bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pertussis (Whooping Cough)
Authors: Decker Michael D , Edwards Kathryn M 
Published: August 2020

AbstractPertussis (whooping cough) is a respiratory infection caused by Bordetella pertussis. All ages are susceptible. In the prevaccine era, almost all children became infected. Pertussis is particularly dangerous in young infants, who account for practically all hospitalizations and deaths, but clinical disease is burdensome at any age. Widespread use of pertussis vaccines dramatically reduced cases, but concern over adverse reactions led to the replacement of standard whole-cell by acellular pertussis vaccines that contain only a few selected pertussis antigens and are far less reactogenic. Routine administration of acellular pertussis vaccines combined with diphtheria and tetanus toxoids is recommended in infancy with toddler and preschool boosters, at age 11, and during pregnancy. Boosting in the second half of every pregancy is critical to protection of the newborn. Waning of vaccine immunity over time has become an increasing concern, and several new pertussis vaccines are being evaluated to address this problem.
Clinical and Epidemiological Features of 46 Children &lt;1 Year Old With Coronavirus Disease 2019 in Wuhan, China: A Descriptive Study
Authors: Liu Xinghua , Tang Jianqiao , Xie Rong , Li Wei , Chen Jianying , Guo Yan , Zhang Bo , Zhang Yue , Wang Juanjuan , Peng Cao , Lei Xiao , Luo Qunying , Zhang Qiong , Li Yunqiao 
Published: August 2020

AbstractThe number of coronavirus disease 2019 (COVID-19) cases has exceeded 10 million. However, little is known about the epidemiology and clinical characteristics of COVID-19 infants. We collected medical information of 46 confirmed patients (&lt;1 year old) and retrospectively analyzed epidemiological history, clinical symptoms, and laboratory test results. The median age was 5 (interquartile range, 2–7) months. Sixteen cases had fever and 27 cases had cough. Moderate disease was present in 40 cases and cardiac injury occurred in 38 cases, following by liver dysfunction in 20 cases and lymphopenia in no cases. Of all infant patients, 2 received invasive mechanical ventilation and 1 died with multiple organ dysfunction syndrome.
Relative Severity of Common Human Coronaviruses and Influenza in Patients Hospitalized With Acute Respiratory Infection: Results From 8-Year Hospital-Based Surveillance in Quebec, Canada
Authors: Gilca Rodica , Carazo Sara , Amini Rachid , Charest Hugues , De Serres Gaston 
Published: August 2020

Abstract

Background
Few data exist concerning the role of common human coronaviruses (HCoVs) in patients hospitalized for acute respiratory infection (ARI) and the severity of these infections compared with influenza.

Methods
Prospective data on the viral etiology of ARI hospitalizations during the peaks of 8 influenza seasons (from 2011–2012 to 2018–2019) in Quebec, Canada, were used to compare patients with HCoV and those with influenza infections; generalized estimation equations models were used for multivariate analyses.

Results
We identified 340 HCoV infections, which affected 11.6% of children (n = 136) and 5.2% of adults (n = 204) hospitalized with ARI. The majority of children (75%) with HCoV infections were also coinfected with other respiratory viruses, compared with 24% of the adults (P &lt; .001). No deaths were recorded in children; 5.8% of adults with HCoV monoinfection died, compared with 4.2% of those with influenza monoinfection (P = .23). The risk of pneumonia was nonsignificantly lower in children with HCoV than in those with influenza, but these risks were similarly high in adults. Markers of severity (length of stay, intensive care unit admissions, and case-fatality ratio) were comparable between these infections in multivariate analyses, in both children and adults.

Conclusions
In children and adults hospitalized with ARI, HCoV infections were less frequent than influenza infections, but were as severe as influenza monoinfections.
Under the Radar: Epidemiology of Plasmodium ovale in the Democratic Republic of the Congo
Authors: Mitchell Cedar L , Brazeau Nicholas F , Keeler Corinna , Mwandagalirwa Melchior Kashamuka , Tshefu Antoinette K , Juliano Jonathan J , Meshnick Steven R 
Published: August 2020

Abstract

Background
Plasmodium ovale is an understudied malaria species prevalent throughout much of sub-Saharan Africa. Little is known about the distribution of ovale malaria and risk factors for infection in areas of high malaria endemicity.

Methods
Using the 2013 Democratic Republic of the Congo (DRC) Demographic and Health Survey, we conducted a risk factor analysis for P. ovale infections. We evaluated geographic clustering of infections and speciated to P. ovale curtisi and P. ovale wallikeri through deep sequencing.

