bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Task-Specific Algorithm to Estimate Occupational (1→3)-β-D-glucan Exposure for Farmers in the Biomarkers of Exposure and Effect in Agriculture Study
Authors: Friesen Melissa C , Hung Felicia , Xie Shuai , Viet Susan M , Deziel Nicole C , Locke Sarah J , Josse Pabitra R , Sauvé Jean-François , Andreotti Gabriella , Thorne Peter S , Beane-Freeman Laura E , Hofmann Jonathan N 
Published: June 2022

Abstract

Objectives
Farmers may be exposed to glucans (a cell component of molds) through a variety of tasks. The magnitude of exposure depends on each farmer’s activities and their duration. We developed a task-specific algorithm to estimate glucan exposure that combines measurements of (1→3)-β-D-glucan with questionnaire responses from farmers in the Biomarkers of Exposure and Effect in Agriculture (BEEA) study.

Methods
To develop the algorithm, we first derived task-based geometric means (GMs) of glucan exposure for farming tasks using inhalable personal air sampling data from a prior air monitoring study in a subset of 32 BEEA farmers. Next, these task-specific GMs were multiplied by subject-reported activity frequencies for three time windows (the past 30 days, past 7 days, and past 1 day) to obtain subject-, task-, and time window-specific glucan scores. These were summed together to obtain a total glucan score for each subject and time window. We examined the within- and between-task correlation in glucan scores for different time frames. Additionally, we assessed the algorithm for the ‘past 1 day’ time window using full-shift concentrations from the 32 farmers who participated in air monitoring the day prior to an interview using multilevel statistical models to compare the measured glucan concentration with algorithm glucan scores.

Results
We focused on the five highest exposed tasks: poultry confinement (300 ng/m3), swine confinement (300 ng/m3), clean grain bins (200 ng/m3), grind feed (100 ng/m3), and stored seed or grain (50 ng/m3); the remaining tasks were &lt;50 ng/m3 and had similar concentrations to each other. Overall, 67% of the participants reported at least one of these tasks. The most prevalent task was stored seed or grain (64%). The highest median glucan scores were observed for poultry confinement and swine confinement; these tasks were reported by 2% and 8% of the participants, respectively. The correlation between scores for the same task but different time windows was high for swine confinement and poultry confinement, but low for clean grain bins. Task-specific scores had low correlation with other tasks. Prior day glucan concentration was associated with the total glucan ‘past 1 day’ score and with swine confinement and clean grain bin task scores.

Conclusions
This study provides insight into the variability and key sources of glucan exposure in a US farming population. It also provides a framework for better glucan exposure assessment in epidemiologic studies and is a crucial starting point for evaluating health risks associated with glucans in future epidemiologic evaluations of this population.
Characterization of carbohydrate metabolism in in vivo- and in vitro-grown and matured mouse antral follicles
Authors: Herta Anamaria-Cristina , von Mengden Lucia , Akin Nazli , Billooye Katy , Coucke Wim , van Leersum Julia , Cava-Cami Berta , Saucedo-Cuevas Laura , Klamt Fábio , Smitz Johan , Anckaert Ellen 
Published: June 2022

AbstractEstablishing an ideal human follicle culture system for oncofertility patients relies mainly on animal models since donor tissue is scarce and often of suboptimal quality. The in vitro system developed in our laboratory supports the growth of prepubertal mouse secondary follicles up to mature oocytes. Given the importance of glucose in preparing the oocyte for proper maturation, a baseline characterization of follicle metabolism both in the culture system and in vivo was carried out. Markers of glucose-related pathways (glycolysis, tricarboxylic acid [TCA] cycle, pentose phosphate pathway [PPP], polyol pathway, and hexosamine biosynthetic pathway), as well as the antioxidant capacity, were measured in the different follicle cell types by both enzymatic activities (spectrophotometric detection) and gene expression (qPCR). This study confirmed that in vivo the somatic cells, mainly granulosa, exhibit intense glycolytic activity, while oocytes perform PPP. Throughout the final maturation step, oocytes in vivo and in vitro showed steady levels for all the key enzymes and metabolites. On the other hand, ovulation triggers a boost of pyruvate and lactate uptake in cumulus cells in vivo, consumes reduced nicotinamide adenine dinucleotide phosphate, and increases TCA cycle and small molecules antioxidant capacity activities, while in vitro, the metabolic upregulation in all the studied pathways is limited. This altered metabolic pattern might be a consequence of cell exhaustion because of culture conditions, impeding cumulus cells to fulfill their role in providing proper support for acquiring oocyte competence.
From self-help to self-advocacy for people with disadvantages: narrating problems through Japanese community radio
Authors: Ogawa Akiko 
Published: June 2022

