EASTR: Identifying and eliminating systematic alignment errors in multi-exon genes.

Accurate alignment of transcribed RNA to reference genomes is a critical step in the analysis of gene expression, which in turn has broad applications in biomedical research and in the basic sciences. We reveal that widely used splice-aware aligners, such as STAR and HISAT2, can introduce erroneous spliced alignments between repeated sequences, leading to the inclusion of falsely spliced transcripts in RNA-seq experiments. In some cases, the 'phantom' introns resulting from these errors make their way into widely-used genome annotation databases. To address this issue, we present EASTR (Emending Alignments of Spliced Transcript Reads), a software tool that detects and removes falsely spliced alignments or transcripts from alignment and annotation files. EASTR improves the accuracy of spliced alignments across diverse species, including human, maize, and Arabidopsis thaliana, by detecting sequence similarity between intron-flanking regions. We demonstrate that applying EASTR before transcript assembly substantially reduces false positive introns, exons, and transcripts, improving the overall accuracy of assembled transcripts. Additionally, we show that EASTR's application to reference annotation databases can detect and correct likely cases of mis-annotated transcripts.

Comparison of BioLIFT versus LIFT for the treatment of trans-sphincteric anal fistula: a protocol for systematic review and meta-analysis.

INTRODUCTION: Identifying the optimal treatment for anal fistula has been challenging. Since first reported in 2007, the ligation of the intersphincteric fistula tract (LIFT) procedure has reported healing rates between 40% and 95% and is being increasingly adopted. The BioLIFT is an augmentation of the LIFT with an intersphincteric bioprosthetic mesh and has reported healing rates between 69% and 94%. Despite increased costs and potential complications associated with mesh, the evidence comparing healing rates between BioLIFT and LIFT is unknown. This study details the protocol for a systematic review and meta-analysis of BioLIFT and LIFT to compare outcomes associated with each procedure. METHODS AND ANALYSIS: MEDLINE, EMBASE and the Cochrane Database will be searched from inception using a search strategy designed by an information specialist. Randomised controlled trials, prospective and retrospective cohort studies, consecutive series, cross-sectional studies and case series with more than five patients will be included. Both comparative and single group studies will be included. The eligible population will be adult patients undergoing BioLIFT or LIFT for trans-sphincteric anal fistula. The primary outcome will be primary healing rate. Secondary outcomes will capture secondary healing rate and complications. Abstract, full text and data extraction will be completed independently and in duplicate by two reviewers. Study risk of bias will be assessed using Risk of Bias In Non-randomized Studies - of Interventions and the Risk of Bias (RoB 2.0) tool. Quality of evidence for outcomes will be evaluated using Grading of Recommendations, Assessment, Development and Evaluations criteria. A meta-analysis will be performed using a random-effects inverse variance model. Subgroup and sensitivity analyses will be explored in relation to complex fistula characteristics and patients who have undergone previous LIFT. Heterogeneity will be assessed using the I2 statistic. ETHICS AND DISSEMINATION: This review does not require research ethics board approval. This study will be completed in September 2022. The findings of this study will be disseminated through peer-reviewed international conferences and journals. PROSPERO REGISTRATION NUMBER: CRD42020127996.

Video-based interviewing in medicine: a scoping review.

