Expression and function of transient receptor potential melastatin 3 in the spinal afferent innervation of the mouse colon.

Abdominal pain is a cardinal symptom of inflammatory bowel disease (IBD). Transient receptor potential (TRP) channels contribute to abdominal pain in preclinical models of IBD, and TRP melastatin 3 (TRPM3) has recently been implicated in inflammatory bladder and joint pain in rodents. We hypothesized that TRPM3 is involved in colonic sensation and is sensitized during colitis. We used immunohistochemistry, ratiometric Ca2+ imaging, and colonic afferent nerve recordings in mice to evaluate TRPM3 protein expression in colon-projecting dorsal root ganglion (DRG) neurons, as well as functional activity in DRG neurons and colonic afferent nerves. Colitis was induced using dextran sulfate sodium (DSS) in drinking water. TRPM3 protein expression was observed in 76% of colon-projecting DRG neurons and was often colocalized with calcitonin gene-related peptide. The magnitudes of intracellular Ca2+ transients in DRG neurons in response to the TRPM3 agonists CIM-0216 and pregnenolone sulfate sodium were significantly greater in neurons from mice with colitis compared with controls. In addition, the percentage of DRG neurons from mice with colitis that responded to CIM-0216 was significantly increased. CIM-0216 also increased the firing rate of colonic afferent nerves from control and mice with colitis. The TRPM3 inhibitor isosakuranetin inhibited the mechanosensitive response to distension of wide dynamic range afferent nerve units from mice with colitis but had no effect in control mice. Thus, TRPM3 contributes to colonic sensory transduction and may be a potential target for treating pain in IBD.NEW & NOTEWORTHY This is the first study to characterize TRPM3 protein expression and function in colon-projecting DRG neurons. A TRPM3 agonist excited DRG neurons and colonic afferent nerves from healthy mice. TRPM3 agonist responses in DRG neurons were elevated during colitis. Inhibiting TRPM3 reduced the firing of wide dynamic range afferent nerves from mice with colitis but had no effect in control mice.

A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks.

The organisation of the genome in nuclear space is an important frontier of biology. Chromosome conformation capture methods such as Hi-C and Micro-C produce genome-wide chromatin contact maps that provide rich data containing quantitative and qualitative information about genome architecture. Most conventional approaches to genome-wide chromosome conformation capture data are limited to the analysis of pre-defined features, and may therefore miss important biological information. One constraint is that biologically important features can be masked by high levels of technical noise in the data. Here we introduce a replicate-based method for deep learning from chromatin conformation contact maps. Using a Siamese network configuration our approach learns to distinguish technical noise from biological variation and outperforms image similarity metrics across a range of biological systems. The features extracted from Hi-C maps after perturbation of cohesin and CTCF reflect the distinct biological functions of cohesin and CTCF in the formation of domains and boundaries, respectively. The learnt distance metrics are biologically meaningful, as they mirror the density of cohesin and CTCF binding. These properties make our method a powerful tool for the exploration of chromosome conformation capture data, such as Hi-C capture Hi-C, and Micro-C.

Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes.

DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N = 190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P < 1 × 10-7). We connect obesity-associated methylation variations to transcriptomic changes at >500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions.

Chromatin jets define the properties of cohesin-driven in vivo loop extrusion.

Complex genomes show intricate organization in three-dimensional (3D) nuclear space. Current models posit that cohesin extrudes loops to form self-interacting domains delimited by the DNA binding protein CTCF. Here, we describe and quantitatively characterize cohesin-propelled, jet-like chromatin contacts as landmarks of loop extrusion in quiescent mammalian lymphocytes. Experimental observations and polymer simulations indicate that narrow origins of loop extrusion favor jet formation. Unless constrained by CTCF, jets propagate symmetrically for 1-2 Mb, providing an estimate for the range of in vivo loop extrusion. Asymmetric CTCF binding deflects the angle of jet propagation as experimental evidence that cohesin-mediated loop extrusion can switch from bi- to unidirectional and is controlled independently in both directions. These data offer new insights into the physiological behavior of in vivo cohesin-mediated loop extrusion and further our understanding of the principles that underlie genome organization.

Psychosocial influences in the development of cumulative trauma disorders.

