bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study
Authors: Nduva George M , Otieno Frederick , Kimani Joshua , Wahome Elizabeth , McKinnon Lyle R , Cholette Francois , Majiwa Maxwell , Masika Moses , Mutua Gaudensia , Anzala Omu , Graham Susan M , Gelmon Larry , Price Matt A , Smith Adrian D , Bailey Robert C , Baele Guy , Lemey Philippe , Hassan Amin S , Sanders Eduard J , Esbjörnsson Joakim 
Published: March 2022

Abstract
In Kenya, HIV-1 key populations including men having sex with men (MSM), people who inject drugs (PWID) and female sex workers (FSW) are thought to significantly contribute to HIV-1 transmission in the wider, mostly heterosexual (HET) HIV-1 transmission network. However, clear data on HIV-1 transmission dynamics within and between these groups are limited. We aimed to empirically quantify rates of HIV-1 flow between key populations and the HET population, as well as between different geographic regions to determine HIV-1 ‘hotspots’ and their contribution to HIV-1 transmission in Kenya. We used maximum-likelihood phylogenetic and Bayesian inference to analyse 4058 HIV-1 pol sequences (representing 0.3 per cent of the epidemic in Kenya) sampled 1986–2019 from individuals of different risk groups and regions in Kenya. We found 89 per cent within-risk group transmission and 11 per cent mixing between risk groups, cyclic HIV-1 exchange between adjoining geographic provinces and strong evidence of HIV-1 dissemination from (i) West-to-East (i.e. higher-to-lower HIV-1 prevalence regions), and (ii) heterosexual-to-key populations. Low HIV-1 prevalence regions and key populations are sinks rather than major sources of HIV-1 transmission in Kenya. Targeting key populations in Kenya needs to occur concurrently with strengthening interventions in the general epidemic.
Iron deficiency anemia in pregnancy
Authors: Igbinosa Irogue , Berube Caroline , Lyell Deirdre J. 
Published: March 2022

Purpose of review
Anemia in pregnancy is associated with increased maternal and neonatal morbidity. There is increasing awareness amongst obstetricians about the need to screen for iron deficiency anemia (IDA), as well as growing literature on diagnosis and treatment. This review aims to summarize causes, consequences, treatment, and evaluation of IDA in pregnancy.

Recent Findings
National guidelines provide varying guidance on diagnosis and treatment of IDA in pregnancy. Serum ferritin is a helpful adjunct for the diagnosis of IDA. Oral iron remains an option for treatment; absorption is improved with every other day dosing and is effective for patients able to tolerate. Emerging studies on modern generations of intravenous (IV) iron demonstrate shorter infusion times and improved safety profiles. Notably, recent UK guidelines provide consideration for universal IV iron supplementation for treatment of anemia beyond 34 weeks of pregnancy.

Summary
Iron, in dietary, oral, and IV forms, has been found effective in resolving anemia in pregnancy. Pregnant people with IDA in the third trimester are more likely to benefit from IV iron. Future studies designed and powered to assess maternal and perinatal morbidity indicators and blood transfusion rates can strengthen recommendations.
Development and Structure of an Accurate Machine Learning Algorithm to Predict Inpatient Mortality and Hospice Outcomes in the Coronavirus Disease 2019 Era
Authors: Chi Stephen , Guo Aixia , Heard Kevin , Kim Seunghwan , Foraker Randi , White Patrick , Moore Nathan 
Published: March 2022

Background:
The coronavirus disease 2019 (COVID-19) pandemic has challenged the accuracy and racial biases present in traditional mortality scores. An accurate prognostic model that can be applied to hospitalized patients irrespective of race or COVID-19 status may benefit patient care.

Research Design:
This cohort study utilized historical and ongoing electronic health record features to develop and validate a deep-learning model applied on the second day of admission predicting a composite outcome of in-hospital mortality, discharge to hospice, or death within 30 days of admission. Model features included patient demographics, diagnoses, procedures, inpatient medications, laboratory values, vital signs, and substance use history. Conventional performance metrics were assessed, and subgroup analysis was performed based on race, COVID-19 status, and intensive care unit admission.