BACKGROUND: The Coronavirus 2019 pandemic necessitated a rapid uptake of video-based interviewing within the personnel selection process in healthcare. While video-based interviews have been evaluated previously, we identified a gap in the literature on the implementation of video-based interviews and how they compare to their face-to-face counterparts. METHODS: A scoping review was conducted to consolidate the available literature on the benefits and limitations of video-based interviews and to understand the perceived barriers associated with transitioning away from face-to-face interviews. A search strategy, developed in concert with an academic health sciences librarian, was run on Ovid MEDLINE, Embase, PsycInfo, and Cochrane Central. The search was performed on March 31, 2020, and updated on February 21, 2021. Studies that implemented and evaluated the impact of video-based interviewing in healthcare were included in our study. Review articles and editorials were excluded. RESULTS: Forty-three studies were included in our scoping review, of which 17 were conference abstracts and 26 were peer-reviewed manuscripts. The risk of bias was moderate or high in most studies, with only four studies having a low risk of bias. Both financial costs and opportunity costs associated with the selection process were reported to be improved with video-based interviewing, while no studies explored the impact on environmental costs. Technical limitations, which were not prevalent, were easily managed during the interview process. Overall, video-based interviews were well received by both applicants and interviewers, although most participants still reported a preference for face-to-face interviews. CONCLUSIONS: While video-based interviewing has become necessary during the Coronavirus 2019 era, there are benefits from a financial, opportunistic, and environmental point of view that argue for its continued use even after the pandemic. Despite its successful implementation with minimal technical issues, a preference still remains for face-to-face interviews. Reasons for this preference are not clear from the available literature. Future studies on the role of nonverbal communication during the video-based interview process are important to better understand how video-based interviewing can be optimized. SYSTEMATIC REVIEW REGISTRATION: This scoping review was registered with Open Science Framework.

Comparison of non-operative versus operative management of resectable colorectal cancer in elderly patients: study protocol for a systematic review.

BACKGROUND: In the 2021 Statistics Canada census, 18.5% of the Canadian population were senior (65 years and older), among those 1.7 million (4.5%) were aged 80 years and older. Colorectal cancer (CRC) is the third most common cancer in both men and women, with its highest incidence rate in septu- and octogenarians. As clinicians encounter a growing number of very elderly patients (80 years and older) with resectable colorectal cancer, justifying major surgery in a comorbid population with limited life expectancy is difficult. Therefore, this study aims to systemically review the available literature to compare non-operative management to surgical resection with respect to overall survival and quality of life. METHOD: We designed and registered a study protocol for a systematic review. We will include all patients above the age of 80 with resectable colorectal cancer. We will search MEDLINE, EMBASE, and the Cochrane Database of Controlled Trials from January 2000 onwards. We will include randomized, non-randomized controlled trials and observational studies comparing non-operative versus operative management of resectable colorectal cancer in elderly patients. The primary outcomes will be overall survival and mortality. Secondary outcomes will include quality of life, and health services/ resources utilization (e.g., treatments, change of level of care…). Two reviewers will independently screen all citations, full-text articles, and abstract data. Potential conflicts will be resolved through discussion. The study methodological quality (or bias) will be appraised using the ROB-2 and ROBIN-I tools. If feasible, we will conduct random effects meta-analysis. Additional analyses will be conducted to explore the potential sources of heterogeneity (e.g., study design and methodological quality). DISCUSSION: This systematic review will synthesize the existing data on the management of colorectal cancer in the very elderly patients, and identify the gap in the literature for potential future research. More specifically, we aim to streamline non-operative outcome data on resectable colorectal cancers to aid clinicians' decision-making with respect to survival outcomes and quality of life. The results of this study will be of interest to multiple audiences including patients, their families, caregivers, healthcare professionals, and policy makers. Results will be published in a peer-reviewed journal.

Sequestration of Intestinal Acidic Toxins by Cationic Resin Attenuates Pancreatic Cancer Progression through Promoting Autophagic Flux for YAP Degradation.

Pancreatic cancer is driven by risk factors such as diabetes and chronic pancreatic injury, which are further associated with gut dysbiosis. Intestinal toxins such as bile acids and bacterial endotoxin (LPS), in excess and persistence, can provoke chronic inflammation and tumorigenesis. Of interest is that many intestinal toxins are negatively charged acidic components in essence, which prompted us to test whether oral administration of cationic resin can deplete intestinal toxins and ameliorate pancreatic cancer. Here, we found that increased plasma levels of endotoxin and bile acids in Pdx1-Cre: LSL-KrasG12D/+ mice were associated with the transformation of the pancreatic ductal carcinoma (PDAC) state. Common bile-duct-ligation or LPS injection impeded autolysosomal flux, leading to Yap accumulation and malignant transformation. Conversely, oral administration of cholestyramine to sequestrate intestinal endotoxin and bile acids resumed autolysosomal flux for Yap degradation and attenuated metastatic incidence. Conversely, chloroquine treatment impaired autolysosomal flux and exacerbated malignance, showing jeopardization of p62/ Sqxtm1 turnover, leading to Yap accumulation, which is also consistent with overexpression of cystatin A (CSTA) in situ with pancreatic cancer cells and metastatic tumor. At cellular levels, chenodeoxycholic acid or LPS treatment activated the ligand-receptor-mediated AKT-mTOR pathway, resulting in autophagy-lysosomal stress for YAP accumulation and cellular dissemination. Thus, this work indicates a potential new strategy for intervention of pancreatic metastasis through sequestration of intestinal acidic toxins by oral administration of cationic resins.

