bluuebunny/crossref_metadata_2025_split huggingface dataset:
SpinFlowSim: a blood flow simulation framework for histology-informed diffusion MRI microvasculature mapping in cancer
Authors: Voronova Anna , Grigoriou Athanasios , Bernatowicz Kinga , Simonetti Sara , Serna Garazi , Roson Núria , Escobar Manuel , Vieito Maria , Nuciforo Paolo , Toledo Rodrigo , Garralda Elena , Sala-Llonch Roser , Fieremans Els , Novikov Dmitry S. , Palombo Marco , Perez-Lopez Raquel , Grussu Francesco 
Published: July 2024

AbstractDiffusion Magnetic Resonance Imaging (dMRI) sensitises the MRI signal to spin motion. This includes Brownian diffusion, but also flow across intricate networks of capillaries. This effect, the intra-voxel incoherent motion (IVIM), enables microvasculature characterisation with dMRI, through metrics such as the vascular signal fractionfVor Apparent Diffusion Coefficient (ADC)D*. The IVIM metrics, while sensitive to perfusion, are in general protocol-dependent, and their interpretation can change depending on the flow regime spins experience during the dMRI measurements (e.g., diffusive vs ballistic), which is in general not known — facts that hamper their clinical utility. Innovative vascular dMRI models are needed to enable thein vivocalculation of biologically meaningful markers of capillary flow. These could have relevant applications in cancer, for instance assessing responses to anti-angiogenic therapies targeting tumor vessels. This paper tackles this need by introducingSpinFlowSim, an open-source simulator of dMRI signals arising from blood flow within pipe networks. SpinFlowSim, tailored for the laminar flow patterns in capillaries, enables the synthesis of highly-realistic microvascular dMRI signals, given networks reconstructed from histology. We showcase the simulator by generating synthetic signals for 15 networks, reconstructed from liver biopsies, and containing cancerous and non-cancerous tissue. Signals exhibit com-plex, non-mono-exponential behaviours, pointing towards the co-existence of different flow regimes within the same network, and diffusion time dependence. We also demonstrate the potential utility of SpinFlowSim by devising a strategy for microvascular property mapping informed by the synthetic signals, focussing on the quantification of blood velocity distribution moments, and of anapparent network branchingindex. These were estimatedin silicoandin vivo, in healthy volunteers and in 13 cancer patients, scanned at 1.5T. In conclusion, realistic flow simulations, as those enabled by SpinFlowSim, may play a key role in the development of the next-generation of dMRI methods for microvascular mapping, with immediate applications in oncology.
Multiplexed detection of febrile infections using CARMEN
Authors: Kamariza M. , McMahon K. , Kim L. , Welch N.L. , Stenson L. , Allan-Blitz L. , Sanders G. , Eromon P. , Iluoreh A.M. , Sijuwola A. , Ope-ewe O.O. , Ayinla A.O. , l’Anson C. , Baudi I. , Paye M.F. , Wilkason C. , Lemieux J. , Ozonoff A. , Stachler E. , Happi C.T. , Sabeti P.C. 
Published: July 2024

AbstractDetection and diagnosis of bloodborne pathogens are critical for patients and for preventing outbreaks, yet challenging due to these diseases’ nonspecific initial symptoms. We advanced CRISPR-based Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN) technology for simultaneous detection of pathogens on numerous samples. We developed three specialized panels that target viral hemorrhagic fevers, mosquito-borne viruses, and sexually transmitted infections, collectively identifying 23 pathogens. We used deep learning to design CARMEN assays with enhanced sensitivity and specificity, validating them and evaluating their performance on synthetic targets, spiked healthy normal serum samples, and patient samples forNeisseria gonorrhoeaein the United States and for Lassa and mpox virus in Nigeria. Our results show multiplexed CARMEN assays match or outperform individual assay RT-PCR in sensitivity, with matched specificity. These findings underscore CARMEN’s potential as a highly effective tool for rapid, accurate pathogen detection for clinical diagnosis and public health surveillance.
Heart-retina time analysis using electrocardiogram-coupled time-resolved dynamic optical coherence tomography
Authors: Valmaggia Philippe , Wolleb Julia , Bieder Florentin , Scholl Hendrik P.N. , Cattin Philippe C. , Maloca Peter M. 
Published: July 2024