Abstract
This study explores an alternative way for tojisha—a Japanese term that usually translates to ‘the parties concerned’ and ‘who face challenges’—to represent themselves. Specifically, it investigates how tojisha can develop self-advocacy skills using the narrative method that facilitates storytelling and community broadcasting. To this end, we scheduled community radio programmes with the aid of a local social worker, five individuals involved in self-help activities, and their supporters. The structured format of the broadcast enabled the tojisha to talk about their difficulties, desires, and ambitions. Data acquired through pre- and post-activity interviews were analysed to understand how storytelling and community radio help tojisha acquire self-advocacy skills. First, we found that the narrative method enabled the participants to bridge their past and future and contemplate the significance of their difficult experiences. Second, the ‘public’ experience of broadcasting helped the participants gain social awareness, particularly regarding the significance of how their storytelling can initiate social change. The broadcast format developed for this study will be useful to other disadvantaged groups considering the use of media for self-advocacy.
Population Immunity to Pre-Omicron and Omicron Severe Acute Respiratory Syndrome Coronavirus 2 Variants in US States and Counties Through 1 December 2021
Authors: Klaassen Fayette , Chitwood Melanie H , Cohen Ted , Pitzer Virginia E , Russi Marcus , Swartwood Nicole A , Salomon Joshua A , Menzies Nicolas A 
Published: June 2022

Abstract

Background
Both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) vaccination contribute to population-level immunity against SARS-CoV-2. This study estimated the immunological exposure and effective protection against future SARS-CoV-2 infection in each US state and county over 2020–2021 and how this changed with the introduction of the Omicron variant.

Methods
We used a Bayesian model to synthesize estimates of daily SARS-CoV-2 infections, vaccination data and estimates of the relative rates of vaccination conditional on infection status to estimate the fraction of the population with (1) immunological exposure to SARS-CoV-2 (ever infected with SARS-CoV-2 and/or received ≥1 doses of a COVID-19 vaccine), (2) effective protection against infection, and (3) effective protection against severe disease, for each US state and county from 1 January 2020 to 1 December 2021.

Results
The estimated percentage of the US population with a history of SARS-CoV-2 infection or vaccination as of 1 December 2021 was 88.2% (95% credible interval [CrI], 83.6%–93.5%). Accounting for waning and immune escape, effective protection against the Omicron variant on 1 December 2021 was 21.8% (95% CrI, 20.7%–23.4%) nationally and ranged between 14.4% (13.2%–15.8%; West Virginia) and 26.4% (25.3%–27.8%; Colorado). Effective protection against severe disease from Omicron was 61.2% (95% CrI, 59.1%–64.0%) nationally and ranged between 53.0% (47.3%–60.0%; Vermont) and 65.8% (64.9%–66.7%; Colorado).

Conclusions
While more than four-fifths of the US population had prior immunological exposure to SARS-CoV-2 via vaccination or infection on 1 December 2021, only a fifth of the population was estimated to have effective protection against infection with the immune-evading Omicron variant.
Tuberculosis Molecular Bacterial Load Assay Reveals Early Delayed Bacterial Killing in Patients With Relapse
Authors: Ntinginya Nyanda Elias , Bakuli Abhishek , Mapamba Daniel , Sabiiti Wilber , Kibiki Gibson , Minja Lilian Tina , Kuchaka Davis , Reither Klaus , Phillips Patrick Peter John , Boeree Martin Johan , Gillespie Stephen H , Hoelscher Michael , Heinrich Norbert ,   for the Pan African Consortium for the Evaluation of Antituberculosis Antibiotics (PanACEA) Consortium
Published: June 2022

