bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolving biology’s dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon
Authors: Hartop Emily , Lee Leshon , Srivathsan Amrita , Jones Mirkka , Peña-Aguilera Pablo , Ovaskainen Otso , Roslin Tomas , Meier Rudolf 
Published: September 2024

Abstract
Background
Zoology’s dark matter comprises hyperdiverse, poorly known taxa that are numerically dominant but largely unstudied, even in temperate regions where charismatic taxa are well understood. Dark taxa are everywhere, but high diversity, abundance, and small size have historically stymied their study. We demonstrate how entomological dark matter can be elucidated using high-throughput DNA barcoding (“megabarcoding”). We reveal the high abundance and diversity of scuttle flies (Diptera: Phoridae) in Sweden using 31,800 specimens from 37 sites across four seasonal periods. We investigate the number of scuttle fly species in Sweden and the environmental factors driving community changes across time and space.

Results
Swedish scuttle fly diversity is much higher than previously known, with 549 putative species detected, compared to 374 previously recorded species. Hierarchical Modelling of Species Communities reveals that scuttle fly communities are highly structured by latitude and strongly driven by climatic factors. Large dissimilarities between sites and seasons are driven by turnover rather than nestedness. Climate change is predicted to significantly affect the 47% of species that show significant responses to mean annual temperature. Results were robust regardless of whether haplotype diversity or species-proxies were used as response variables. Additionally, species-level models of common taxa adequately predict overall species richness.

Conclusions
Understanding the bulk of the diversity around us is imperative during an era of biodiversity change. We show that dark insect taxa can be efficiently characterised and surveyed with megabarcoding. Undersampling of rare taxa and choice of operational taxonomic units do not alter the main ecological inferences, making it an opportune time to tackle zoology’s dark matter.
Dietary patterns and cardiorespiratory fitness in midlife and subsequent all-cause dementia: findings from the Cooper Center Longitudinal Study
Authors: Meernik Clare , Eilat-Adar Sigal , Leonard David , Barlow Carolyn E. , Gerber Yariv , Tesler Riki , Byker Shanks Carmen , Pettee Gabriel Kelley , Pavlovic Andjelka , DeFina Laura F. , Shuval Kerem 
Published: September 2024

Abstract
Background
Identifying lifestyle factors that independently or jointly lower dementia risk is a public health priority given the limited treatment options available to patients. In this cohort study, we examined the associations between Mediterranean or Dietary Approaches to Stop Hypertension (DASH) diet adherence and cardiorespiratory fitness (CRF) with later-life dementia, and assessed whether the associations between dietary pattern and dementia are modified by CRF.

Methods
Data are from 9,095 adults seeking preventive care at the Cooper Clinic (1987–1999) who completed a 3-day dietary record and a maximal exercise test. Alzheimer’s disease and related disorders or senile dementia (i.e., all-cause dementia) was identified from Medicare administrative claims (1999–2019). Illness-death models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the associations between Mediterranean or DASH diet adherence (primary exposure), CRF (secondary exposure), and all-cause dementia, adjusted for demographic and clinical factors. An interaction term was included between diet score and CRF to assess effect modification by CRF.

Results
The mean age at baseline was 50.6 (standard deviation [SD]: 8.4) years, and a majority of the study sample were men (77.5%) and White (96.4%). 1449 cases of all-cause dementia were identified over a mean follow-up of 9.2 (SD: 5.8) years. Neither Mediterranean nor DASH diet adherence was associated with dementia risk in fully adjusted models (HR per SD of Mediterranean diet score: 1.00, 95% CI: 0.94, 1.05; HR per SD of DASH diet score: 1.02, 95% CI: 0.96, 1.08). However, participants with higher CRF had a decreased hazard of dementia (HR, per metabolic equivalent of task [MET] increase, Mediterranean model: 0.95, 95% CI: 0.92, 0.98; HR, per MET increase, DASH model: 0.96, 95% CI: 0.92, 0.97). No effect modification by CRF was observed in the association between diet and dementia.

