Read Mapping for Hi-C Analysis.

Hi-C is a popular ligation-based technique to detect 3D physical chromosome structure within the nucleus using cross-linking and next-generation sequencing. As an unbiased genome-wide assay based on chromosome conformation capture, it provides rich insights into chromosome structure, dynamic chromosome folding and interactions, and the regulatory state of a cell. Bioinformatics analyses of Hi-C data require dedicated protocols as most genome alignment tools assume that both paired-end reads will map to the same chromosome, resulting in large two-dimensional matrices as processed data. Here, we outline the necessary steps to generate high-quality aligned Hi-C data by separately mapping each read while correcting for biases from restriction enzyme digests. We introduce our own custom open-source pipeline, which enables users to select an aligner of their choosing with high accuracy and performance. This enables users to generate high-resolution datasets with fast turnaround and fewer unmapped reads. Finally, we discuss recent innovations in experimental techniques, bioinformatics techniques, and their applications in clinical testing for diagnostics.

Measurement of fast neutron induced (n,γ) reaction cross-section of 68Zn, 96Zr, 121Sb and 123Sb in the energy range of 1 to 2 MeV.

The (n,γ) reaction cross-section for the elements 68Zn, 96Zr, 121Sb and 123Sb, present in the reactor structural/shielding materials, was measured by neutron activation technique in the neutron energy region of 1-2 MeV as very limited data is available in this energy range. Further, the neutron spectrum peaks in this energy region for the fast breeder reactors and proposed accelerator driven sub-critical systems. The natural strontium (natSr) element was used as a neutron flux monitor by considering effective combined reaction cross-section for 86Sr(n,γ)87Srm and 87Sr(n,n')87Srm reactions. The pellets of mixture of sample and monitor were irradiated by a quasi-mono energetic fast neutron beam, generated by 7Li(p,n)7Be reaction at FOTIA, Bhabha Atomic Research Centre, Mumbai, India. The activity of activation products was measured by off-line gamma-ray spectrometry using High Purity Germanium Detector (HPGe). The present data with improved uncertainty and covariance analysis enhance the cross-section data base for better constraining the evaluated data and theoretical models. The theoretical (n,γ) reaction cross-sections were calculated using TALYS 1.96, which could reasonably explain the present data with the Fermi gas level density prescription.

Mapping between measurement scales in meta-analysis, with application to measures of body mass index in children.

Quantitative evidence synthesis methods aim to combine data from multiple medical trials to infer relative effects of different interventions. A challenge arises when trials report continuous outcomes on different measurement scales. To include all evidence in one coherent analysis, we require methods to "map" the outcomes onto a single scale. This is particularly challenging when trials report aggregate rather than individual data. We are motivated by a meta-analysis of interventions to prevent obesity in children. Trials report aggregate measurements of body mass index (BMI) either expressed as raw values or standardized for age and sex. We develop three methods for mapping between aggregate BMI data using known or estimated relationships between measurements on different scales at the individual level. The first is an analytical method based on the mathematical definitions of z-scores and percentiles. The other two approaches involve sampling individual participant data on which to perform the conversions. One method is a straightforward sampling routine, while the other involves optimization with respect to the reported outcomes. In contrast to the analytical approach, these methods also have wider applicability for mapping between any pair of measurement scales with known or estimable individual-level relationships. We verify and contrast our methods using simulation studies and trials from our data set which report outcomes on multiple scales. We find that all methods recreate mean values with reasonable accuracy, but for standard deviations, optimization outperforms the other methods. However, the optimization method is more likely to underestimate standard deviations and is vulnerable to non-convergence.

Accelerated 2D radial Look-Locker T1 mapping using a deep learning-based rapid inversion recovery sampling technique.