Results
Of 18 149 adults tested, we detected 143 prevalent P. ovale infections (prevalence estimate 0.8%; 95% confidence interval [CI], .59%–.98%). Prevalence ratios (PR) for significant risk factors were: male sex PR = 2.12 (95% CI, 1.38–3.26), coprevalent P. falciparum PR = 3.52 (95% CI, 2.06–5.99), and rural residence PR = 2.19 (95% CI, 1.31–3.66). P. ovale was broadly distributed throughout the DRC; an elevated cluster of infections was detected in the south-central region. Speciation revealed P. ovale curtisi and P. ovale wallikeri circulating throughout the country.

Conclusions
P. ovale persists broadly in the DRC, a high malaria burden country. For successful elimination of all malaria species, P. ovale needs to be on the radar of malaria control programs.
Upsurge of Conjugate Vaccine Serotype 4 Invasive Pneumococcal Disease Clusters Among Adults Experiencing Homelessness in California, Colorado, and New Mexico
Authors: Beall Bernard , Walker Hollis , Tran Theresa , Li Zhongya , Varghese Jasmine , McGee Lesley , Li Yuan , Metcalf Benjamin J , Gierke Ryan , Mosites Emily , Chochua Sopio , Pilishvili Tamara 
Published: August 2020

Abstract
After 7-valent pneumococcal conjugate vaccine introduction in the United States in 2000, invasive pneumococcal disease (IPD) due to serotype 4 greatly decreased in children and adults. Starting in 2013, serotype 4 IPD incidence increased among adults within 3 of 10 Active Bacterial Core surveillance sites. Of 325 serotype 4 cases among adults in 2010–2018, 36% were persons experiencing homelessness (PEH); incidence of serotype 4 IPD among PEH was 100–300 times higher than in the general population within these 3 areas. Genome sequencing for isolates recovered 2015–2018 (n = 246), revealed that increases in serotype 4 IPD were driven by lineages ST10172, ST244, and ST695. Within each lineage, clusters of near-identical isolates indicated close temporal relatedness. Increases in serotype 4 IPD were limited to Colorado, California, and New Mexico, with highest increases among PEH, who were at increased risk for exposure to and infections caused by these strains.
Pretransplant CMV-Specific T-Cell Immunity But Not Dose of Antithymocyte Globulin Is Associated With Recovery of Specific Immunity After Kidney Transplantation
Authors: Páez-Vega Aurora , Cantisán Sara , Agüera Maria L , Suñer Marta , Facundo Carmen , Yuste Jose R , Fernández-Ruiz Mario , Montejo Miguel , Redondo-Pachón Dolores , López-Oliva Maria O , Fernández-Rodríguez Ana , Fariñas Maria C , Hernández Domingo , Len Oscar , Muñoz Patricia , Valle-Arroyo Jorge , Rodelo-Haad Cristian , Cordero Elisa , Torre-Cisneros Julián 
Published: August 2020

Abstract

Background
This is a prospective, multicenter, observational study in cytomegalovirus (CMV)-seropositive kidney transplant recipients with pretransplant CMV-specific cell-mediated immunity (CMV-CMI) receiving antithymocyte globulin (ATG). We aimed to investigate posttransplant CMV-CMI over time and the impact of the dose-dependent ATG.

Methods
CMV-CMI was assessed at days +30, +45, +60, and +90 after transplantation with the QuantiFERON-CMV assay. A reactive result (interferon-γ [IFN-γ] ≥ 0.2 IU/mL) indicated a positive CMV-CMI.

Results
A total of 78 positive CMV-CMI patients were enrolled in the study, of which 59.5% had a positive CMV-CMI at day +30 and 82.7% at day +90. Multivariate logistic regression analysis showed that ATG dose was not associated with positive CMV-CMI at any point. However, pretransplant IFN-γ level (&gt;12 IU/mL vs ≤12 IU/mL) was associated with positive CMV-CMI at day +30 (odds ratio, 12.9; 95% confidence interval, 3.1–53.3; P &lt; .001). In addition, all the patients who did not recover CMV-CMI at day +90 had a pretransplant IFN-γ level ≤12 IU/mL.

