bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sleep and circadian informatics data harmonization: a workshop report from the Sleep Research Society and Sleep Research Network
Authors: Mazzotti Diego R , Haendel Melissa A , McMurry Julie A , Smith Connor J , Buysse Daniel J , Roenneberg Till , Penzel Thomas , Purcell Shaun , Redline Susan , Zhang Ying , Merikangas Kathleen R , Menetski Joseph P , Mullington Janet , Boudreau Eilis 
Published: January 2022

Abstract
The increasing availability and complexity of sleep and circadian data are equally exciting and challenging. The field is in constant technological development, generating better high-resolution physiological and molecular data than ever before. Yet, the promise of large-scale studies leveraging millions of patients is limited by suboptimal approaches for data sharing and interoperability. As a result, integration of valuable clinical and basic resources is problematic, preventing knowledge discovery and rapid translation of findings into clinical care. To understand the current data landscape in the sleep and circadian domains, the Sleep Research Society (SRS) and the Sleep Research Network (now a task force of the SRS) organized a workshop on informatics and data harmonization, presented at the World Sleep Congress 2019, in Vancouver, Canada. Experts in translational informatics gathered with sleep research experts to discuss opportunities and challenges in defining strategies for data harmonization. The goal of this workshop was to fuel discussion and foster innovative approaches for data integration and development of informatics infrastructure supporting multi-site collaboration. Key recommendations included collecting and storing findable, accessible, interoperable, and reusable data; identifying existing international cohorts and resources supporting research in sleep and circadian biology; and defining the most relevant sleep data elements and associated metadata that could be supported by early integration initiatives. This report introduces foundational concepts with the goal of facilitating engagement between the sleep/circadian and informatics communities and is a call to action for the implementation and adoption of data harmonization strategies in this domain.
High-cited favorable studies for COVID-19 treatments ineffective in large trials
Authors: Ioannidis John P.A. 
Published: January 2022

ABSTRACTImportanceCOVID-19 has resulted in massive production, publication and wide dissemination of clinical studies trying to identify effective treatments. However, several widely touted treatments failed to show effectiveness in large well-done randomized controlled trials (RCTs).ObjectiveTo evaluate for COVID-19 treatments that showed no benefits in subsequent large RCTs how many of their most-cited clinical studies had declared favorable results for these interventions.MethodsScopus (last update December 23, 2021) identified articles on lopinavir-ritonavir, hydroxycholoroquine/azithromycin, remdesivir, convalescent plasma, colchicine or interferon (index interventions) that represented clinical trials and that had received >150 citations. Their conclusions were assessed and correlated with study design features. The ten most recent citations for the most-cited article on each index intervention were examined on whether they were critical to the highly-cited study. Altmetric scores were also obtained.Findings40 articles of clinical studies on these index interventions had received >150 citations (7 exceeded 1,000 citations). 20/40 (50%) had favorable conclusions and 4 were equivocal. Highly-cited articles with favorable conclusions were rarely RCTs while those without favorable conclusions were mostly RCTs (3/20 vs 15/20, p=0.0003). Only 1 RCT with favorable conclusions had sample size >160. Citation counts correlated strongly with Altmetric scores, in particular news items. Only 9 (15%) of 60 recent citations to the most highly-cited studies with favorable or equivocal conclusions were critical to the highly-cited study.ConclusionMany clinical studies with favorable conclusions for largely ineffective COVID-19 treatments are uncritically heavily cited and disseminated. Early observational studies and small randomized trials may cause spurious claims of effectiveness that get perpetuated.
MS1Connect: a mass spectrometry run similarity measure
Authors: Lin Andy , Kaiser Brooke L. Deatherage , Hutchison Janine R. , Bilmes Jeffrey A. , Noble William Stafford 
Published: January 2022

