bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting olfactory loss in chronic rhinosinusitis using machine learning
Authors: Ramakrishnan Vijay R , Arbet Jaron , Mace Jess C , Suresh Krithika , Shintani Smith Stephanie , Soler Zachary M , Smith Timothy L 
Published: September 2021

AbstractObjectiveCompare machine learning (ML)-based predictive analytics methods to traditional logistic regression in classification of olfactory dysfunction in chronic rhinosinusitis (CRS-OD) and identify predictors within a large multi-institutional cohort of refractory CRS patients.MethodsAdult CRS patients enrolled in a prospective, multi-institutional, observational cohort study were assessed for baseline CRS-OD using a smell identification test (SIT) or brief SIT (bSIT). Four different ML methods were compared to traditional logistic regression for classification of CRS normosmics versus CRS-OD.ResultsData were collected for 611 study participants who met inclusion criteria between 2011 April and 2015 July. Thirty-four percent of enrolled patients demonstrated olfactory loss on psychophysical testing. Differences between CRS normosmics and those with smell loss included objective disease measures (CT and endoscopy scores), age, sex, prior surgeries, socioeconomic status, steroid use, polyp presence, asthma, and aspirin sensitivity. Most ML methods performed favorably in terms of predictive ability. Top predictors include factors previously reported in the literature, as well as several socioeconomic factors.ConclusionOlfactory dysfunction is a variable phenomenon in CRS patients. ML methods perform well compared to traditional logistic regression in classification of normosmia versus smell loss in CRS, and are able to include numerous risk factors into prediction models. Several actionable features were identified as risk factors for CRS-OD. These results suggest that ML methods may be useful for current understanding and future study of hyposmia secondary to sinonasal disease, the most common cause of persistent olfactory loss in the general population.
Rapid Emergence and Spread of Severe Acute Respiratory Syndrome Coronavirus 2 Gamma (P.1) Variant in Haiti
Authors: Tagliamonte Massimiliano S , Mavian Carla , Zainabadi Kayvan , Cash Melanie N , Lednicky John A , Magalis Brittany Rife , Riva Alberto , Deschamps Marie Marcelle , Liautaud Bernard , Rouzier Vanessa , Fitzgerald Daniel W , Pape Jean William , Morris J Glenn , Salemi Marco 
Published: September 2021

Abstract
After an initial wave of coronavirus disease 2019 (COVID-19) in Haiti in summer 2020 (primarily lineage B.1), seropositivity for anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G (IgG) was ~40%. Variant P.1 (gamma) was introduced in February 2021, with an initially limited introduction followed by exponential local dissemination within this unvaccinated population with prior exposure to earlier SARS-CoV-2 lineages.
Similar Antibody Responses Against Severe Acute Respiratory Syndrome Coronavirus 2 in Individuals Living Without and With Human Immunodeficiency Virus on Antiretroviral Therapy During the First South African Infection Wave
Authors: Snyman Jumari , Hwa Shi Hsia , Krause Robert , Muema Daniel , Reddy Tarylee , Ganga Yashica , Karim Farina , Leslie Alasdair , Sigal Alex , Ndung’u Thumbi ,   COVID-19 Mechanisms and Multi-omics at the Intersection of TB and HIV in KwaZulu-Natal (COMMIT-KZN Team), Archary Moherndran , Dullabh Kaylesh J , Goulder Philip , Harling Guy , Harrichandparsad Rohen , Herbst Kobus , Jeena Prakash , Khoza Thandeka , Klein Nigel , Kløverpris Henrik , Madansein Rajhmun , Marakalala Mohlopheni , Mazibuko Matilda , Moshabela Mosa , Mthabela Ntombifuthi , Naidoo Kogie , Ndhlovu Zaza , Nyamande Kennedy , Padayatchi Nesri , Patel Vinod , Smit Theresa , Steyn Adrie , Wong Emily 
Published: September 2021

Abstract

Background
There is limited understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis in African populations with a high burden of infectious disease comorbidities such as human immunodeficiency virus (HIV). The kinetics, magnitude, and duration of virus-specific antibodies and B-cell responses in people living with HIV (PLWH) in sub-Saharan Africa have not been fully characterized.