Efficient abdominal coverage with T1-mapping methods currently available in the clinic is limited by the breath hold period (BHP) and the time needed for T1 recovery. This work develops a T1-mapping framework for efficient abdominal coverage based on rapid T1 recovery curve (T1RC) sampling, slice-selective inversion, optimized slice interleaving, and a convolutional neural network (CNN)-based T1 estimation. The effect of reducing the T1RC sampling was evaluated by comparing T1 estimates from T1RC ranging from 0.63 to 2.0 s with reference T1 values obtained from T1RC = 2.5-5 s. Slice interleaving methodologies were evaluated by comparing the T1 variation in abdominal organs across slices. The repeatability of the proposed framework was demonstrated by performing acquisition on test subjects across imaging sessions. Analysis of in vivo data based on retrospectively shortening the T1RC showed that with the CNN framework, a T1RC = 0.84 s yielded T1 estimates without significant changes in mean T1 (p > 0.05) or significant increase in T1 variability (p > 0.48) compared to the reference. Prospectively acquired data using T1RC = 0.84 s, an optimized slice interleaving scheme, and the CNN framework enabled 21 slices in a 20 s BHP. Analyses across abdominal organs produced T1 values within 2% of the reference. Repeatability experiments yielded Pearson's correlation, repeatability coefficient, and coefficient of variation of 0.99, 2.5%, and 0.12%, respectively. The proposed T1 mapping framework provides full abdominal coverage within a single BHP.

Early Detection of Myocardial Involvement in Thalassemia Intermedia Patients: Multiparametric Mapping by Magnetic Resonance Imaging.

BACKGROUND: No study has assessed myocardial T1 and T2 values in patients with beta-thalassemia intermedia (ß-TI). PURPOSE: To assess the prevalence of myocardial involvement in ß-TI patients by T2* relaxometry and native T1 and T2 mapping and to determine the correlation of myocardial relaxation times with demographic and clinical parameters. STUDY TYPE: Prospective matched-cohort study. SUBJECTS: 42 ß-TI patients (27 females, 39.65 ± 12.32 years), enrolled in the Extension-Myocardial Iron Overload in Thalassaemia Network, and 42 age- and sex-matched healthy volunteers (27 females, 40.01 ± 11.36 years) and thalassemia major (TM) patients (27 females, 39.27 ± 11.57 years). FIELD STRENGTH/SEQUENCE: 1.5 T/multi-echo gradient echo, modified Look-Locker inversion recovery, multi-echo fast-spin-echo, cine balanced steady-state-free precession, and late gadolinium enhancement (LGE) sequences. ASSESSMENT: Hepatic, pancreatic, and left ventricular (LV) T2* values, LV native T1 and T2 values, biventricular ejection fractions and volumes, and presence and extent of replacement myocardial fibrosis. STATISTICAL TESTS: Comparisons between two groups were performed with two-sample t tests, Wilcoxon's signed rank tests, or χ2 testing. Correlation analysis was performed using Pearson's or Spearman's test. P < 0.05 was considered statistically significant. RESULTS: ß-TI patients had significantly higher LV T2 values than healthy subjects (56.84 ± 4.03 vs. 52.46 ± 2.50 msec, P < 0.0001) and significantly higher LV T1 values than TM patients (1018.32 ± 48.94 vs. 966.66 ± 66.47 msec, P < 0.0001). In ß-TI, female gender was associated with significantly increased LV T1 (P = 0.041) and T2 values (P < 0.0001), while splenectomy and presence of regular transfusions were associated with significantly lower LV T1 values (P = 0.014 and P = 0.001, respectively). In ß-TI patients, all LV relaxation times were significantly correlated with each other (T2*-T1: P = 0.003; T2*-T2: P = 0.003; T1-T2: P < 0.0001). Two patients with a reduced LV T2* also had a reduced LV T1, while only one had a reduced LV T2. Three patients had a reduced LV T1 but a normal LV T2*; 66.7% of the patients had an increased LV T2. All LV relaxation times were significantly correlated with pancreas T2* values (T2*: P = 0.033; T1: P < 0.0001; T2: P = 0.014). No LV relaxation time was associated (P > 0.05) with hepatic iron concentration, biventricular function parameters, or LGE presence. CONCLUSION: The combined use of all three myocardial relaxation times has potential to improve sensitivity in the detection of early/subclinical myocardial involvement in ß-Tl patients. LEVEL OF EVIDENCE: 2 TECHNICAL EFFICACY: Stage 2.

Current state of data stewardship tools in life science.

In today's data-centric landscape, effective data stewardship is critical for facilitating scientific research and innovation. This article provides an overview of essential tools and frameworks for modern data stewardship practices. Over 300 tools were analyzed in this study, assessing their utility, relevance to data stewardship, and applicability within the life sciences domain.