AbstractInterpretation of newly acquired mass spectrometry data can be improved by identifying, from an online repository, previous mass spectrometry runs that resemble the new data. However, this retrieval task requires computing the similarity between an arbitrary pair of mass spectrometry runs. This is particularly challenging for runs acquired using different experimental protocols. We propose a method, MS1Connect, that calculates the similarity between a pair of runs by examining only the intact peptide (MS1) scans, and we show evidence that the MS1Connect score is accurate. Specifically, we show that MS1Connect outperforms several baseline methods on the task of predicting the species from which a given proteomics sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities computed from fragment (MS2) scans, even though this data is not used by MS1Connect. The MS1Connect software will be made available upon acceptance at https://github.com/bmx8177/MS1Connect.
Harmonized-Multinational qEEG Norms (HarMNqEEG)
Authors: Li Min , Wang Ying , Lopez-Naranjo Carlos , Abd Hamid Aini Ismafairus , Evans Alan C. , Savostyanov Alexander N. , Calzada-Reyes Ana , Areces-Gonzalez Ariosky , Villringer Arno , Tobon-Quintero Carlos A. , Garcia-Agustin Daysi , Paz-Linares Deirel , Yao Dezhong , Dong Li , Aubert-Vazquez Eduardo , Reza Faruque , Omar Hazim , Abdullah Jafri Malin , Galler Janina R. , Ochoa-Gomez John F. , Prichep Leslie S. , Galan-Garcia Lidice , Morales-Chacon Lilia , Valdes-Sosa Mitchell J. , Tröndle Marius , Mohd Zulkifly Mohd Faizal Bin , Abdul Rahman Muhammad Riddha Bin , Milakhina Natalya S. , Langer Nicolas , Rudych Pavel , Hu Shiang , Koenig Thomas , Virues-Alba Trinidad A. , Lei Xu , Bringas-Vega Maria L. , Bosch-Bayard Jorge F. , Valdes-Sosa Pedro Antonio 
Published: January 2022

AbstractThis paper extends our frequency domain quantitative electroencephalography (qEEG) methods pursuing higher sensitivity to detect Brain Developmental Disorders. Prior qEEG work lacked integration of cross-spectral information omitting important functional connectivity descriptors. Lack of geographical diversity precluded accounting for site-specific variance, increasing qEEG nuisance variance. We ameliorate these weaknesses. i) Create lifespan Hermitian Riemannian multinational qEEG norms for cross-spectral tensors. These norms result from the HarMNqEEG project fostered by the Global Brain Consortium. We calculate the norms with data from 9 countries, 12 devices, and 14 studies, including 1564 subjects. Instead of raw data, only anonymized metadata and EEG cross-spectral tensors were shared. After visual and automatic quality control developmental equations for the mean and standard deviation of qEEG traditional and Hermitian Riemannian descriptive parameters were calculated using additive mixed-effects models. We demonstrate qEEG “batch effects” and provide methods to calculate harmonized z-scores. ii) We also show that the multinational harmonized Hermitian Riemannian norms produce z-scores with increased diagnostic accuracy to predict brain dysfunction at school-age produced by malnutrition only in the first year of life. We provide data and software for constructing norms. iii) We offer open code and data to calculate different individual z-scores from the HarMNqEEG dataset. These results contribute to developing bias-free, low-cost neuroimaging technologies applicable in various health settings.HighlightsWe create lifespan Hermitian Riemannian qEEG norms for cross-spectral tensors.The norms are based on 9 countries, 12 devices, and 14 studies, with 1564 subjects.We demonstrate qEEG “batch effects”, providing harmonization methods to remove them.Multinational harmonized z-scores increase diagnostic accuracy of brain dysfunction.Data and software are available for norm and individual z-scores calculation.
The blowflyChrysomya latifronsinhabits fragmented rainforests, but lacks genetic diversity and population structure
Authors: Butterworth Nathan J. , Wallman James F. , Johnston Nikolas P. , Dawson Blake M. , McGaughran Angela 
Published: January 2022