Abstract
Bacterial killing in patients with tuberculosis (TB) relapse was compared to that in patients achieving cure, measured by TB molecular bacterial load assay (TB-MBLA) or mycobacteria growth indicator tube (MGIT) time to positivity (TTP). TB-MBLA in 4 relapsed patients was significantly different compared to 132 cured patients after 2 weeks of treatment; MGIT TTP showed a significant difference from week 8.
TheStaphylococcus aureusNetwork Adaptive Platform Trial Protocol: New Tools for an Old Foe
Authors: Tong Steven Y C , Mora Jocelyn , Bowen Asha C , Cheng Matthew P , Daneman Nick , Goodman Anna L , Heriot George S , Lee Todd C , Lewis Roger J , Lye David C , Mahar Robert K , Marsh Julie , McGlothlin Anna , McQuilten Zoe , Morpeth Susan C , Paterson David L , Price David J , Roberts Jason A , Robinson J Owen , van Hal Sebastiaan J , Walls Genevieve , Webb Steve A , Whiteway Lyn , Yahav Dafna , Davis Joshua S ,   for the Staphylococcus aureus Network Adaptive Platform (SNAP) Study Group, Anagnostou Nick , Archuleta Sophia , Athan Eugene , Barina Lauren , Best Emma , Bloomfield Max , Bostock Jennifer , Botheras Carly , Bowen Asha , Britton Philip , Burden Hannah , Campbell Anita , Carter Hannah , Cheng Matthew , Chew Ka Lip , Chong Russel Lee Ming , Coombs Geoff , Daley Peter , Daneman Nick , Davies Jane , Davis Joshua , Dishon Yael , Dotel Ravindra , Dunlop Adrian , Flack Felicity , Flanagan Katie , Foo Hong , Ghanem-Zoubi Nesrin , Giulieri Stefano , Goodman Anna , Grant Jennifer , Gregson Dan , Guy Stephen , Gwee Amanda , Hardy Erica , Henderson Andrew , Heriot George , Howden Benjamin , Hudson Fleur , Johnstone Jennie , Kalimuddin Shirin , Kretser Dana de , Kwa Andrea , Lee Todd , Legg Amy , Lewis Roger , Llewelyn Martin , Lumley Thomas , Lye David , MacFadden Derek , Mahar Robert , Malhamé Isabelle , Marks Michael , Marsh Julie , Martinello Marianne , Matthews Gail , McArthur Colin , McGlothlin Anna , McKew Genevieve , McMullan Brendan , McQuilten Zoe , Milliken Eliza , Mora Jocelyn , Morpeth Susan , Murthy Srinivas , Nourse Clare , O'Sullivan Matthew , Paterson David , Paul Mical , Petersiel Neta , Petrella Lina , Pett Sarah , Price David , Roberts Jason , Robinson Owen , Rogers Ben , Saville Benjamin , Scarborough Matthew , Scheetz Marc , Scheuerman Oded , Schwartz Kevin , Smith Simon , Snelling Tom , Soares Marta , Sommerville Christine , Stewardson Andrew , Stone Neil , Sud Archana , Tilley Robert , Tong Steven , Turner Rebecca , Underwood Jonathan , Hal Sebastiaan van , Voss Lesley , Walls Genevieve , Webb Rachel , Webb Steve , Whiteway Lynda , Wilson Heather , Wuerz Terry , Yahav Dafna 
Published: June 2022

AbstractStaphylococcus aureus bloodstream (SAB) infection is a common and severe infectious disease, with a 90-day mortality of 15%–30%. Despite this, &lt;3000 people have been randomized into clinical trials of treatments for SAB infection. The limited evidence base partly results from clinical trials for SAB infections being difficult to complete at scale using traditional clinical trial methods. Here we provide the rationale and framework for an adaptive platform trial applied to SAB infections. We detail the design features of the Staphylococcus aureus Network Adaptive Platform (SNAP) trial that will enable multiple questions to be answered as efficiently as possible. The SNAP trial commenced enrolling patients across multiple countries in 2022 with an estimated target sample size of 7000 participants. This approach may serve as an exemplar to increase efficiency of clinical trials for other infectious disease syndromes.
Coronavirus Disease 2019 (COVID-19) Severity Among Women of Reproductive Age With Symptomatic Laboratory-Confirmed Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection by Pregnancy Status—United States, 1 January 2020–25 December 2021
Authors: Strid Penelope , Zapata Lauren B , Tong Van T , Zambrano Laura D , Woodworth Kate R , Riser Aspen P , Galang Romeo R , Gilboa Suzanne M , Ellington Sascha R 
Published: June 2022

Abstract

Background
Information on the severity of coronavirus disease 2019 (COVID-19) attributable to the Delta variant in the United States among pregnant people is limited. We assessed the risk for severe COVID-19 by pregnancy status in the period of Delta variant predominance compared with the pre-Delta period.

