Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome

Interspersed repeat composition and distribution in mammals have been best characterized in the human and mouse genomes. The bovine genome contains typical eutherian mammal repeats, but also has a significant number of long interspersed nuclear element RTE (BovB) elements proposed to have been horizontally transferred from squamata. Our analysis of the BovB repeats has indicated that only a few of them are currently likely to retrotranspose in cattle. However, bovine L1 repeats (L1 BT) have many likely active copies. Comparison of substitution rates for BovB and L1 BT indicates that L1 BT is a younger repeat family than BovB. In contrast to mouse and human, L1 occurrence is not negatively correlated with G+C content. However, BovB, Bov A2, ART2A, and Bov-tA are negatively correlated with G+C, although Bov-tAs correlation is weaker. Also, by performing genome wide correlation analysis of interspersed and simple sequence repeats, we have identified genome territories by repeat content that appear to define ancestral vs. ruminant-specific genomic regions. These ancestral regions, enriched with L2 and MIR repeats, are largely conserved between bovine and human.     

Epidemiology of sporadic bloody diarrhea in rural Western Kenya

We conducted laboratory-based surveillance and a case-control study to characterize the epidemiology of bloody diarrhea in rural Western Kenya. From May 1997 through April 2001, we collected stool from 451 persons with bloody diarrhea presenting to four rural clinics. Cultures of 231 (51%) specimens yielded 247 bacterial pathogens: 198 Shigella (97 S. flexneri, 41 S. dysenteriae type 1, 39 S. dysenteriae type non-1, 13 S. boydii, 8 S. sonnei), 33 Campylobacter, 15 non-typhoidal Salmonella, and 1 Vibrio cholerae O1. More than 90% of the isolates (excluding Campylobacter) were resistant to trimethoprim-sulfamethoxazole and tetracycline, and more than 80% were resistant to ampicillin. Most (74%) ill persons received medication to which their isolate was resistant. Drinking Lake Victoria water and sharing latrines between multiple households increased risk of bloody diarrhea. Washing hands after defecating was protective. Providing safe drinking water and more latrines, and promoting hand washing could reduce the burden of illness from bloody diarrhea while limiting injudicious antimicrobial use.     

Motivations,Barriers, and Outcomes of Patient-Reported Shared Decision Making in Eosinophilic Esophagitis

Digestive Diseases and Sciences - Little is known about patient choice in treatment of eosinophilic esophagitis (EoE). Determine motivators and barriers to using common EoE therapies and describe...     

Immune evasion in HPV− head and neck precancer–cancer transition is driven by an aneuploid switch involving chromosome 9p loss

An aneuploid-immune paradox encompasses somatic copy-number alterations (SCNAs), unleashing a cytotoxic response in experimental precancer systems, while conversely being associated with immune suppression and cytotoxic-cell depletion in human tumors, especially head and neck cancer (HNSC). We present evidence from patient samples and cell lines that alterations in chromosome dosage contribute to an immune hot-to-cold switch during human papillomavirus-negative (HPV⁻) head and neck tumorigenesis. Overall SCNA (aneuploidy) level was associated with increased CD3⁺ and CD8⁺ T cell microenvironments in precancer (mostly CD3⁺, linked to trisomy and aneuploidy), but with T cell-deficient tumors. Early lesions with 9p21.3 loss were associated with depletion of cytotoxic T cell infiltration in TP53 mutant tumors; and with aneuploidy were associated with increased NK-cell infiltration. The strongest driver of cytotoxic T cell and Immune Score depletion in oral cancer was 9p-arm level loss, promoting profound decreases of pivotal IFN-γ-related chemokines (e.g., CXCL9) and pathway genes. Chromosome 9p21.3 deletion contributed mainly to cell-intrinsic senescence suppression, but deletion of the entire arm was necessary to diminish levels of cytokine, JAK-STAT, and Hallmark NF-κB pathways. Finally, 9p arm-level loss and JAK2-PD-L1 codeletion (at 9p24) were predictive markers of poor survival in recurrent HPV⁻ HNSC after anti–PD-1 therapy; likely amplified by independent aneuploidy-induced immune-cold microenvironments observed here. We hypothesize that 9p21.3 arm-loss expansion and epistatic interactions allow oral precancer cells to acquire properties to overcome a proimmunogenic aneuploid checkpoint, transform and invade. These findings enable distinct HNSC interception and precision-therapeutic approaches, concepts that may apply to other CN-driven neoplastic, immune or aneuploid diseases, and immunotherapies.

