bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrasting cytosolic glutathione redox dynamics under abiotic and biotic stress in barley as revealed by the biosensor Grx1–roGFP2
Authors: Bohle Finja , Klaus Alina , Ingelfinger Julian , Tegethof Hendrik , Safari Nassim , Schwarzländer Markus , Hochholdinger Frank , Hahn Matthias , Meyer Andreas J , Acosta Ivan F , Müller-Schüssele Stefanie J 
Published: February 2024

Abstract
Barley is a staple crop of major global importance and relatively resilient to a wide range of stress factors in the field. Transgenic reporter lines to investigate physiological parameters during stress treatments remain scarce. We generated and characterized transgenic homozygous barley lines (cv. Golden Promise Fast) expressing the genetically encoded biosensor Grx1–roGFP2, which indicates the redox potential of the major antioxidant glutathione in the cytosol. Our results demonstrated functionality of the sensor in living barley plants. We determined the glutathione redox potential (EGSH) of the cytosol to be in the range of –308 mV to –320 mV. EGSH was robust against a combined NaCl (150 mM) and water deficit treatment (–0.8 MPa) but responded with oxidation to infiltration with the phytotoxic secretome of the necrotrophic fungus Botrytis cinerea. The generated reporter lines are a novel resource to study biotic and abiotic stress resilience in barley, pinpointing that even severe abiotic stress leading to a growth delay does not automatically induce cytosolic EGSH oxidation, while necrotrophic pathogens can undermine this robustness.
Normalization of kinship relations to enrich family network analysis: case study on China biographical database
Authors: Li Bin , Yuan Yiguo , Lu Xuehui , Bol Peter K 
Published: February 2024

Abstract
Kinship is an important issue in history studies. The kinship database is the key resource to analyze the structure, succession, and evolution of families. However, one kinship could be expressed by different words, and one kinship word may be vague and ambiguous in natural languages, especially in pre-modern Chinese. As in the well-known China Biographical Database, which contains 484,066 kinship instances, there are more than 400 kinship words. Thus, the relations extracted from history texts cannot be directly used to build family networks. In this article, we put forward a novel method to normalize kinship relations by three basic relations: father–descendant, mother–descendant, and husband–wife, as well as the gender of each person. All types of kinships are normalized to these three basic relations. In this way, we identified 178,390 basic kinship relations to fully describe the original 462,147 unambiguous kinship instances, while finding 3,989 inconsistencies and inferring 5,805 missing persons. Then, we generate 29,423 families by basic kinship relations and analyze the properties of families, such as their sizes, depths, and intermarriages across families. This type of family analysis had been almost impossible prior to normalizing kinship relations. Therefore, this technique enables improved family database construction and deeper quantitative analysis.
An integrated in vitro carcinogenicity test that distinguishes between genotoxic carcinogens, non-genotoxic carcinogens, and non-carcinogens
Authors: Chapman Katherine E , Shah Ume-Kulsoom , Fletcher Jessica F , Johnson George E , Doak Shareen H , Jenkins Gareth J S 
Published: February 2024

Abstract
Chemical safety testing plays a crucial role in product and pharmacological development, as well as chemoprevention; however, in vitro genotoxicity safety tests do not always accurately predict the chemicals that will be in vivo carcinogens. If chemicals test positive in vitro for genotoxicity but negative in vivo, this can contribute to unnecessary testing in animals used to confirm erroneous in vitro positive results. Current in vitro tests typically evaluate only genotoxicity endpoints, which limits their potential to detect non-genotoxic carcinogens. The frequency of misleading in vitro positive results can be high, leading to a requirement for more informative in vitro tests. It is now recognized that multiple-endpoint genotoxicity testing may aid more accurate detection of carcinogens and non-carcinogens. The objective of this review was to evaluate the utility of our novel, multiple-endpoint in vitro test, which uses multiple cancer-relevant endpoints to predict carcinogenic potential. The tool assessed micronucleus frequency, p53 expression, p21 expression, mitochondrial respiration, cell cycle abnormalities and, uniquely, cell morphology changes in human lymphoblastoid cell lines, TK6 and MCL-5. The endpoints were used to observe cellular responses to 18 chemicals within the following categories: genotoxic carcinogens, non-genotoxic carcinogens, toxic non-carcinogens, and misleading in vitro positive and negative agents. The number of endpoints significantly altered for each chemical was considered, alongside the holistic Integrated Signature of Carcinogenicity score, derived from the sum of fold changes for all endpoints. Following the calculation of an overall score from these measures, carcinogens exhibited greater potency than non-carcinogens. Genotoxic carcinogens were generally more potent than non-genotoxic carcinogens. This novel approach therefore demonstrated potential for correctly predicting whether chemicals with unknown mechanism may be considered carcinogens. Overall, while further validation is recommended, the test demonstrates potential for the identification of carcinogenic compounds. Adoption of the approach could enable reduced animal use in carcinogenicity testing.
Identification of Hammerhead-variant ribozyme sequences in SARS-CoV-2
Authors: Liu Getong , Jiang Hengyi , Chen Dongrong , Murchie Alastair I H 
Published: February 2024

