdiabetes and joint testing of Gxdiabetes, G-colorectal cancer association and/or G-diabetes correlation (2,3-degrees of freedom joint tests; d.f.). Based on the joint tests, variant rs3802177 inSLC30A8(p-value3-d.f.:5.46×10−11; regulates phosphorylation of the insulin receptor and phosphatidylinositol-3 kinase activity) and rs9526201 inLRCH1(p-value2-d.f.:7.84×10−09; regulates T cell migration and Natural Killer Cell cytotoxicity) were associated with colorectal cancer. These results suggest that variation in genes related to insulin signalling and immune function may modify the association of diabetes with colorectal cancer and provide novel insights into the biology underlying the diabetes and colorectal cancer relationship.