bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Comprehensive Battery to Collect Social and Structural Determinants of Health (SSDOH) in Cognitively Normal or Very Mildly Impaired Persons
Authors: Streitz Marissa L. , Denny Andrea , Xiong Chengjie , McCue Lena , Stites Shana D. , Midgett Sharnita , Mechanic-Hamilton Dawn , Moulder Krista L. , Morris John C. , Balls-Berry Joyce 
Published: April 2022

Introduction:
Research addressing Alzheimer disease and related dementias must examine nonbiological factors influencing the risk for and expression of Alzheimer disease and related dementias. These factors address the interplay of cognition with lived experiences and social and structural determinants of health (SSDOH). However, coordinated measures of SSDOH are limited.

Methods:
The Knight Alzheimer Disease Research Center (ADRC) at Washington University in St. Louis developed and piloted a comprehensive battery to measure SSDOH. One hundred and twelve participants, very mildly cognitively impaired or unimpaired, enrolled in memory studies completed the electronic SSDOH battery. The Clinical Dementia Rating (CDR) determined the presence or absence of cognitive impairment.

Results:
Four domains demonstrated above acceptable intraclass correlation scores for test-retest reliability (≥0.70), including adverse childhood events, discrimination, social status, and early education. Twenty very mildly impaired participants completed the electronic pilot study.

Conclusion:
Our findings indicate that participants with early-stage symptomatic Alzheimer disease are able to participate in electronic SSDOH data collection. In collaboration with the University of Pennsylvania ADRC, we replaced/modified certain assessments to increase intraclass correlation. The resulting battery, Social and Structural Life-courses Influencing Aging and Dementia (SS-DIAD), can serve as a SSDOH collection tool and is currently utilized in cognitively impaired and unimpaired research participants at both ADRCs.
Nonutility of procalcitonin for diagnosing bacterial pneumonia in COVID-19
Authors: Cohen Avi J. , Glick Laura R. , Lee Seohyuk , Kunitomo Yukiko , Tsang Derek A. , Pitafi Sarah , Toro Patricia Valda , Zhang Ethan , Datta Rupak , Dela Cruz Charles S. , Gautam Samir 
Published: April 2022

AbstractPatients hospitalized with COVID-19 are at significant risk for superimposed bacterial pneumonia. However, diagnosing superinfection is challenging due to its clinical resemblance to severe COVID-19. We therefore evaluated whether the immune biomarker, procalcitonin, could facilitate the diagnosis of bacterial superinfection. To do so, we identified 185 patients with severe COVID-19 who underwent lower respiratory culture; 85 had superinfection. Receiver operating characteristic curve analysis showed that procalcitonin at the time of culture was incapable of distinguishing patients with bacterial infection (AUC, 0.52). We conclude that static measurement of procalcitonin does not aid in the diagnosis of superinfection in severe COVID-19.
Cohort profile: The Pregnancy, Arsenic, and Immune Response (PAIR) Study, a longitudinal pregnancy and birth cohort in rural northern Bangladesh
Authors: Avolio Lindsay N. , Smith Tyler J. S. , Navas-Acien Ana , Kruczynski Kate , Pisanic Nora , Randad Pranay R. , Detrick Barbara , Fry Rebecca C. , van Geen Alexander , Goessler Walter , Karron Ruth A. , Klein Sabra L. , Ogburn Elizabeth L. , Wills-Karp Marsha , Alland Kelsey , Ayesha Kaniz , Dyer Brian , Islam Md. Tanvir , Oguntade Habibat A. , Rahman Md. Hafizur , Ali Hasmot , Haque Rezwanul , Shaikh Saijuddin , Schulze Kerry J. , Muraduzzaman A. K. M. , Alamgir A. S. M. , Flora Meerjady Sabrina , West Keith P. , Labrique Alain B. , Heaney Christopher D. ,   the JiVitA Maternal and Child Health and Nutrition Research Project
Published: April 2022