Abstract
The SARS-CoV-2 RNA virus and variants, responsible for the COVID-19 pandemic has become endemic, raised a need for further understanding of the viral genome and biology. Despite vast research on SARS-CoV-2, no ribozymes have been found in the virus genome. Here we report the identification of 39 Hammerhead-variant ribozyme sequences (CoV-HHRz) in SARS-CoV-2. These sequences are highly conserved within SARS-CoV-2 variants but show large diversity among other coronaviruses. In vitro CoV-HHRz sequences possess the characteristics of typical ribozymes; cleavage is pH and ion dependent, although their activity is relatively low and Mn2+ is required for cleavage. The cleavage sites of four CoV-HHRz coincide with the breakpoint of expressed subgenomic RNA (sgRNAs) in SARS-CoV-2 transcriptome data suggesting in vivo activity. The CoV-HHRz are involved in processing sgRNAs for ORF7b, ORF 10 and ORF1ab nsp13 which are essential for viral packaging and life cycle.
Linear DNA-driven recombination in mammalian mitochondria
Authors: Fragkoulis Georgios , Hangas Anu , Fekete Zsófia , Michell Craig , Moraes Carlos T , Willcox Smaranda , Griffith Jack D , Goffart Steffi , Pohjoismäki Jaakko L O 
Published: February 2024

Abstract
Mitochondrial DNA (mtDNA) recombination in animals has remained enigmatic due to its uniparental inheritance and subsequent homoplasmic state, which excludes the biological need for genetic recombination, as well as limits tools to study it. However, molecular recombination is an important genome maintenance mechanism for all organisms, most notably being required for double-strand break repair. To demonstrate the existence of mtDNA recombination, we took advantage of a cell model with two different types of mitochondrial genomes and impaired its ability to degrade broken mtDNA. The resulting excess of linear DNA fragments caused increased formation of cruciform mtDNA, appearance of heterodimeric mtDNA complexes and recombinant mtDNA genomes, detectable by Southern blot and by long range PacBio® HiFi sequencing approach. Besides utilizing different electrophoretic methods, we also directly observed molecular complexes between different mtDNA haplotypes and recombination intermediates using transmission electron microscopy. We propose that the known copy-choice recombination by mitochondrial replisome could be sufficient for the needs of the small genome, thus removing the requirement for a specialized mitochondrial recombinase. The error-proneness of this system is likely to contribute to the formation of pathological mtDNA rearrangements.
Curriculum and Competency Guidelines for the Advanced Care Practitioner in Infectious Disease
Authors: Smith Miriam A , Zelenetz Paul , Kim Angela , Donaghy Henry , Gould J Scott , McLeod-Sordjan Renee 
Published: February 2024

Abstract

Background
Changes in the health care delivery system have altered the way internal medicine (IM) is practiced, with inclusion of subspecialty advanced care practitioners (ACPs) as vital members of the health care team.

Methods
ACPs are provided the clinical settings and educational resources within an academic center to become competent in recognizing and managing common and complicated infectious diseases (ID). The ID ACP will be given progressive responsibility with expectations for achievement of milestones as they develop into competent practitioners. We seek to ensure quality, cost-effective, and comprehensive patient-centered care on the ID service in the inpatient and ambulatory settings in compliance with national standards and scope of practice recommendations and regulations.

Results
In recognition of the expanding role of ACPs, we developed a curriculum and guidelines in the subspecialty of ID.

