Genome wide analysis of gene expression changes in skin from patients with type 2 diabetes

Non-healing chronic ulcers are a serious complication of diabetes and are a major healthcare problem. While a host of treatments have been explored to heal or prevent these ulcers from forming, these treatments have not been found to be consistently effective in clinical trials. An understanding of the changes in gene expression in the skin of diabetic patients may provide insight into the processes and mechanisms that precede the formation of non-healing ulcers. In this study, we investigated genome wide changes in gene expression in skin between patients with type 2 diabetes and non-diabetic patients using next generation sequencing. We compared the gene expression in skin samples taken from 27 patients (13 with type 2 diabetes and 14 non-diabetic). This information may be useful in identifying the causal factors and potential therapeutic targets for the prevention and treatment of diabetic related diseases

Dopamine, affordance and active inference.

The role of dopamine in behaviour and decision-making is often cast in terms of reinforcement learning and optimal decision theory. Here, we present an alternative view that frames the physiology of dopamine in terms of Bayes-optimal behaviour. In this account, dopamine controls the precision or salience of (external or internal) cues that engender action. In other words, dopamine balances bottom-up sensory information and top-down prior beliefs when making hierarchical inferences (predictions) about cues that have affordance. In this paper, we focus on the consequences of changing tonic levels of dopamine firing using simulations of cued sequential movements. Crucially, the predictions driving movements are based upon a hierarchical generative model that infers the context in which movements are made. This means that we can confuse agents by changing the context (order) in which cues are presented. These simulations provide a (Bayes-optimal) model of contextual uncertainty and set switching that can be quantified in terms of behavioural and electrophysiological responses. Furthermore, one can simulate dopaminergic lesions (by changing the precision of prediction errors) to produce pathological behaviours that are reminiscent of those seen in neurological disorders such as Parkinson's disease. We use these simulations to demonstrate how a single functional role for dopamine at the synaptic level can manifest in different ways at the behavioural level

The Pre-Operative Evaluation Clinic: An Underutilized Service in Optimizing Analgesic Outcomes in Patients on Buprenorphine, Methadone, and Naltrexone for Substance Use Disorder or Chronic Pain

Addyson E Sand,1 Tyler E Powell,1 Helen T Marry,1 Heather R Rathbun,1 Jenna R Steege,1 Allison LeMahieu,2 Adam K Jacob,1 Ryan S D’Souza,1 Oludare O Olatoye1 1Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, USA; 2Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USACorrespondence: Oludare O Olatoye, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA, Email [email protected]: Patients receiving methadone, buprenorphine, and naltrexone for either chronic pain or substance use disorder (SUD) pose perioperative challenges. Due to their complex pharmacology, perioperative recommendations continue to evolve. Deviations from these recommendations may result in worse perioperative outcomes. A formal preoperative evaluation (POE) and optimization of patients on these medications are recommended to address these concerns.Methods: A single-center retrospective electronic health record review was performed with adult patients on methadone, buprenorphine, and naltrexone undergoing elective surgery between January 1, 2010 and December 31, 2020. The primary outcome of interest was the percentage of patients referred to the POE clinic for evaluation prior to the scheduled elective surgery. In addition, we assessed differences in variables (perioperative opioid, hospital length of stay, perioperative multimodal analgesics, perioperative complications, inpatient pain service consult, readmission within 30 days, cancellation of surgery, addiction medicine consult) based on POE clinic evaluation. This analysis was performed separately for patients prescribed these medications for SUD versus chronic pain. Continuous outcomes were analyzed using linear regression with generalized estimating equations (GEE) and robust variance estimates.Results: A total of 714 patients were included in the final analysis, of which 572 (80%) took buprenorphine, methadone, or naltrexone for chronic pain and 142 (20%) took these medications for SUD. Within the chronic pain and SUD subpopulations, 193 (34%) and 35 (25%) patients had formal POE clinic assessments, respectively. Among those taking these medications for chronic pain, POE clinic evaluation was associated with a higher likelihood for receiving non-opioid multimodal analgesics perioperatively (p = 0.016).Conclusion: Formal preoperative evaluations are currently underutilized in patients who take buprenorphine, methadone, or naltrexone for chronic pain or SUD. These patients may benefit from POE clinic assessment to optimize perioperative outcomes.Keywords: preoperative evaluation, chronic opioid therapy, substance use disorder, naltrexone, buprenorphine, methadone, perioperative pain managemen

Misinformation Persists in Complementary Health: Evaluating the Reliability and Quality of YouTube-Based Information on the Use of Acupuncture for Chronic Pain