Conclusions
In this sample of apparently healthy middle-aged adults seeking preventive care, higher CRF at midlife was associated with a lower risk of all-cause dementia, though adherence to a Mediterranean or DASH diet was not, and CRF did not modify the diet-dementia association. CRF should be emphasized in multimodal interventions for dementia prevention and investigated among diverse samples.
Differential susceptibility of human motor neurons to infection with Usutu and West Nile virus
Authors: Marshall Eleanor M. , Bauer Lisa , Nelemans Tessa , Sooksawasdi Na Ayudhya Syriam , Benavides Feline , Lanko Kristina , de Vrij Femke M. S. , Kushner Steven A. , Koopmans Marion , van Riel Debby , Rockx Barry 
Published: September 2024

AbstractWest Nile virus (WNV) and Usutu virus (USUV) are closely related flaviviruses with differing capacities to cause neurological disease in humans. WNV is thought to use a transneural route of neuroinvasion along motor neurons and causes severe motor deficits. The potential for use of transneural routes of neuroinvasion by USUV has not been investigated experimentally, and evidence from the few clinical case reports of USUV-associated neuroinvasive disease is lacking. We hypothesised that, compared with WNV, USUV is less able to infect motor neurons, and therefore determined the susceptibility of human induced pluripotent stem cell (iPSC)-derived spinal cord motor neurons to infection. Both viruses could grow to high titres in iPSC-derived neural cultures. However, USUV could not productively infect motor neurons due to restriction by the antiviral response, which was not induced upon WNV infection. Inhibition of the antiviral response allowed for widespread infection and transportation of USUV along motor neurons within a compartmented culture system. These results show a stark difference in the ability of these two viruses to evade initiation of intrinsic antiviral immunity. Our data suggests that USUV cannot infect motor neurons in healthy individuals but in case of immunodeficiency may pose a risk for motor-related neurological disease and transneural invasion.
Assessing the health status of migrants upon arrival in Europe: a systematic review of the adverse impact of migration journeys
Authors: Canova Cristina , Dansero Lucia , Destefanis Cinzia , Benna Clara , Rosato Isabella 
Published: September 2024

Abstract
Background
Numerous studies have explored the impact of pre- and post-migration factors on the overall health of migrant populations. The objective of this study is to enhance our understanding of additional determinants affecting migrants' health by examining the impact of the migration phase and related journeys in the European context.

Methods
We conducted a systematic review of studies published in the MEDLINE, Embase, and Scopus databases from 2003 up to January 5, 2024. We included observational studies reporting information on the health status of migrant populations recorded upon arrival in a country situated in Europe, and on the transit phase, including specific risk factors experienced during the journey or its characteristics. Title and abstract screening were performed using active learning techniques provided by ASReview software. The results of the included studies were presented qualitatively, with a focus on publications that formally assessed the association between the journey and the investigated health outcomes. The systematic review was registered on PROSPERO, CRD42024513421.

Results
Out of 11,370 records screened, we ultimately included 25 studies, all conducted since 2017. Most adopted a cross-sectional design and a quantitative approach, with relatively small sample sizes. The majority of the studies were conducted in Serbia and Italy. Only 14 of them formally assessed the association between different exposures in the transit phase and health outcomes, including mental health, well-being and quality of life, infectious and non-communicable diseases.

Conclusion
Epidemiological research focusing on the transit phase in Europe remains limited, with few available studies facing challenges related to data collection, study design and analysis, thereby limiting the interpretability and generalisability of their results. These findings underscore the need for action, prompting the development of adequate and feasible strategies to conduct additional studies focusing on migrant populations during migration journeys.
PROs for RARE: protocol for development of a core patient reported outcome set for individuals with genetic intellectual disability
Authors: van Silfhout Nadia Y. , van Muilekom Maud M. , van Karnebeek Clara D. , Haverman Lotte , van Eeghen Agnies M. 
Published: September 2024

Abstract
Introduction
Rare genetic neurodevelopmental disorders and intellectual disability (ID), collectively called genetic ID (GID), can profoundly impact daily functioning and overall well-being of affected individuals. To improve our understanding of the impact of GID and advancing both care and research, measuring relevant patient reported outcomes (PROs) is crucial. Currently, various PROs are measured for GID. Given the shared comorbidities across disorders, we aim to develop a generic core PRO set for children and adults with GID.

