bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stabilization of the human cytomegalovirus UL136p33 reactivation determinant overcomes the requirement for UL135 for replication in hematopoietic cells
Authors: Moy Melissa A. , Collins-McMillen Donna , Crawford Lindsey , Parkins Christopher , Zeltzer Sebastian , Caviness Katie , Zaidi Syed Shujaat Ali , Caposio Patrizia , Goodrum Felicia 
Published: August 2023

ABSTRACT

Human cytomegalovirus (HCMV) is a beta herpesvirus that persists indefinitely in the human host through a latent infection. The polycistronic
UL133–UL138
gene locus of HCMV encodes genes regulating latency and reactivation. While
UL138
is pro-latency, restricting virus replication in CD34
+
hematopoietic progenitor cells (HPCs),
UL135
overcomes this restriction and is required for reactivation. By contrast,
UL136
is expressed with later kinetics and encodes multiple proteins with differential roles in latency and reactivation. Like
UL135
, the largest
UL136
isoform, UL136p33, is required for reactivation from latency in HPCs; viruses failing to express either protein are unresponsive to reactivation stimuli. Furthermore, UL136p33 is unstable, and its instability is important for the establishment of latency, and sufficient accumulation of UL136p33 is a checkpoint for reactivation. We hypothesized that stabilizing UL136p33 might overcome the requirement of
UL135
for replication. We generated recombinant viruses lacking
UL135
that expressed a stabilized variant of UL136p33. Stabilizing UL136p33 did not impact the replication of the
UL135
mutant virus in fibroblasts. However, in the context of infection in HPCs, stabilization of UL136p33 strikingly compensated for the loss of
UL135,
resulting in increased replication in CD34
+
HPCs and in humanized NOD-
scid
IL2Rγ
c
null
(huNSG) mice. This finding suggests that while
UL135
is essential for replication in HPCs, it functions largely at steps preceding the accumulation of UL136p33, and that stabilized expression of UL136p33 largely overcomes the requirement for
UL135
. Taken together, our genetic evidence indicates an epistatic relationship between UL136p33 and
UL135
, whereby
UL135
may initiate events early in reactivation that drive the accumulation of UL136p33 to a threshold required for productive reactivation.

IMPORTANCE
Human cytomegalovirus (HCMV) is one of nine human herpesviruses and a significant human pathogen. While HCMV establishes a lifelong latent infection that is typically asymptomatic in healthy individuals, its reactivation from latency can have devastating consequences in the immunocompromised. Defining viral genes important in the establishment of or reactivation from latency is important to defining the molecular basis of latent and replicative states and in controlling infection and CMV disease. Here we define a genetic relationship between two viral genes in controlling virus reactivation from latency using primary human hematopoietic progenitor cells and humanized mouse models.
Euo is a developmental regulator that represses late genes and activates midcycle genes in
Chlamydia trachomatis
Authors: Hakiem Owais R. , Rizvi Syed M. A. , Ramirez Cuper , Tan Ming 
Published: August 2023

ABSTRACT

The pathogenic bacterium
Chlamydia
reproduces via an unusual intracellular developmental cycle in which it converts from a dividing form (reticulate body or RB) to an infectious form (elementary body or EB). The transcription factor Euo has been proposed as a developmental regulator in
Chlamydia trachomatis
because it repressed a number of late chlamydial promoters, which are transcribed during RB-to-EB conversion. To define the Euo regulon, we performed a genome-wide study that combined Euo DNA immunoprecipitation-seq (DIP-seq) studies with RNA-seq analysis of HeLa cells infected with an Euo-overexpressing
C. trachomatis
strain. We demonstrate that Euo directly regulates ~7% of
C. trachomatis
genes. However, only about half were downregulated (28/61; 45.9%) by Euo overexpression while paradoxically the other half were upregulated (33/61; 54.1%). Intriguingly, all downregulated genes were late genes, while the majority of upregulated genes were midcycle genes, which are transcribed during RB replication. DIP analysis showed that Euo occupancy sites were restricted to the core promoter region for downregulated genes but were located over a wider region immediately upstream of the promoter for upregulated genes. We also found that Euo controls its own expression through a negative feedback mechanism. Electron microscopy analysis of cells infected with the Euo-overexpressing strain showed fewer EBs, consistent with a block in RB-to-EB conversion, as well as fewer and larger RBs. Together, these findings broaden the role of Euo as a developmental regulator that functions as both a transcriptional repressor of late genes and a transcriptional activator of midcycle genes in
C. trachomatis
.