Methods
Laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections among symptomatic women of reproductive age (WRA) were assessed. We calculated adjusted risk ratios for severe disease including intensive care unit (ICU) admission, receipt of invasive ventilation or extracorporeal membrane oxygenation (ECMO), and death comparing the pre-Delta period (1 January 2020–26 June 2021) and the Delta period (27 June 2021–25 December 2021) for pregnant and nonpregnant WRA.

Results
Compared with the pre-Delta period, the risk of ICU admission during the Delta period was 41% higher (adjusted risk ratio [aRR], 1.41 [95% confidence interval {CI}, 1.17–1.69]) for pregnant WRA and 9% higher (aRR, 1.09 [95% CI, 1.00–1.18]) for nonpregnant WRA. The risk of invasive ventilation or ECMO was higher for pregnant (aRR, 1.83 [95% CI, 1.26–2.65]) and nonpregnant (aRR, 1.34 [95% CI, 1.17–1.54]) WRA in the Delta period. During the Delta period, the risk of death was 3.33 (95% CI, 2.48–4.46) times the risk in the pre-Delta period among pregnant WRA and 1.62 (95% CI, 1.49–1.77) among nonpregnant WRA.

Conclusions
Compared with the pre-Delta period, pregnant and nonpregnant WRA were at increased risk for severe COVID-19 in the Delta period.
Kinetics of Maternally Derived Anti–Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibodies in Infants in Relation to the Timing of Antenatal Vaccination
Authors: Rottenstreich Amihai , Zarbiv Gila , Oiknine-Djian Esther , Vorontsov Olesya , Zigron Roy , Kleinstern Geffen , Porat Shay , Wolf Dana G 
Published: June 2022

AbstractBackgroundSARS-CoV-2 infection during early infancy can result in severe disease. We evaluated the durability of maternally-derived anti-SARS-CoV-2 antibodies in infants and its relation to antenatal vaccination timing.MethodsSera were prospectively collected at birth and 3 months after delivery from mother-infant pairs following antenatal BNT162b2 vaccination. SARS-CoV-2 receptor binding domain (RBD)-specific IgG levels and neutralizing activity were evaluated.Results56 mother-infant pairs were included: 15 (26.8%) were vaccinated in the first trimester, 16 (28.6%) in the second trimester, and 25 (44.6%) in the third trimester.At the time of delivery, all neonates were positive for anti-RBD-specific IgG with a median concentration of 4046 [IQR 2446–7896] AU/mL, with the highest concentration found after third trimester vaccination (median 6763 [IQR 3857–12561] AU/mL). At 3 months after delivery, anti RBD-specific IgG levels in infants significantly waned with a median concentration of 545 [IQR 344–810] AU/mL (P &lt; .001). The half-life of anti-RBD-specific IgG was 66 days among mothers and 30 days among infants. While at the time of delivery, all neonates had detectable neutralizing activity regardless of gestational age at vaccination, at 3-months of age, a higher proportion of infants born to mothers vaccinated in third trimester had persistent neutralizing activity as compared to those born to mothers vaccinated in second trimester.ConclusionsMaternal vaccination leads to efficient transplacental antibody transfer, with persistent anti-SARS-CoV-2 antibodies detected at 3 months of age in all infants. The observed effect of antenatal immunization timing on the kinetics of maternally-derived antibodies may have implications for SARS-CoV-2 vaccination strategies.
Prevalence, Outcome, and Prevention of Congenital Cytomegalovirus Infection in Neonates Born to Women With Preconception Immunity (CHILd Study)
Authors: Lilleri Daniele , Tassis Beatrice , Pugni Lorenza , Ronchi Andrea , Pietrasanta Carlo , Spinillo Arsenio , Arossa Alessia , Achille Cristian , Vergani Patrizia , Ornaghi Sara , Riboni Silvia , Cavoretto Paolo , Candiani Massimo , Gaeta Gerarda , Prefumo Federico , Fratelli Nicola , Fichera Anna , Vignali Michele , Barbasetti Di Prun Allegra , Fabbri Elisa , Cetin Irene , Locatelli Anna , Consonni Sara , Rutolo Simona , Miotto Elena , Savasi Valeria , Di Giminiani Maria , Cromi Antonella , Binda Sandro , Fiorina Loretta , Furione Milena , Cassinelli Gabriela , Klersy Catherine ,   for the CHILd Study Group, Piccini Stefania , Marrazzi Valentina , Muscettola Giulia , Zelini Paola , d’Angelo Piera , De Cicco Marica , Cirasola Daniela , Zavaglio Federica , Testa Lea , Ballerini Claudia , Stachetti Rebecca , Fondazione Marta Ruggiero , De Liso Federica , Cavallero Annalisa , Tessitore Isadora Vaglio , Ventura Maria Luisa , Pozzoni Mirko , Merlo Camilla , Rivetti Giulia , Spinoni Vania , Belloni Gaia , Querzola Camilla , Pessina Marta , Ligato Elisa , Zavatta Alice , Balconi Marta , Mussi Serena , Biraghi Patrizia , Cammarata Selene , Ghezzi Fabio , Agosti Massimo , Pellegrinelli Laura , Galli Cristina , Primache Valeria 
Published: June 2022