AbstractThe eye and the heart are two closely interlinked organs, and many diseases affecting the cardiovascular system manifest in the eye. To contribute to the understanding of blood flow propagation towards the retina, we developed a method to acquire electrocardiogram (ECG) coupled time-resolved dynamic optical coherence tomography (OCT) images. This method allows for continuous synchronised monitoring of the cardiac cycle and retinal blood flow dynamics. The dynamic OCT measurements were used to calculate time-resolved blood flow profiles using fringe washout analysis. The relative fringe washout was computed to generate the flow velocity profiles within arterioles at the optic nerve head rim. We found that the blood column between the heart and the retina propagates within one cardiac cycle, denoting the arrival time as the heart-retina time (HRT). In a group of healthy subjects, the HRT was 144 ± 19 ms (mean ± SD). The HRT could provide a novel potential biomarker for cardiovascular health in direct relation to retinal perfusion.
Breathome discriminate Ischemic Heart Disease
Authors: Marzoog Basheer Abdullah , Chomakhidze Peter , Gognieva Daria , Gagarina Nina Vladimirovna , Silantyev Artemiy , Suvorov Alexander , Fominykha Ekaterina , Kopylov Philipp 
Published: July 2024

AbstractBackgroundIschemic heart disease (IHD) impacts the quality of life and has the highest mortality rate in between other cardiovascular disease in the globe.ObjectivesIHD early diagnosis, management, and prevention remain underestimated due to the poor diagnostic and therapeutic strategies including the early prevention methods.AimsTo assess the changes in the exhaled breath analysis, volatile organic compounds (VOCs), in patients with ischemic heart disease confirmed by stress computed tomography myocardial perfusion (CTP) imaging.Materials and methodsA single center observational study included 80 participants from Moscow. The participants aged ≥ 40 years and given a written consent to participate in the study. Both groups, G1=31 with vs G2=49 without post stress induced myocardial perfusion defect, passed cardiologist consultation, anthropometric measurements, blood pressure and pulse rate, echocardiography, real time breathing at rest into PTR-TOF-MS-1000, cardio-ankle vascular index, performing bicycle ergometry, and immediately after performing bicycle ergometry repeating the breathing analysis into the PTR-TOF-MS-1000, and after three minutes from the second breath, repeat the breath into the PTR-TOF-MS-1000, then performing CTP. LASSO regression with nested cross-validation was used to find association between VOCs and existence of perfusion defect. Statistical processing was carried out using the R programming language v4.2 and Python v.3.10 [^R], STATISTICA, and IBM SPSS.ResultsThe specificity 77.6 % [95 % confidence interval (CI); 0.666; 0.889], sensitivity 83.9 % [95 % CI; 0.692; 0.964], and accuracy of the diagnostic method using exhaled breath analysis, area under the curve (AUC) 83.8 % [95 % CI; 0.73655857; 0.91493173]. Whereas, the AUC of the bicycle ergometry 50.7 % [95 % CI; 0.388; 0.625], specificity 53.1 % [95 % CI; 0.392; 0.673], and sensitivity 48.4 % [95 % CI; 0.306; 0.657].ConclusionVOCs analysis appear to discriminate individuals with and without IHD with clinically acceptable diagnostic accuracy.OtherThe exhaled breath analysis reflects the myocardiocytes metabolomic signature and related intercellular homeostasis changes and regulation perturbances. Exhaled breath analysis poses a promise result to improve the diagnostic accuracy of the physical stress tests.
The novel duodenal isolateStreptococcus salivariusAGIRA0003 promotes barrier dysfunction and IgG responses in functional dyspepsia
Authors: Burns Grace L. , Wark Jasmine A. , Hoedt Emily C. , Minahan Kyra , Sherwin Simonne , Bruce Jessica K. , Lim Yenkai , Teh Jing Jie , Jamaluddin M. Fairuz B. , Soh Wai Sinn , Caban Shandelle , Fowler Sophie , Almazi Juhura G. , Woldu Ameha S. , Dun Matthew D. , Tanwar Pradeep S. , Potter Michael D. E. , Shanahan Erin R. , Holtmann Gerald , Morrison Mark , Talley Nicholas J. , Keely Simon 
Published: July 2024