Methods
We longitudinally followed SARS-CoV-2–infected individuals in Durban, KwaZulu-Natal, South Africa, and characterized SARS-CoV-2 receptor-binding domain-specific immunoglobulin (Ig) M, IgG, and IgA weekly for 1 month and at 3 months post-diagnosis. Thirty of 72 (41.7%) were PLWH, 25/30 (83%) of whom were on antiretroviral therapy (ART) with full HIV suppression. Plasma neutralization was determined using a live virus neutralization assay, and antibody-secreting cell population frequencies were determined by flow cytometry.

Results
Similar seroconversion rates, time to peak antibody titer, peak magnitude, and durability of anti–SARS-CoV-2 IgM, IgG, and IgA were observed in people not living with HIV and PLWH with complete HIV suppression on ART. In addition, similar potency in a live virus neutralization assay was observed in both groups. Loss of IgA was significantly associated with age (P = .023) and a previous diagnosis of tuberculosis (P = .018).

Conclusions
Similar antibody responses and neutralization potency in people not living with HIV and PLWH on stable ART in an African setting suggest that coronavirus disease 2019 (COVID-19) natural infections may confer comparable antibody immunity in these groups. This provides hope that COVID-19 vaccines will be effective in PLWH on stable ART.
Evolution of Coronavirus Disease 2019 (COVID-19) Symptoms During the First 12 Months After Illness Onset
Authors: Wynberg Elke , van Willigen Hugo D G , Dijkstra Maartje , Boyd Anders , Kootstra Neeltje A , van den Aardweg Joost G , van Gils Marit J , Matser Amy , de Wit Marije R , Leenstra Tjalling , de Bree Godelieve , de Jong Menno D , Prins Maria ,   RECoVERED Study Group, Agard Ivette , Ayal Jane , Cavdar Floor , Craanen Marianne , Davidovich Udi , Deuring Annemarieke , van Dijk Annelies , Ersan Ertan , del Grande Laura , Hartman Joost , Koedoot Nelleke , Lebbink Romy , Loomans Dominique , Makowska Agata , du Maine Tom , de Man Ilja , van der Meij Lizenka , van Polanen Marleen , Oud Maria , Reid Clark , Storey Leeann , van Wijk Marc 
Published: September 2021

Abstract

Background
Few robust longitudinal data on long-term coronavirus disease 2019 (COVID-19) symptoms are available. We evaluated symptom onset, severity and recovery across the full spectrum of disease severity, up to one year after illness onset.

Methods
The RECoVERED Study is a prospective cohort study based in Amsterdam, the Netherlands. Participants aged ≥18 years were enrolled following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis via the local public health service and from hospitals. Standardized symptom questionnaires were completed at enrollment, 1 week and month later, and monthly thereafter. Clinical severity was defined according to World Health Organization (WHO) criteria. Kaplan-Meier methods were used to compare time from illness onset to symptom recovery, by clinical severity. We examined determinants of time to recovery using multivariable Cox proportional hazards models.

Results
Between 11 May 2020 and 1 May 2021, 342 COVID-19 patients (192 [56%] male) were enrolled, of whom 99/342 (29%) had mild, 145/342 (42%) moderate, 56/342 (16%) severe, and 42/342 (12%) critical disease. The proportion of participants who reported at least 1 persistent symptom at 12 weeks after illness onset was greater in those with severe/critical disease (86.7% [95% confidence interval {CI} = 76.5–92.7%]) compared to those with mild or moderate disease (30.7% [95% CI = 21.1–40.9%] and 63.8% [95% CI = 54.8–71.5%], respectively). At 12 months after illness onset, two-fifths of participants (40.7% [95% CI = 34.2–7.1]) continued to report ≥1 symptom. Recovery was slower in female compared to male participants (adjusted hazard ratio [aHR] 0.65 [95% CI = .47–.92]) and those with a body mass index [BMI]  ≥30kg/m2 compared to BMI &lt;25kg/m2 (hazard ratio [HR] 0.62 [95% CI = .39–.97]).

Conclusions
COVID-19 symptoms persisted for one year after illness onset, even in some individuals with mild disease. Female sex and obesity were the most important determinants of speed of recovery from symptoms.
Association of E484K Spike Protein Mutation With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Vaccinated Persons: Maryland, January–May 2021
Authors: Feder Kenneth A , Patel Ami , Vepachedu Venkata R , Dominguez Catherine , Keller Eric N , Klein Liore , Kim Curi , Blood Tim , Hyun Judie , Williams Thelonious W , Feldman Katherine A , Mostafa Heba H , Morris C Paul , Ravel Jacques , Duwell Monique , Blythe David , Myers Robert 
Published: September 2021