Hepatitis B Virus X Protein (HBx) Suppresses Transcription Factor EB (TFEB) Resulting in Stabilization of Integrin Beta 1 (ITGB1) in Hepatocellular Carcinoma Cells.

Hepatitis B virus (HBV) infection is a major etiological risk for the incidence of hepatocellular carcinoma (HCC), and HBV X protein (HBx) is essential for oncogenic transformation. It is not known that if HBx can sabotage the lysosomal system for transformation and tumorigenesis, or its mechanism if it does have an effect. Examining clinical data, we observed that the downregulation of lysosomal components and transcription factor EB (TFEB) was associated with a poor prognosis of HCC patients. In HCC cells, we found that expression of HBx suppressed TFEB, impaired biogenesis of autophagic-lysosome, and promoted cellular dissemination. HBx mediated downregulation of TFEB led to impairment of autophagic/lysosomal biogenesis and flux, and consequently, accumulation of integrin beta 1 (ITGB1) for motility of HCC cells. Conversely, TFEB, in a steady-state condition, through induction of lysosomal biogenesis restrained ITGB1 levels and limited mobility of HCC cells. Specifically, overexpression of TFEB upregulated and activated the cysteine proteases including cathepsin L (CTSL) to degrade ITGB1. Conversely, expression of cystatin A (CSTA) or cystatin B (CSTB), the cellular inhibitors of lysosomal cysteine proteinases, spared ITGB1 from degradation and promoted dissemination of HCC cells. Taken together, this study suggests a potential mechanism for HBV-mediated malignancy, showing that HBx mediated downregulation of TFEB leads to accumulation of ITGB1 for HCC cell migration.

Association Between Patient Activation and Health Care Utilization After Thoracic and Abdominal Surgery.

Importance: Increased patient activation (PA) (ie, knowledge, skills, motivation, confidence to participate in care) may result in improved outcomes, especially in surgical settings. Objective: To estimate the extent to which PA is associated with 30-day postdischarge unplanned health care utilization after major thoracic or abdominal surgery. Design, Setting, and Participants: This cohort study was performed at 2 centers of a tertiary care hospital network between October 2017 and January 2019. Adult patients undergoing thoracic or abdominal surgery were included. Of 880 patients assessed for eligibility, 692 were deemed eligible, of whom 34 declined to participate, 1 withdrew consent, and 4 were excluded after consent. Exposures: Patient activation was measured immediately after surgery during the initial admission using the Patient Activation Measure (score range, 0-100). Patients were dichotomized into low and high PA groups using previously described thresholds (Patient Activation Measure score, ≤55.1). Main Outcomes and Measures: The primary outcome was unplanned 30-day postdischarge health care utilization (composite including emergency department and outpatient clinic visits and/or hospital readmission). Secondary outcomes were length of stay, 30-day emergency department visits, 30-day readmissions, and postoperative complications. Results: A total of 653 patients admitted for thoracic, general, colorectal, and gynecologic surgery were included in the study (mean [SD] age, 58 [15] years; 369 women [56%]; 366 [56%] had minimally invasive surgery; 52 [8%] had emergency surgery), of which 152 (23%) had a low level of PA. Baseline characteristics were similar between patients with low- and high-level PA. Low PA was associated with unplanned health care utilization (odds ratio [OR], 3.15; 95% CI, 2.05-4.86; P < .001), emergency department visits (OR, 1.64; 95% CI, 1.02-2.64; P = .04), complications (OR, 1.63; 95% CI, 1.11-2.41; P = .01), and length of stay (adjusted mean difference, 1.19 days; 95% CI, 0.06-2.33; P = .04). Low PA was not associated with a higher risk of readmission (adjusted OR, 1.04; 95% CI, 0.56-1.93; P = .90). Conclusions and Relevance: In this study, low level of PA was associated with postdischarge unplanned health care use, hospital stay, and complications after major surgery. Identification of patients with low activation may allow the implementation of interventions to improve health care knowledge and support self-management postdischarge.