AbstractBackground and aimsFunctional dyspepsia (FD) is a highly prevalent disorder of gut-brain interaction (DGBI) that is associated with an altered duodenal microbiota, unexplained low grade duodenal inflammation and altered intestinal permeability. This study aimed to investigate if novel FD-derived bacterial isolates elicited immune responses in FD and the capacity of an immune-stimulating isolate, AGIRA0003 to breach the duodenal epithelial barrier.MethodsBacterial lysates were investigated for immune reactivity using immunoblotting of patient plasma. Immunoblots were probed with plasma from FD patients (n=44, 46.6±17.5 years, 79.6% female) or controls (n=30, 48.9±15.7 years, 63.3% female). Peripheral gut-homing T cells were quantified by flow cytometry and histological analysis used to investigate duodenal biopsies. Polarised Caco-2 cells and FD duodenal spheroids (n=4 lines) were exposed toStreptococcus salivariusAGIRA0003 at a multiplicity of infection of 10 bacterial cells to 1 mammalian cell for 6 hours.ResultsThe presence of plasma IgG antibodies againstS. salivariusAGIRA0003 was significantly associated with FD (χ215.7, 1,p<0.0001). Patients with these IgG antibodies had increased gut-homing lymphocytes (0.33±0.77% vs 1.00±1.46%,p=0.046). Strain AGIRA0003, but not related commensal strains, disrupted tight junction proteins in Caco-2 monolayers, and decreased claudin 1 (CLDN1; 0.49±0.11,p=0.03), desmocollin 2 (DSC2; 0.64±0.33,p=0.03) and desmoglein 2 (DSG2; 0.30±0.12,p=0.03) in spheroid monolayers. In addition, DSC2 (2.19±0.97 vs 1.48±0.85,p=0.02) and DSG2 (23.22±15.92 vs 12.38±7.34,p=0.04) protein levels were decreased in IgG+FD biopsies compared to controls.ConclusionsS. salivariusAGIRA0003 is a potential pathobiont capable of impairing duodenal epithelial barrier defences that elicits an immune response in FD patients.
Prospective classification of functional dependence: Insights from machine learning and the Canadian Longitudinal Study on Aging
Authors: van Allen Zachary M. , Boisgontier Matthieu P. 
Published: July 2024

AbstractPurposeFunctional dependence is a multifactorial health condition affecting well-being and life expectancy. To better understand the mechanisms underlying this condition, we aimed to identify the variables that best prospectively classify adults with and without limitations in basic and instrumental activities of daily living.MethodsA filtering approach was used to select the best predictors of functional status from 4,248 candidate predictors collected in 39,927 participants aged 44 to 88 years old at baseline. Several machine learning models using the selected baseline variables (2010-2015) were compared for their ability to classify participants by functional status (dependent vs. independent) at follow up (2018-2021) on a training dataset (n=31,941) of participants from the Canadian Longitudinal Study on Aging. The best performing model was then examined on a test dataset (n=7,986) to confirm sensitivity, specificity, and accuracy.ResultsEighteen candidate baseline variables were identified as the best predictors of functional status at follow up. Logistic regression was the best performing model for classifying participants by functional status and achieved balanced accuracy of 81.9% on the test dataset. The absence of functional limitations at baseline, stronger grip strength, being free of pain and of chronic conditions, being a female, having a drivers license, and good memory were associated with greater odds functionally independence at follow-up. In contrast, older age, psychological distress, walking slowly, being retired, having one or more chronic conditions, and never going for walks were associated with greater odds of functional dependence at follow-up.ConclusionFunctional status can be best prospectively estimated by health condition, age, muscle strength, short-term memory, physical activity, psychological distress, and sex. These predictors can estimate functional status over 6 years ahead with high accuracy. This early identification of people at risk of functional dependence allows sufficient time for the implementation of interventions aiming to delay functional decline.
Hypnotherapy for major depressive disorder: a systematic review of randomized clinical trials
Authors: Souza Filipe Luís , Moura Murilo Schiefler , Elkins Gary , Silva Juliana Vieira Almeida 
Published: July 2024