Conclusions
Our proposal greatly adds to the available literature for ACPs to provide the full spectrum of ID practice.
Characteristics and Outcomes of Pregnant Women Hospitalized With Laboratory-Confirmed Respiratory Syncytial Virus Before and During the COVID-19 Pandemic
Authors: Milucky Jennifer , Patel Kadam , Patton Monica E , Kirley Pam Daily , Austin Elizabeth , Meek James , Anderson Evan J , Brooks Alicia , Brown Chloe , Mumm Erica , Salazar-Sanchez Yadira , Barney Grant , Popham Kevin , Sutton Melissa , Talbot H Keipp , Crossland Melanie T , Havers Fiona P ,   RSV-NET Surveillance Team, Chai Shua J , Armistead Isaac , Yousey-Hindes Kimberly , Openo Kyle P , Henderson Justin , Bye Erica , Pacheco Francesca , Rowlands Jemma V , Bennett Nancy M , Hendrick M Andraya , Schaffner William , Hill Mary 
Published: February 2024

Abstract

Background
Respiratory syncytial virus (RSV) can cause severe disease among infants and older adults. Less is known about RSV among pregnant women.

Methods
To analyze hospitalizations with laboratory-confirmed RSV among women aged 18 to 49 years, we used data from the RSV Hospitalization Surveillance Network (RSV-NET), a multistate population-based surveillance system. Specifically, we compared characteristics and outcomes among (1) pregnant and nonpregnant women during the pre–COVID-19 pandemic period (2014–2018), (2) pregnant women with respiratory symptoms during the prepandemic and pandemic periods (2021–2023), and (3) pregnant women with and without respiratory symptoms in the pandemic period. Using multivariable logistic regression, we examined whether pregnancy was a risk factor for severe outcomes (intensive care unit admission or in-hospital death) among women aged 18 to 49 years who were hospitalized with RSV prepandemic.

Results
Prepandemic, 387 women aged 18 to 49 years were hospitalized with RSV. Of those, 350 (90.4%) had respiratory symptoms, among whom 33 (9.4%) were pregnant. Five (15.2%) pregnant women and 74 (23.3%) nonpregnant women were admitted to the intensive care unit; no pregnant women and 5 (1.6%) nonpregnant women died. Among 279 hospitalized pregnant women, 41 were identified prepandemic and 238 during the pandemic: 80.5% and 35.3% had respiratory symptoms, respectively (P &lt; .001). Pregnant women were more likely to deliver during their RSV-associated hospitalization during the pandemic vs the prepandemic period (73.1% vs 43.9%, P &lt; .001).

Conclusions
Few pregnant women had severe RSV disease, and pregnancy was not a risk factor for a severe outcome. More asymptomatic pregnant women were identified during the pandemic, likely due to changes in testing practices for RSV.
Confronting the Disruption of the Infectious Diseases Workforce by Artificial Intelligence: What This Means for Us and What We Can Do About It
Authors: Langford Bradley J , Branch-Elliman Westyn , Nori Priya , Marra Alexandre R , Bearman Gonzalo 
Published: February 2024

Abstract
With the rapid advancement of artificial intelligence (AI), the field of infectious diseases (ID) faces both innovation and disruption. AI and its subfields including machine learning, deep learning, and large language models can support ID clinicians’ decision making and streamline their workflow. AI models may help ensure earlier detection of disease, more personalized empiric treatment recommendations, and allocation of human resources to support higher-yield antimicrobial stewardship and infection prevention strategies. AI is unlikely to replace the role of ID experts, but could instead augment it. However, its limitations will need to be carefully addressed and mitigated to ensure safe and effective implementation. ID experts can be engaged in AI implementation by participating in training and education, identifying use cases for AI to help improve patient care, designing, validating and evaluating algorithms, and continuing to advocate for their vital role in patient care.
Epidemiology, Clinical Characteristics, and Diagnostic Testing Practices for Pneumocystis Pneumonia–Associated Hospitalizations, United States, 2019–2022
Authors: Benedict Kaitlin , Baggs James , Gold Jeremy A W 
Published: February 2024