Majesty Greer,1 Sai Kamma,2 Henry Tran,2 Bright Etumuse,2 Jay D Shah,3 Youshaa El-Abed,4 Jane O Onyemachi,2 Nasir Hussain,5 Thomas P Pittelkow,6 Ryan S D’Souza6 1Howard University College of Medicine, Washington, DC, USA; 2University of Texas Medical Branch School of Medicine, Galveston, TX, USA; 3Department of Anesthesiology, Baylor College of Medicine, Houston, TX, USA; 4College of Osteopathic Medicine, Kansas City University, Kansas City, MO, USA; 5Department of Anesthesiology, The Ohio State University Wexner Medical Center, Columbus, OH, USA; 6Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, USACorrespondence: Ryan S D’Souza, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, 200 First St. SW, Rochester, MN, 55905, USA, Email [email protected]: Acupuncture is commonly used to treat chronic pain. Patients often access public social media platforms for healthcare information when querying acupuncture. Our study aims to appraise the utility, accuracy, and quality of information available on YouTube, a popular social media platform, on acupuncture for chronic pain treatment.Methods: Using search terms such as “acupuncture for chronic pain” and “acupuncture pain relief”, the top 54 videos by view count were selected. Included videos were > 1 minute duration, contained audio in English, had > 7000 views, and was related to acupuncture. One primary outcome of interest was categorizing each video’s usefulness as useful, misleading, or neither. Another primary outcome of interest was the quality and reliability of each video using validated instruments, including the modified DISCERN (mDISCERN) tool and the Global Quality Scale (GQS). The means were calculated for the video production characteristics, production sources, and mDISCERN and GQS scores. Continuous and categorical outcomes were compared using Student’s t-test and chi-square test, respectively.Results: Of the 54 videos, 57.4% were categorized as useful, 14.8% were misleading, and 27.8% were neither. Useful videos had a mean GQS and mDISCERN score of 3.77± 0.67 and 3.48± 0.63, respectively, while misleading videos had mean GQS and mDISCERN score of 2.50± 0.53 and 2.38± 0.52, respectively. 41.8% of the useful videos were produced by a healthcare institution while none of the misleading videos were produced by a healthcare institution. However, 87.5% of the misleading videos were produced by health media compared to only 25.8% of useful videos from health media.Discussion: As patients increasingly depend on platforms like YouTube for trustworthy information on complementary health practices such as acupuncture, our study emphasizes the critical need for more higher-quality videos from unbiased healthcare institutions and physicians to ensure patients are receiving reliable information regarding this topic.Keywords: acupuncture, chronic pain, social media, anesthesia, information dissemination, interne

Prognostic model to predict postoperative acute kidney injury in patients undergoing major gastrointestinal surgery based on a national prospective observational cohort study.

Background: Acute illness, existing co-morbidities and surgical stress response can all contribute to postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery. The aim of this study was prospectively to develop a pragmatic prognostic model to stratify patients according to risk of developing AKI after major gastrointestinal surgery. Methods: This prospective multicentre cohort study included consecutive adults undergoing elective or emergency gastrointestinal resection, liver resection or stoma reversal in 2-week blocks over a continuous 3-month period. The primary outcome was the rate of AKI within 7 days of surgery. Bootstrap stability was used to select clinically plausible risk factors into the model. Internal model validation was carried out by bootstrap validation. Results: A total of 4544 patients were included across 173 centres in the UK and Ireland. The overall rate of AKI was 14·2 per cent (646 of 4544) and the 30-day mortality rate was 1·8 per cent (84 of 4544). Stage 1 AKI was significantly associated with 30-day mortality (unadjusted odds ratio 7·61, 95 per cent c.i. 4·49 to 12·90; P < 0·001), with increasing odds of death with each AKI stage. Six variables were selected for inclusion in the prognostic model: age, sex, ASA grade, preoperative estimated glomerular filtration rate, planned open surgery and preoperative use of either an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker. Internal validation demonstrated good model discrimination (c-statistic 0·65). Discussion: Following major gastrointestinal surgery, AKI occurred in one in seven patients. This preoperative prognostic model identified patients at high risk of postoperative AKI. Validation in an independent data set is required to ensure generalizability

Impaired RNA incorporation and dimerization in live attenuated leader-variants of SIV(mac239)

BACKGROUND: The 5' untranslated region (UTR) or leader sequence of simian immunodeficiency virus (SIV(mac239)) is multifunctional and harbors the regulatory elements for viral replication, persistence, gene translation, expression, and the packaging and dimerization of viral genomic RNA (vRNA). We have constructed a series of deletions in the SIV(mac239 )leader sequence in order to determine the involvement of this region in both the packaging and dimerization of viral genomic RNA. We also assessed the impact of these deletions upon viral infectiousness, replication kinetics and gene expression in cell lines and monkey peripheral blood mononuclear cells (PBMC). RESULTS: Regions on both sides of the major splice donor (SD) were found to be necessary for the efficiency and specificity of viral genome packaging. However, stem-loop1 is critical for both RNA encapsidation and dimerization. Downstream elements between the splice donor and the initiation site of SIV-Gag have additive effects on RNA packaging and contribute to a lesser degree to RNA dimerization. The targeted disruption of structures on both sides of the SD also severely impacts viral infectiousness, gene expression and replication in both CEMx174 cells and rhesus PBMC. CONCLUSION: In the leader region of SIV(mac239), stem-loop1 functions as the primary determinant for both RNA encapsidation and dimerization. Downstream elements between the splice donor and the translational initiation site of SIV-Gag are classified as secondary determinants and play a role in dimerization. Collectively, these data signify a linkage between the primary encapsidation determinant of SIV(mac239 )and RNA dimerization