AbstractClimate change and deforestation are causing rainforests to become increasingly fragmented, placing them at heightened risk of biodiversity loss. Invertebrates constitute the greatest proportion of this biodiversity, yet we lack basic knowledge of their population structure and ecology. It is not currently feasible to assess the population structure of every invertebrate species, so there is a compelling need to identify ‘indicator species’ that are broadly indicative of habitat-level patterns and processes. Blowflies are an ideal candidate, because they are widespread, abundant, and can be easily collected within rainforests.Here, we present the first study of the blowflyChrysomya latifrons, which is endemic to the rainforests of New South Wales, Australia. We genotyped 188 flies from 15 isolated rainforests and found low overall genetic diversity and a complete lack of genetic structure between populations – suggesting the presence of a single large panmictic population along ~1,000 km of the Australian east coast. This highlights that: (1)Ch. latifronsinhabits every rainforest in NSW and undoubtedly plays an important role in these ecosystems, but low genetic diversity may cause it to struggle to adapt to a changing climate; (2) strongly dispersing insects have the capacity to migrate between isolated rainforests, likely carrying pollen, parasites, phoronts, and pathogens with them to form crucial trophic networks; and (3) there is an urgent need for similar studies on poorly dispersing rainforest insects, as these may be the most fragmented and at highest risk of local extinction.
A digital self-care intervention for Ugandan patients with heart failure and their clinicians: User-centred design and usability study
Authors: Hearn Jason , Wali Sahr , Birungi Patience , Cafazzo Joseph A. , Ssinabulya Isaac , Akiteng Ann R. , Ross Heather J. , Seto Emily , Schwartz Jeremy I. 
Published: January 2022

AbstractBackgroundThe prevalence of heart failure (HF) is increasing in Uganda. Ugandan patients with HF report receiving limited information about their illness, disease management, or empowerment to engage in self-care behaviors. Interventions targeted at improving HF self-care have been shown to improve patient quality of life and to reduce hospitalizations in high-income countries. However, such interventions remain underutilized in resource-limited settings like Uganda.ObjectiveTo develop a digital health intervention that enables improved self-care amongst HF patients in Uganda.MethodsWe implemented a user-centred design process to develop a self-care intervention entitled Medly Uganda. The ideation phase comprised a systematic scoping review and preliminary data collection amongst HF patients and clinicians in Uganda. An iterative design process was then used to advance an initial prototype into a fully-functional digital health intervention. The evaluation phase involved usability testing of the developed intervention amongst Ugandan patients with HF and their clinicians.ResultsMedly Uganda is a digital health intervention that is fully integrated within a government-operated mobile health platform. The system allows patients to report daily HF symptoms, receive tailored treatment advice, and connect with a clinician when showing signs of decompensation. Medly Uganda harnesses Unstructured Supplementary Service Data technology that is already widely used in Uganda for mobile phone-based financial transactions. Usability testing showed the system to be accepted by patients, caregivers, and clinicians.ConclusionsMedly Uganda is a fully-functional and well-accepted digital health intervention that enables Ugandan HF patients to better care for themselves. Moving forward, we expect the system to help decongest cardiac clinics and improve self-care efficacy amongst HF patients in Uganda.
Associations between multiple long-term conditions and mortality in diverse ethnic groups
Authors: Stafford Mai , Knight Hannah , Hughes Jay , Alarilla Anne , Mondor Luke , Kone Anna Pefoyo , Wodchis Walter , Deeny Sarah R 
Published: January 2022