Subjects:
A total of 35,521 patients hospitalized between April 2020 and October 2020 at a single health care system including a tertiary academic referral center and 9 community hospitals.

Results:
Of 35,521 patients, including 9831 non-White patients and 2020 COVID-19 patients, 2838 (8.0%) met the composite outcome. Patients who experienced the composite outcome were older (73 vs. 61 y old) with similar sex and race distributions between groups. The model achieved an area under the receiver operating characteristic curve of 0.89 (95% confidence interval: 0.88, 0.91) and an average positive predictive value of 0.46 (0.40, 0.52). Model performance did not differ significantly in White (0.89) and non-White (0.90) subgroups or when grouping by COVID-19 status and intensive care unit admission.

Conclusion:
A deep-learning model using large-volume, structured electronic health record data can effectively predict short-term mortality or hospice outcomes on the second day of admission in the general inpatient population without significant racial bias.
Caregiver Burden in Caregivers of Children With Special Health Care Needs and Association With Chronic Pain
Authors: Camelo Castillo Wendy , Onasanya Oluwadamilola , dosReis Susan , Hogans Beth , Reeves Gloria 
Published: March 2022

Background/Objectives:
Chronic noncancer pain (CNCP) affects millions of individuals in the United States but evidence of its prevalence among caregivers of children with special health care needs is sparse. We sought to estimate the prevalence of CNCP and its association with caregiver burden, in a nationally representative sample.

Methods:
Retrospective cross-sectional study using pooled Medical Expenditure Panel Survey data for 2010–2015. Within interviewed households, family groups consisting of at least 1 parent and 1 child (0–17 y) were identified. CNCP was identified by one or more International Classification of Diseases, Ninth Revision (ICD-9)-CM codes utilizing previously published approaches. Level of caregiver burden was defined using a validated screener questionnaire identifying children with high burden of care (ie, special health care needs), for example, high or low burden. We estimated prevalence of CNCP as a function of caregiver burden, as well as the association of risk factors with CNCP, including parent sociodemographic features, clinical diagnoses, and family level characteristics.

Results:
We identified 46,525 caregivers of whom 3.6% reported experiencing high caregiving burden. The prevalence of CNCP was 25.5% and 14.0% among parents with high compared with low caregiving burden, respectively. Odds of CNCP were higher among parents with high compared to those with lower caregiver burden (odds ratio=1.29, 95% confidence interval=1.06–1.55). Being obese, experiencing disability, and having a mental health diagnosis were associated with higher odds of CNCP.

Conclusions:
Chronic pain is more common among caregivers with high caregiver burden. Our findings highlight the need to further explore the nature and impact of risk factors on caregiver health and disability.
Parashewanella hymeniacidonis sp. nov., isolated from marine sponge (Hymeniacidon sinapium)
Authors: Kim Soo-Bin , Park Jin-Sook 
Published: March 2022

A flagella bacterium, designated strain 202IG2-18T was isolated from a marine sponge Hymeniacidon sinapium from Ulleung-do in the Republic of Korea. Cells were Gram-stain-negative, motile, aerobic, rod-shaped and non-pigmented. The strain was able to grow at pH 5.5–9.5 (optimum, pH 7.5), in the presence of 1–5 % (w/v) NaCl (optimum, 3 %, w/v) and at 18–30 °C (optimum, 30 °C). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 202IG2-18T belonged to the family

Shewanellaceae

, and was most closely related to [

Shewanella

] irciniae NRRL B-41466T (97.9 %), followed by

Parashewanella tropica

KCCM 43304T (97.1 %),

Parashewanella curva

KCTC 62318T (96.3 %) and

Parashewanella spongiae

KCTC 22492T (96.2 %). The predominant fatty acids were iso-C15 : 0 (25.7 %), C17 : 1
ω8c (13.5 %), summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c, 12.7 %), iso-C13 : 0 (10.4 %) and C16 : 0 (9.6 %). The only detected respiratory quinone was ubiquinone Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified glycolipids, two unidentified aminophospholipids, an unidentified phospholipid and an unidentified aminolipid. The G+C content of the genomic DNA was 39.8 mol%. The average nucleotide identity values compared to all other related species was below 72.8 % and digital DNA–DNA hybridization values were 21.1–22.3 %, all below the threshold for bacterial species delineation. Phenotypic, phylogenetic, genomic and chemotaxonomic characteristics showed that strain 202IG2-18T represents a novel species of the genus