Functional Recovery after Surgery for Lumbar Spinal Stenosis in Patients with Hypertension.

Hypertension is a prevalent condition that is associated with lower health status in patients with lumbar spinal stenosis. The study determined whether hypertension is a prognostic factor associated with functional recovery after spine surgery for lumbar spinal stenosis. This was a secondary analysis of the Alberta Lumbar Spinal Stenosis Study in which patients were identified as participants at the time of lumbosacral magnetic resonance imaging or computed tomography in Calgary, Alberta, Canada. Multivariable linear regression analyses were performed to examine hypertension as a prognostic factor of functional recovery after surgery (Oswestry Disability Index, the Swiss Spinal Stenosis (SSS)-Symptom Severity and SSS-Physical Function scales). Of the 97 surgical participants, 49 who were hypertensive were older (76.8, SD 11.4 years) than the 48 non-hypertensive participants (66.7, SD 12.4 years) (p < 0.001). No significant associations between hypertension and post-operative function in any of the three multivariable models were seen. The Oswestry Disability Index mean score improved after surgery (effect size: 1.73; 95%CI: 1.39, 2.06), with no differences seen between those with and without hypertension (p = 0.699). Large changes were seen after surgery for the SSS-Symptom Severity (effect size: 1.0, 95%CI 0.7, 1.3) and SSS-Physical Function (effect size: 0.9, 95%CI 0.6, 1.2) scales. Hypertension alone does not negatively impact functional recovery following surgery.

Liver Injury Impaired 25-Hydroxylation of Vitamin D Suppresses Intestinal Paneth Cell defensins, leading to Gut Dysbiosis and Liver Fibrogenesis.

Vitamin D deficiency is co-prevalent with various liver diseases including cirrhosis, while the underlying mechanism remains elusive. Vitamin D receptor (VDR) is abundantly expressed in the distal region of small intestine, where the Paneth cells are enriched, suggesting that vitamin D signaling may modulates the intestinal Paneth cells and their production of defensins to restrain microbiome growth in the small intestine. In this study we found that in carbon tetrachloride-induced liver injury, hepatic 25-hydroxylation of vitamin D was impaired, leading to down regulated expression of Paneth cell fensins in the small intestine, gut dysbiosis, and endotoxinemia. While intraperitoneal injection of endotoxin (lipopolysaccharides) alone did not elicit liver fibrosis, it exacerbated the carbon tetrachloride initiated liver fibrogenesis. Oral gavage of synthetic Paneth cell alpha-defensin 5 (DEFA5) restored the homeostasis of gut microbiota, reduced endotoxemia, relieved liver inflammation, and ameliorated liver fibrosis. Likewise, Cholestyramine, cationic resin that can sequestrate endotoxin in the intestine, attenuated the liver fibrosis as well. Fecal transplant of the microbes derived from the DEFA5-treated donors improved liver fibrosis in the recipient mice. The intestinal Vdrconditional knockout mice exhibited reduction of Paneth cell defensins and lysozyme production, and worsened liver injury and fibrogenesis. Thus, liver injury impairs synthesis of 25(OH)VD3, which consequently impedes the Paneth cells functions in the small intestine, leading to gut dysbiosis for liver fibrogenesis.

Video-based interviewing in medicine: protocol for a scoping review.