AbstractBackgroundMultiple conditions are more prevalent in some minoritised ethnic groups and are associated with higher mortality rate but studies examining differential mortality once conditions are established is US-based. Our study tested whether the association between multiple conditions and mortality varies across ethnic groups in England.Methods and FindingsA random sample of primary care patients from Clinical Practice Research Datalink (CPRD) was followed from 1st January 2015 until 31st December 2019. Ethnicity, usually self-ascribed, was obtained from primary care records if present or from hospital records. Cox regression models were used to estimate mortality by number of long-term conditions, ethnicity and their interaction, with adjustment for age and sex for 532,059 patients with complete data.During five years of follow-up, 5.9% of patients died. Each additional long-term condition at baseline was associated with increased mortality. This association differed across ethnic groups. Compared with 50-year-olds of white ethnicity with no conditions, the mortality rate was higher for white 50-year-olds with two conditions (HR 1.77) or four conditions (HR 3.13). Corresponding figures were higher for 50-year-olds of Black Caribbean ethnicity with two conditions (HR=2.22) or four conditions (HR 4.54). The direction of the interaction of number of conditions with ethnicity showed higher mortality associated with long-term conditions in nine out of ten minoritised ethnic groups, attaining statistical significance in four (Pakistani, Black African, Black Caribbean and Black other ethnic groups).ConclusionsThe raised mortality rate associated with having multiple conditions is greater in minoritised ethnic groups compared with white people. Research is now needed to identify factors that contribute to these inequalities. Within the health care setting, there may be opportunities to target clinical and self-management support for people with multiple conditions from minoritised ethnic groups.
SARS-CoV-2 Omicron Neutralization After Heterologous Vaccine Boosting
Authors: Lyke Kirsten E. , Atmar Robert L. , Islas Clara Dominguez , Posavad Christine M. , Szydlo Daniel , PaulChourdhury Rahul , Deming Meagan E. , Eaton Amanda , Jackson Lisa A. , Branche Angela R. , Sahly Hana M. El , Rostad Christina A. , Martin Judith M. , Johnston Christine , Rupp Richard E. , Mulligan Mark J. , Brady Rebecca C. , Frenck Robert W. , Bäcker Martín , Kottkamp Angelica C. , Babu Tara M. , Rajakumar Kumaravel , Edupuganti Srilatha , Dobrzynski David , Coler Rhea N. , Archer Janet I. , Crandon Sonja , Zemanek Jillian A. , Brown Elizabeth R. , Neuzil Kathleen M. , Stephens David S. , Post Diane J. , Nayak Seema U. , Roberts Paul C. , Beigel John H. , Montefiori David ,   the DMID 21-0012 Study Group
Published: January 2022

AbstractAs part of an ongoing study assessing homologous and heterologous booster vaccines, following primary EUA series, we assessed neutralization of D614G and Omicron variants prior to and 28 days after boost. Subset analysis was done in six combinations (N = 10/group): four homologous primary-booster combinations included mRNA-1273 two-dose priming followed by boosting with 100-μg or 50-μg mRNA-1273, Ad26.COV2.S single-dose priming followed by Ad26.COV2.S booster and BNT162b2 two-dose priming followed by BNT162b2 boosting; and two heterologous primary-booster combinations: BNT162b2 followed by Ad26.COV2.S and Ad26.COV2.S followed by BNT162b2. Neutralizing antibody (Nab) titers to D614G on the day of boost (baseline) were detected in 85-100% of participants, with geometric mean titers (GMT) of 71-343 in participants who received an mRNA vaccine series versus GMTs of 35-41 in participants primed with Ad26.OV2.S. Baseline NAb titers to Omicron were detected in 50-90% of participants who received an mRNA vaccine series (GMT range 12.8-24.5) versus 20-25% among participants primed with Ad26.COV2.S. The booster dose increased the neutralizing GMT in most combinations to above 1000 for D614G and above 250 for Omicron by Day 29. Homologous prime-boost Ad26.COV2.S had the lowest NAb on Day 29 (D614G GMT 128 and Omicron GMT 45). Results were similar between age groups. Most homologous and heterologous boost combinations examined will increase humoral immunity to the Omicron variant.
A national survey of early treatment seeking behavior among those with incident SARS-CoV-2 infection
Authors: Kojima Noah , Brobeck Matthew , Slepnev Vladimir , Klausner Jeffrey D. 
Published: January 2022