Parashewanella

, for which the name Parashewanella hymeniacidonis sp. nov. is proposed. The type strain is 202IG2-18T (=KACC 22256T=LMG 32203T).
Hymenobacter armeniacus sp. nov. and Hymenobacter montanus sp. nov., two radiation-resistant bacteria from soil
Authors: Park Yuna , Chang Yoonjee , Kim Myung Kyum 
Published: March 2022

Two bacterial strains, designated BT189T and BT664T, were isolated from soil sampled in the Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains BT189T and BT664T belonged to the genus

Hymenobacter

, family

Hymenobacteraceae

(order

Cytophagales

). The 16S rRNA genes of the two strains shared a sequence similarity of 93.7 %. The closely related species of strain BT189T were

Hymenobacter rubidus

DG7BT (97.1 % 16S rRNA similarity) and

Hymenobacter terrae

DG7AT (96.7 %). The closest related species to strain BT664T were

Hymenobacter sedentarius

DG5BT (95.3 %) and

Hymenobacter terrenus

MIMtkLc17T (95.2 %). The genome sizes of strains BT189T and BT664T were 5 285 287 and 5 475 357 bp, respectively. The genomic DNA G+C contents of strains BT189T and BT664T were 63.2 and 59.3 mol%, respectively. The main fatty acids of strain BT189T were iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1
ω6c/C16 : 1
ω7c), and those of strain BT664T were iso-C15 : 0, C16 : 1
ω5c and summed feature 3 (C16 : 1
ω6c/C16 : 1
ω7c). The main polar lipid in both strains was phosphatidylethanolamine and the predominant respiratory quinone was MK-7, supporting the affiliation of these strains with the genus

Hymenobacter

. Based on the results of biochemical, chemotaxonomic and phylogenetic analyses, two novel species, Hymenobacter armeniacus BT189T (=KCTC 72341T=NBRC 114843T) and Hymenobacter montanus BT664T (KACC 21967T=NBRC 114856T), are proposed.
Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant
Authors: Ciubotariu Ilinca I. , Dorman Jack , Perry Nicole M. , Gorenstein Lev , Kattoor Jobin J. , Fola Abebe A. , Zine Amy , Hendrix G. Kenitra , Wilkes Rebecca P. , Kitchen Andrew , Carpi Giovanna 
Published: March 2022

ABSTRACTUsing a combination of data from routine surveillance, genomic sequencing, and phylogeographic analysis we tracked the spread and introduction events of SARS-CoV-2 variants focusing on a large university community. Here, we sequenced and analyzed 677 high-quality SARS-CoV-2 genomes from positive RNA samples collected from Purdue University students, faculty, and staff who tested positive for the virus between January 2021 and May 2021, comprising an average of 32% of weekly cases across the time frame. Our analysis of circulating SARS-CoV-2 variants over time revealed periods when Variant of Concern (VOC) Alpha (B.1.1.7) and Iota (B.1.526) reached rapid dominance and documented that VOC Gamma (P.1) was increasing in frequency as campus surveillance was ending. Phylodynamic analysis of Gamma genomes from campus alongside a subsampling of >20,000 previously published P.1 genomes revealed ten independent introductions of this variant into the Purdue community, predominantly from elsewhere in the United States, with introductions from within the state of Indiana and from Illinois, and possibly Washington and New York, suggesting a degree of domestic spread. We conclude that a robust and sustained active and passive surveillance program coupled with genomic sequencing during a pandemic offers important insights into the dynamics of pathogen arrival and spread in a campus community and can help guide mitigation measures.
Statistical notes on false positive and negative error rates in the evaluation of long-term carcinogenicity bioassays
Authors: Hothorn Ludwig A. 
Published: March 2022

