bluuebunny/crossref_metadata_2025_split huggingface dataset:
CellBoost: A pipeline for machine assisted annotation in neuroanatomy
Authors: Qian Kui , Friedman Beth , Takatoh Jun , Wang Fan , Kleinfeld David , Freund Yoav 
Published: September 2023

AbstractOne of the important yet labor intensive tasks in neuroanatomy is the identification of select populations of cells. Current high-throughput techniques enable marking cells with histochemical fluorescent molecules as well as through the genetic expression of fluorescent proteins. Modern scanning microscopes allow high resolution multi-channel imaging of the mechanically or optically sectioned brain with thousands of marked cells per square millimeter. Manual identification of all marked cells is prohibitively time consuming. At the same time, simple segmentation algorithms suffer from high error rates and sensitivity to variation in fluorescent intensity and spatial distribution. We present a methodology that combines human judgement and machine learning that serves to significantly reduce the labor of the anatomist while improving the consistency of the annotation. As a demonstration, we analyzed murine brains with marked premotor neurons in the brainstem. We compared the error rate of our method to the disagreement rate among human anatomists. This comparison shows that our method can reduce the time to annotate by as much as ten-fold without significantly increasing the rate of errors. We show that our method achieves significant reduction in labor while achieving an accuracy that is similar to the level of agreement between different anatomists.
Characterization of sinking and suspended microeukaryotic communities in spring Oyashio waters
Authors: Yang Qingwei , Yang Yanhui , Xia Jun , Fukuda Hideki , Okazaki Yusuke , Nagata Toshi , Ogata Hiroyuki , Endo Hisashi 
Published: September 2023

AbstractMicroeukaryotes are important components of sinking particles contributing to carbon export from the surface to deep oceans. The knowledge of the sinking microeukaryotic communities and their dynamics is limited. We applied 18S rDNA metabarcoding method to investigate the microeukaryotic communities in sinking and suspended particles distinguished by marine snow catchers (MSC) during spring in the Oyashio region. Sinking particles displayed distinct communities and lower diversity than did suspended particles. The community compositions of the sinking particles varied with depth, suggesting that microeukaryotes were selectively removed through disaggregation or decomposition during settling. Prymnesiophyceae and diatoms were effectively removed, as indicated by their decreased abundance in the sinking particles at increasing depths. Conversely, phototrophic dinoflagellates maintained a higher abundance in the sinking particles across depths, indicating resistance to disaggregation and decomposition. Heterotrophic dinoflagellates and Spirotrichea were enriched in sinking particles and marine stramenopiles (MAST) groups were enriched in suspended particles. Sinking heterotrophic protist communities in the deep layers were similar to those in the surface layers, whereas they differed from the suspended ones in the same layer. Therefore, heterotrophic protists in surface layers were transported to deeper layers. Overall, our results demonstrate the functional differences among microeukaryotes in the biological carbon pump.
Selection of Ethanol Tolerant Strains ofCandida albicansby Repeated Ethanol Exposure Results in Strains with Reduced Susceptibility to Fluconazole
Authors: Day Andrew W. , Kumamoto Carol A. 
Published: September 2023

AbstractCandida albicansis a commensal yeast that has important impacts on host metabolism and immune function, and can establish life-threatening infections in immunocompromised individuals. Previously,C. albicanscolonization has been shown to contribute to the progression and severity of alcoholic liver disease. However, relatively little is known about howC. albicansresponds to changing environmental conditions in the GI tract of individuals with alcohol use disorder, namely repeated exposure to ethanol. In this study, we repeatedly exposedC. albicansto high concentrations (10% vol/vol) of ethanol—a concentration that can be observed in the upper GI tract of humans following consumption of alcohol. Following this repeated exposure protocol, ethanol small colony (Esc) variants ofC. albicansisolated from these populations exhibited increased ethanol tolerance, altered transcriptional responses to ethanol, and cross-resistance/tolerance to the frontline antifungal fluconazole. These Esc strains exhibited chromosomal copy number variations and carried polymorphisms in genes previously associated with the acquisition of fluconazole resistance during human infection. This study identifies a selective pressure that can result in evolution of fluconazole tolerance and resistance without previous exposure to the drug.
Hepatitis C Virus Infection and Risk of Non-Hodgkin’s Lymphoma: A Case-control Study in Mainland China
Authors: Hao Miao , Wang Wenjun , Lu Rui , Liu Yixin , Wu Fengping , Li Yaping , Jia Xiaoli , Dang Shuangsuo , Zhang Xin 
Published: September 2023