STUDY DESIGN: This study is a single-phase, qualitative study using grounded theory methodology. INTRODUCTION: Cumulative trauma disorders (CTDs) are musculoskeletal disorders that impact health and productivity. CTD risk factors are present in the workplace, home, and community. Occupational and physical therapists specializing in hand and upper extremity rehabilitation (hand therapists) are widely involved with this population. Hand therapists often employ a medical model in the assessment and treatment of these conditions; however, the medical model has not proven to be consistently effective in relieving symptoms or producing a durable return to daily living activities. PURPOSE OF THE STUDY: The purpose of this study was to explore the lived experiences of individuals diagnosed with CTD, and investigate the psychosocial phenomena influencing CTD development as an impediment to occupational performance. METHODS: The principal investigator recruited 11 participants who met specific inclusion criteria, then used semi-structured interviews aimed at exploring the lived experiences of the participants while investigating the psychosocial phenomenon influencing CTD development. Interviews were transcribed and analyzed using a process of constant comparison, up until saturation occurred. Trustworthiness techniques were used in the data analysis phase and included peer reviews and member checking. FINDINGS: The findings suggest that many psychosocial factors contribute to the development and impact of CTDs, at both onset of symptoms and throughout the duration of the condition. A significant number of contextual factors influence participants' function, behavior, relationships, and the course of medical care. Themes derived from the participants' expressions, included the following: 1) an initial strategy of "work through the pain," can be detrimental to symptom resolution and leads to progressive failure to meet role expectations, 2) a pervasive notion of CTDs as "an invisible disability," leaving participants feeling isolated and frustrated when significant others fail to offer support or reject them, 3) participants often delayed reporting symptom development to employers, family members, and medical personnel, risking permanent injury and disability, 4) a "stigma" is attached to CTDs that encourages isolation; however, the social support of even one significant other in a person's life can facilitate adaptation. DISCUSSION AND CONCLUSION: All participants experienced hardship because of their conditions; however, two of the eleven participants capably navigated the process, using past experience and support from family and employer to successfully adapt. These findings offer support that CTDs are adaptive disorders. The study's conclusion suggests a new model to describe CTD dysfunction and presents new ways of thinking for clinicians who treat the CTD population.

Conserved non-coding elements: developmental gene regulation meets genome organization.

Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks-dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.

Mapping communication spaces: The development and use of a tool for analyzing the impact of EHRs on interprofessional collaborative practice.

INTRODUCTION: Members of the healthcare team must access and share patient information to coordinate interprofessional collaborative practice (ICP). Although some evidence suggests that electronic health records (EHRs) contribute to in-team communication breakdowns, EHRs are still widely hailed as tools that support ICP. If EHRs are expected to promote ICP, researchers must be able to longitudinally study the impact of EHRs on ICP across communication types, users, and physical locations. OBJECTIVE: This paper presents a data collection and analysis tool, named the Map of the Clinical Interprofessional Communication Spaces (MCICS), which supports examining how EHRs impact ICP over time, and across communication types, users, and physical locations. METHODS: The tool's development evolved during a large prospective longitudinal study conducted at a Canadian pediatric academic tertiary-care hospital. This two-phased study [i.e., pre-implementation (phase 1) and post implementation (phase 2)] of an EHR employed a constructivist grounded theory approach and triangulated data collection strategies (i.e., non-participant observations, interviews, think-alouds, and document analysis). The MCICS was created through a five-step process: (i) preliminary structural development based on the use of the paper-based chart (phase 1); (ii) confirmatory review and modification process (phase 1); (iii) ongoing data collection and analysis facilitated by the map (phase 1); (iv) data collection and modification of map based on impact of EHR (phase 2); and (v) confirmatory review and modification process (phase 2). RESULTS: Creating and using the MCICS enabled our research team to locate, observe, and analyze the impact of the EHR on ICP, (a) across oral, electronic, and paper communications, (b) through a patient's passage across different units in the hospital, (c) across the duration of the patient's stay in hospital, and (d) across multiple healthcare providers. By using the MCICS, we captured a comprehensive, detailed picture of the clinical milieu in which the EHR was implemented, and of the intended and unintended consequences of the EHR's deployment. The map supported our observations and analysis of ICP communication spaces, and of the role of the patient chart in these spaces. CONCLUSIONS: If EHRs are expected to help resolve ICP challenges, it is important that researchers be able to longitudinally assess the impact of EHRs on ICP across multiple modes of communication, users, and physical locations. Mapping the clinical communication spaces can help EHR designers, clinicians, educators and researchers understand these spaces, appreciate their complexity, and navigate their way towards effective use of EHRs as means for supporting ICP. We propose that the MCICS can be used "as is" in other academic tertiary-care pediatric hospitals, and can be tailored for use in other healthcare institutions.