The HAPPY concept mapping study: "To prevent injuries in young handball players it's important to " - Perceptions among stakeholders.

OBJECTIVES: This study aimed to identify facilitators for implementing injury prevention initiatives in youth handball, and to assess stakeholders' perceptions of their importance and feasibility. DESIGN: Mixed-method concept mapping study. METHODS: Four stakeholder groups - coaches, administrators, health staff and players - participated in this mixed-method concept mapping study. Participants (n = 224; 19 % coaches, 22 % health staff, 63 % players, 18 % administrators) first provided statements about facilitators for implementing injury prevention initiatives in youth handball, then thematically grouped them (n = 47), before rating them (n = 57) for importance and feasibility (5-point Likert scales). Stakeholder-specific cluster maps and Go-Zone scatter plots were created. Statements rated above average for both importance and feasibility were considered as prioritized (Go-Zone 1). RESULTS: 87 unique statements were generated during brainstorming. Multidimensional scaling and hierarchical cluster analysis resulted in similar sorting data clustering patterns for coaches, health staff, and administrators, which included federation strategies, club strategies, and coach and athlete education/knowledge. All clusters were rated >3 on average ratings of importance by all stakeholder groups. Six statements were in Go-Zone 1 for all stakeholder groups, including three statements about coach knowledge and education. Players' importance and feasibility ratings had limited overlap with other stakeholder groups' Go-Zone 1 statements. Players' Go-Zone 1 statements mainly addressed individual load management and practical training setup. CONCLUSIONS: Coach knowledge and education, alongside collaboration among stakeholder groups, are essential when implementing injury prevention initiatives in youth handball. Stakeholder groups have varying perspectives, underscoring the importance of understanding and addressing these diverse viewpoints when implementing injury prevention initiatives in youth handball.

Multielectrode Catheter-Based Pulsed Field Ablation of Persistent and Long-Standing Persistent Atrial Fibrillation.

BACKGROUND AND AIMS: Rhythm control of non-paroxysmal atrial fibrillation (AF) is significantly more challenging, as a result of arrhythmia perpetuation promoting atrial substrate changes and AF maintenance. We describe a tailored ablation strategy targeting multiple left atrial (LA) sites via a pentaspline pulsed field ablation (PFA) catheter in persistent AF sustained beyond 6 months (PerAF>6m) and long-standing persistent AF (LSPAF). METHODS: The ablation protocol included the following stages: pulmonary vein antral and posterior wall isolation plus anterior roof line ablation (Stage 1); electrogram-guided substrate ablation (Stage 2); atrial tachyarrhythmia regionalization and ablation (Stage 3). RESULTS: Seventy-two [age:68±10years, 61.1%males; AF history: 25 (18-45) months] patients with PerAF>6m (52.8%) and LSPAF (47.2%) underwent their first PFA via the FarapulseTM system. LA substrate ablation (Stage 1 and 2) led to AF termination in 95.8% of patients. AF organized into a left-sided atrial flutter (AFlu) in 46 (74.2%) patients. The PFA catheter was used to identify LA sites showing diastolic, low-voltage electrograms and entrainment from its splines was performed to confirm the pacing site was inside the AFlu circuit. Left AFlu termination was achieved in all cases via PFA delivery. Total procedural and LA dwell times were 112±25min and 59±22 min, respectively. Major complications occurred in 2 (2.8%) patients. Single-procedure success rate was 74.6% after 14.9±2.7 months of follow-up; AF-free survival was 89.2%. CONCLUSIONS: In our cohort, PFA-based AF substrate ablation led to AF termination in 95.8% of cases. Very favorable clinical outcomes were observed during >1year of follow-up.