SummaryIn order to evaluate the association between hepatitis C virus (HCV) and non-Hodgkin’s lymphoma (NHL) in Mainland China, we conducted a hospital case-control study. Cases were newly diagnosed patients with NHL between 2009 and 2015 admitted to the Second Affiliated Hospital of Xi’an Jiaotong University. Controls were gender and age matched patients admitted to the same hospital due to acute conditions. A total of 694 cases and controls (1 : 1 ratio) were identified. Anti-HCV prevalence was 1.7% in NHL cases and 2.3% in controls (6/347vs. 8/347, OR = 0.75, 95% CI 0.26-2.17). Such prevalence in NHL cases (1.7%; 95% CI 0.6%-3.7%) does not differ from that in the Xi’an population (1.9%) or that in the general Chinese population (1.3%). HCV-RNA positivity was 0.9% in both NHL cases and controls using the available data (OR = 1.00, 95% CI 0.20-4.99). Subgroup analyses by histologic type of NHL or Epstein-Barr virus infection also showed no associations between anti-HCV and NHL. In conclusion, HCV is not associated with NHL risk in Mainland China, suggesting that the role of HCV in the occurrence of NHL is not significant in this population.
Estimating the population effectiveness of interventions against COVID-19 in France: a modelling study
Authors: Ganser Iris , Buckeridge David L , Heffernan Jane , Prague Mélanie , Thiébaut Rodolphe 
Published: September 2023

AbstractBackgroundNon-pharmaceutical interventions (NPIs) and vaccines have been widely used to manage the COVID-19 pandemic. However, uncertainty persists regarding the effectiveness of these interventions due to data quality issues, methodological challenges, and differing contextual factors. Accurate estimation of their effects is crucial for future epidemic preparedness.MethodsTo address this, we developed a population-based mechanistic model that includes the impact of NPIs and vaccines on SARS-CoV-2 transmission and hospitalization rates. Our statistical approach estimated all parameters in one step, accurately propagating uncertainty. We fitted the model to comprehensive epidemiological data in France from March 2020 to October 2021. With the same model, we simulated scenarios of vaccine rollout.ResultsThe first lockdown was the most effective, reducing transmission by 84% (95% confidence interval (CI) 83-85). Subsequent lockdowns had diminished effectiveness (reduction of 74% (69-77) and 11% (9-18), respectively). A 6 pm curfew was more effective than one at 8 pm (68% (66-69) vs. 48% (45-49) reduction), while school closures reduced transmission by 15% (12-18). In a scenario without vaccines before November 2021, we predicted 159,000 or 168% (95% prediction interval (PI) 70-315) more deaths and 1,488,000 or 300% (133-492) more hospitalizations. If a vaccine had been available after 100 days, over 71,000 deaths (16,507-204,249) and 384,000 (88,579-1,020,386) hospitalizations could have been averted.ConclusionOur results highlight the substantial impact of NPIs, including lockdowns and curfews, in controlling the COVID-19 pandemic. We also demonstrate the value of the 100 days objective of the Coalition for Epidemic Preparedness Innovations (CEPI) initiative for vaccine availability.
Genetic Variations in TrkB.T1 Isoform and Their Association with Somatic and Psychological Symptoms in Individuals with IBS
Authors: Hong H. , Mocci E. , Kamp K. , Zhu S. , Cain K.C. , Burr R. L. , Perry J. , Heitkemper M. M , Weaver-Toedtman K. R. , Dorsey S.G 
Published: September 2023