AbstractThe appropriate interpretation of mortality-adjusted tumor incidences in long-term carcinogenicity bioassays depends substantially on the actual false positive and false negative error rates. These depend, among other things, on the type of analysis of multiple correlated tumor sites and the mode of dose-response dependence in relation to the design. Selected quantitative results, such as shape-to-design relationship and discreteness are presented and the influence of further issues is discussed qualitatively.
DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing
Authors: Ni Peng , Zhong Zeyu , Xu Jinrui , Huang Neng , Zhang Jun , Nie Fan , Zhao Haochen , Zou You , Huang Yuanfeng , Li Jinchen , Xiao Chuan-Le , Luo Feng , Wang Jianxin 
Published: March 2022

AbstractLong single-molecular sequencing, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, is advantageous in detecting DNA 5-methylcytosine (5mC) in CpGs, especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence PCR-treated and M.SssI-treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 AUC on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5mCs using PacBio CCS.
Internationalization motives, location advantages and performance: the case of Indian firms from knowledge-intensive industries
Authors: Ahsan Faisal Mohammad , Sinha Ashutosh Kumar 
Published: March 2022

PurposeRecent empirical findings on the relationship between internationalization and firm performance (I–P) suggest a significant role of firm's context. Extending this line of argument, the authors study the effect of internationalization on firm's performance for emerging market firms from knowledge-intensive industries, taking into account the firm's motive of internationalization and host country’s location-based advantages.Design/methodology/approachThe authors link host country-specific advantages (CSAs) with firm-specific advantages (FSAs) to identify three distinct settings of internationalization for emerging economy firms – (1) asset-exploitative internationalization in developing or least developed countries, (2) asset-exploitative internationalization in developed countries and (3) strategic asset-seeking internationalization. The authors test this study’s hypotheses on a sample of 415 Indian firms from knowledge-intensive industries.FindingsThe authors find that firm's performance upon internationalization is non-linear in each of the three different settings. The nature of the non-linear relationship depends upon location-based advantages of the host country and the motive of internationalization.Originality/valueThe motive of internationalization and the location-based advantages sought during internationalization are unique for emerging economy firms. Hence, the study extends understanding of the I–P linkage in an emerging economy context.
Scale development for analyzing the fit of real and virtual world integration: an example of Pokémon Go
Authors: Shiau Wen-Lung , Huang Li-Chun 
Published: March 2022

PurposeAugmented reality (AR) has become a trend, and the effects of Pokémon Go, the most popular online and mobile game, have been explored in many studies. However, few studies have developed questionnaires of fit to investigate the relationship between the fit and the integration of the game's virtual world and reality. The paper intends to integrate the models of stimulus-organism-response (S-O-R) and information systems success with cognitive fit theory to explore the fit and reactions of users in the integration of real and virtual worlds.Design/methodology/approachFollowing MacKenzie's scale development, two surveys were conducted. The first survey was conducted to perform a scale development of fit. The second survey was collected from 315 Pokémon Go players to validate the fit scale and it was analyzed via structural equation modeling.FindingsThe results show that scale development of fit has good reliability and validity. Furthermore, game information quality, game system quality and virtual (Pokémon) characteristics have significantly positive effects on cognitive and emotional fit. Cognitive and emotional fit have significant positive effects on user satisfaction, and user satisfaction has significant positive effects on continued intention to play. The results suggest that maintaining the quality of the game and improving the virtual interface will provide a better fit between the real and virtual worlds, enhancing user satisfaction with the fit as well as their intention for continued use.Originality/valueAlthough fit has been widely studied in various contexts, the application of AR has been rarely discussed. This study develops a scale of fit and takes Pokémon Go as the subject to validate the fit measurement and discuss players' cognition and feelings regarding the game. The authors measure user reactions to different stimuli and explore cognitive and emotional fit as well as the integration of virtual worlds and reality. In sum, to the best of the authors’ knowledge, this is one of the earliest studies to explore and develop a cognitive and emotional fit scale for future researchers and practitioners.
Unlocking value with a crowdsourcing configuration of smart city: a system dynamic simulation
Authors: Caporuscio Andrea , Pietronudo Maria Cristina , Schiavone Francesco , Leone Daniele 
Published: March 2022