ABSTRACTIntroduction:Major Depressive Disorder (MDD) is one of the most debilitating diseases worldwide and has seen a significant increase in diagnoses during the pandemic, demanding more and better therapeutic tools to manage the post-pandemic scenario.Objective:The aim of this systematic review is to provide a comprehensive analysis of the last 20 years of clinical research on Hypnotherapy (HT) to determine whether this intervention has evidence to support its recommendation for the treatment of MDD.Methods:This review included only randomized clinical trials (RCTs) involving adult populations diagnosed with MDD, regardless of the severity level (mild, moderate, or severe) according to any validated diagnostic criteria, compared to a control group (active treatment or none), with any follow-up duration and free access to the manuscript. The bibliographic survey was planned to be as sensitive as possible, conducted across seven distinct databases: MEDLINE (PubMed), Embase, CENTRAL, PsycINFO, Scopus, ScieELO, and Latin American and Caribbean Health Sciences Literature (LILACS). To identify potentially eligible studies in the grey literature, researchers also searched the U.S. National Library of Medicine (ClinicalTrials.gov). The risk of bias was assessed by two independent investigators using Cochrane’s revised tool (RoB 2), and the final judgment was made by consensus. To better analyze the included studies, the certainty of the evidence was evaluated through the Grading of Recommendations Assessment, Development and Evaluation (GRADE). Due to the lack of comparable studies, it was not possible to perform a meta-analysis; therefore, the studies were graphically displayed in Descriptive Forest Plots.Results:There is very low-quality evidence suggesting that hypnosis-based interventions may reduce the severity of depression, which precludes the clinical recommendation of this intervention for patients in the real world, pending the production of better evidence of effectiveness and safety, although no evidence of significant adverse effects was found.Other:This review was pre-registered with PROSPERO and can be accessed using the registration number CRD42023409631.
Correlation analysis of latent hepatitis B virus infection gene mutation in unpaid blood donors
Authors: Yu Wei , Wang Fang , Liu Qiang 
Published: July 2024

AbstractObjectiveTo analyze the HBV S region gene mutation in serum samples of occult hepatitis B virus (HBV) infection (OB1), and to further analyze the mechanism of gene mutation and OBI.MethodsBlood samples from unpaid blood donors from January 2022 to December 2023 were collected and analyzed for serology, liver function indicators, viral load and gene mutation.ResultsA total of 90 OBI cases were detected, the detection rate was 0.051%, and the incidence of OBI was correlated with age. The sequence amplification of s region in the blood samples showed the presence of C type and B type genes, both of which occurred in the hydrophilic region.ConclusionThere is no abnormal liver function between OBI and hepatitis B population, and there is no difference in viral load between different serum modes. Mutations in the HBVS region are more likely to cause OBI, which provides a scientific basis for more sensitive HBV detection.
Blastocystisin the cervix of Polish women: a subtype found in a parenteral location is different to that found in the anus
Authors: Suchońska Barbara , Kaczmarek Adam , Wesołowska Maria , Młocicki Daniel , Sałamatin Rusłan 
Published: July 2024

AbstractObjectiveThe presence ofBlastocystisspp. in a parenteral location—in the female genital tract—has been reported three times. The genetic material of the protozoan has been identified only once.MethodsBlastocystisDNA was detected using real-time PCR.ResultsThirty patients with so-called cervical erosions were examined. The presence ofBlastocystisgenetic material was confirmed in nine women. The authors are the first to confirm and identify the DNA ofBlastocystissubtype ST1, ST6, and ST7 in samples taken from the ectocervix and the distal part of the cervical canal of women with large, symptomatic glandular ectopies which were resistant to standard treatment. In one case, in material from the cervix we identified aBlastocystissubtype which was different to that found in the anus of the same woman.ConclusionsOur findings indicate that the presence ofBlastocystisin the cervix is not, in any obvious way, associated with hygienic issues or neglect, but could be the result of women having vaginal intercourse with heterosexual men in whose semen this protozoan occurs. The possibility ofBlastocystisoccurrence in semen has been confirmed by recent publications as well as our own unpublished results. This discovery gives hope for the eradication of these organisms and thus to curing patients with chronic gynaecological problems.
The role of specific and non-specific factors in a brief group psychological intervention for psychological distress: a randomised clinical trial
Authors: Keyan Dharani , Dawson Katie , Azevedo Suzanna , Yadav Srishti , Choi-Christou Jasmine , Maliakkal Deepthi J. , Pillai Mohan K. , Thomas Elizabeth , George Tony S. , Bryant Richard A. 
Published: July 2024