The genetic bases for predisposition, and neoplastic transformation, to cancer have been increasingly well described. However, it remains less clear how early, precancer cells employ these genetic alterations to acquire the characteristic features and properties (1) of malignant disease. For example, studies of the immune landscape led to breakthrough trials of programmed death-1 (PD-1) inhibitors for recurrent, metastatic head and neck squamous cell carcinoma (HNSC) therapy (2–4). This underscores the importance of immune modulation in these tumors, despite a still suboptimal overall response rate of less than 20% in advanced cancers. Immune response within tumors has been observed to be strongest at the earliest neoplastic stages, as reported recently in lung adenocarcinoma precursors (5). As such, new, immune-based strategies could be developed to reduce the high global burden of HNSC, by intercepting the most common precursor of the most common HNSC presentation: HPV⁻ oral squamous cell carcinomas (6–8).Studies of chromosome somatic copy-number (CN) alteration (SCNA) profiles have reported the impact of 3p14, 9p21, or 17p13 loss in molecular models of HNSC progression (9) and risk (10–15). Early studies reported that patients with oral precancers harboring 9p21 and/or 3p14 loss were at significantly greater cancer risk than those with retention at these loci (10, 16). A comprehensive, prospective validation study examined the relative contribution of six candidate chromosome-arm regions. 9p21 loss had the greatest influence on cancer risk (13). The mechanism underlying the association between CN and malignant transformation of precancers, however, is unclear (17–20). Studies of CN-altered neoplastic cells have shown that SCNAs can trigger a cytotoxic response in experimental precancer systems (21, 22) but, paradoxically, were associated with immune evasion (23) and suppression (24) in computational studies of naturally occurring human cancers. The latter, in melanoma, found that nonresponders to PD-1 and CTLA-4 blockade had higher CN alteration and loss burdens, which correlated with immunologically cold tumors, characterized by cytotoxic-cell, marker, and metric reductions, and suppressive microenvironment cell, network, and signal increases (23–26). This SCNA-cold association was particularly strong in our previous, pan-The Cancer Genome Atlas (TCGA) computational study in HNSC (23). These data point to a putative in vivo switch from immune hot-to-cold in the precancer–cancer transition, and raise the hypothesis that SCNAs in precursor lesions contribute to malignant transformation through genomic events and mechanisms that enable the acquisition of immune-suppressive, evasive properties. To test this hypothesis, we evaluated CN influence on immune profiles and outcomes in a large prospective oral precancer patient cohort, and HPV⁻ HNSC (tissue specimens and cell lines) and anti–PD-1–treated recurrent-disease cohorts.     

Heterozygous Mutations in Natriuretic Peptide Receptor‐B (NPR2) Gene as a Cause of Short Stature

Based on the observation of reduced stature in relatives of patients with acromesomelic dysplasia, Maroteaux type (AMDM), caused by homozygous or compound heterozygous mutations in natriuretic peptide receptor‐B gene (NPR2), it has been suggested that heterozygous mutations in this gene could be responsible for the growth impairment observed in some cases of idiopathic short stature (ISS). We enrolled 192 unrelated patients with short stature and 192 controls of normal height and identified seven heterozygous NPR2 missense or splice site mutations all in the short stature patients, including one de novo splice site variant. Three of the six inherited variants segregated with short stature in the family. Nine additional rare nonsynonymous NPR2 variants were found in three additional cohorts. Functional studies identified eight loss‐of‐function mutations in short individuals and one gain‐of‐function mutation in tall individuals. With these data, we were able to rigorously verify that NPR2 functional haploinsufficiency contributes to short stature. We estimate a prevalence of NPR2 haploinsufficiency of between 0 and 1/26 in people with ISS. We suggest that NPR2 gain of function may be a more common cause of tall stature than previously recognized.     

Psychometric properties of the Zephyr bioharness device: a systematic review

Background

Technological development and improvements in Wearable Physiological Monitoring devices, have facilitated the wireless and continuous field-based monitoring/capturing of physiologic measures in healthy, clinical or athletic populations. These devices have many applications for prevention and rehabilitation of musculoskeletal disorders, assuming reliable and valid data is collected. The purpose of this study was to appraise the quality and synthesize findings from published studies on psychometric properties of heart rate measurements taken with the Zephyr Bioharness device.

Methods

We searched the Embase, Medline, PsycInfo, PuMed and Google Scholar databases to identify articles. Articles were appraised for quality using a structured clinical measurement specific appraisal tool. Two raters evaluated the quality and conducted data extraction. We extracted data on the reliability (intra-class correlation coefficients and standard error of measurement) and validity measures (Pearson/Spearman’s correlation coefficients) along with mean differences. Agreement parameters were summarised by the average biases and 95% limits of agreement.

Results

A total of ten studies were included: quality ratings ranged from 54 to 92%. The intra-class correlation coefficients reported ranged from 0.85–0.98. The construct validity coefficients compared against gold standard calibrations or other commercially used devices, ranged from 0.74–0.99 and 0.67–0.98 respectively. Zephyr Bioharness agreement error ranged from ??4.81 (under-estimation) to 3.00 (over-estimation) beats per minute, with varying 95% limits of agreement, when compared with gold standard measures.

Conclusion

Good to excellent quality evidence from ten studies suggested that the Zephyr Bioharness device can provide reliable and valid measurements of heart rate across multiple contexts, and that it displayed good agreements vs. gold standard comparators – supporting criterion validity.

     

The development of an instrument to evaluate interprofessional student team competency

Healthcare institutions, accreditation agencies for higher learning, and organizations such as the National Academy of Medicine in the United States, support interprofessional education (IPE) opportunities. However, incorporating IPE opportunities into academic settings remains difficult. One challenge is assessing IPE learning and practice outcomes, especially at the level of student performance to ensure graduates are “collaboration-ready”. The Creighton-Interprofessional Collaborative Evaluation (C-ICE) instrument was developed to address the need for a measurement tool for interprofessional student team performance. Four interprofessional competency domains provide the framework for the C-ICE instrument. Twenty-six items were identified as essential to include in the C-ICE instrument. This instrument was found to be both a reliable and a valid instrument to measure interprofessional interactions of student teams. Inter-rater reliability as measured by Krippendorff’s nominal alpha (nKALPHA) ranged from .558 to .887; with four of the five independent assessments achieving nKALPHA greater than or equal to 0.796. The findings indicated that the instrument is understandable (Gwet’s alpha coefficient (gAC) 0.63), comprehensive (gAC = 0.62), useful and applicable (gAC = 0.54) in a variety of educational settings. The C-ICE instrument provides educators a comprehensive evaluation tool for assessing student team behaviors, skills, and performance.