IMPORTANCE

In this study, we developed a correlative approach that combined DNA immunoprecipitation-seq and RNA-seq analyses to define the regulon of the
Chlamydia trachomatis
transcription factor Euo. We confirmed the proposed role of Euo as a transcriptional repressor of late chlamydial genes but also showed that Euo activates transcription of a subset of midcycle genes and autoregulates its own expression via negative feedback. This study validates and expands the role of Euo as an important developmental regulator in
C. trachomatis
. In addition, this genome-wide correlative approach can be applied to study transcription factors in other pathogenic bacteria.
Characterization of A/H7 influenza virus global antigenic diversity and key determinants in the hemagglutinin globular head mediating A/H7N9 antigenic evolution
Authors: Kok Adinda , Scheuer Rachel , Bestebroer Theo M. , Burke David F. , Wilks Samuel H. , Spronken Monique I. , de Meulder Dennis , Lexmond Pascal , Pronk Mark , Smith Derek J. , Herfst Sander , Fouchier Ron A. M. , Richard Mathilde 
Published: August 2023

ABSTRACT
Avian A/H7 influenza viruses are a global threat to animal and human health. These viruses continue to cause outbreaks in poultry and have caused the highest number of reported zoonotic infections to date, highlighting their pandemic threat. Evidence for antigenic diversification of avian A/H7 influenza viruses exists; however, knowledge of the drivers and molecular basis of antigenic evolution of these viruses is limited. Here, antigenic cartography was used to analyze the global antigenic diversity of A/H7 influenza viruses and to determine the molecular basis of antigenic change in A/H7N9 viruses. A phylogenetic tree based on all available A/H7 HA sequences was generated, from which 52 representative, genetically diverse, antigens were selected for antigenic characterization using hemagglutination inhibition assays. The resulting data were used to compute an antigenic map using multidimensional scaling algorithms. High antigenic relatedness was observed between antigens and sera belonging to genetically divergent A/H7 (sub)lineages. The most striking antigenic change relative to the timespan of virus isolation was observed for the A/H7N9 viruses isolated between 2013 and 2019 in China. Amino acid changes at positions 116, 118, 125, 130, 151, and 217 in the hemagglutinin globular head were found to be the main determinants of antigenic evolution between A/H7N9 influenza virus prototypes. The A/H7 antigenic map and knowledge of the molecular determinants of their antigenic evolution will aid pandemic preparedness against A/H7 influenza viruses, specifically regarding the design of novel vaccines and vaccination strategies.

IMPORTANCE
A/H7 avian influenza viruses cause outbreaks in poultry globally, resulting in outbreaks with significant socio-economical impact and zoonotic risks. Occasionally, poultry vaccination programs have been implemented to reduce the burden of these viruses, which might result in an increased immune pressure accelerating antigenic evolution. In fact, evidence for antigenic diversification of A/H7 influenza viruses exists, posing challenges to pandemic preparedness and the design of vaccination strategies efficacious against drifted variants. Here, we performed a comprehensive analysis of the global antigenic diversity of A/H7 influenza viruses and identified the main substitutions in the hemagglutinin responsible for antigenic evolution in A/H7N9 viruses isolated between 2013 and 2019. The A/H7 antigenic map and knowledge of the molecular determinants of their antigenic evolution add value to A/H7 influenza virus surveillance programs, the design of vaccines and vaccination strategies, and pandemic preparedness.
Celiac—the lone horse? An autoimmune condition without signals of microbiota dysbiosis
Authors: Turjeman Sondra , Sharon Efrat , Levin Rachel , Oralewska Beata , Szaflarska-Popławska Anna , Bierła Joanna B. , Cukrowska Bożena , Koren Omry 
Published: August 2023