ABSTRACTPurposeArsenic exposure and micronutrient deficiencies may alter immune reactivity to influenza vaccination in pregnant women, transplacental transfer of maternal antibodies to the fetus, and maternal and infant acute morbidity. The Pregnancy, Arsenic, and Immune Response (PAIR) Study is a longitudinal pregnancy and birth cohort designed to assess whether arsenic exposure and micronutrient deficiencies alter maternal or newborn immunity and acute morbidity following maternal seasonal influenza vaccination during pregnancy.ParticipantsWe enrolled 784 pregnant women in rural Gaibandha District in northern Bangladesh between October 2018 and March 2019. Women received a quadrivalent seasonal inactivated influenza vaccine at enrollment in the late first or early second trimester between 11 and 17 weeks of gestational age. Follow-up included up to 13 visits between enrollment and three months postpartum as well as weekly telephone surveillance to ascertain influenza-like illness and other acute morbidity symptoms in women and infants. Tube well drinking water and urine specimens were collected to assess arsenic exposure. Of 784 women who enrolled, 736 (93.9%) delivered live births and 551 (70.3%) completed follow-up visit to three months postpartum.Findings to DateArsenic was ≥0.02 µg/L in 97.9% of water specimens collected from participants at enrollment. The medians (interquartile ranges) of water and urinary arsenic were 5.1 (0.5-25.1) µg/L and 33.1 (19.6-56.5) µg/L, respectively. Water and urinary arsenic were strongly correlated (Spearman’s ρ=0.72) among women with water arsenic ≥ median but weakly correlated (ρ=0.18) among women with water arsenic < median.Future PlansThe PAIR Study is well positioned to examine the effects of low-moderate arsenic exposure and micronutrient deficiencies on immune outcomes in women and infants.RegistrationNCT03930017
Classification of Omicron BA.1, BA.1.1 and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data
Authors: Hirotsu Yosuke , Maejima Makoto , Shibusawa Masahiro , Natori Yume , Nagakubo Yuki , Hosaka Kazuhiro , Sueki Hitomi , Mochizuki Hitoshi , Tsutsui Toshiharu , Kakizaki Yumiko , Miyashita Yoshihiro , Omata Masao 
Published: April 2022

AbstractObjectiveRecently, the Omicron strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread and replaced the previously dominant Delta strain. Several Omicron sublineages (BA.1, BA.1.1 and BA.2) have been identified, with in vitro and preclinical reports showing that the pathogenicity and therapeutic efficacy differs between BA.1 and BA.2. We sought to develop a TaqMan assay to identify these subvariants.MethodsA TaqMan assay was constructed for rapid identification and genotyping of Omicron sublineages. We analyzed three characteristic mutations of the spike gene, Δ69–70, G339D and Q493R, by TaqMan assay. The accuracy of the TaqMan assay was examined by comparing its results with the results of whole genome sequencing (WGS) analysis.ResultsA total of 169 SARS-CoV-2 positive samples were analyzed by WGS and TaqMan assay. The 127 samples determined as BA.1/BA.1.1 by WGS were all positive for Δ69–70, G339D and Q493R by TaqMan assay. Forty-two samples determined as BA.2 by WGS were negative for Δ69–70 but positive for G339D and Q493R by TaqMan. The concordance rate between WGS and the TaqMan assay was 100% (169/169).ConclusionTaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages.
Automated Enhancement and Curation of Healthcare Data
Authors: Greer Melody , Zayas Cilia , Bhattacharyya Sudeepa 
Published: April 2022

AbstractSocial and behavioral aspects of our lives significantly impact our health, yet minimal social determinants of health (SDOH) data elements are collected in the healthcare system. In this study we developed a repeatable SDOH enrichment and integration process to incorporate dynamically evolving SDOH domain concepts from consumers into clinical data. This process included SDOH mapping, linking compiled consumer data, data quality analysis and preprocessing, storage, and visualization. Our preliminary analysis shows commercial consumer data can be a viable source of SDOH factor at an individual-level for clinical data thus providing a path for clinicians to improve patient treatment and care.
Effectiveness of a nation-wide COVID-19 vaccination program in Mexico
Authors: Bello-Chavolla Omar Yaxmehen , Antonio-Villa Neftali Eduardo , Valdés-Ferrer Sergio Iván , Fermín-Martínez Carlos A. , Fernández-Chirino Luisa , Ramírez-García Daniel , Mancilla-Galindo Javier , Kammar-García Ashuin , Ávila-Funes José Alberto , Zúñiga-Gil Clemente Humberto , García-Grimshaw Miguel , Ceballos-Liceaga Santa Elizabeth , Carbajal-Sandoval Guillermo , Montes-González José Antonio , Zaragoza-Jiménez Christian Arturo , García-Rodríguez Gabriel , Cortés-Alcalá Ricardo , Reyes-Terán Gustavo , López-Gatell Hugo , Gutiérrez-Robledo Luis Miguel 
Published: April 2022