Methods and results
Developing the generic core PRO set entails the following steps: 1) providing an overview of potentially relevant PROs by scoping reviews and qualitative research; 2) integrating and conceptualizing these PROs (i.e., describing the content of the PROs in detail) into a pilot generic core PRO set; and 3) prioritizing relevant PROs by a European Delphi survey and consensus meetings.

Conclusions
This protocol presents the steps for developing a generic core PRO set for children and adults with GID. The next step involves selecting suitable patient reported outcome measures (PROMs) to adequately measure these PROs: the generic core PROM set. This generic core PROM set needs validation in the GID population, and eventually implementation in care and research, facilitating the aggregation and analysis of PRO data and guaranteeing continuous integration of the patient perspective in both care and research.
Real-world treatment outcomes for Hodgkin lymphoma in South Africa: a prospective observational study
Authors: Vogt Samantha L. , Laudin Garrick , Zahurak Marianna , Vaughan Jenifer , Lakha Atul , Pather Sugeshnee , Waja Ziyaad , Chetty Deshan , Omar Tanvier , Stevens Wendy , Ashmore Philippa , Otwombe Kennedy , Hlongwane Khuthadzo , Varadhan Ravi , Patel Moosa , Ambinder Richard F. , Martinson Neil A. , Xian Rena R. , Philip Vinitha 
Published: September 2024

Abstract
Background
Prospective data from sub-Saharan Africa suggests that treatment outcomes for people living with HIV (PWH) with Hodgkin lymphoma (HL) are similar to those without HIV. However, real-world data from high-resource settings and retrospective studies from sub-Saharan Africa, suggest inferior outcomes. We set out to evaluate the real-world treatment outcomes for HL in South Africa to better understand the disparate outcomes.

Methods
We established a prospective, observational cohort of newly diagnosed, adult (≥ 18 years) HL cases recruited from Chris Hani Baragwanath Academic and Netcare Olivedale Hospitals in Johannesburg, South Africa between March 2021 and March 2023. Participants were followed for up to 18 months after enrollment with data censored on December 23rd, 2023. The primary endpoint was 1-year overall survival.

Results
We enrolled 47 participants with HL including 31 PWH and 16 HIV-negative. Advanced stage disease and B symptoms were common at time of diagnosis irrespective of HIV status. Bone marrow biopsy, performed during the work-up and evaluation of cytopenias, provided the initial diagnosis of HL in 16/31 (52%) PWH. HIV status and bone marrow involvement were associated with early mortality (within 3 months of diagnosis) and a poorer 1-year overall survival from diagnosis (HIV: 55% vs. 88%; p = 0.03; bone marrow involvement: 50% vs. 80%; p = 0.02). Among evaluable participants, those that received at least 6 cycles of chemotherapy and underwent response assessment, there was no difference between those with and without HIV.

Conclusion
Traditional laboratory markers of poor prognosis including anemia, lymphopenia and hypoalbuminemia were more common among PWH and those with bone marrow involvement and suggest high risk disease. A better understanding of the drivers of these aggressive presentations is warranted to ensure more PWH are able to tolerate chemotherapy.
Imerslund-Gräsbeck syndrome in a child with a novel compound heterozygous mutations in the AMN gene: a case report
Authors: Zhang Dedong , Liu Siying , Xi Bixin , Zhu Yongbing , Chen Yu , Zhang Jiasi , Liu Aiguo 
Published: September 2024

Abstract
Background
Imerslund-Gräsbeck syndrome (IGS) is an autosomal recessive disorder characterized by selective vitamin B12 malabsorption, resulting in vitamin B12 deficiency and impaired reabsorption of proximal tubular proteins.This case highlights a previously unidentified compound heterozygous variant in the Amnionless (AMN) gene that causes IGS syndrome and underscores the importance of long-term oral vitamin B12 replacement therapy in managing the condition.