Differential patterns of antibody response against SARS-CoV-2 nucleocapsid epitopes detected in sera from patients in acute phase of COVID-19, convalescents and pre-pandemic individuals.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have already infected more than 0.7 billion people and caused over 7 million deaths worldwide. At the same time, our knowledge about this virus is still incipient. In some cases, there is a pre-pandemic immunity, however its source is unknown. The analysis of patients' humoral responses might shed a light on this puzzle. In this paper, we evaluated the antibody recognition of nucleocapsid protein, one of the structural proteins of SARS-CoV-2. For this purpose, we used pre-pandemic, acute COVID-19 and convalescent patients' sera to identify and map nucleocapsid protein epitopes. We identified a common epitope KKSAAEASKKPRQKRTATKA recognized by sera antibodies from all three groups. Some motifs of this sequence are widespread among various coronaviruses, plant or human proteins indicating that there might be more sources of nucleocapsid-reactive antibodies than previous infection with seasonal coronavirus. The two sequences MSDNGPQNQRNAPRITFGGP and KADETQALPQRQKKQQTVTL were detected as specific for sera from patients in acute phase of infection and convalescents making them suitable for future development of vaccine against SARS-CoV-2. Knowledge of the humoral response to SARS-CoV-2 infection is essential for the design of appropriate diagnostic tools and vaccine antigens.

Use of implementation mapping to develop a multifaceted implementation strategy for an electronic prospective surveillance model for cancer rehabilitation.

BACKGROUND: Electronic Prospective Surveillance Models (ePSMs) remotely monitor the rehabilitation needs of people with cancer via patient-reported outcomes at pre-defined time points during cancer care and deliver support, including links to self-management education and community programs, and recommendations for further clinical screening and rehabilitation referrals. Previous guidance on implementing ePSMs lacks sufficient detail on approaches to select implementation strategies for these systems. The purpose of this article is to describe how we developed an implementation plan for REACH, an ePSM system designed for breast, colorectal, lymphoma, and head and neck cancers. METHODS: Implementation Mapping guided the process of developing the implementation plan. We integrated findings from a scoping review and qualitative study our team conducted to identify determinants to implementation, implementation actors and actions, and relevant outcomes. Determinants were categorized using the Consolidated Framework for Implementation Research (CFIR), and the implementation outcomes taxonomy guided the identification of outcomes. Next, determinants were mapped to the Expert Recommendations for Implementing Change (ERIC) taxonomy of strategies using the CFIR-ERIC Matching Tool. The list of strategies produced was refined through discussion amongst our team and feedback from knowledge users considering each strategy's feasibility and importance rating via the Go-Zone plot, feasibility and applicability to the clinical contexts, and use among other ePSMs reported in our scoping review. RESULTS: Of the 39 CFIR constructs, 22 were identified as relevant determinants. Clinic managers, information technology teams, and healthcare providers with key roles in patient education were identified as important actors. The CFIR-ERIC Matching Tool resulted in 50 strategies with Level 1 endorsement and 13 strategies with Level 2 endorsement. The final list of strategies included 1) purposefully re-examine the implementation, 2) tailor strategies, 3) change record systems, 4) conduct educational meetings, 5) distribute educational materials, 6) intervene with patients to enhance uptake and adherence, 7) centralize technical assistance, and 8) use advisory boards and workgroups. CONCLUSION: We present a generalizable method that incorporates steps from Implementation Mapping, engages various knowledge users, and leverages implementation science frameworks to facilitate the development of an implementation strategy. An evaluation of implementation success using the implementation outcomes framework is underway.

Systematic review: locating qualitative academic publications for reviewing tenants' and landlords' renting experiences and interaction in the Majority World.

This methodological protocol describes the step-by-step process of identifying the relevant international academic literature to be reviewed within the project 'The affective economies of emerging private renting markets: understanding tenants and landlords in postcommunist Romania" (AFFECTIVE-PRS). It presents: (1) the preliminary decisions taken related to the breadth of the review (choice of databases, type of research, type of reference, searching fields); (2) the operationalisation of keywords and Boolean strings; (3) the further calibration of the searching parameters through piloting; (4) the final retrieval of relevant references through systematic and manual searches; and (5) the geographical coverage of the retained literature. While the paper demonstrates the rigour of the methodological approach taken, it also opens up the space for other scholars to scrutinise, replicate or adjust this approach to their own work.

How to optimize the CAR-T Cell therapy process? A group concept mapping analysis of preconditions for a frictionless process from a German multistakeholder perspective.