ABSTRACT

Accumulating evidence supports the role of microbiota in autoimmune processes, but research regarding the role of the gut microbiota in celiac disease (CD) is still emerging, and a consistent CD-associated dysbiosis pattern has not yet been defined. Here, we characterized the microbiota of children newly diagnosed with CD, with their unaffected family members as a healthy control group to reduce confounding factors including genetic background, hygiene, dietary habits, and environment, and followed children with CD over 1 year of dietary intervention (exclusion of gluten) to understand if the microbiota is associated with CD and its mediation. We did not find differences in the microbiota of siblings with and without CD, despite a wealth of evidence in the literature supporting CD-specific microbiota. CD is common among first-degree relatives, so this could suggest that unaffected family members in this study may be living in a pre-CD state, currently below clinical detection. Interestingly, despite the effectiveness of diet in CD control, we did not observe diet-mediated microbiota changes, except for short-term increase in
Akkermansia muciniphila
. This lack of effect could suggest a very strong CD microbial signature even when controlled or could be a technical shortcoming. Expanded future studies with both related and unrelated controls and diet interventions in both the CD and control arms can provide further context to our findings.

IMPORTANCE

The microbiota is the community of microbes that live in and on us. These microbes are essential to our health and everyday function. Disruption of the community is associated with diseases ranging from metabolic syndrome to autoimmune diseases to mental disorders. In the case of celiac disease (CD), research remains inconclusive regarding implications of the microbiota in etiology. Here, we compared microbiota of children with CD to those of their unaffected family members and found very few differences in microbiota profiles. We next examined how gluten elimination in CD patients affects the microbiota. Surprisingly, despite diet adherence, microbiota shifts were minimal, with only a short-term increase in
Akkermansia muciniphila
. Previous studies suggest that family members of CD patients may be living in a pre-CD state, which could explain their microbial similarity. A larger study with unrelated controls and increased microbiota monitoring during diet intervention should give our findings more perspective.
Supplemental Material: Late orogenic high-temperature overprint in (ultra)high-pressure ([U]HP) metamorphic rocks of the North Qinling Orogen, Central China: Insights into the geodynamics of the exhumation of (U)HP metamorphic rocks
Authors: Li Xin , Liu Liang , et al.  
Published: August 2023

<p>Text S1: Analytical methods of whole-rock major element analyses, mineral chemistry measurements, zircon U-Pb dating, and trace element measurements. Figure S1: P/T–H2O/O diagrams for samples QL2105 and QL2106. Figure S2: P–T diagram calculated with an effective bulk-rock composition for sample QL2106. Figure S3: Representative Raman spectra of mineral inclusions in zircons with different ages from samples QL2105 and QL2106. Table S1: Selected microprobe analyses of garnet, amphibole, biotite, plagioclase, and phengite for samples QL2105, QL2106, and QL2107. Table S2: Zircon U-Pb isotopic and age data as well as trace element compositions of zircons of samples QL2105, QL2106, and QL2107. </p>
Cancer rehabilitation support by cancer counselling centres (CARES): study protocol of a quasi-experimental feasibility study
Authors: Hiltrop Kati , Heidkamp Paula , Breidenbach Clara , Kowalski Christoph , Bruns Gudrun , Ernstmann Nicole 
Published: August 2023

IntroductionWhile maintaining or restoring work ability after a cancer diagnosis is an essential aim of the rehabilitation process for working-age patients, problems can arise during the return to work (RTW) or when retaining work. Counselling could provide support for patients with or after cancer with employment-related questions (eg, questions related to RTW and work retention). Outpatient psychosocial cancer counselling centres in Germany offer counselling on work-related questions; however, resources for this are limited. This protocol presents a feasibility study of an intensified needs-based counselling intervention that supports those seeking employment-related advice.Methods and analysisThe CARES (cancer rehabilitation support by cancer counselling centres) project is a feasibility study for a newly developed counselling intervention. The intervention is being developed as part of the project and piloted in about 20 outpatient cancer counselling centres. The CARES study has a quasi-experimental pre–post design with a control cohort. First, patients who undergo regular counselling are recruited. Second, after the counsellors have been trained for the newly developed intervention, participants for the intervention group are recruited from the cancer counselling centres. Quantitative and formative evaluations will be performed in accordance with the existing guidelines. The quantitative evaluation comprises three patient surveys (at the beginning of the counselling process, 3 months into the counselling process and, for the intervention group, at the end of the counselling process) and routine data of the counselling process. The formative evaluation includes interviews with patients, counsellors and other stakeholders, as well as participatory observations of counselling sessions.Ethics and disseminationApproval has been obtained from the ethics committee of the Medical Faculty of the University Bonn (061/22; 09.04.2022). A data protection concept ensures adherence to data protection regulations for the handled data. The dissemination strategies include discussing the results with the cancer counselling centres.Trial registration numberGerman Clinical Trials Register (DRKS00028121); Pre-results.
Does medical education reform change who is selected? A national cross-sectional survey from China
Authors: You You , Wang Weimin , Cleland Jennifer 
Published: August 2023