AbstractIrritable bowel syndrome (IBS), a disorder of gut-brain interaction, is often comorbid with somatic pain and psychological disorders. Dysregulated signaling of brain-derived neurotrophic factor (BDNF) and its receptor, tropomyosin-related kinase B (TrkB), has been implicated in somatic-psychological symptoms in individuals with IBS. Thus, we investigated the association of 10 single nucleotide polymorphisms (SNPs) in the regulatory 3’ untranslated region (UTR) ofNTRK2(TrkB) kinase domain-deficient truncated isoform (TrkB.T1) and theBDNFVal66Met SNP with somatic and psychological symptoms and quality of life in a U.S. cohort (IBS n=464; healthy controls n=156). We found that the homozygous recessive genotype (G/G) of rs2013566 in individuals with IBS is associated with worsened somatic symptoms, including headache, back pain, joint pain, muscle pain, and somatization as well as diminished sleep quality, energy level and overall quality of life. Validation using U.K. BioBank (UKBB) data confirmed the association of rs2013566 with increased likelihood of headache. Several SNPs (rs1627784, rs1624327, rs1147198) showed significant associations with muscle pain in our U.S. cohort. Notably, these SNPs are predominantly located in H3K4Me1-enriched regions, suggesting their enhancer and/or transcription regulation potential. Together, our findings suggest that genetic variation within the 3’UTR region of the TrkB.T1 isoform may contribute to comorbid conditions in individuals with IBS, resulting in a spectrum of somatic and psychological symptoms that may influence their quality of life. These findings advance our understanding of the genetic interaction between BDNF/TrkB pathways and somatic-psychological symptoms in IBS, highlighting the importance of further exploring this interaction for potential clinical applications.
Qualitative exploration of patients’ experiences with Intrabeam targeted intraoperative radiotherapy (TARGIT-IORT) and External-Beam Radiotherapy Treatment (EBRT)
Authors: Bagga Sandeep , Swiderska Natalie , Hooker Charlotte , Royle Jenny , O’Connor Marie Ennis , Freeney Siobhan , Watson Dympna , Woolcock Robin 
Published: September 2023

AbstractFor patients with early breast cancer undergoing breast conserving surgery, radiotherapy is given either as a post-operative course of External-Beam RadioTherapy (EBRT), given daily for over a number of days and often weeks, or with TARGeted Intrabeam Intraoperative radioTherapy (TARGIT-IORT), which is delivered, during surgery under the same anaesthetic. Several studies have reported the quantitative Quality-of-Life (QoL) benefits of TARGIT-IORT over EBRT. This qualitative study was designed to gather a deep understanding of the benefits and impacts of receiving EBRT or TARGIT-IORT as perceived by patients. It also captured how differently the treatments affected the lived experience of the patient and their care partner through their treatment journey.A patient-led Working Group was established to guide study design, delivery and to help validate findings. Patients with experience of receiving EBRT or TARGIT-IORT were first purposively sampled by Hampshire Hospitals NHS Foundation Trust after which a randomiser was applied to ensure the final selection process was free from bias. In February and March 2023, 29 semi-structured interviews (15 EBRT, 14 TARGIT-IORT) were conducted virtually via Zoom. Thematic analysis of verbatim interview transcripts was then carried out by two coders generating 11 themes related to either EBRT or TARGIT-IORT.A number of procedural grievances were noted among EBRT patients. EBRT was perceived as being disruptive to a range of normal routines (work, home-life, and the burden of travel), and dissatisfying due to discomfort of side effects. TARGIT-IORT was perceived by patients and care partners as being efficient (given while they are asleep during surgery and without additional hospital visits) with minimal if any disruptions to QoL and that it was the safer option. The need for adequate, accessible information provision at the right time to reduce anxieties was noted in both cohorts. These new insights are valuable for healthcare staff and policy makers and could help incorporate the two treatments into routine practice. Further research is now needed to explore TARGIT-IORT in more diverse populations and in the 35 other countries where it is already a well- established treatment option.
Mechanisms for Integrating Real Data into Search Game Simulations: An Application to Winter Health Service Pressures and Preventative Policies
Authors: Chapman Martin , G-Medhin Abigail , Daneshi Kian , Bramwell Tom , Durbaba Stevo , Curcin Vasa , Parmar Divya , Boulding Harriet , Becares Laia , Morgan Craig , Molokhia Mariam , McBurney Peter , Harding Seeromanie , Wolfe Ingrid , Ashworth Mark , Poston Lucilla 
Published: September 2023