BACKGROUND: Careers in healthcare involve an extensive interview process as transitions are made from one level of training to the next. For physicians, interviews mark the gateway from entrance into medical school, acceptance into residency, fellowships, and subsequent job opportunities. Previous literature outlining the costs associated with face-to-face interviews and concerns regarding the climate crisis has triggered an interest in video-based interviews. Barriers to transitioning away from in-person interviews include concerns regarding lack of rapport between applicants and interviewers, and applicants being less able to represent themselves. In a new era ushered in by COVID where many of us have utilized virtual meetings more than any prior time both personally and for work, we wanted to consolidate the current literature on the use of video-based interviews in healthcare and summarize the findings. METHODS: A scoping review will be conducted to explore the benefits and limitations of video-based interviews for both applicants and interviewers within healthcare fields, as well as the perceived barriers associated with transitioning away from face-to-face interviews. The scoping review methodology outlined by Arksey and O'Malley will be implemented. The search strategy developed by the authors in collaboration with an academic health sciences librarian will be conducted across four electronic databases (Embase, MEDLINE, Cochrane Central, and PsycInfo) and supplemented by a review of the grey literature and reference lists of included studies. The study selection process will be documented using the PRISMA flow diagram, and reasons for exclusion following full-text review will be recorded. The extracted data will be analyzed using quantitative and qualitative analysis. DISCUSSION: Despite previous literature on the costs associated with face-to-face interviews, there has been hesitancy with transitioning to video-based interviews due to concerns of lack of rapport between applicants and interviewers, and applicants being less able to represent themselves. While these limitations have been explored in previous studies, a succinct review of the current literature to guide the effective restructuring of the interview process is lacking. With our scoping review, we hope to fill this gap in the literature to better understand barriers to transitioning from face-to-face interviews and directions for future research.

Reinventing community in COVID-19: a case in Canberra, Australia.

In this essay, I share my experiences and reflections of fighting COVID-19 from the perspective of a resident and a planner living and working in Canberra, Australia. I focus on three themes of building community compassion and collaboration and regard them as potential opportunities deriving from this crisis. First, COVID-19 presents a compulsory situation for establishing a virtual community and practising smart work. Second, COVID-19 helps rediscover a local community and nurture a special community spirit under the social distancing circumstance. Third, COVID-19 creates more opportunities of engaging and understanding nature, interestingly, in a context of staying home. These three themes are in large part rooted in the local communities of a city that is known for low density and being a 'bush capital' and possibly suggest some rethinking about the city's planning legacy.

Digital biomarkers of spine and musculoskeletal disease from accelerometers: Defining phenotypes of free-living physical activity in knee osteoarthritis and lumbar spinal stenosis.

BACKGROUND CONTEXT: Lumbar spinal stenosis (LSS) and knee osteoarthritis (OA) are 2 of the leading causes of disability worldwide. In order to provide disease-specific prescriptions for physical activity, there is a clear need to better understand physical activity in daily life (performance) in these populations. PURPOSE: To discover performance phenotypes for LSS and OA by applying novel analytical methods to accelerometry data. Specific objectives include the following: (1) to identify characteristic features (phenotypes) of free-living physical activity unique to individuals with LSS and OA, and (2) to determine which features can best differentiate between these conditions. STUDY DESIGN AND SETTING: Leveraging data from 3 existing cross-sectional cohorts, accelerometry signal feature characterization and selection were performed in a computational laboratory. PATIENT SAMPLE: Data from a total of 4,028 individuals were analyzed from the following 3 datasets: LSS Accelerometry Database (n=75); OA Initiative (n=1950); and the 2003 to 2004 National Health and Nutrition Examination Survey (pain-free controls, n=2003). METHODS: In order to characterize the accelerometry signals, data were examined using (1) standard intervals for counts/minute from Freedson et al. and (2) the physical performance intervals for mobility-limited pain populations. From this, 42 novel accelerometry features were defined and evaluated for significance in discriminating between the groups (LSS, OA, and controls) in order to then determine which sparse set of features best differentiates between the groups. These sparse sets of features defined the performance phenotypes. OUTCOME MEASURES: Accelerometry features and their ability to differentiate between individuals with LSS, OA, and controls. RESULTS: Given age and gender, classification rates were at least 80% accurate (pairwise) between diseased and pain-free populations (LSS vs. controls and OA vs. controls). The most important features to distinguish between disease groups corresponded to measures in the light and sedentary activity intervals. The more subtle classification between diseased populations (LSS vs. OA) was 72% accurate, with light and moderate activity providing the prominent distinguishing features. CONCLUSIONS: We describe the discovery of performance phenotypes of LSS and OA from accelerometry data, revealed through a novel set of features that characterize daily patterns of movement in people with LSS and OA. These performance phenotypes provide a new method for analyzing free-living physical activity (performance) in LSS and OA, and provide the groundwork for more personalized approaches to measuring and improving function.