Abstract
Among 9048 people infected with SARS-CoV-2 between January and May 2021 in Maryland, in regression-adjusted analysis, SARS-CoV-2 viruses carrying the spike protein mutation E484K were disproportionately prevalent among persons infected after full vaccination against COVID-19 compared with infected persons who were not fully vaccinated (aOR, 1.96; 95% CI: 1.36–2.83).
Adalimumab and Infliximab Impair SARS-CoV-2 Antibody Responses: Results from a Therapeutic Drug Monitoring Study in 11 422 Biologic-Treated Patients
Authors: Chanchlani Neil , Lin Simeng , Chee Desmond , Hamilton Benjamin , Nice Rachel , Arkir Zehra , Bewshea Claire , Cipriano Bessie , Derikx Lauranne A A P , Dunlop Allan , Greathead Louise , Griffiths Rachel L , Ibraheim Hajir , Kelleher Peter , Kok Klaartje B , Lees Charlie W , MacDonald Jonathan , Sebastian Shaji , Smith Philip J , McDonald Timothy J , Irving Peter M , Powell Nick , Kennedy Nicholas A , Goodhand James R , Ahmad Tariq 
Published: September 2021

Abstract

Background and Aims
Infliximab attenuates serological responses to SARS-CoV-2 infection. Whether this is a class effect, or if anti-tumour necrosis factor [anti-TNF] level influences serological responses, remains unknown.

Methods
Seroprevalence and the magnitude of SARS-CoV-2 nucleocapsid antibody responses were measured in surplus serum from 11 422 (53.3% [6084] male; median age 36.8 years) patients with immune-mediated inflammatory diseases, stored at six therapeutic drug monitoring laboratories between January 29 and September 30, 2020. Data were linked to nationally held SARS-CoV-2 PCR results to July 11, 2021.

Results
Rates of PCR-confirmed SARS-CoV-2 infection were similar across treatment groups. Seroprevalence rates were lower in infliximab- and adalimumab- than vedolizumab-treated patients (infliximab: 3.0% [178/5893], adalimumab: 3.0% [152/5074], vedolizumab: 6.7% [25/375], p = 0.003). The magnitude of SARS-CoV-2 reactivity was similar in infliximab- vs adalimumab-treated patients (median 4.30 cut-off index [COI] [1.94–9.96] vs 5.02 [2.18–18.70], p = 0.164), but higher in vedolizumab-treated patients (median 21.60 COI [4.39–68.10, p &lt; 0.004). Compared to patients with detectable infliximab and adalimumab drug levels, patients with undetectable drug levels [&lt;0.8 mg/L] were more likely to be seropositive for SARS-CoV-2 antibodies. One-third of patients who had PCR testing prior to antibody testing failed to seroconvert, all were treated with anti-TNF. Subsequent positive PCR-confirmed SARS-CoV-2 was seen in 7.9% [12/152] of patients after a median time of 183.5 days [129.8–235.3], without differences between drugs.

Conclusion
Anti-TNF treatment is associated with lower SARS-CoV-2 nucleocapsid seroprevalence and antibody reactivity when compared to vedolizumab-treated patients. Higher seropositivity rates in patients with undetectable anti-TNF levels support a causal relationship, although confounding factors, such as combination therapy with a immunomodulator, may have influenced the results.
Unexpected genomic features of high current density-producing Geobacter sulfurreducens strain YM18
Authors: Fujikawa Takashi , Ogura Yoshitoshi , Ishigami Koki , Kawano Yoshihiro , Nagamine Miyuki , Hayashi Tetsuya , Inoue Kengo 
Published: September 2021

ABSTRACT
Geobacter sulfurreducens produces high current densities and it has been used as a model organism for extracellular electron transfer studies. Nine G. sulfurreducens strains were isolated from biofilms formed on an anode poised at –0.2 V (vs SHE) in a bioelectrochemical system in which river sediment was used as an inoculum. The maximum current density of an isolate, strain YM18 (9.29 A/m2), was higher than that of the strain PCA (5.72 A/m2), the type strain of G. sulfurreducens, and comparable to strain KN400 (8.38 A/m2), which is another high current-producing strain of G. sulfurreducens. Genomic comparison of strains PCA, KN400 and YM18 revealed that omcB, xapD, spc and ompJ, which are known to be important genes for iron reduction and current production in PCA, were not present in YM18. In the PCA and KN400 genomes, two and one region(s) encoding CRISPR/Cas systems were identified, respectively, but they were missing in the YM18 genome. These results indicate that there is genetic variation in the key components involved in extracellular electron transfer among G. sulfurreducens strains.
897Environmental contamination of Coxiella burnetii in and around an endemically infected goat farm
Authors:   Hasanthi Abeykoon Abeykoon Mudiyanselage, Hou Kangwei , Vincent Gemma A. , Stevenson Mark A. , Firestone Simon M. , Wiethoelter Anke 
Published: September 2021