Conclusions
More than half of CMV-seropositive kidney transplant recipients receiving ATG recover (or maintain) CMV-CMI by the first month after transplantation. The pretransplant IFN-γ level, but not the ATG dose, shows a strong association with the kinetics of this recovery.
The role of non-governmental development organizations in the implementation of lymphatic filariasis programmes
Authors: Bush Simon , Richards Frank O , Zhang Yaobi 
Published: August 2020

Abstract
The Lymphatic Filariasis (LF) Non-governmental Development Organization (NGDO) Network was established to engage in supporting both international and national LF elimination agendas covering areas such as assisting ministries of health as an on-the-ground link between communities and programmes, which additionally gives the Network members an important voice from the field at international meetings; playing key roles in programme evolution (especially helping to both scale up and scale down mass drug administration [MDA] as elimination thresholds are met); having a role in operational research and developing new programme delivery models that can be taken to scale (such as linkages with other disease programmes and approaches to morbidity management and disability prevention); developing advocacy and policy approaches with other partners; convening other important stakeholders (academic, technical, programmatic and funding); mobilizing financial and technical resources to support programmes; supporting national human resource capacity building to catalyse national ownership of LF programmes; providing leadership in LF governance structures and working in areas of conflict to ensure that everybody in LF-endemic areas enjoys treatment services. Three case studies will illustrate the roles identified for NGDOs in LF programmes covering development of operational research, policy and advocacy linkage between LF and malaria programmes; launching LF morbidity management projects and NGDO's ability to work and deliver LF services in areas of conflict. In addition, the case studies will show the role of NGDOs in mobilising financial and technical resources that support national human resources, leading to national ownership of programmes. Conclusions will be drawn on the role of NGDOs in the Global Alliance for LF elimination and the need for continued partnerships to reach programme goals.
Multiple developmental pathways lead to the generation of CD4 T-cell memory
Authors: Hojyo Shintaro , Tumes Damon , Murata Akihiko , Tokoyoda Koji 
Published: August 2020

Abstract
Long-term immunological memory mediated by CD4 T cells provides a rapid protection against previously encountered pathogens or antigens. However, it is still controversial how memory CD4 T cells are generated and maintained. Unclear definitions of T-cell memory may be partially responsible for this controversy. It is becoming clear that diverse pathways are responsible for the differentiation and long-term persistence of memory T cells. We herein discuss the diversity of memory cell generation, describing a novel population of resting memory CD4 T cells and their precursors.
Multiplex real-time PCR assays for the prediction of cephalosporin, ciprofloxacin and azithromycin antimicrobial susceptibility of positive Neisseria gonorrhoeae nucleic acid amplification test samples
Authors: Peterson S W , Martin I , Demczuk W , Barairo N , Naidu P , Lefebvre B , Allen V , Hoang L , Hatchette T F , Alexander D , Tomas K , Trubnikov M , Wong T , Mulvey M R 
Published: August 2020

Abstract

Background
The incidence of antimicrobial-resistant Neisseria gonorrhoeae (GC) is rising in Canada; however, antimicrobial resistance (AMR) surveillance data are unavailable for infections diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs), representing over 80% of diagnoses. We developed a set of 10 improved molecular assays for surveillance of GC-AMR and prediction of susceptibilities in NAAT specimens.

Methods
Multiplex real-time PCR (RT–PCR) assays were developed to detect SNPs associated with cephalosporin (ponA, porB, mtrR −35delA, penA A311V, penA A501, N513Y, G545S), ciprofloxacin (gyrA S91, parC D86/S87/S88) and azithromycin [23S (A2059G, C2611T), mtrR meningitidis-like promoter] resistance. The assays were validated on 127 gonococcal isolates, 51 non-gonococcal isolates and 50 NAATs with matched culture isolates. SNPs determined from the assay were compared with SNPs determined from in silico analysis of WGS data. MICs were determined for culture isolates using the agar dilution method.

Results
SNP analysis of the 50 NAAT specimens had 96% agreement with the matched culture RT–PCR analysis. When compared with MICs, presence of penA A311V or penA A501 and two or more other SNPs correlated with decreased susceptibility and presence of three or more other SNPs correlated with intermediate susceptibility to cephalosporins; presence of any associated SNP correlated with ciprofloxacin or azithromycin resistance. NAAT-AMR predictions correlated with matched-culture cephalosporin, ciprofloxacin and azithromycin MICs at 94%, 100% and 98%, respectively.