Accuracy of Adverse Drug Reaction Documentation upon Implementation of an Ambulatory Electronic Health Record System.

BACKGROUND: Detection, monitoring and treatment of adverse drug reactions (ADRs) are paramount to patient safety. The use of a comprehensive electronic health record (EHR) system has the potential to address inadequacies in ADR documentation and to facilitate ADR reporting to health agencies. However, effective methods to maintain the quality of documented ADRs within an EHR have not been well studied. OBJECTIVE: To evaluate the accuracy and effectiveness of ADR documentation transfer throughout the implementation of a comprehensive EHR system. METHODS: Retrospective analysis of ADR documentation at a tertiary care pediatric hospital between January 2013 and June 2014. ADRs documented in the newly implemented ambulatory EHR, pharmacy system and hybrid health record system were extracted. Documentation inconsistencies and processes for managing ADR documentation within the EHR were reviewed. RESULTS: A total of 115 patients with 260 unique ADRs were identified. Only 155 (60 %) of the identified ADRs were found in the ambulatory EHR system. The remaining 105 ADRs (40 %) were missing from the EHR when it was compared with the other systems. Seventy-two patients (63 %) returned for a follow-up visit, and each had their ADR documentation reviewed in the ambulatory EHR. Following the visit, 44 % of these ambulatory EHR records still included incorrect information. CONCLUSIONS: We identified discrepancies in ADR documentation within hospital systems, which need to be addressed as healthcare institutions transition to EHRs. Processes related to the transfer of ADR information into the EHR should be clearly defined. To improve the quality of ADR documentation, steps to force complete and continual ADR verification should be introduced at early stages of implementation of a new EHR, and all responsible providers should play a role.

The impact of adopting EHRs: how losing connectivity affects clinical reasoning.

CONTEXT: As electronic health records (EHRs) are adopted by teaching hospitals, educators must examine how this change impacts trainee development. OBJECTIVES: We investigate this influence by studying clinician experiences of a hospital's move from paper charts to an EHR. We ask: how does each chart modality present conceptions of time and data interconnections? How do these conceptions affect clinical reasoning? METHODS: This two-phase, longitudinal study employed constructivist grounded theory. Data were collected at a paediatric teaching hospital before (Phase 1), during and after (Phase 2) the transition from a paper chart to an EHR system. Data collection consisted of field observations (146 hours involving 300 health care providers, 22 patients and 32 patient family members), think-aloud (n = 13) and think-after (n = 11) sessions, interviews (n = 39) and document retrieval (n = 392). Theories of rhetorical genre studies and visual rhetoric informed analysis. RESULTS: In the paper flowsheet, clinicians recorded and viewed patient data in chronologically organised displays that emphasised data interconnections. In the EHR flowsheet, clinicians viewed and recorded individual data points that were largely chronologically and contextually isolated. Clinicians reported that this change resulted in: (i) not knowing the patient's evolving status; (ii) increased cognitive workload, and (iii) loss of clinical reasoning support mechanisms. CONCLUSIONS: Understanding how patient data are interconnected is essential to clinical reasoning. The use of EHRs supports this goal because the EHR is a tool for collecting dispersed data; however, these collections often deconstruct data interconnections. Where the paper flowsheet emphasises chronology and interconnectedness, the EHR flowsheet emphasises individual data values that are largely independent of time and other patient data. To prepare trainees to work with EHRs, the ways of thinking and acting that were implicitly learned through the use of paper charts must be made explicit. To support clinical reasoning, medical educators should provide lessons in connectivity ­ the chronologically framed data interconnections upon which clinicians rely to provide patient care.