Introduction: Treatment with chimeric antigen receptor T (CAR-T) cells involves a large number of interdisciplinary stakeholders and is associated with complex processes ranging from patient-specific production to follow-up care. Due to the complexity, maximum process optimization is required in order to avoid efficiency losses. This study aimed at systematically determining the preconditions for a frictionless flow of the CAR-T process by surveying the stakeholders involved. Methods: A Group Concept Mapping (GCM) analysis, a mixed-methods participatory research, was conducted. CAR-T experts from different professional backgrounds went through three steps: 1) Brainstorming relevant aspects (statements) for a frictionless process, 2) Sorting the collected statements based on their similarity, and 3) Rating the importance and feasibility of each statement. A cluster map reflecting the overarching topics was derived, and mean ratings per statement and cluster were calculated. Results: Overall, 20 CAR-T experts participated. A total of 80 statements were collected, resulting in a map of the following 10 clusters (mean importance/feasibility): Information for patients and physicians (4.16/3.77), Supportive network (4.03/3.53), Eligibility of patients (4.41/3.63), Evidence, transparency and communication (4.01/3.33), Paperwork (4.1/2.52), Interface with pharmaceutical manufacturer (4.03/2.85), Reimbursement (4.29/2.31), Quality Management (4.17/3.18), Infrastructure of CAR-T clinics (4.1/2.93), and Patient-oriented processes (4.46/3.32). Discussion: The 80 statements underlined the complex and manifold nature of the CAR-T treatment process. Our results reflect the first step in overcoming hurdles: identifying potential hurdles and required preconditions. Decision-makers and stakeholders can use the results to derive strategies and measures to further promote a frictionless process.

A missense mutation in the tyrosinase gene explains acromelanism in domesticated canaries.

Acromelanism is a form of albinism observed in several vertebrate species. In mammals, acromelanism is known to be caused by mutations in the tyrosinase gene (TYR) that induce a temperature-sensitive behavior of melanin synthesis, resulting in a characteristic hair color gradient. In birds, several phenotypes consistent with acromelanism have been reported, but their genetic basis remains unknown. This study aimed to identify the genetic basis of an acromelanistic phenotype in domesticated canaries known as pearl and test whether it is caused by the same molecular mechanism described for mammals. To do this, we compared the genomes of pearl and non-pearl canaries and searched for potentially causative genetic mutations. Our results suggest that the pearl phenotype is caused by a mutation in the TYR gene encoding a TYR-P45H missense substitution. Our findings further suggest that reports of acromelanism in other bird species might be explained by TYR mutations.

Computed Tomographic Angiography in Planning Thoraco-dorsal Artery Perforator Flap in Breast and Soft Tissue Reconstruction: A Systematic Review.

OBJECTIVES: Thoraco-dorsal Artery Perforator (TDAP) flaps have been increasingly used in breast and soft tissue reconstruction. Perforator localization is often done using a hand-held doppler, however, false results are not uncommon. This study aimed to systematically review the literature on the value of preoperative Computed Tomographic Angiography (CTA) in TDAP flaps examining scanning protocol, mapping technique, concordance with operative findings and disadvantages. METHODS: A PRISMA-compliant comprehensive search of Medline, Embase, Cochrane Library and CINAHL databases was conducted in November 2023. We included studies evaluating CTA mapping of free and pedicled TDAPs for breast or soft tissue reconstruction using The Joanna Briggs Institute (JBI) Critical Appraisal Tools. RESULTS: Five studies were included and considered at high risk of bias. The studies included 72 patients with a mean age of 43.8 years. Concordance between CT findings and Doppler mapping or operative visualization was reported in two studies. In three studies, CTA was combined with Doppler flowmetry, whilst dynamic infrared thermography was used in one study. Standardized scanning protocol and patient positioning were lacking in all reports. CONCLUSIONS: This study highlights the paucity of evidence on the value of CTA in TDA perforator mapping with inconsistent outcomes and non-standardized scanning protocols. Despite difficult imaging acquisition and interpretation, 3D reconstructed images and detailed vascular anatomy may facilitate planning. ADVANCES IN KNOWLEDGE: Further research is required to explore the practical value of CTA in TDAP planning and standardizing protocols.

Systematic analysis and network mapping of disease associations in autoimmune polyglandular syndrome.