Chlorophyllin Modulates Gut Microbiota and Inhibits Intestinal Inflammation to Ameliorate Hepatic Fibrosis in Mice.

Liver fibrosis is an abnormal wound healing response and a common consequence of chronic liver diseases from infection or alcohol/xenobiotic exposure. At the cellular level, liver fibrosis is mediated by trans-differentiation of hepatic stellate cells (HSCs), which is driven by persistent hepatic and systemic inflammation. However, impaired enterohepatic circulation and gut dysbiosis may indirectly contribute to the liver fibrogenesis. The composition of the gut microbiota depends on diet composition and host factors. In this study, we examined chlorophyllin, derived from green pigment chlorophyll, on gut microbiota, the intestinal mucosal barrier, and liver fibrosis. BALB/c mice received carbon tetrachloride through intraperitoneal injection to induce liver fibrosis and chlorophyllin was administrated in drinking water. The effects of chlorophyllin on liver fibrosis were evaluated for (1) survival rate, (2) hepatic morphologic analysis, (3) inflammatory factors in both the small intestine and liver, and (4) gut microbiota. Our results indicate that oral administration of chlorophyllin could attenuate intestinal and hepatic inflammation and ameliorate liver fibrosis. Importantly, oral administration of chlorophyllin promptly rebalanced the gut microbiota, exhibiting down-regulation of the phylum Firmicutes and up-regulation of the phylum Bacteroidetes. In vitro experiments on intestinal epithelial cells showed that chlorophyllin exposure could inhibit NF-κB pathway via IKK-phosphorylation suppression. In conclusion, this study demonstrates potential application of chlorophyllin to regulate the intestinal microbiota and ameliorate hepatic fibrosis.

Objective measurement of function following lumbar spinal stenosis decompression reveals improved functional capacity with stagnant real-life physical activity.

BACKGROUND CONTEXT: Lumbar spinal stenosis (LSS) is a prevalent and costly condition associated with significant dysfunction. Alleviation of pain and improvement of function are the primary goals of surgical intervention. Although prior studies have measured subjective improvements in function after surgery, few have examined objective markers of functional improvement. PURPOSE: We aimed to objectively measure and quantify changes in physical capacity and physical performance following surgical decompression of LSS. STUDY DESIGN/SETTING: Prospective cohort study. PATIENT SAMPLE: Thirty-eight patients with LSS determined by the treating surgeon's clinical and imaging evaluation, and who were scheduled for surgical treatment, were consecutively recruited at two academic medical facilities, with 28 providing valid data for analysis at baseline and 6 months after surgery. OUTCOME MEASURES: Before surgery and at 6 months after surgery, participants provided 7 days of real-life physical activity (performance) using ActiGraph accelerometers; completed two objective functional capacity measures, the Short Physical Performance Battery and Self-Paced Walking Test; and completed three subjective functional outcome questionnaires, Oswestry Disability Index, Spinal Stenosis Symptom Questionnaire, and Short-Form 36. METHODS: Physical activity, as measured by continuous activity monitoring, was analyzed as previously described according to the 2008 American Physical Activity Guidelines. Paired t tests were performed to assess for postsurgical changes in all questionnaire outcomes and all objective functional capacity measures. Chi-square analysis was used to categorically assess whether patients were more likely to meet these physical activity recommendations after surgery. RESULTS: Participants were 70.1 years old (±8.9) with 17 females (60.7%) and an average body mass index of 28.4 (±6.2). All subjective measures (Oswestry Disability Index, Spinal Stenosis Symptom Questionnaire, and Short-Form 36) improved significantly at 6 months after surgery, as did objective functional measures of capacity including balance, gait speed, and ambulation distance (Short Physical Performance Battery, Self-Paced Walking Test). However, objectively measured performance (real-life physical activity) did not change following surgery. Although fewer participants qualified as inactive (54% vs. 71%), and more (11% vs. 4%) met the physical activity guideline recommendations at the 6-month follow-up, these differences were not statistically significant (p=.22) CONCLUSIONS: This is the first study, of which we are aware, to objectively evaluate changes in postsurgical performance (real-life physical activity) in people with LSS. We found that at 6 months after surgery for LSS, participants demonstrated significant improvements in self-reported function and objectively measured physical capacity, but not physical performance as measured by continuous activity monitoring. This lack of improvement in performance, despite improvements in self-reported function and objective capacity, suggests a role for postoperative rehabilitation focused specifically on increasing performance after surgery in the LSS population.