Case presentation
In this retrospective analysis, we present the clinical data of a 3-year and 6-month-old female child diagnosed with IGS at Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, China, in November 2018. The child was admitted to the hospital due to a history of anemia persisting for over a month. There was no previous significant medical history. The admission examination revealed megaloblastic anemia with proteinuria. Serum vitamin B12 levels were decreased, while folic acid and renal function were normal. The patient was diagnosed with megaloblastic anemia and started long-term oral vitamin B12 replacement therapy. Throughout the follow-up period, blood tests consistently showed normal results, while proteinuria persisted. In November 2019, the child and her parents underwent whole exome sequencing analysis, which revealed a novel compound heterozygous variant in the AMN gene: c.162 + 1G > A and c.922 C > T (p.Q308X) in the child, c.162 + 1G > A in the father, and c.922 C > T (p.Q308X) in the mother. Therefore, this child was further diagnosed with IGS.

Conclusions
In this case, whole exome sequencing proves to be highly practical in daily healthcare for diagnosing and refining rare or ultra-rare diseases with ambiguous phenotypes or genetic diversity. It is also valuable for prognostic evaluation and personalized management. Additionally, the oral vitamin B12 treatment demonstrated positive clinical effects for the child, offering a new option for patients unable to undergo intramuscular vitamin B12 replacement therapy.
The effect of benzylpenicillin prohylaxis after birth on length and weight of syphilis-exposed infants in eastern China
Authors: Chen Kejin , Zhao Xiaoyan , Wu Wei , Jiang Lihua , Yuan Xiaojie , Bian Chaorong 
Published: September 2024

Abstract
Background
We conducted this study to assess the impact of an intervention to interrupt mother-to-child transmission on the height and weight of syphilis-exposed infants after receiving penicillin prophylaxis after birth and to provide a scientific basis for further elimination of mother-to-child transmission.

Methods
We recruited 419 infants born to syphilis-infected mothers from 2015 to 2020 in Changzhou, and performed 1:1 matching to infants born to syphilis-free mothers during the same period. All infants were followed up to 18 months of age. We collected height and weight data and compared them.

Results
At 18 months of age, the height and weight of the syphilis-exposed infants were almost greater than the WHO reference standards. However, when compared with local unexposed infants, there were almost no differences. The boys born to mothers who received two courses of treatment had longer body lengths at 18 months of age than did those born to mothers who did not receive two courses of treatment, and the girls born to mothers who did not receive treatment had lower body weights at 3 months of age than did both treated groups.

Conclusion
The growth trajectory of infants without congenital syphilis born to syphilis-infected mothers is virtually indistinguishable from that of the general local population. Syphilis-exposed newborns can receive preventive treatment as a public health intervention.
PMS2 mutation spectra in Norway and risk of cancer for carriers of pathogenic variants
Authors: Sjursen Wenche , Hyldebrandt Hanne K. , Lavik Liss Anne S. , Haukanes Bjørn Ivar , Ariansen Sarah , Briskemyr Siri , Sylvander Anna E. , Haavind Marianne T. , Olsen Maren F. , Røyset Elin S. , Vetti Hildegunn , Stormorken Astrid , Grindedal Eli Marie 
Published: September 2024

Abstract
Background
In Norway, we have offered testing of PMS2 since 2006, and have a large national cohort of carriers. The aim of this study was to describe all PMS2 variants identified, and to describe frequency, spectrum and penetrance of cancers in carriers of class 4/5 variants.