BACKGROUND: The purpose of our work was to provide a data-driven perspective to APS, a complex autoimmune disorder, supplementing traditional clinical observations. METHODS: Medical records of 7559 patients were analyzed, autoimmune origin was proved in 3180 cases of which 380 (12%) had APS. Associations of component disorders were investigated by computational methods to reveal typical patterns of disease development. RESULTS: Twenty-eight distinct autoimmune disorders were diagnosed forming 113 combinations. The 10 most frequent combinations were responsible for 51,3% of cases. HT and GD were differentiated as main cornerstones of APS, sharing several comorbidities. HT was the most common manifestation (67.4%), followed by GD (26.8%) and T1D (20.8%). APS started significantly earlier in men than in women. Thyroid autoimmunity was frequently linked to gastrointestinal and systemic manifestations and these patterns of associations substantially differed from that of T1D, AD or CeD when present as first manifestations, suggesting the possibility of a common biological cause. CONCLUSION: APS is more frequent than reported. Classifying APS requires a shift of perspective towards disease associations rather than disorder prevalence.

Quantitative susceptibility mapping at 7 T in COVID-19: brainstem effects and outcome associations.

Post-mortem studies have shown that patients dying from severe acute respiratory syndrome coronavirus (SARS-CoV-2) infection frequently have pathological changes in their CNS, particularly in the brainstem. Many of these changes are proposed to result from para-infectious and/or post-infection immune responses. Clinical symptoms such as fatigue, breathlessness, and chest pain are frequently reported in post-hospitalized coronavirus disease 2019 (COVID-19) patients. We propose that these symptoms are in part due to damage to key neuromodulatory brainstem nuclei. While brainstem involvement has been demonstrated in the acute phase of the illness, the evidence of long-term brainstem change on MRI is inconclusive. We therefore used ultra-high field (7 T) quantitative susceptibility mapping (QSM) to test the hypothesis that brainstem abnormalities persist in post-COVID patients and that these are associated with persistence of key symptoms. We used 7 T QSM data from 30 patients, scanned 93-548 days after hospital admission for COVID-19 and compared them to 51 age-matched controls without prior history of COVID-19 infection. We correlated the patients' QSM signals with disease severity (duration of hospital admission and COVID-19 severity scale), inflammatory response during the acute illness (C-reactive protein, D-dimer and platelet levels), functional recovery (modified Rankin scale), depression (Patient Health Questionnaire-9) and anxiety (Generalized Anxiety Disorder-7). In COVID-19 survivors, the MR susceptibility increased in the medulla, pons and midbrain regions of the brainstem. Specifically, there was increased susceptibility in the inferior medullary reticular formation and the raphe pallidus and obscurus. In these regions, patients with higher tissue susceptibility had worse acute disease severity, higher acute inflammatory markers, and significantly worse functional recovery. This study contributes to understanding the long-term effects of COVID-19 and recovery. Using non-invasive ultra-high field 7 T MRI, we show evidence of brainstem pathophysiological changes associated with inflammatory processes in post-hospitalized COVID-19 survivors.

Invasive management of atrial tachycardias using a novel lattice-tip catheter combining high-density mapping and dual ablation properties: initial real-world experience.

BACKGROUND: Invasive management of atrial tachycardias(ATs) requires proper diagnosis of the mechanism followed by elimination of the responsible substrate. A novel lattice-tip catheter with both high-density mapping and dual ablation properties(radiofrequency-RF/pulsed field ablation-PFA) has been recently introduced for catheter ablation of atrial fibrillation. We present the first study to assess its performance in the management of ATs (diagnostic and therapeutic). METHODS: Patients with documented ATs were selected. Activation mapping was used for the establishment of the AT mechanism. Confirmation with entrainment was performed, whenever appropriate. Accuracy of the activation mapping in diagnosis, acute ablation efficacy, and procedural characteristics were the study endpoints. RESULTS: Twenty patients were included (12 cavotricuspid isthmus-dependent atrial flutters, 5 mitral flutters, 2 roof flutters, and 2 focal ATs). Proper diagnosis was established by activation mapping in all cases. The mean mapping time was 7.85 ± 3.06 min with 296.82 ± 150.9 mean mapping points/minute. The mean ablation time was 54.25 ± 42.97 s. Conversion to sinus rhythm during ablation was achieved in all cases with the exception of a roof flutter that converted to mitral flutter and a case of a parahisian AT in which ablation was not attempted. Patients that received ablation did not experience any arrhythmia recurrence in a mean follow up of 4.14 ± 0.91 months. No major or minor complications occurred. CONCLUSION: The lattice-tip catheter and its dedicated electroanatomical mapping system provided sufficiently detailed activation mapping for the diagnosis of the AT mechanism. The delivered lesions were highly effective acutely, with no adverse events. However, limitations exist and should be acknowledged.

