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.

Exploring Journey Maps as Products From Qualitative Research: Application Through Food Insecure Veterans' Experiences.

Journey maps are graphic representations of participant, user, customer, or patient experiences or "journeys" with a particular phenomenon, product, business, or organization. Journey maps help visualize complex pathways and phases in accessible, digestible ways. They also capture emotions, reactions, and values associated with the processes participants undergo, complemented by images or quotes from participants. Here, we outline the foundations of journey maps in research and in practice settings. Our goal is to describe journey maps to researchers new to the product and emphasize the novelty and utility of journey maps as visual products from qualitative research particularly in a health setting. To explore journey maps-including their benefits, drawbacks, and relevance-we discuss examples including our own process for designing a journey map of food insecure Veterans' experiences using qualitative, in-depth interviews and supported by member checking. Our journey map depicts food insecurity as a repetitive process, a unique contribution given that many journey maps are designed with discrete starting and stopping points. We conclude by discussing the novelty of journey maps as innovative products that researchers can use to identify opportunities for process improvements and innovation using multiple data sources or methods.

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.

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.

Use of multiparametric MRI to noninvasively assess iodinated contrast-induced acute kidney injury.

PURPOSE: To gauge the utility of multiparametric MRI in characterizing pathologic changes after iodinated contrast-induced acute kidney injury (CI-AKI) in rats. METHODS: We randomly grouped 24 rats injected with 8 g iodine/kg of body weight (n = 6 each) and 6 rats injected with saline as controls. All rats underwent T1, T2 mapping and diffusion kurtosis imaging (DKI) after contrast injection at 0 (control), 1, 3, 7, 13 days. T1, T2, and mean kurtosis (MK) values were performed in renal outer/inner stripes of outer medulla (OSOM and ISOM) and cortex (CO), and their diagnosis performance for CI-AKI also been evaluated. Serum creatinine (SCr), insulin-like growth factor-binding protein 7 (IGFBP7), tissue inhibitor metalloproteinase 2 (TIMP-2), aquaporin-1 (AQP1), α-smooth muscle actin (α-SMA), and histologic indices were examined. RESULTS: Compared with controls, urinary concentrations of both TIMP-2 and IGFBP7 were obviously elevated from Day 1 to Day 13 (all p < 0.05). T2 values were significantly higher than control group for Days 1 and 3, and T1 and MK increased were more remarkable at all time points (Days 1-13) in CI-AKI (all p < 0.05) than control group. Changes in T1 and MK strongly correlated with renal injury scores of all anatomical compartments and with expression levels of AQP1 and moderately correlated with α-SMA. Changes in T2 values correlating moderately with renal scores of CO, ISOM and OSOM and AQP1. The MK obtained the highest area under the receiver operating characteristic (ROC) curve of 0.846 with a sensitivity of 70.8 % and specificity of 88.9 %. CONCLUSIONS: Combined use of multiparametric MRI could be a valid noninvasive method for comprehensive monitoring of CI-AKI. Among these parameters, MK may achieve the best diagnostic performance for CI-AKI.

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.

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.

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.