Abstract
Among 9196 hospitalizations involving Pneumocystis pneumonia, those without HIV had higher in-hospital mortality (24.3% vs 10.5%, P &lt; .001) when compared with those with HIV. These findings underscore the continued importance of Pneumocystis pneumonia clinical awareness and the need for comprehensive prophylaxis guidance, particularly for certain patients without HIV who are immunosuppressed.
Cholera Deaths During Outbreaks in Uvira, Eastern Democratic Republic of the Congo, 10–35 Months After Mass Vaccination
Authors: Bugeme Patrick Musole , Xu Hanmeng , Hutchins Chloe , Dent Juan , Saidi Jaime Mufitini , Rumedeka Baron Bashige , Itongwa Moïse , Mashauri Joël Faraja Zigashane , Masembe Lulela Faraja , Bengehya Justin , Kulondwa Jean-Claude , Debes Amanda K , Ciglenecki Iza , Tshiwedi Esperance , Kitoga Faida , Bodisa-Matamu Tavia , Nadège Taty , Kavunga-Membo Hugo , Lunguya Octavie , Welo Placide Okitayemba , Knee Jackie , Mukadi-Bamuleka Daniel , Azman Andrew S , Malembaka Espoir Bwenge 
Published: February 2024

Abstract
Our understanding of the burden and drivers of cholera mortality is hampered by limited surveillance and confirmation capacity. Leveraging enhanced clinical and laboratory surveillance in the cholera-endemic community of Uvira, eastern Democratic Republic of Congo, we describe cholera deaths across 3 epidemics between September 2021 and September 2023 following mass vaccination.
Discovery of diffuse radio source in Abell 1060
Authors: Kurahara Kohei , Akahori Takuya , Oki Aika , Omiya Yuki , Nakazawa Kazuhiro 
Published: February 2024

Abstract
Non-thermal components in the intra-cluster medium (ICM), such as turbulence, magnetic field, and cosmic rays, imprint the past and current energetic activities of jets from active galactic nuclei (AGN) of member galaxies as well as disturbance caused by galaxy cluster mergers. Meter- and centimeter-radio observations of synchrotron radiation allow us to diagnose the nonthermal component. Here we report on our discovery of an unidentified diffuse radio source, named the Flying Fox, near the center of the Abell 1060 field. The Flying Fox has an elongated ring-like structure and a central bar shape, but there is no obvious host galaxy. The average spectral index of the Flying Fox is −1.4, which is steeper than that for radio sources seen at meter wavelengths. We discussed the possibilities of radio lobes, phoenixes, radio halos and relics, and an odd radio circle. In conclusion, the Flying Fox is not clearly explained by known radio sources.
Hydrostatic pressure impedes the degradation of sinking copepod carcasses and fecal pellets
Authors: Franco-Cisterna Belén , Stief Peter , Glud Ronnie N 
Published: February 2024

Abstract
Fast-sinking zooplankton carcasses and fecal pellets appear to contribute significantly to the vertical transport of particulate organic carbon (POC), partly because of low temperature that decreases microbial degradation during the descent into the deep ocean. Increasing hydrostatic pressure could further reduce the degradation efficiency of sinking POC, but this effect remains unexplored. Here, the degradation of carcasses and fecal pellets of the abundant marine copepod Calanus finmarchicus was experimentally studied as a function of pressure (0.1–100 MPa). Samples were either exposed to elevated pressure in short 1-day incubations or a gradual pressure increase, simulating continuous particle sinking during a 20-day incubation. Both experiments revealed gradual inhibition of microbial respiration in the pressure range of 20–100 MPa, corresponding to 2–10-km depth. This suggests that hydrostatic pressure impedes carbon mineralization of fast-sinking carcasses and fecal pellets and enhances the deep-sea deposition rate of zooplankton-derived organic material.
Age-specific transmission dynamics of SARS-CoV-2 during the first 2 years of the pandemic
Authors: Boldea Otilia , Alipoor Amir , Pei Sen , Shaman Jeffrey , Rozhnova Ganna 
Published: February 2024

Abstract
During its first 2 years, the SARS-CoV-2 pandemic manifested as multiple waves shaped by complex interactions between variants of concern, non-pharmaceutical interventions, and the immunological landscape of the population. Understanding how the age-specific epidemiology of SARS-CoV-2 has evolved throughout the pandemic is crucial for informing policy decisions. In this article, we aimed to develop an inference-based modeling approach to reconstruct the burden of true infections and hospital admissions in children, adolescents, and adults over the seven waves of four variants (wild-type, Alpha, Delta, and Omicron BA.1) during the first 2 years of the pandemic, using the Netherlands as the motivating example. We find that reported cases are a considerable underestimate and a generally poor predictor of true infection burden, especially because case reporting differs by age. The contribution of children and adolescents to total infection and hospitalization burden increased with successive variants and was largest during the Omicron BA.1 period. However, the ratio of hospitalizations to infections decreased with each subsequent variant in all age categories. Before the Delta period, almost all infections were primary infections occurring in naive individuals. During the Delta and Omicron BA.1 periods, primary infections were common in children but relatively rare in adults who experienced either reinfections or breakthrough infections. Our approach can be used to understand age-specific epidemiology through successive waves in other countries where random community surveys uncovering true SARS-CoV-2 dynamics are absent but basic surveillance and statistics data are available.
Prediction of general practice licensure/certification examination performance by a measure of ‘questionable’ activities in clinical practice: a retrospective cohort study
Authors: Magin Parker , Ralston Anna , Fielding Alison , Holliday Elizabeth , Tran Michael , Tapley Amanda , van Driel Mieke , Ball Jean , Moad Dominica , Mitchell Ben , Fisher Katie , FitzGerald Kristen , Spike Neil , Turner Rachel , Davey Andrew 
Published: February 2024