ABSTRACTBACKGROUNDVaccination has been effective in ameliorating the impact of COVID-19. However, estimation of vaccine effectiveness (VE) is still unavailable for some widely used vaccines and underrepresented groups. Here, we report on the effectiveness of a nation-wide COVID-19 vaccination program in Mexico.METHODSWe used a test-negative design within a national COVID-19 surveillance system to assess VE of the BNT162b2, mRNA-12732, Gam-COVID-Vac, Ad5-nCoV, Ad26.COV2.S, ChAdOx1 and CoronaVac vaccines, against SARS-CoV-2 infection, COVID-19 related hospitalization and death for adults ≥18 years in Mexico. VE was estimated using Cox proportional hazard models considering time-varying vaccination status in partial and fully vaccinated individuals compared to unvaccinated adults, adjusted by age, sex, comorbidities and municipality. We also estimated VE for adults ≥60 years, for cases with diabetes and comparing periods with predominance of variants B.1.1.519 and B.1.617.2.RESULTSWe assessed 793,487 vaccinated compared to 4,792,338 unvaccinated adults between December 24th, 2020, and September 27th, 2021. VE against SARS-CoV-2 infection was highest for fully vaccinated individuals with mRNA-12732 (91.5%, 95%CI 90.3-92.4) and Ad26.COV2.S (82.2%, 95%CI 81.4-82.9), whereas for COVID-19 related hospitalization were BNT162b2 (84.3%, 95%CI 83.6-84.9) and Gam-COVID-Vac (81.4% 95%CI 79.5-83.1) and for mortality BNT162b2 (89.8%, 95%CI 89.2-90.2) and mRNA-12732 (93.5%, 95%CI 86.0-97.0). VE for all evaluated vaccines was reduced for adults ≥60 years, people with diabetes, and in periods of Delta variant predominance.CONCLUSIONSAll evaluated vaccines were effective against SARS-CoV-2 infection and COVID-19 related hospitalization and death. Mass vaccination campaigns with multiple vaccine products are feasible and effective to maximize vaccination coverage.
The network of SARS-CoV-2—cancer molecular interactions and pathways
Authors: Erola Pau , Martin Richard M. , Gaunt Tom R. 
Published: April 2022

AbstractBackgroundRelatively little is known about the long-term impacts of SARS-CoV-2 biology, including whether it increases the risk of cancer. This study aims to identify the molecular interactions between COVID-19 infections and cancer processes.Materials and MethodsWe integrated recent data on SARS-CoV-2 – host protein interactions, risk factors for critical illness, known oncogenes, tumor suppressor genes and cancer drivers in EpiGraphDB, a database of disease biology and epidemiology. We used these data to reconstruct the network of molecular links between SARS-CoV-2 infections and cancer processes in various tissues expressing the angiotensin-converting enzyme 2 (ACE2) receptor. We applied community detection algorithms and Gene Set Enrichment Analysis (GSEA) to identify cancer-relevant pathways that may be perturbed by SARS-CoV-2 infection.ResultsIn lung tissue, the results showed that 4 oncogenes are potentially targeted by SARS-CoV-2, and 92 oncogenes interact with other human genes targeted by SARS-CoV-2. We found evidence of potential SARS-CoV-2 interactions with Wnt and hippo signaling pathways, telomere maintenance, DNA replication, protein ubiquitination and mRNA splicing. Some of these pathways were potentially affected in multiple tissues.ConclusionsThe long-term implications of SARS-CoV-2 infection are still unknown, but our results point to the potential impact of infection on pathways relevant to cancer affecting cell proliferation, development and survival, favoring DNA degradation, preventing the repair of damaging events and impeding the translation of RNA into working proteins. This highlights the need for further research to investigate whether such effects are transient or longer lasting. Our results are openly available in the EpiGraphDB platform at https://epigraphdb.org/covid-cancer and the repository https://github.com/MRCIEU/covid-cancer (https://doi.org/10.5281/zenodo.6391588).
The theta paradox: 4-8 Hz EEG oscillations reflect both local sleep and cognitive control
Authors: Snipes Sophia , Krugliakova Elena , Meier Elias , Huber Reto 
Published: April 2022