Methods
All detected PMS2 variants were collected from the diagnostic laboratories and reclassified according to ACMG criteria and gene specific guidelines. Data on variant, gender, cancer diagnosis, age at diagnosis, and age at last known follow-up was collected on all carriers of class 4/5 variants from electronic patient records. The Kaplan-Meier algorithm was used to calculate cumulative risk of any cancer, colorectal cancer and endometrial cancer.

Results
In total, 220 different PMS2 variants were detected. Twenty nine class 4/5 variants were identified in 482 carriers. The most common pathogenic variant was the founder mutation c.989-1G > T, detected in 204 patients from 58 families. Eighty seven out of 482 (18.0%) had been diagnosed with colorectal cancer, 10 of these (11.8%) before 40 years. Cumulative risk at 70 years in our cohort was 34.7% for colorectal cancer and 26.1% for endometrial cancer.

Conclusions
After 15 years of genetic testing, 29 different class 4/5 variants have been detected in Norway. Almost half of Norwegian PMS2 carriers have the founder variant 989-1G > T. Penetrance of colorectal cancer in our cohort was moderate but variable, as 11.5% of those diagnosed were younger than 40 years.
Recommendations for developing accessible patient information leaflets for clinical trials to address English language literacy as a barrier to research participation
Authors: Wylde Vikki , Brennan Sharon , Johnson Emma , Roberts Kirsty , Beswick Andrew D. , Jameson Catherine 
Published: September 2024

Abstract
Background
Low English language literacy is a common barrier to participation in clinical trials. Patient information leaflets (PILs) used in clinical trials are often lengthy, complex and have poor readability; this is a persistent and prevalent problem common to trials across the world. Simplifying the information provided in PILs can lead to improved understanding, comprehension and knowledge.
The aim of this project was to develop recommendations for developing accessible PILs for clinical trials through a literature review of published and grey literature and co-working with marginalised communities, patients, and health and social care charities.

Methods
A literature review of MEDLINE, Embase and online resources was conducted, and recommendations for developing accessible PILs were extracted from eligible published and grey literature. Grey literature which contained insights into more inclusive forms of communication was also identified and summarised. Meetings were held with two racially marginalised community groups, two groups involving autistic adults and/or adults with learning difficulties and a patient advisory group. Examples of accessible PILs were shared and discussions held about the content and format of the PILs and suggestions for changes/improvements. National Voices, a coalition of health and social care charities in England, held a national online workshop with charities and lived experience partners. Recommendations identified from the multiple sources were coded, collated and refined to develop an overarching framework of recommendations.

Results
The framework consists of 74 recommendations for developing accessible PILs for clinical trials. Recommendations cover the five topics of formatting, information presentation, writing style, content and accessibility.

Conclusions
This project has developed a comprehensive framework of recommendations to guide researchers in the development of accessible PILs for clinical trials. Findings from previous research and from co-working with marginalised communities, patients and health and social care charities were collated to ensure that a diverse range of voices and experiences informed the framework. These recommendations aim to support researchers to develop better study information to reduce English language literacy as a barrier to participation in clinical trials.
Research progress and challenges of the PD-1/PD-L1 axis in gliomas
Authors: Jiacheng Dong , Jiayue Cui , Ying Guo , Shaohua Wang , Wenhui Liu , Xinyu Hong 
Published: September 2024

AbstractThe emergence of programmed death-1 (PD-1) and programmed death ligand 1 (PD-L1) immunosuppressants provides new therapeutic directions for various advanced malignant cancers. At present, PD-1/PD-L1 immunosuppressants have made significant progress in clinical trials of some gliomas, but PD-1/PD-L1 inhibitors have not yet shown convincing clinical efficacy in gliomas. This article summarizes the research progress of the PD-1 /PD-L1 pathway in gliomas through the following three aspects. It mainly includes the complex expression levels and regulatory mechanisms of PD-1/PD-L1 in the glioma microenvironment, the immune infiltration in glioma immunosuppressive microenvironment, and research progress on the application of PD-1/PD-L1 immunosuppressants in clinical treatment trials for gliomas. This will help to understand the current treatment progress and future research directions better.