ObjectivesApproximately 10 years ago, China introduced an education plan to improve the overall quality of medical education and to better serve the population’s health needs. Many medical schools were then recognised and financed by China’s Ministry of Education to develop and operationalise new pilot programmes (PPs) aligned with this plan. These ran in parallel with the traditional programmes (TPs). One way to achieve the plan’s first aim, improving the quality of medical education, is to select academically stronger candidates. We, thus, examined and compared who were selected into PPs and TPs.DesignCross-sectional study.SettingData were collected from 123 medical schools across China via the 2021 China Medical Student Survey.ParticipantsParticipants were undergraduate clinical medicine students across all year groups.Primary and secondary outcome measuresMedical school selection was via the National College Entrance Examination (NCEE). Medical students’ NCEE performance and their sociodemographics were used as the primary and secondary outcome measures. Mann-Whitney or χ2tests were used to compare the means between educational programmes (PPs vs TPs) and various selection outcomes. Multilevel mixed-effects regressions were employed to account for school idiosyncratic selection results.ResultsOf the 204 817 respondents, 194 163 (94.8%) were in a TP and 10 654 (5.2%) a PP. PP respondents (median=75.2, IQR=69.5–78.8) had significantly higher NCEE scores than their TP counterparts (median=73.9, IQR=68.5–78.7). Holding constant their NCEE score, PP respondents were significantly more likely to come from urban areas, not be first-generation college students, and have parents with higher occupational status and income.ConclusionsAssuming quality can be indicated by prior academic achievement at the point of selection, PPs achieved this mission. However, doing so limited medical students’ diversity. This may be unhelpful in achieving the Education Plan’s goal to better serve China’s health needs.
Glycaemic monitoring and control among high-risk patients with type 2 diabetes in Australian general practice during COVID-19
Authors: Barlow Kirrilee Jane , Fahey Paul P , Atlantis Evan 
Published: August 2023

BackgroundThe COVID-19 pandemic disrupted general practice worldwide, primarily due to public health measures that restricted access to care for chronic diseases, such as type 2 diabetes. These measures disproportionately affected higher risk groups with type 2 diabetes, such as older people and those with obesity. This study aims to identify factors that may have influenced the rates of compliance with testing guidelines and target glycaemic control in Australian general practice settings during the COVID-19 pandemic.MethodsWe used a serial cross-sectional study design of patient record data from general practices representative of the Nepean Blue Mountains Local Health District between 2020 and 2022. Aggregated patient records were analysed to determine percentages of subgroups with a blood glycaemic testing interval consistent with guidelines (≥1 within 15 months) and achieving target glycaemic control (by glycated haemoglobin of ≤7%). Linear regression models were used to test the association between independent and dependent variables, and to generate regression coefficients and 95% CI, corrected for time trends.ResultsOf the average 14 356 patient records per month, 55% were male, 53% had a body mass index (BMI) <30 and 55% were aged 55–74 years. Compliance to testing guidelines slightly decreased (75–73%) but was positively associated with male sex (2.5%, 95% CI 1.7%, 3.4%), BMI≥30 (9.6%, 95% CI 8.8%, 10.4%) and 55–74 years (7.5%, 95% CI 6.6%, 8.5%) and 75 years and over age groups (7.1%, 95% CI 6.2%, 7.9%). Mean percentage of patient records achieving target glycaemic control slightly increased and was negatively associated with male sex (−3.7%, 95% CI −5.2%, –2.2%), but positively associated with 55–74 years (4.5%, 95% CI 3.8%, 5.1%) and 75 years and over age groups (12.2%, 95% CI 4.5%, 20.0%). Compliance to testing guidelines increased with each additional general practice per 10 000 persons (8.4%, 95% CI 4.9%, 11.8%).ConclusionsDuring the COVID-19 pandemic, people with type 2 diabetes in Australia continued to follow glycaemic testing guidelines at the same rate. In fact, there was a slight improvement in glycaemic control among all subgroups of patients, including those at higher risk. These findings are encouraging, but the longer term impact of COVID-19 on type 2 diabetes care is still unclear.
Growth differentiation factor-15 in patients with or at risk of heart failure but before first hospitalisation
Authors: Bradley Joshua , Schelbert Erik B , Bonnett Laura J , Lewis Gavin A , Lagan Jakub , Orsborne Christopher , Brown Pamela Frances , Black Nicholas , Naish Josephine H , Williams Simon G , McDonagh Theresa , Schmitt Matthias , Miller Christopher A 
Published: August 2023