AbstractWhile modelling and simulation are powerful techniques for exploring complex phenomena, if they are not coupled with suitable real-world data any results obtained are likely to require extensive validation. We consider this problem in the context of search game modelling, and suggest that both demographic and behaviour data are used to configure certain model parameters. We show this integration in practice by using a combined dataset of over 150,000 individuals to configure a specific search game model that captures the environment, population, interventions and individual behaviours relating to winter health service pressures. The presence of this data enables us to more accurately explore the potential impact of service pressure interventions, which we do across 33,000 simulations using a computational version of the model. We find government advice to be the best-performing intervention in simulation, in respect of improved health, reduced health inequalities, and thus reduced pressure on health service utilisation.
Are the rise in childhood obesity rates leading an increase in hospitalizations due to dengue?
Authors: Jeewandara Chandima , Karunananda Maneshka Vindesh , Fernando Suranga , Danasekara Saubhagya , Jayakody Gamini , Arulkumaran S. , Samaraweera N.Y. , Kumarawansha Sarathchandra , Sivaganesh Subramaniyam , Amarasinghe P. Geethika , Jayasinghe Chintha , Wijesekara Dilini , Marasinghe Manonath Bandara , Mambulage Udari , Wijayatilake Helanka , Senevirathne Kasun , Bandara A.D.P , Gallage C.P. , Colambage N.R. , Udayasiri A.A. Thilak , Lokumarambage Tharaka , Upasena Y. , Weerasooriya W.P.K.P. ,   seroprevalence study group, Ogg Graham S. , Malavige Gathsaurie Neelika 
Published: September 2023

AbstractBackgroundObesity and diabetes are known risk factors for severe dengue. The prevalence of obesity has markedly increased in many dengue endemic countries and the association of obesity with increased risk of hospitalization has not been previously been studied.Methods and findingsChildren aged 10 to 20 years (n=5207), were recruited from nine districts in Sri Lanka using a stratified multi-stage cluster sampling method. Details of previous admissions to hospital due to dengue and anthropometric measurements were recorded and seropositivity rates for dengue were assessed. The body mass index centile (BMI) in children aged 10 to 18, was derived by plotting the values on the WHO BMI-for-age growth charts, to acquire the percentile ranking. For participants aged >18 years of age, BMI was calculated and interpretated as for adults and a BMI of > 23.9 kg/m2were considered as obese.Although the dengue seropositivity rates were similar in children of the different BMI centiles, 12/66 (18.2%) seropositive children with BMI centile >97th, had been hospitalized for dengue, compared to 103/1086 (9.48%) of children with a BMI centile of <97th. Therefore, those with a BMI centile of >97th, were twice as likely (odds ratio 2.1, 95% CI, 1.1 to 3.9, p=0.03) to have been hospitalized for dengue compared to children with a lower BMI. In those >18 years of age, obese individuals were again significantly more likely to have been hospitalized compared to leaner individuals (odds ratio 2.6, 95% CI, 1.0 to 6.1, p=0.04).ConclusionsObesity appears to increase the risk of hospitalization in those with dengue, highlighting the importance of creating awareness regarding obesity and risk of severe disease and hospitalization in dengue endemic countries.
Outbreak of severe community-acquired bacterial infections fromStreptococcus pyogenes, Streptococcus pneumoniae, Neisseria meningitidis, andHaemophilus influenzaeamong children in North Rhine-Westphalia (Germany), October to December 2022
Authors: Goretzki Sarah C. , van der Linden Mark , Itzek Andreas , Hühne Tom , Adelmann Roland O. , Ala Eldin Firas , Albarouni Mohamed , Becker Jan-Claudius , Berghäuser Michael A. , Boesing Thomas , Boeswald Michael , Brasche Milian , Brevis Francisco , Camara Rokya , Deibert Clara , Dohle Frank , Dolgner Jörg , Dziobaka Jan , Eifinger Frank , Elting Natalie , Endmann Matthias , Engelmann Guido , Frenzke Holger , Gappa Monika , Gharavi Bahman , Goletz Christine , Hahn Eva , Heidenreich Yvonne , Heimann Konrad , Hensel Kai O. , Hoffmann Hans-Georg , Hoppenz Marc , Horneff Gerd , Klassen Helene , Körner-Rettberg Cordula , Längler Alfred , Lenz Pascal , Lohmeier Klaus , Müller Andreas , Niemann Frank , Paulussen Michael , Pentek Falk , Perez Ruy , Pingel Markus , Repges Philip , Rothoeft Tobias , Rübo Jochen , Schade Herbert , Schmitz Robert , Schonhoff Peter , Schwade Jan N. , Schwarz Tobias , Seiffert Peter , Selzer Georg , Spille Uwe , Thiel Carsten , Thimm Ansgar , Urgatz Bartholomäus , van den Heuvel Alijda , van Hop Tan , Giesen Verena , Wirth Stefan , Wollbrink Thomas , Wüller Daniel , Felderhoff-Müser Ursula , Dohna-Schwake Christian , Lâm Thiên-Trí , Claus Heike , Bruns N. 
Published: September 2023