Murine leukemia virus RNA dimerization is coupled to transcription and splicing processes

Most of the cell biological aspects of retroviral genome dimerization remain unknown. Murine leukemia virus (MLV) constitutes a useful model to study when and where dimerization occurs within the cell. For instance, MLV produces a subgenomic RNA (called SD') that is co-packaged with the genomic RNA predominantly as FLSD' heterodimers. This SD' RNA is generated by splicing of the genomic RNA and also by direct transcription of a splice-associated retroelement of MLV (SDARE). We took advantage of these two SD' origins to study the effects of transcription and splicing events on RNA dimerization. Using genetic approaches coupled to capture of RNA heterodimer in virions, we determined heterodimerization frequencies in different cellular contexts. Several cell lines were stably established in which SD' RNA was produced by either splicing or transcription from SDARE. Moreover, SDARE was integrated into the host chromosome either concomitantly or sequentially with the genomic provirus. Our results showed that transcribed genomic and SD' RNAs preferentially formed heterodimers when their respective proviruses were integrated together. In contrast, heterodimerization was strongly affected when the two proviruses were integrated independently. Finally, dimerization was enhanced when the transcription sites were expected to be physically close. For the first time, we report that splicing and RNA dimerization appear to be coupled. Indeed, when the RNAs underwent splicing, the FLSD' dimerization reached a frequency similar to co-transcriptional heterodimerization. Altogether, our results indicate that randomness of heterodimerization increases when RNAs are co-expressed during either transcription or splicing. Our results strongly support the notion that dimerization occurs in the nucleus, at or near the transcription and splicing sites, at areas of high viral RNA concentration

Whole Genome Sequence Analysis of Cryptococcus gattii from the Pacific Northwest Reveals Unexpected Diversity

A recent emergence of Cryptococcus gattii in the Pacific Northwest involves strains that fall into three primarily clonal molecular subtypes: VGIIa, VGIIb and VGIIc. Multilocus sequence typing (MLST) and variable number tandem repeat analysis appear to identify little diversity within these molecular subtypes. Given the apparent expansion of these subtypes into new geographic areas and their ability to cause disease in immunocompetent individuals, differentiation of isolates belonging to these subtypes could be very important from a public health perspective. We used whole genome sequence typing (WGST) to perform fine-scale phylogenetic analysis on 20 C. gattii isolates, 18 of which are from the VGII molecular type largely responsible for the Pacific Northwest emergence. Analysis both including and excluding (289,586 SNPs and 56,845 SNPs, respectively) molecular types VGI and VGIII isolates resulted in phylogenetic reconstructions consistent, for the most part, with MLST analysis but with far greater resolution among isolates. The WGST analysis presented here resulted in identification of over 100 SNPs among eight VGIIc isolates as well as unique genotypes for each of the VGIIa, VGIIb and VGIIc isolates. Similar levels of genetic diversity were found within each of the molecular subtype isolates, despite the fact that the VGIIb clade is thought to have emerged much earlier. The analysis presented here is the first multi-genome WGST study to focus on the C. gattii molecular subtypes involved in the Pacific Northwest emergence and describes the tools that will further our understanding of this emerging pathogen

DMSO and Betaine Greatly Improve Amplification of GC-Rich Constructs in De Novo Synthesis

In Synthetic Biology, de novo synthesis of GC-rich constructs poses a major challenge because of secondary structure formation and mispriming. While there are many web-based tools for codon optimizing difficult regions, no method currently exists that allows for potentially phenotypically important sequence conservation. Therefore, to overcome these limitations in researching GC-rich genes and their non-coding elements, we explored the use of DMSO and betaine in two conventional methods of assembly and amplification. For this study, we compared the polymerase (PCA) and ligase-based (LCR) methods for construction of two GC-rich gene fragments implicated in tumorigenesis, IGF2R and BRAF. Though we found no benefit in employing either DMSO or betaine during the assembly steps, both additives greatly improved target product specificity and yield during PCR amplification. Of the methods tested, LCR assembly proved far superior to PCA, generating a much more stable template to amplify from. We further report that DMSO and betaine are highly compatible with all other reaction components of gene synthesis and do not require any additional protocol modifications. Furthermore, we believe either additive will allow for the production of a wide variety of GC-rich gene constructs without the need for expensive and time-consuming sample extraction and purification prior to downstream application