ABSTRACTHuman brain activity generates electroencephalographic (EEG) oscillations that characterize specific behavioral and vigilance states. The frequency of these oscillations is typically sufficient to distinguish a given state, however theta oscillations (4-8 Hz) have instead been found in near-opposite conditions of drowsiness during sleep deprivation and alert cognitive control. While the latter has been extensively studied and is often referred to as “frontal midline theta”, the former has been investigated far less but is considered to be a marker for local sleep during wake. In this study we investigated to what extent theta oscillations differed during cognitive tasks and sleep deprivation. We measured high-density EEG in 18 young healthy adults performing 6 tasks under 3 levels of sleep deprivation. We found both cognitive load and sleep deprivation increased theta power in medial prefrontal cortical areas, however sleep deprivation caused additional increases in theta in many other, predominantly frontal, areas. The sources of sleep deprivation theta were task-dependent, with a visual-spatial task and short-term memory task showing the most widespread effects. Notably, theta was highest in supplementary motor areas during passive music listening, and highest in the inferior temporal cortex during a spatial game. This suggests that theta caused by sleep deprivation may preferentially occur in cortical areas not involved in ongoing behavior. While our results find differences in topography from frontal midline theta, they raise the possibility that a common mechanism may underly both theta oscillations during cognition and during sleep deprivation.
Low-dose IL-2 reduces IL-21+T cells and induces a long-lived anti-inflammatory gene expression signature inversely modulated in COVID-19 patients
Authors: Zhang Jia-Yuan , Hamey Fiona , Trzupek Dominik , Mickunas Marius , Lee Mercede , Godfrey Leila , Yang Jennie H.M. , Pekalski Marcin L , Kennet Jane , Waldron-Lynch Frank , Evans Mark L. , Tree Timothy I. M. , Wicker Linda S. , Todd John A. , Ferreira Ricardo C. 
Published: April 2022

AbstractDespite early clinical successes, the mechanisms of action of low-dose interleukin-2 (LD-IL-2) immunotherapy remain only partly understood. Here, we examined the effects of interval administration of low-dose recombinant IL-2 (iLD-IL-2) using high-resolution, single-cell multiomics and flow cytometry. We confirmed that iLD-IL-2 selectively expands thymic-derived FOXP3+HELIOS+Tregs and CD56brNK cells, and showed that treatment reduced the frequency of IL-21-producing CD4+T cells and of two subsets of innate-like CD8+T cells, mucosal-associated invariant T cells and Vγ9Vδ2T cells. The cellular changes induced by LD-IL-2 were associated with an anti-inflammatory gene expression signature, which remains detectable in all T and NK cell subsets analysed one month after treatment. The anti-inflammatory nature of this gene expression signature was supported by the observation that the same genes were also modulated in COVID-19 patients, but in the opposite direction. These findings warrant continued investigations of the potential clinical benefits of iLD-IL-2 in immunotherapy and further understanding of the development of long-term sequelae in convalescent COVID-19 patients.
Diabetes Management Beliefs among Adults Diagnosed with Type 2 Diabetes in Iran: A Theory Informed Approach from a Theory of Planned Behavior Framework
Authors: Ghaffari Mohammad Payam , White Katherine M. , Djafarian Kourosh , Cartledge Susie , Keshavarz Seyed Ali , Daryabeygi-Khotbehsara Reza , Shariful Islam Sheikh Mohammad 
Published: April 2022

AbstractObjectiveThe current study was informed by the belief basis of Ajzen’s (1991) Theory of Planned Behavior (TPB) to identify the important behavioral (advantages and disadvantages), normative (important referents) and control (barriers and facilitators) beliefs associated with the key recommended prevention and management behaviors for adults in Iran diagnosed with Type 2 diabetes (T2D).MethodsA cross-sectional study was conducted. A total of 115 adults diagnosed with T2D completed a questionnaire examining behavioral, normative and control beliefs and intention in relation to the three diabetes management behaviors including low fat food consumption, carbohydrate counting and physical activity. For each behavior, intention was considered as dependent variable; beliefs were independent variables. Analyses involved three multivariate one-way analysis of variance (MANOVAs).ResultsThe findings for carbohydrate counting and physical activity suggested behavioral and control beliefs as differentiating high from low intenders to perform the behavior. For carbohydrate counting, behavioral beliefs such as weight control, improving one’s health, feeling good and controlling diabetic complications differed significantly between low and high intenders. For physical activity, feeling good, controlling blood sugar and tiredness were among behavioral beliefs differentiating low and high intenders. Medical advice from professionals and greater knowledge were identified as facilitators of carbohydrate counting. High costs were identified as a key barrier preventing individuals from engaging in physical activity. Spouse was the single significant referent influencing carbohydrate counting.Conclusions & ImplicationsIdentifying the underlying beliefs of key diabetes management behaviors can assist in the design of tailored educational interventions for individuals with T2D.
Canonical Strigolactones Are Not the Tillering-Inhibitory Hormone but Rhizospheric Signals in Rice
Authors: Ito Shinsaku , Braguy Justine , Wang Jian You , Yoda Akiyoshi , Fiorilli Valentina , Takahashi Ikuo , Jamil Muhammad , Felemban Abrar , Miyazaki Sho , Mazzarella Teresa , Shinozawa Akihisa , Balakrishna Aparna , Berqdar Lamis , Rajan Chakravarty , Ali Shawkat , Haider Imran , Sasaki Yasuyuki , Yajima Shunsuke , Akiyama Kohki , Lanfranco Luisa , Zurbriggen Matias , Nomura Takahito , Asami Tadao , Al-Babili Salim 
Published: April 2022