Conclusions
We expanded molecular tests for N. gonorrhoeae AMR prediction by adding new loci and multiplexing reactions to improve surveillance where culture isolates are unavailable.
A randomized, double-blind, placebo-controlled, single and multiple ascending dose Phase 1 study to determine the safety, pharmacokinetics and food and faecal microbiome effects of ibezapolstat administered orally to healthy subjects
Authors: Garey Kevin W , Begum Khurshida , Lancaster Chris , Gonzales-Luna Anne , Bui Dinh , Mercier Julie , Seng Yue Corinne , Ducharme Murray P , Hu Ming , Vince Bradley , Silverman Michael H , Alam M Jahangir , Kankam Martin 
Published: August 2020

AbstractBackgroundClostridioides difficile infection is the most common cause of healthcare-associated infections in the USA, with limited treatment options. Ibezapolstat is a novel DNA polymerase IIIC inhibitor with in vitro activity against C. difficile.Objectives and methodsRandomized, double-blind, placebo-controlled study to assess the safety, tolerability and pharmacokinetics of ibezapolstat in healthy volunteers. Microbiome changes associated with ibezapolstat were compared with vancomycin over a 10 day course using shotgun metagenomics.ResultsA total of 62 subjects aged 31 ± 7 years (45% female; average BMI: 25 ± 3 kg/m2) were randomized. Ibezapolstat was well tolerated with a safety signal similar to placebo. Ibezapolstat had minimal systemic absorption with the majority of plasma concentrations less than 1 µg/mL. In the multiday, ascending dose study, ibezapolstat concentrations of 2000 µg/g of stool were observed by Day 2 and for the remainder of the dosing time period. In the multiday, multiple-dose arm, baseline microbiota was comparable between subjects that received ibezapolstat compared with vancomycin. At Day 10 of dosing, differential abundance analysis and β-diversity demonstrated a distinct difference between the microbiome in subjects given vancomycin compared with either dose of ibezapolstat (P = 0.006). α-Diversity changes were characterized as an increase in the Actinobacteria phylum in subjects that received ibezapolstat and an increase in Proteobacteria in subjects given vancomycin.ConclusionsIbezapolstat was shown to be safe and well tolerated, with minimal systemic exposure, high stool concentrations and a distinct microbiome profile compared with oral vancomycin. These results support further clinical development of ibezapolstat for patients with C. difficile infection.
Comparison of a Point-of-Care Assay and a High-Complexity Assay for Detection of SARS-CoV-2 RNA
Authors: Stevens Bryan , Hogan Catherine A , Sahoo Malaya K , Huang ChunHong , Garamani Natasha , Zehnder James , Kurzer Jason , Pinsky Benjamin A 
Published: August 2020

Abstract

Background
Numerous nucleic acid amplification assays utilizing different target genes of the SARS-CoV-2 genome have received emergency use authorization (EUA) by the United States Food and Drug Administration (FDA). Limited data are available comparing the test performance characteristics of these assays.

Methods
A diagnostic comparison study was performed to evaluate the performance of the Cepheid Xpert Xpress SARS-CoV-2 assay compared to the Hologic Panther Fusion SARS-CoV-2 assay using clinical nasopharyngeal specimens. Agreement between the two assays was assessed by overall, positive, and negative percent agreement and Cohen’s kappa coefficient.

Results
A total of 104 (54 positive and 50 negative) clinical nasopharyngeal samples were tested by both assays. Using the Panther Fusion as a reference standard, the Xpert demonstrated an overall agreement of 99.0% [95% confidence interval (CI): 94.8–100], positive percent agreement of 98.1% (95% CI: 90.1–100), and a negative percent agreement of 100% (95% CI: 94.2–100). The kappa coefficient was 0.98 (95% CI: 0.94–1.0). One sample positive by the Panther Fusion with a cycle threshold (Ct) of 38.6 was found to be reproducibly negative by the Xpert assay.

Conclusions
The Cepheid Xpert Xpress SARS-CoV-2 assay provides test performance comparable to the Hologic Panther Fusion SARS-CoV-2 assay while offering laboratories rapid, on-demand testing capacity.
An approach to predicting patient experience through machine learning and social network analysis
Authors: Bari Vitej , Hirsch Jamie S , Narvaez Joseph , Sardinia Robert , Bock Kevin R , Oppenheim Michael I , Meytlis Marsha 
Published: August 2020

Abstract

Objective
Improving the patient experience has become an essential component of any healthcare system’s performance metrics portfolio. In this study, we developed a machine learning model to predict a patient’s response to the Hospital Consumer Assessment of Healthcare Providers and Systems survey’s “Doctor Communications” domain questions while simultaneously identifying most impactful providers in a network.

Materials and Methods
This is an observational study of patients admitted to a single tertiary care hospital between 2016 and 2020. Using machine learning algorithms, electronic health record data were used to predict patient responses to Hospital Consumer Assessment of Healthcare Providers and Systems survey questions in the doctor domain, and patients who are at risk for responding negatively were identified. Model performance was assessed by area under receiver-operating characteristic curve. Social network analysis metrics were also used to identify providers most impactful to patient experience.

