Sport Biomechanics Applications Using Inertial, Force, and EMG Sensors: A Literature Overview

In the last few decades, a number of technological developments have advanced the spread of wearable sensors for the assessment of human motion. These sensors have been also developed to assess athletes’ performance, providing useful guidelines for coaching, as well as for injury prevention. The data from these sensors provides key performance outcomes as well as more detailed kinematic, kinetic, and electromyographic data that provides insight into how the performance was obtained. From this perspective, inertial sensors, force sensors, and electromyography appear to be the most appropriate wearable sensors to use. Several studies were conducted to verify the feasibility of using wearable sensors for sport applications by using both commercially available and customized sensors. The present study seeks to provide an overview of sport biomechanics applications found from recent literature using wearable sensors, highlighting some information related to the used sensors and analysis methods. From the literature review results, it appears that inertial sensors are the most widespread sensors for assessing athletes’ performance; however, there still exist applications for force sensors and electromyography in this context. The main sport assessed in the studies was running, even though the range of sports examined was quite high. The provided overview can be useful for researchers, athletes, and coaches to understand the technologies currently available for sport performance assessment

Gut Microbiota Composition Modulates the Magnitude and Quality of Germinal Centers during Plasmodium Infections

Gut microbiota composition is associated with human and rodent Plasmodium infections, yet the mechanism by which gut microbiota affects the severity of malaria remains unknown. Humoral immunity is critical in mediating the clearance of Plasmodium blood stage infections, prompting the hypothesis that mice with gut microbiota-dependent decreases in parasite burden exhibit better germinal center (GC) responses. In support of this hypothesis, mice with a low parasite burden exhibit increases in GC B cell numbers and parasite-specific antibody titers, as well as better maintenance of GC structures and a more targeted, qualitatively different antibody response. This enhanced humoral immunity affects memory, as mice with a low parasite burden exhibit robust protection against challenge with a heterologous, lethal Plasmodium species. These results demonstrate that gut microbiota composition influences the biology of spleen GCs as well as the titer and repertoire of parasite-specific antibodies, identifying potential approaches to develop optimal treatments for malaria

Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data

The adaptive immune receptor repertoire (AIRR) contains information on an individuals' immune past, present and potential in the form of the evolving sequences that encode the B cell receptor (BCR) repertoire. AIRR sequencing (AIRR-seq) studies rely on databases of known BCR germline variable (V), diversity (D), and joining (J) genes to detect somatic mutations in AIRR-seq data via comparison to the best-aligning database alleles. However, it has been shown that these databases are far from complete, leading to systematic misidentification of mutated positions in subsets of sample sequences. We previously presented TIgGER, a computational method to identify subject-specific V gene genotypes, including the presence of novel V gene alleles, directly from AIRR-seq data. However, the original algorithm was unable to detect alleles that differed by more than 5 single nucleotide polymorphisms (SNPs) from a database allele. Here we present and apply an improved version of the TIgGER algorithm which can detect alleles that differ by any number of SNPs from the nearest database allele, and can construct subject-specific genotypes with minimal prior information. TIgGER predictions are validated both computationally (using a leave-one-out strategy) and experimentally (using genomic sequencing), resulting in the addition of three new immunoglobulin heavy chain V (IGHV) gene alleles to the IMGT repertoire. Finally, we develop a Bayesian strategy to provide a confidence estimate associated with genotype calls. All together, these methods allow for much higher accuracy in germline allele assignment, an essential step in AIRR-seq studies

The nonperturbative functional renormalization group and its applications

The renormalization group plays an essential role in many areas of physics, both conceptually and as a practical tool to determine the long-distance low-energy properties of many systems on the one hand and on the other hand search for viable ultraviolet completions in fundamental physics. It provides us with a natural framework to study theoretical models where degrees of freedom are correlated over long distances and that may exhibit very distinct behavior on different energy scales. The nonperturbative functional renormalization-group (FRG) approach is a modern implementation of Wilson's RG, which allows one to set up nonperturbative approximation schemes that go beyond the standard perturbative RG approaches. The FRG is based on an exact functional flow equation of a coarse-grained effective action (or Gibbs free energy in the language of statistical mechanics). We review the main approximation schemes that are commonly used to solve this flow equation and discuss applications in equilibrium and out-of-equilibrium statistical physics, quantum many-particle systems, high-energy physics and quantum gravity.Comment: v2) Review article, 93 pages + bibliography, 35 figure

Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

Abstract: Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls

Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group

Funder: U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)Funder: National Center for Research Resources under award number 1 C06 RR12463-01, VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service, the DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558), the DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440), the DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329), the Ohio Third Frontier Technology Validation Fund, the Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering and the Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University.Funder: Susan G Komen Foundation (CCR CCR18547966) and a Young Investigator Grant from the Breast Cancer Alliance.Funder: The Canadian Cancer SocietyFunder: Breast Cancer Research Foundation (BCRF), Grant No. 17-194Abstract: Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring

Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials

Funder: Breast Cancer Research Foundation (BCRF); doi: https://doi.org/10.13039/100001006Abstract: Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting

Genomic tools and models for investigating the role of germline diversity in mouse antibody repertoire development.

Given the diversity and complexity within immunoglobulin (IG) loci, effective mouse models first require characterization of intra-strain differences and construction of high-quality reference assemblies for IG loci in several representative strains. To understand light chain germline diversity across biomedically significant mouse strains, we profiled the expressed IGK and IGL repertoires of 18 commonly used laboratory mouse strains using AIRR-seq. Across strains, we observed germline IGKV sequences shared by three different IGK haplotypes and a more conserved IGLV germline repertoire among common laboratory strains. Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing was used to sequence and assemble bacterial artificial chromosomes (BAC) clones spanning the IGH locus in BALB/cByJ and the IGK locus in NOD/LtJ, which represented divergent IG haplotypes. We assembled the BALB/cByJ-IGH assembly into five independent contigs containing 192 functional and 135 non-functional IGHV genes, 30 IGHD genes, 4 IGHJ genes, and 8 IGHC genes. The NOD/ShiLtJ-IGK assembly was assembled into two independent contigs, which contained 82 functional and 31 non-functional IGKV genes. These data guided construction of congenic strains on a C57BL/6 background that carried divergent BALB/cByJ or NOD/ShiLtJ IGH or IGK loci from, respectively. In addition, bulk AIRR-seq data from the BALB/cByJ-IGH congenic strain showed that divergent IGH haplotype influenced usage frequencies of germline IGKV and IGLV repertoire. Overall, this work revealed significant unexplored IG haplotype diversity through AIRR-seq, generated new IG reference assemblies, identified incomplete germline gene databases that lacked haplotype diversity, and provided evidence that heavy and light chain pairing frequencies are likely influenced by underlying IG haplotype variation

MRI findings are more common in selected patients with acute low back pain than controls?

Purpose The purpose of this study is to investigate if lumbar disc pathology identified on MRI scans is more common in patients with acute, likely discogenic, low back pain than matched controls. Methods We compared rates of MRI findings between 30 cases with low back pain and 30 pain-free controls. Cases were patients presenting for care with likely discogenic low back pain (demonstrated centralisation with repeated movement testing), of moderate intensity and with minimal past history of back pain. Controls were matched for age, gender and past history of back pain. Cases and controls underwent MRI scanning which was read for the presence of a range of MRI findings by two blinded assessors. Results The presence of disc degeneration, modic changes and disc herniation significantly altered the odds of a participant being a case or control. For example subjects were 5.2 times more likely to be a case than a control when disc degeneration grade of C3 was present, and 6.0 times more likely with modic changes. The presence of a high-intensity zone or annular tear was found to significantly alter odds for one assessor but not the other assessor. Conclusion MRI findings including disc degeneration, modic changes and herniation are more common in selected people with current acute (likely discogenic) low back pain than in controls without current low back pain. Further investigation of the value of MRI findings as prognostic factors and as treatment effect modifiers is required to assess the potential clinical importance of these findings.7 page(s

Transit Foods (Semester Unknown) IPRO 315: TransitFoodsIPRO315FinalPresentationSu10

Most of the existing large scale urban food depositories / pantries are based on a model of food production and distribution which has not changed in the last forty years. It is essentially the same model used by large private grocery chains, involving off-site food acquisition (either through production or donation) and dissemination to large distribution centers. In some cases, these distribution centers are then accessed by either individuals or organizations which truck the goods to smaller, local urban distribution points. In other cases, patrons are required to visit the large facility, which it typically in a less accessible location.Deliverable