AbstractBackgroundDespite effective means to treat SARS-CoV-2 infection, the early treatment seeking behavior of those newly diagnosed with infection is not clear.MethodsWe surveyed users of a national SARS-CoV-2 testing company to assess the frequency and correlates of early treatment seeking behavior for a positive test result. We recruited adults (18 years or older) who had tested positive for SARS-CoV-2 by PCR at a large clinical laboratory. To be eligible, individuals had to have a positive test result within 7 days of enrollment. Surveys were anonymous and voluntary. We collected data on demographic characteristics, general health care access and utilization, awareness of treatment for COVID-19, treatment seeking behavior, and treatments received. Descriptive statistics and odds ratios (OR) with 95% confidence intervals (95% CI) were calculated on StataSE.ResultsParticipants were surveyed from 3-7 January 2022: among the 15,991 who viewed a survey request, 7,647 individuals were eligible and provided responses. The median age of a respondent was 42 years (interquartile range: 32 to 54), 68.9% of respondents were women, and respondents represented 33 different states, districts, and territories. Among respondents, 23.1% reported they had sought treatment or medical advice for their current COVID-19 diagnosis. Of those who were very aware of treatment for COVID-19, 31.0% sought treatment versus 16.7% who were unaware (p-value< 0.001). The odds of treatment seeking behavior were higher for those that were contacted by a medical professional after their diagnosis (OR: 4.57 [95% CI: 3.89 to 5.37]), those with a primary doctor (OR: 2.94 [95% CI: 2.52 to 3.43]), those who self-measured their oxygen saturation (OR: 2.53 [95% CI: 2.25 to 2.84]), and those over 65 years of age (OR: 2.36 [95% CI: 2.02 to 2.76]). There was no difference in those seeking treatment based on heritage, ethnicity, prior COVID-19 diagnosis, state political affiliation, or vaccination status. The odds of seeking treatment were lower among men (OR: 0.88 [95% CI: 0.78 to 0.99]) and those without insurance (OR: 0.62 [95% CI: 0.52 to 0.72]). The most common treatment locations were clinics and most common treatments were Vitamin C, Vitamin D, Zinc, Tylenol, and NSAIDs.ConclusionMore public outreach is needed to raise awareness of the benefits of treatment for COVID-19. We found that people who were more aware about treatment for COVID-19 were more likely to seek medical advice or therapy. Efforts to increase awareness might increase early treatment for SARS-CoV-2 infection. Increased outreach with treatment facilitation from medical professionals and/or public health staff to those with newly detected SARS-CoV-2 infections, particularly among those at higher-risk of complications, might also be helpful.
Cost of tuberculosis-related aeromedical retrievals in the Torres Strait, Australia
Authors: Foster J’Belle , Judge Daniel , Mendez Diana , Marais Ben J. , Peniyamina Dunstan , McBryde Emma S. 
Published: January 2022

ABSTRACTTuberculosis (TB) remains a disease of public health significance at the Australia / Papua New Guinea (PNG) international border. In the remote Torres Strait Islands, aeromedical evacuation is a necessary but costly component of TB management and patients with critical care needs require support to prevent onward TB transmission. A detailed costing of an exemplar TB patient from PNG who presented to a Queensland Health facility in the Torres Strait and required urgent aeromedical evacuation was performed. Data were drawn from patient charts, financial and clinical information systems used within Queensland Health and the Torres and Cape Hospital and Health Service. The total cost of aeromedical evacuation was AUD 124,280; 54% of the cost was attributed to travel. Between 2016 and 2019, 19 patients diagnosed with TB were medically evacuated from an outer Torres Strait Island with a median length of hospital stay of 57 days. Aeromedical evacuation and medical management costs require adequate budget allocation.
Rapid detection of single nucleotide polymorphisms using the MinION nanopore sequencer: a feasibility study for perioperative precision medicine
Authors: Tabata Yoshiteru , Matsuo Yoshiyuki , Fujii Yosuke , Ohta Atsufumi , Hirota Kiichi 
Published: January 2022

AbstractIntroductionPrecision medicine is a phrase used to describe personalized medical care tailored to specific patients based on their clinical presentation and genetic makeup. However, despite the fact that several single nucleotide polymorphisms (SNPs) have been reported to be associated with increased susceptibility to particular anesthetic agents and the occurrence of perioperative complications, genomic profiling and thus precision medicine has not been widely applied in perioperative management.MethodsWe validated six SNP loci known to affect perioperative outcomes in Japanese patients using genomic DNA from saliva specimens and nanopore sequencing of each SNP loci to facilitate allele frequency calculations and then compared the nanopore results to those produced using the conventional dideoxy sequencing method.ResultsNanopore sequencing reads clustered into the expected genotypes in both homozygous and heterozygous cases. In addition, the nanopore sequencing results were consistent with those obtained using conventional dideoxy sequencing and the workflow provided reliable allele frequency estimation, with a total analysis time of less than 4 h.ConclusionThus, our results suggest that nanopore sequencing may be a promising and versatile tool for SNP genotyping, allowing for rapid and feasible risk prediction of perioperative outcomes.