Alternation of Gut Microbiota in Patients with Pulmonary Tuberculosis.

One-third of the world's population has been infected with Mycobacterium tuberculosis (M. tuberculosis), a primary pathogen of the mammalian respiratory system, while about 10% of latent infections progress to active tuberculosis (TB), indicating that host and environmental factors may determine the outcomes such as infection clearance/persistence and treatment prognosis. The gut microbiota is essential for development of host immunity, defense, nutrition and metabolic homeostasis. Thus, the pattern of gut microbiota may contribute to M. tuberculosis infection and prognosis. In current study we characterized the differences in gut bacterial communities in new tuberculosis patients (NTB), recurrent tuberculosis patients (RTB), and healthy control. The abundance-based coverage estimator (ACE) showed the diversity index of the gut microbiota in the patients with recurrent tuberculosis was increased significantly compared with healthy controls (p < 0.05). At the phyla level, Actinobacteria and Proteobacteria, which contain many pathogenic species, were significantly enriched in the feces RTB patients. Conversely, phylum Bacteroidetes, containing a variety of beneficial commensal organisms, was reduced in the patients with the recurrent tuberculosis compared to healthy controls. The Gram-negative genus Prevotella of oral origin from phylum of Bacteroidetes and genus Lachnospira from phylum of Firmicutes were significantly decreased in both the new and recurrent TB patient groups, compared with the healthy control group (p < 0.05). We also found that there was a positive correlation between the gut microbiota and peripheral CD4+ T cell counts in the patients. This study, for the first time, showed associations between gut microbiota with tuberculosis and its clinical outcomes. Maintaining eubiosis, namely homeostasis of gut microbiota, may be beneficial for host recovery and prevention of recurrence of M. tuberculosis infection.

M2-like macrophages in the fibrotic liver protect mice against lethal insults through conferring apoptosis resistance to hepatocytes.

Acute injury in the setting of liver fibrosis is an interesting and still unsettled issue. Most recently, several prominent studies have indicated the favourable effects of liver fibrosis against acute insults. Nevertheless, the underlying mechanisms governing this hepatoprotection remain obscure. In the present study, we hypothesized that macrophages and their M1/M2 activation critically involve in the hepatoprotection conferred by liver fibrosis. Our findings demonstrated that liver fibrosis manifested a beneficial role for host survival and apoptosis resistance. Hepatoprotection in the fibrotic liver was tightly related to innate immune tolerance. Macrophages undertook crucial but divergent roles in homeostasis and fibrosis: depleting macrophages in control mice protected from acute insult; conversely, depleting macrophages in fibrotic liver weakened the hepatoprotection and gave rise to exacerbated liver injury upon insult. The contradictory effects of macrophages can be ascribed, to a great extent, to the heterogeneity in macrophage activation. Macrophages in fibrotic mice exhibited M2-preponderant activation, which was not the case in acutely injured liver. Adoptive transfer of M2-like macrophages conferred control mice conspicuous protection against insult. In vitro, M2-polarized macrophages protected hepatocytes against apoptosis. Together, M2-like macrophages in fibrotic liver exert the protective effects against lethal insults through conferring apoptosis resistance to hepatocytes.