Abstract

Purpose
‘Low-value’ clinical care and medical services are ‘questionable’ activities, being more likely to cause harm than good or with disproportionately low benefit relative to cost. This study examined the predictive ability of the QUestionable In Training Clinical Activities Index (QUIT-CAI) for general practice (GP) registrars’ (trainees’) performance in Australian GP Fellowship examinations (licensure/certification examinations for independent GP).

Methods
The study was nested in ReCEnT, an ongoing cohort study in which Australian GP registrars document their in-consultation clinical practice. Outcome factors in analyses were individual registrars’ scores on the three Fellowship examinations (‘AKT’, ‘KFP’, and ‘OSCE’ examinations) and pass/fail rates during 2012–21. Analyses used univariable and multivariable regression (linear or logistic, as appropriate). The study factor in each analysis was ‘QUIT-CAI score percentage’—the percentage of times a registrar performed a QUIT-CAI clinical activity when ‘at risk’ (i.e. when managing a problem where performing a QUIT-CAI activity was a plausible option).

Results
A total of 1265, 1145, and 553 registrars sat Applied Knowledge Test, Key Features Problem, and Objective Structured Clinical Exam examinations, respectively. On multivariable analysis, higher QUIT-CAI score percentages (more questionable activities) were significantly associated with poorer Applied Knowledge Test scores (P = .001), poorer Key Features Problem scores (P = .003), and poorer Objective Structured Clinical Exam scores (P = .005). QUIT-CAI score percentages predicted Royal Australian College of General Practitioner exam failure [odds ratio 1.06 (95% CI 1.00, 1.12) per 1% increase in QUIT-CAI, P = .043].

Conclusion
Performing questionable clinical activities predicted poorer performance in the summative Fellowship examinations, thereby validating these examinations as measures of actual clinical performance (by our measure of clinical performance, which is relevant for a licensure/certification examination).
Patient preference, efficacy, and compliance with zoledronic acid for glucocorticoid-induced osteoporosis in patients with autoimmune diseases
Authors: Kim Ji-Won , Jung Ju-Yang , Kim Hyoun-Ah , Son Heejun , Suh Chang-Hee 
Published: February 2024

AbstractPurposeWe evaluated the preference, patient satisfaction, and efficacy of zoledronic acid compared with oral bisphosphonates (BPs) for glucocorticoid-induced osteoporosis (GIOP) in patients with autoimmune diseases.MethodsWe enrolled 50 patients with new fractures or osteoporosis detected on follow-up bone densitometry after at least 1 year of oral BP use among patients diagnosed with GIOP during treatment for autoimmune diseases. After 1 year of zoledronic acid treatment, patients completed a survey for preference and satisfaction assessment. Treatment efficacy was analysed by comparing bone mineral density changes and fractures with those in a control group of patients who continued oral BP use.ResultsAge, sex, treatment duration, and medication history did not differ significantly between the two groups. Among the participants, 86.7% preferred and were more satisfied with intravenous zoledronic acid than with oral BPs, primarily because of the convenience of its administration interval. Only two patients (4%) reported infusion-related adverse events with zoledronic acid. Furthermore, no significant differences were observed in the annualized percentage change in the bone mineral density of the lumbar spine, femur neck, and hip between patients receiving zoledronic acid and those receiving oral BPs. The occurrence of new fractures was consistent across both groups, with two cases in each, showing no significant differences.ConclusionPatients showed a preference for and greater satisfaction with zoledronic acid, and its efficacy in treating osteoporosis was comparable to that of oral BPs. Therefore, zoledronic acid is a suitable treatment option for GIOP in patients with autoimmune diseases.