Abstract

Background
Coxiella burnetii is the cause of Q fever, a zoonotic disease spread by aerosol transmission. This study investigated C. burnetii environmental contamination in and around an endemically infected, intensively managed dairy goat farm in Victoria, Australia.

Methods
Dust, soil and water were collected in and around kidding pens. Samplings were collected before, during and after each kidding season. Soil was sampled along a 500 m transect from the main kidding pen in the predominant wind direction to assess the risk of C. burnetii spread from the main farm shed as a point source. DNA extraction and quantitative PCRs targeting the IS1111 and com1 genes were performed. Analyses are ongoing to describe the change in the frequency of C. burnetii positive environmental samples as a function of distance from the main farm shed.

Results
Dust inside the kidding pen contained C. burnetii DNA at all time points, with higher loads during the kidding seasons. Soil samples were positive for both PCR targets and were evenly dispersed within close ranges (500 m) from the main farm shed. Only those water samples taken from close to the main farm shed were positive.

Conclusions
C. burnetii was readily found in dust and soil in and around a farm shed where coxiellosis was endemic. Further environmental sampling will allow us to estimate the distance over which C. burnetii contamination occurs around a known point source.

Key messages
Results of this study will provide information critical for estimating Q fever risk around livestock facilities.
1227Colorectal cancer risk prediction models incorporating lifestyle and biomarker data: Results from the EPIC cohort
Authors: Aleksandrova Krasimira , Reichmann Robin , Jenab Mazda , Rinaldi Sabina , Kaaks Rudolf , de-Mesquita Bas Bueno- , Riboli Elio , Gunter Marc 
Published: September 2021

Abstract

Background
Colorectal cancer represents a major public health concern and there is a worrying tendency of increasing incidence rates among younger people in the last decades. Risk stratification of high-risk individuals may aid targeted disease prevention. We therefore aimed to evaluate the predictive value of a wide range of lifestyle and biomarker variables using data within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort.

Methods
A range of lifestyle, anthropometric and dietary variables in 329,885 participants in the EPIC cohort were evaluated as potential predictors for risk of colorectal cancer over 10 years. Biomarker measurements of 41 parameters were available for 1,320 CRC cases and 1,320 controls selected using incidence density matching. Best sets of predictors were selected using elastic net regularization with bootstrapping. Random survival forest was applied as a novel technique to validate the set of selected predictors taking variable interactions into account.

Results
The results suggested a set of lifestyle factors including age, waist circumference, height, smoking, alcohol consumption, physical activity, vegetables, dairy products, processed meat, and sugar and confectionary that showed good discrimination (Harrell's C-index: 0.710) and excellent calibration. The analyses further revealed a set of biomarkers that increased the predictive performance beyond age, sex and lifestyle factors.

Conclusions
Risk prediction models based on lifestyle and biomarker data may prove useful in the identification of individuals at high risk for colorectal cancer.

Key messages
Risk prediction models incorporating lifestyle and biomarker data could contribute to developing strategies for targeted colorectal cancer prevention.
1493Trends of Rotavirus Gastroenteritis during a Conflict Time, Yemen, 2014-2019
Authors: Ghaleb Yasser , alkuhlani Sharaf , Serouri Abdul Wahed Al , Ghaleb Yasser 
Published: September 2021

Abstract

Background
The Rotavirus Gastroenteritis (RVG) is a contagious vaccine-preventable disease that contributes to the high morbidity and mortality among under 5 children. In Yemen, Rotavirus Surveillance System (RVS) was launched in 2007 as sentinel surveillance and the vaccine was introduced in 2012. However, the current protracted conflict led to a significant breakdown of health services including immunization and water, sanitation and hygiene. The aim is to describe the pattern of RVG during the conflict time: 2014-2019.

Methods
2014-2019 RVS data that covers demographic variables, clinical symptoms, vaccination status and laboratory results were analyzed using Epi.info 7.2.