AbstractThe plant hormones strigolactones (SLs) regulate shoot branching and mediate the communication with symbiotic mycorrhizal fungi, but also with noxious root parasitic weeds, such as Striga spp. SLs derive from carlactone (CL) and are divided structurally into canonical and non-canonical SLs. However, the questions about particular biological functions of the two groups and the identification of the SL that inhibits shoot branching are still unanswered, hampering targeted modification of SL pattern towards improving plant architecture and resistance against Striga. Here, we reported that 4-deoxyorobanchol (4DO) and orobanchol, the two canonical SLs in rice, do not have major role in determining rice shoot architecture. CRISPR/Cas9 mediated Osmax1-900 mutants, lacking these two SLs, do not show the high tillering and dwarf phenotype typical for SL-deficient plants. However, the absence of 4DO and orobanchol in root exudates significantly decreased their capability in inducing Striga seed germination, while caused only a delay in root colonization by mycorrhizal fungi. To confirm the genetic evidence, we used the SL-biosynthesis inhibitor TIS108. Our results showed that TIS108 is a MAX1-specific inhibitor that lowers 4DO and orobanchol synthesis, conferring a resistance to Striga without a severe impact on rice architecture. Hence, our work uncovers the specific function of canonical SLs as rhizospheric signals and paves the way for establishing chemical and genetic based approaches for combating the root parasitic weeds, by targeted depletion of their release.
Single-cell transcriptomics to definePlasmodium falciparumstage-transition in the mosquito midgut
Authors: Mohammed Mubasher , Dziedziech Alexis , Sekar Vaishnovi , Ernest Medard , Alves E Silva Thiago Luiz , Balan Balu , Emami S. Noushin , Biryukova Inna , Friedländer Marc R. , Jex Aaron , Lorena Marcelo Jacobs , Henriksson Johan , Rodriguez Joel Vega , Ankarklev Johan 
Published: April 2022

AbstractMalaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory vector mosquito provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzedPlasmodium falciparumdevelopment in the mosquito gut, from unfertilized female gametes through the first 20 hours post blood feeding, including the zygote and ookinete stages. This study revealed the transcriptional trajectories of the ApiAP2 family of transcription factors, and of parasite stress genes in response to the harsh environment of the mosquito midgut. Further, employing structure-based functional predictions we found several upregulated genes predicted to encode intrinsically disordered proteins (IDPs), a category of proteins known for their importance in regulation of transcription, translation and protein-protein interactions. IDPs are known for their antigenic properties and may serve as suitable targets for antibody or peptide-based transmission suppression strategies.
Direct evidence for pinning of single, ice-bound antifreeze proteins by subzero nanoscopy
Authors: Tas Roderick P. , Hendrix Marco M. R. M. , Voets Ilja K. 
Published: April 2022

AbstractIce-binding by antifreeze proteins (AFPs) reduces freezing temperatures and arrests ice-crystal ripening, making AFPs essential for survival in ice-laden environments and attractive as biocompatible antifreezes. Whilst their activity was identified over 50 years ago, the physical mechanisms are still debated because experimental insights at the molecular scale remain elusive. Here we introduce optical nanoscopy to resolve the ice/water interfacial dynamics of single AFPs. Using this method, we demonstrate pinning of individual proteins. Surprisingly, this quasi-permanent pinning is lost when freezing point depression activity is inhibited by a single mutation in the ice-binding site. These findings provide direct experimental evidence for the adsorption-inhibition paradigm, pivotal to all theoretical descriptions of activity and offer new insights in the molecular mechanisms by which these biological antifreezes function.