Combining Quantitative Susceptibility Mapping With the Gray Matter Volume to Predict Neurological Deficits in Patients With Small Artery Occlusion.

BACKGROUND: Currently, there is still a lack of valuable neuroimaging markers to assess the clinical severity of stroke patients with small artery occlusion (SAO). Quantitative susceptibility mapping (QSM) is a quantitative processing method for neuroradiological diagnostics. Gray matter (GM) volume changes in stroke patients are also proved to be associated with neurological deficits. This study aims to explore the predictive value of QSM and GM volume in neurological deficits of patients with SAO. METHODS: As neurological deficits, the National Institutes of Health Stroke Scale (NIHSS) was used. Sixty-six SAO participants within 24 h of first onset were enrolled and divided into mild and moderate groups based on NIHSS. QSM values of infarct area and GM volume were calculated from magnetic resonance imaging (MRI) data. Two-sample t-tests were used to compare differences in QSM value and GM volume between the two groups, and the diagnostic efficacy of the combination of QSM value and GM volume was evaluated. RESULTS: The results revealed both the QSM value and GM volume within the infarct area of the moderate group were lower compared to the mild group. Moderate group exhibited lower GM volume in some specific gyrus compared with mild group in the case of voxel-wise GM volume on whole-brain voxel level. The support vector machine (SVM) classifier's analysis showed a high power for the combination of QSM value, GM volume within the infarct area, and voxel-wise GM volume. CONCLUSION: Our research first reported the combination of QSM value, GM volume within the infarct area, and voxel-wise GM volume could be used to predict neurological impairment of patients with SAO, which provides new insights for further understanding the SAO stroke.

Automated single-cell omics end-to-end framework with data-driven batch inference.

To facilitate single-cell multi-omics analysis and improve reproducibility, we present single-cell pipeline for end-to-end data integration (SPEEDI), a fully automated end-to-end framework for batch inference, data integration, and cell-type labeling. SPEEDI introduces data-driven batch inference and transforms the often heterogeneous data matrices obtained from different samples into a uniformly annotated and integrated dataset. Without requiring user input, it automatically selects parameters and executes pre-processing, sample integration, and cell-type mapping. It can also perform downstream analyses of differential signals between treatment conditions and gene functional modules. SPEEDI's data-driven batch-inference method works with widely used integration and cell-typing tools. By developing data-driven batch inference, providing full end-to-end automation, and eliminating parameter selection, SPEEDI improves reproducibility and lowers the barrier to obtaining biological insight from these valuable single-cell datasets. The SPEEDI interactive web application can be accessed at https://speedi.princeton.edu/. A record of this paper's transparent peer review process is included in the supplemental information.

High-content phenotypic analysis of a C. elegans recombinant inbred population identifies genetic and molecular regulators of lifespan.

Lifespan is influenced by complex interactions between genetic and environmental factors. Studying those factors in model organisms of a single genetic background limits their translational value for humans. Here, we mapped lifespan determinants in 85 C. elegans recombinant inbred advanced intercross lines (RIAILs). We assessed molecular profiles-transcriptome, proteome, and lipidome-and life-history traits, including lifespan, development, growth dynamics, and reproduction. RIAILs exhibited large variations in lifespan, which correlated positively with developmental time. We validated three longevity modulators, including rict-1, gfm-1, and mltn-1, among the top candidates obtained from multiomics data integration and quantitative trait locus (QTL) mapping. We translated their relevance to humans using UK Biobank data and showed that variants in GFM1 are associated with an elevated risk of age-related heart failure. We organized our dataset as a resource that allows interactive explorations for new longevity targets.