Results
6,663 suspected RVG cases were reported. The most affected age group was 9-12 months and cases were higher among males (59%). RVG shows a seasonal pattern where RVG was predominantly reported in the cold season. Only 24% needed admission due to severe dehydration. Only 65% of cases were vaccinated, of them 85% received two doses. The case fatality rate was 1.1%, and was significantly higher among unvaccinated (1.8 vs. 0.6%, P &lt; 0.0001). Of the 5,875 samples collected, only one third found positive to Rotavirus where the predominant genotypes were G12 P [8] and G 2 P [4].

Conclusions
The findings highlight that RVG is still an ongoing cause of morbidity among under 5 children in Yemen that upsurges with the low Rotavirus immunization coverage. Therefore, boosting immunization coverage together with other diarrhea prevention strategies are required. Furthermore, ongoing surveillance is important to monitor the RVG epidemiology and to evaluate vaccine effectiveness against the currently circulating genotypes.

Key messages
It is First research about rota that done in Yemen during conflict so it gives opportunity for future increased scientific rigor, outcomes-focused research, and health informatics.
It provides policy makers by recommendation for improving public health and surveillance system during crisis.
750Hospital admissions for patients with rheumatoid arthritis in Western Australia hospitals have declined over time
Authors: Almutairi Khalid ,   FRACP, Rheumatology Johannes Nossent,   UWA, Public Health David Preen,   FRACP Helen Keen,   RACP, Rheumatology and Gerontology Charles Inderjeeth
Published: September 2021

Abstract

Background
Rheumatoid arthritis (RA) imposes a considerable burden on society in terms of morbidity, long-term disability, and costs. RA prevalence is poorly described in Australia, and linked health datasets can provide a more meaningful picture for RA epidemiology in the Australian population.

Methods
We extracted data on all patients identified in the WA Hospital Morbidity Data Collection between 1995 and 2014, with the International Classification of Diseases (ICD) codes for RA (ICD 10 M05.00–M06.99, and the corresponding ICD 9 codes). We estimated period prevalence rates per 1000 hospital separations and annual average percentage changes, with the total number of hospital separations each year.

Results
A total of 17,125 patients were admitted to WA hospitals with a diagnostic code for RA over the study period (1995-2014). The total number of hospital separations for RA patients was 50,353, indicating an average of three hospital separations per patient over twenty years. The RA prevalence was 3.4 per 1000 separations over the study period, with a -2.89% annual average decrease since 1995.

Conclusion
These data demonstrate that hospitalisation for RA has decreased considerably in WA over the last two decades. As this decrease roughly coincides with the introduction of biological drug treatment for RA, the reduced need for hospital admission is likely due to improvements in RA management.

Key messages
The RA prevalence was 3.4 per 1000 separations over the study period (1995-2014).
749The global prevalence of Rheumatoid Arthritis: A meta-analysis
Authors: Almutairi Khalid ,   Johannes Nossent,   David Preen,   Helen Keen,   Charles Inderjeeth
Published: September 2021

Abstract

Background
To determine the global prevalence of rheumatoid arthritis (RA) based on published studies and reveal factors which influence the RA prevalence estimates.

Methods
Four electronic databases- ProQuest Central, MEDLINE, Web of Science, and EMBASE were searched for publications from 1980 and 2019, reporting prevalence estimates of RA. A random-effect meta-analysis model was used to produce the pooled prevalence estimates. The potential sources of between-study heterogeneity were identified using sensitivity analysis, sub-group and meta-regression analyses.

Results
A total of 67 studies consisting of 212,335,171 patients were included in the meta-analysis. The global prevalence of RA was estimated 0.46% (95% CI: 0.39-0.54; I2=99.9%) with a 95% prediction interval (0.06–1.27). The point-prevalence of RA was 0.45% (95% CI: 0.38- 0.53%), while the pooled period-prevalence was 0.46% (0.36% and 0.57%). The highest RA pooled prevalence was estimated at 0.69% (95% CI: 0.47–0.95) derived from linked data sources studies. Based on subgroup analyses, the pooled prevalence of RA was influenced by geographical location, the risk bias of studies, period-prevalence method and urban population setting over the stratified periods.

Conclusion
The global prevalence of RA was 460 per 100,000 population from 1980–2018, with a 95% prediction interval (0.06– 1.27%). RA prevalence estimates were influenced by geographical location, the risk bias assessment of studies, period-prevalence method and urban population setting over time.

Key messages
The global prevalence of RA was 460 per 100,000 population from 1980–2018, with a 95% prediction interval (0.06– 1.27%).