ObjectiveIdentification of patients at risk of adverse outcome from heart failure (HF) at an early stage is a priority. Growth differentiation factor (GDF)-15 has emerged as a potentially useful biomarker. This study sought to identify determinants of circulating GDF-15 and evaluate its prognostic value, in patients at risk of HF or with HF but before first hospitalisation.MethodsProspective, longitudinal cohort study of 2166 consecutive patients in stage A–C HF undergoing cardiovascular magnetic resonance and measurement of GDF-15. Multivariable linear regression investigated determinants of GDF-15. Cox proportional hazards modelling, Net Reclassification Improvement and decision curve analysis examined its incremental prognostic value. Primary outcome was a composite of first hospitalisation for HF or all-cause mortality. Median follow-up was 1093 (939–1231) days.ResultsMajor determinants of GDF-15 were age, diabetes and N-terminal pro-B-type natriuretic peptide, although despite extensive phenotyping, only around half of the variability of GDF-15 could be explained (R20.51). Log-transformed GDF-15 was the strongest predictor of outcome (HR 2.12, 95% CI 1.71 to 2.63) and resulted in a risk prediction model with higher predictive accuracy (continuous Net Reclassification Improvement 0.26; 95% CI 0.13 to 0.39) and with greater clinical net benefit across the entire range of threshold probabilities.ConclusionIn patients at risk of HF, or with HF but before first hospitalisation, GDF-15 provides unique information and is highly predictive of hospitalisation for HF or all-cause mortality, leading to more accurate risk stratification that can improve clinical decision making.Trial registration numberNCT02326324.
Palliative sedation: ethics in clinical practice guidelines – systematic review
Authors: Tomczyk Martyna , Jaques Cécile , Jox Ralf J 
Published: August 2023

ObjectivesThe objective of our study was to determine whether, and to what degree, the ethical dimension was present in clinical practice guidelines (CPGs) on palliative sedation, and to identify the ethical issues with respect to the different forms of this practice. The purpose was purely to be descriptive; our aim was not to make any kind of normative judgements on these ethical issues or to develop our own ethical recommendations.MethodsWe performed a systematic review of CPGs on the palliative sedation of adults, focusing our analysis on the ethical dimension of these texts and the ethical issues of this practice. The study protocol is registered on PROSPERO.ResultsIn total, 36 current CPGs from four continents (and 14 countries) were included in our analysis. Generally, ethics was rarely referred to or absent from the CPGs. Only six texts contained a specific section explicitly related to ethics. Ethical issues were named, conceptualised and presented in heterogeneous, often confusing ways. It was impossible to identify the ethical issues of each form of palliative sedation. Ethics expertise was not involved in the development of most of the CPGs and, if it was, this did not always correlate with the ethical dimension of the document.ConclusionsEffective cooperation between palliative care clinicians and ethicists should be encouraged, in order to integrate in particular the crucial ethical issues of continuous deep sedation until death when developing or updating CPGs on palliative sedation.