Abstract

Background
Human cytomegalovirus (HCMV) is the leading infectious cause of congenital disabilities. We designed a prospective study to investigate the rate, outcome, and risk factors of congenital CMV (cCMV) infection in neonates born to immune women, and the potential need and effectiveness of hygiene recommendations in this population.

Methods
The study was composed of 2 sequential parts: an epidemiology (part 1) and a prevention (part 2) study. Performance of part 2 depended upon a cCMV rate &gt;0.4%. Women enrolled in part 1 did not receive hygiene recommendations. Newborns were screened by HCMV DNA testing in saliva and cCMV was confirmed by urine testing.

Results
Saliva swabs were positive for HCMV DNA in 45/9661 newborns and cCMV was confirmed in 18 cases. The rate of cCMV was .19% (95% confidence interval [CI]: .11–.29%), and 3 out of 18 infants with cCMV had symptoms of CMV at birth. Age, nationality, occupation, and contact with children were similar between mothers of infected and noninfected newborns. Twin pregnancy (odds ratio [OR]: 7.2; 95% CI: 1.7–32.2; P = .037) and maternal medical conditions (OR: 3.9; 95% CI: 1.5–10.1; P = .003) appeared associated with cCMV. Given the rate of cCMV was lower than expected, the prevention part of the study was cancelled.

Conclusions
Newborns from women with preconception immunity have a low rate of cCMV, which appears to be mostly due to reactivation of the latent virus. Therefore, serological screening in childbearing age would be pivotal to identify HCMV-seropositive women, whose newborns have a low risk of cCMV.

Clinical trials registration
www.clinicaltrials.gov (NCT03973359).
Integration of Sequencing and Epidemiologic Data for Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections in a Tertiary-Care Hospital
Authors: Czech-Sioli Manja , Günther Thomas , Robitaille Alexis , Roggenkamp Hannes , Büttner Henning , Indenbirken Daniela , Christner Martin , Lütgehetmann Marc , Knobloch Johannes , Aepfelbacher Martin , Grundhoff Adam , Fischer Nicole 
Published: June 2022

Abstract

Background
The ongoing coronavirus disease 2019 pandemic significantly burdens hospitals and other healthcare facilities. Therefore, understanding the entry and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for effective prevention and preparedness measures. We performed surveillance and analysis of testing and transmission of SARS-CoV-2 infections in a tertiary-care hospital in Germany during the second and third pandemic waves in fall/winter 2020.

Methods
Between calendar week 41 in 2020 and calendar week 1 in 2021, 40%, of all positive patient and staff samples (284 total) were subjected to full-length viral genome sequencing. Clusters were defined based on similar genotypes indicating common sources of infection. We integrated phylogenetic, spatial, and temporal metadata to detect nosocomial infections and outbreaks, uncover transmission chains, and evaluate containment measures’ effectiveness.

Results
Epidemiologic data and contact tracing readily recognize most healthcare-associated (HA) patient infections. However, sequencing data reveal that temporally preceding index cases and transmission routes can be missed using epidemiologic methods, resulting in delayed interventions and serially linked outbreaks being counted as independent events. While hospital-associated transmissions were significantly elevated at a moderate rate of community transmission during the second wave, systematic testing and high vaccination rates among staff have led to a substantial decrease in HA infections at the end of the second/beginning of the third wave despite high community transmissions.

Conclusions
While epidemiologic analysis is critical for immediate containment of HA SARS-CoV-2 outbreaks, integration of genomic surveillance revealed weaknesses in identifying staff contacts. Our study underscores the importance of high testing frequency and genomic surveillance to detect, contain and prevent SARS-CoV-2–associated infections in healthcare settings.