AbstractBackgroundIn late 2022, a surge of severe bacterial infections caused byS. pyogeneswas reported in several European countries, including Germany. This study assessed disease burden and severity of hospitalizations for community-acquired bacterial infections withS. pyogenes, S. pneumoniae, N. meningitidis, andH. influenzaeamong children in North Rhine-Westphalia (NRW), Germany, during the last quarter of 2022 compared to long-term incidences.MethodsHospital cases due to bacterial infections between October and December 2022 were collected from 59/62 (95 %) children’s hospitals in NRW and combined with surveillance data (2016 - 2023) from the national reference laboratories for streptococci,N. meningitidis, andH. influenzae. Total cases in NRW and incidence rates from January 2016 to March 2023 were estimated by capture-recapture analyses. Expected annual deaths from the studied pathogens were calculated from national death cause statistics.ResultsBetween October and December 2022, 153 cases with high overall disease severity were reported with pneumonia being most common (59 %, n = 91). Incidence rates of bacterial infections declined at the beginning of the COVID-19 pandemic. In late 2022 and early 2023 a massive surge to levels unprecedented since 2016 was observed, mainly driven byS. pyogenesandS. pneumoniae. Observed deaths during the study period exceeded the expected number for the entire year in NRW by far (7 vs. 0.9).DiscussionThe unprecedented peak of bacterial infections in late 2022 and early 2023 was caused by various mechanisms intertwined that require close surveillance and improved precautionary measures for future outbreaks.
How COVID-19 continues to affect contraception in Scotland: a retrospective analysis of Scottish prescribing data between 2016 and 2023
Authors: Johnson-Hall Elliot 
Published: September 2023

AbstractBackgroundIn Scotland, the effects of the COVID-19 pandemic on women’s access to contraception are unknown. Globally, COVID-19 restrictions have led to a shift to telehealth service delivery alongside a reduction in contraceptive provision. Research into whether the effects of COVID-19 on contraception have abated after restrictions have been lifted is lacking.MethodsThis is a retrospective longitudinal study of prescribing data from the Scottish Health and Social Care Open Data repository (https://www.opendata.nhs.scot) between January 2016 and January 2023. Contraceptives were extracted and categorised using truncated British National Formulary codes and analysed using R. Contraceptive provision was compared across four periods: pre-COVID-19 (01/01/2016–23/03/2020), lockdown (24/03/2020–29/05/2020 & 05/01/2021–26/04/2021), restrictions (30/05/2020–04/01/2021 & 27/04/2021–30/04/2022), and post-COVID-19 (01/05/2022–01/01/2023).ResultsDuring lockdowns, contraceptive prescribing in Scotland decreased by 82.90% of pre-COVID-19 levels. This trend was more severe for long-acting reversible contraception which fell to 11.80% of pre-COVID-19 prescriptions. After COVID-19, the level of contraceptive prescribing has risen to 108.23% of its pre-pandemic level. Large increases in subcutaneous medroxyprogesterone acetate (499.05%), progestogen-only pills (125.07%), the patch (165.09%), levonorgestrel-IUS (112.54%), and ulipristal acetate emergency contraception prescribing (357.97%). Conversely, combined oral contraceptive pills (75.04%), Cu-IUD (83.63%), the implant (81.10%), and levonorgestrel emergency contraception (67.42%) prescribing has decreased.ConclusionsCOVID-19 vastly decreased contraceptive prescribing during lockdowns in Scotland. Post-COVID-19, changes in contraceptive prescribing within Scottish general practices are reported, with implications for health policy and service delivery planning.Availability of Data & CodeAll code and data used are fully available from Zenodo (doi:10.5281/zenodo.8310085)The raw dataset used is also publicly available from the Scottish Health and Social Care Open Data repository (opendata.nhs.scot).