PurposeThe paper aims to explore the value generated by a specific configuration of a smart city's infrastructure by proposing a comparison between a silos configuration versus a crowd configuration at the data storage and processing level.Design/methodology/approachA system dynamics simulation is adopted to determine and compare the value created by the two configurations of smart city's infrastructure. The simulation outlines the flow of data and their positive and negative feedback that reinforce and hinder the smart city value generation.FindingsThe results demonstrate the huge impact of the availability of data for App developers when crowdsourcing configuration is adopted. Furthermore, results unveil the potential in value generation of a crowdsourcing smart city platform configuration compared to a silos architecture.Originality/valueThe authors have proposed a comparison between two alternative smart city digital platform configurations. The paper seeks to test the magnitude of the pros and cons of a crowdsourcing approach in setting up a smart city digital platform. The paper provides new guidelines for improving the data management of smart cities.
Comparative microbiome analysis of Diaphorina citri and its associated parasitoids Tamarixia radiata and Diaphorencyrtus aligarhensis reveals Wolbachia as a dominant endosymbiont
Authors: Ashraf Hafiza Javaria , Ramos Aguila Luis Carlos , Akutse Komivi Senyo , Ilyas Muhammad , Abbasi Asim , Li Xiaofang , Wang Liande 
Published: March 2022

SummaryMicrobiome analysis in a host–parasitoid interaction network was conducted to compare the taxonomic composition of bacterial communities of Diaphornia citri, Tamarixia radiata, and Diaphorencyrtus aligarhensis. The comparative analysis revealed differences in the composition and diversity of the symbiont populations across the host and its associated parasitoids. Proteobacteria was the most dominant phylum, representing 67.80% of the total bacterial community, while Candidatus Profftella armature and Wolbachia were the dominant genera across the host and parasitoids. There were clear differences observed in alpha and beta diversity of microbiota through the host and its associated parasitoids. The function prediction of bacterial communities and Pearson correlation analysis showed that specific bacterial communities displayed positive correlations with the carbohydrate metabolism pathway. Furthermore, when symbiotic bacteria were eliminated using a broad‐spectrum antibiotic, tetracycline hydrochloride, the parasitoids' median survival time and longevity were significantly reduced. We confirmed the physiological effects of symbiotic bacteria on the fitness of parasitoids and demonstrated the effect of antibiotics in decreasing the food intake and measurement of amino acids in the hemolymph. This study sheds light on basic information about the mutualism between parasitoids and bacteria, which may be a potential source for biocontrol strategies for citrus psyllid, especially D. citri.
Finding Place in the Archive: A Case Study of St. John [Colored] Missionary Baptist Church, 1866–1900
Authors: Hopkins Portia D. 
Published: March 2022

AbstractThis article explores the ongoing preservation efforts of The St. John Fundraising and Preservation Committee at St. John Missionary Baptist Church (SJMBC). The church, founded in 1869 by former slaves, is located in Fort Bend County, Texas, a county which held the second‐largest slave population in the state in 1860. SJMBC sought to develop an archive of historical records to narrate St. John's early history, particularly at sites it intersected with the history of Fort Bend County, Missouri City, and the Dew Brothers plantation during the nineteenth and early twentieth centuries. Because the majority of the church records were lost in a fire in 2006, Friends of St. John needed to locate other sites in the archive where the church's presence and significance were recorded. They recruited researchers, public scholars and architects and developed relationships with nearby universities and churches to aid in their mission. Highlighting several types of source materials such as a slaver's account book, maps, census, deed, and school records and tax assessments held by the county, SJMBC established a historical narrative of the church through a calculated juxtaposition to well‐established historical narratives of significant white people and events in the county.