Results
Using a random forest algorithm, patients’ responses to the following 3 questions were predicted: “During this hospital stay how often did doctors. 1) treat you with courtesy and respect? 2) explain things in a way that you could understand? 3) listen carefully to you?” with areas under the receiver-operating characteristic curve of 0.876, 0.819, and 0.819, respectively. Social network analysis found that doctors with higher centrality appear to have an outsized influence on patient experience, as measured by rank in the random forest model in the doctor domain.

Conclusions
A machine learning algorithm identified patients at risk of a negative experience. Furthermore, a doctor social network framework provides metrics for identifying those providers that are most influential on the patient experience.
Free Radical Scavenging Activity of Some Legumes Hulls Extract and Its Efficacy on Oil Oxidative Stability
Authors: El-Beltagy Alaa ElDein , Alharthi Salman 
Published: August 2020

Abstract

Background
Synthetic antioxidants have toxigenic effects, there is therefore growing interest in substituting them with natural antioxidants. Attention is being focused on extracting them from agricultural industry residuals to minimize costs. Legume seed hulls could be cheap sources of such natural antioxidants.

Objective
This study aims to unravel potential free radical scavenging activity, antioxidant activity, and total phenolic and flavonoid contents of some legumes’ hulls extracted by different solvents and evaluate their efficacy to enhance sunflower oil stability.

Method
Legume hulls extracted by different solvents were evaluated for their antioxidant activity coefficient (AAC), free radical scavenging activity [by 2,2-diphenyl-1- picrylhydrazyl (DPPH)], and phenolic and flavonoids contents. The protection factor and induction periods (rancimat test) of the highest activity extracts were evaluated.

Results
Sunflower seed hull ethyl acetate extract, lupine seed hull ethanol extract, and mung bean hull petroleum ether extract exhibited stronger DPPH scavenging activity, AAC, and protection factor values than other solvents. Ethyl acetate extracts of sunflower seed hulls showed an antioxidant and scavenging activity close (P&gt;0.05) to that detected for α-tocopherol.

Conclusions
Legume hulls may possess strong free radical scavenging and antioxidant activity. The analogous effect between sunflower hull extract and α-tocopherol make it a potential, cheaper substitute of α-tocopherol in food systems.

Highlights
The analogous effect between sunflower hull extract and α-tocopherol give it the potency to allow substitution at a concentration of 0.5% of sunflower hull ethyl acetate or 1% of lupine hull ethanol extract instead of 0.5% α-tocopherol to enhance induction periods and protection factors of sunflower oil.
LC–MS-MS Determination of 25 Antipsychotic Drugs and Metabolites in Urine for Medication Compliance Monitoring
Authors: Kim Seon Yeong , Kim Hee Seung , Cheong Jae Chul , Kim Jin Young 
Published: August 2020

Abstract
A liquid chromatography–tandem mass spectrometry (LC–MS-MS) method was developed for 25 antipsychotic drugs and their metabolite in urine for monitoring medication compliance of mentally disordered criminals on probation. Target compounds were extracted with a solid-phase extraction technique using a newly developed hydrophilic-lipophilic balanced sorbent to remove interferences and minimize the matrix effect (ME). Extracted sample was injected into the LC–MS-MS with an electrospray ionization source in positive mode and multiple-reaction monitoring mode. The analytes were separated and detected within 10 minutes using a reversed-phase column with a gradient elution method using 0.1% formic acid in water and 0.1% formic acid in methanol as mobile phase. The validation parameters were evaluated as follows: selectivity, limit of detection, lower limit of quantification (LLOQ), linearity, accuracy and precision, stability, dilution integrity, recovery (RE), ME and process efficiency (PE). The LLOQs were 0.1 to 2.0 ng/mL, and determination coefficients of the calibration curve were above 0.9943 over the concentration ranges. The intra-and inter-day accuracy ranged from −10.4% to 9.9% and from −9.6% to 9.4%, while the intra-and inter-day precision were within 10.7% and 9.9%. The bench-top and long-term stability ranged from 92.1% to 109.5% and 88.7% to 111.6%, respectively. The reproducibility of auto-sampler stability was &lt;10% for all analytes. The accuracy and precision of dilution integrity ranged from −11.7% to 10.5% and 0.4% to 9.9%, respectively. The relative standard deviation of RE and ME was from 0.6% to 6.6% and 0.5% to 3.9%, respectively, while that of PE was 1.3% to 4.5%. The developed LC–MS-MS method for medication compliance monitoring was successfully applied to urine samples from mentally disordered probationers and determined to be one of effective ways for preventing the recurrence of mentally disordered crimes.