Long-term evaluation of a Canadian back pain mass media campaign.

PURPOSE: This paper evaluates the long-term impact of a Canadian mass media campaign on general public beliefs about staying active when experiencing low back pain (LBP). METHODS: Changes in beliefs about staying active during an episode of LBP were studied using telephone and web-based surveys. Logistic regression analysis was used to investigate changes in beliefs over time and the effect of exposure to campaign messaging. RESULTS: The percentage of survey respondents agreeing that they should stay active through LBP increased annually from 58.9 to ~72.0%. Respondents reporting exposure to campaign messaging were statistically significantly more likely to agree with staying active than respondents who did not report exposure to campaign messaging (adjusted OR, 95% CI = 1.96, 1.73-2.21). CONCLUSION: The mass media campaign had continued impact on public LBP beliefs over the course of 7 years. Improvements over time were associated with exposure to campaign messaging.

Cationic Polystyrene Resolves Nonalcoholic Steatohepatitis, Obesity, and Metabolic Disorders by Promoting Eubiosis of Gut Microbiota and Decreasing Endotoxemia.

A pandemic of metabolic diseases, consisting of type 2 diabetes, nonalcoholic fatty liver disease, and obesity, has imposed critical challenges for societies worldwide, prompting investigation of underlying mechanisms and exploration of low-cost and effective treatment. In this report, we demonstrate that metabolic disorders in mice generated by feeding with a high-fat diet without dietary vitamin D can be prevented by oral administration of polycationic amine resin. Oral administration of cholestyramine, but not the control uncharged polystyrene, was able to sequester negatively charged bacterial endotoxin in the gut, leading to 1) reduced plasma endotoxin levels, 2) resolved systemic inflammation and hepatic steatohepatitis, and 3) improved insulin sensitivity. Gut dysbiosis, characterized as an increase of the phylum Firmicutes and a decrease of Bacteroidetes and Akkermansia muciniphila, was fully corrected by cholestyramine, indicating that the negatively charged components in the gut are critical for the dysbiosis. Furthermore, fecal bacteria transplant, derived from cholestyramine-treated animals, was sufficient to antagonize the metabolic disorders of the recipient mice. These results indicate that the negatively charged components produced by dysbiosis are critical for biogenesis of metabolic disorders and also show a potential application of cationic polystyrene to treat metabolic disorders through promoting gut eubiosis.

Cathepsin H-Mediated Degradation of HDAC4 for Matrix Metalloproteinase Expression in Hepatic Stellate Cells: Implications of Epigenetic Suppression of Matrix Metalloproteinases in Fibrosis through Stabilization of Class IIa Histone Deacetylases.

In three-dimensional extracellular matrix, mesenchymal cells including hepatic stellate cells (HSCs) gain the ability to express matrix metalloproteinases (MMPs) on injury signals. In contrast, in myofibroblastic HSCs in fibrotic liver, many MMP genes are silenced into an epigenetically nonpermissive state. The mechanism by which the three-dimensional extracellular matrix confers the MMP genes into an epigenetically permissive state has not been well characterized. In continuation of previous work, we show here that the up-regulation of MMP genes is mediated through degradation of class IIa histone deacetylases (HDACs) by certain cysteine cathepsins (Cts). In three-dimensional extracellular matrix culture, CtsH, among other cysteine cathepsins, was up-regulated and localized as puncta in the nuclear and cytoplasmic compartments in a complex with HDAC4 for its degradation. Conversely, along with HSC trans-differentiation, CtsH and CtsL were progressively down-regulated, whereas HDAC4 was concurrently stabilized. The inhibition of cysteine cathepsins by specific proteinase inhibitors or chloroquine, which raises cellular pH, restored HDAC4. Recombinant CtsH could break down HDAC4 in the transfected cells and in vitro at acidic pH. In human cirrhotic liver, activated HSCs express high levels of class IIa HDACs but little CtsH. We propose that cysteine cathepsin-mediated degradation of class IIa HDACs plays a key role in the modulation of MMP expression/suppression and HSC functions in tissue injury and fibrosis.