AbstractAimsAlthough brief psychological interventions in low-and-middle-income-countries have been shown to be effective, they have typically been tested against usual or enhanced usual care (EUC). This design has precluded delineation of the role of specific and non-specific factors in influencing symptom reduction outcomes. This study evaluates the impact of a group psychological intervention (adapted version of WHO’s Problem Management Plus; PM+; titledCoping with COVID) against non-directive group Supportive Counselling (SC) on psychological distress during the COVID-19 pandemic in India.MethodsBetween October 2020 and December 2022, this two-arm single-blind, controlled trial randomised 183 young adults in Bangalore, India who screened positive for psychological distress to eitherCoping with COVID(n = 91) or SC (n=92), on a 1:1 basis.Coping with COVIDcomprised six weekly small group sessions delivered by videoconferencing that taught stress coping strategies. SC also involved six weekly group sessions that were led by a facilitator and offered non-directive support. The primary outcomes were anxiety and depression as measured by the Hospital Anxiety and Depression Scales (HADS) assessed at baseline, post-intervention, 2-months, and 6-months after treatment. The primary outcome timepoint was the 2-month assessment. Secondary outcomes included generalised worry, positive wellbeing, pandemic-related stress, and suicidal ideation.ResultsOne hundred and sixty-one participants (88%) were retained at the 2-month follow-up. Intent-to-treat analyses indicated that theCoping with COVIDcondition did not lead to significant reductions in in anxiety (mean difference 0.24 [95% CI, –1.01,1.48],p>0.05), or depression (mean difference .03 [95% CI, –1.19, 1.26],p>0.05) relative to SC. Similarly, there were no significant differences between conditions for all secondary outcomes.ConclusionsThe findings suggest that the benefits of strategies that comprise transdiagnostic scalable psychological interventions may not surpass non-specific factors in driving symptom reduction. There is a need to further evaluate the non-specific factors in scalable psychological programs because focusing on these may have implications for ease of training and implementation.
Protrudin acts at ER-endosome contacts to promote KIF5-mediated endosomal fission and endosome-to-Golgi transport
Authors: Kleniuk Julia , Nadadhur Aishwarya G. , Wolfenden Emily , Rodger Catherine , Zlamalova Eliska , Reid Evan 
Published: July 2024

AbstractFission of transport tubules from early endosomes is required for endosomal sorting, but mechanisms of endosomal tubule fission (ETF) are incompletely understood. We show protrudin acts at ER-endosome contacts to promote ETF and endosome-to-Golgi traffic. Protrudin-mediated ETF required its ability to interact with ER-localised VAP proteins, endosomal phosphoinositides and KIF5. These properties also regulated the distance between protrudin and endosomal tubules. The defective ETF phenotype of increased endosomal tubulation in cells lacking protrudin was phenocopied by depletion of KIF5, but not FYCO1, a motor protein adaptor implicated in protrudin-dependent late endosome motility. It also required intact microtubules and dynein, consistent with a model where protrudin facilitates a tug-of-war between KIF5 and dynein to fission tubules. In addition to its direct role, protrudin links many other machineries involved in ETF, thus our findings elucidate how ETF is co-ordinated. These machineries are enriched for proteins implicated in hereditary motor neuron disorders, and protrudin or KIF5 depletion caused defective ETF in human neurons.SummaryProtrudin binds ER-localised VAPs and endosomal phosphoinositides to form ER-endosome contacts that promote endosomal tubule fission and endosome-to-Golgi traffic. Protrudin recruits KIF5 to provide a FYCO1-independent force to fission endosomal tubules in neurons and non-polarised cells.