Endoscopic assessment of the J pouch in ulcerative colitis: A narrative review.

Patients with ulcerative colitis sometimes need a total colectomy with ileal pouch-anal anastomosis due to medically refractory disease or colitis-associated neoplasia. Up to 50% of patients with ulcerative colitis postoperatively develop pouchitis and the rate of chronic inflammatory pouch conditions requiring pouch excision or diverting ileostomy is reported to be 10%. In order to diagnose and monitor pouchitis, pouchoscopy is essential to assess endoscopic inflammatory findings of the J pouch and to survey neoplasia development, particularly in the remnant distal rectum. However, endoscopic protocols for the evaluation of the pouch may not be standardized worldwide and the reliability of existing disease activity indices for pouchitis has been questioned due to the lack of validation. Recently, reliable endoscopic scoring systems based on an observation of the anatomical location of the J pouch were reported and a significant association between the distribution pattern of endoscopic inflammation (i.e., endoscopic phenotype) and pouch outcomes was also uncovered. In this review, we discuss how to survey the J pouch using pouchoscopy, endoscopic indices for pouchitis disease activity, endoscopic phenotypes and classification, and the pathological mechanisms of pouchitis phenotype in patients with ulcerative colitis.

Unraveling the mechanisms of triplet state formation in a heavy-atom free photosensitizer.

Triplet excited state generation plays a pivotal role in photosensitizers, however the reliance on transition metals and heavy atoms can limit the utility of these systems. In this study, we demonstrate that an interplay of competing quantum effects controls the high triplet quantum yield in a prototypical boron dipyrromethene-anthracene (BD-An) donor-acceptor dyad photosensitizer, which is only captured by an accurate treatment of both inner and outer sphere reorganization energies. Our ab initio-derived model provides excellent agreement with experimentally measured spectra, triplet yields and excited state kinetic data, including the triplet lifetime. We find that rapid triplet state formation occurs primarily via high-energy triplet states through both spin-orbit coupled charge transfer and El-Sayed's rule breaking intersystem crossing, rather than direct spin-orbit coupled charge transfer to the lowest lying triplet state. Our calculations also reveal that competing effects of nuclear tunneling, electronic state recrossing, and electronic polarizability dictate the rate of non-productive ground state recombination. This study sheds light on the quantum effects driving efficient triplet formation in the BD-An system, and offers a promising simulation methodology for diverse photochemical systems.

Machine learning based DNA melt curve profiling enables automated novel genotype detection.

Surveillance for genetic variation of microbial pathogens, both within and among species, plays an important role in informing research, diagnostic, prevention, and treatment activities for disease control. However, large-scale systematic screening for novel genotypes remains challenging in part due to technological limitations. Towards addressing this challenge, we present an advancement in universal microbial high resolution melting (HRM) analysis that is capable of accomplishing both known genotype identification and novel genotype detection. Specifically, this novel surveillance functionality is achieved through time-series modeling of sequence-defined HRM curves, which is uniquely enabled by the large-scale melt curve datasets generated using our high-throughput digital HRM platform. Taking the detection of bacterial genotypes as a model application, we demonstrate that our algorithms accomplish an overall classification accuracy over 99.7% and perform novelty detection with a sensitivity of 0.96, specificity of 0.96 and Youden index of 0.92. Since HRM-based DNA profiling is an inexpensive and rapid technique, our results add support for the feasibility of its use in surveillance applications.

WNT2B Deficiency Causes Enhanced Susceptibility to Colitis Due to Increased Inflammatory Cytokine Production.

BACKGROUND AND AIMS: Humans with WNT2B deficiency have severe intestinal disease, including significant inflammatory injury, highlighting a critical role for WNT2B. We sought to understand how WNT2B contributes to intestinal homeostasis. METHODS: We investigated the intestinal health of Wnt2b knock out (KO) mice. We assessed the baseline histology and health of the small intestine and colon, as well as the impact of inflammatory challenge using dextran sodium sulfate (DSS). We also evaluated human intestinal tissue. RESULTS: Mice with WNT2B deficiency had normal baseline histology but enhanced susceptibility to DSS colitis due to an increased early injury response. While ISC markers were decreased, epithelial proliferation was similar to controls. Wnt2b KO mice showed an enhanced inflammatory signature after DSS treatment. Wnt2b KO colon and human WNT2B-deficient organoids both had increased levels of CXCR4 and IL6, and biopsy tissue from humans showed increased neutrophils. CONCLUSION: WNT2B is important for regulation of inflammation in the intestine. Absence of WNT2B leads to increased expression of inflammatory cytokines and increased susceptibility to gastrointestinal inflammation, particularly in the colon.

The potential impact of removing a ban on electronic nicotine delivery systems using the Mexico smoking and vaping model (SAVM).

Objective: To develop the Mexico Smoking and Vaping Model (Mexico SAVM) to estimate cigarette and electronic nicotine delivery systems (ENDS) prevalence and the public health impact of legalizing ENDS use. Methods: SAVM, a cohort-based discrete-time simulation model, compares two scenarios. The ENDS-Restricted Scenario estimates smoking prevalence and associated mortality outcomes under the current policy of an ENDS ban, using Mexico-specific population projections, death rates, life expectancy, and smoking and e-cigarette prevalence. The ENDS-Unrestricted Scenario projects smoking and vaping prevalence under a hypothetical scenario where ENDS use is allowed. The impact of legalizing ENDS use is estimated as the difference in smoking- and vaping-attributable deaths (SVADs) and life-years lost (LYLs) between the ENDS-Restricted and Unrestricted scenarios. Results: Compared to a national ENDS ban, The Mexico SAVM projects that legalizing ENDS use could decrease smoking prevalence by 40.1% in males and 30.9% in females by 2049 compared to continuing the national ENDS ban. This reduction in prevalence would save 2.9 (2.5 males and 0.4 females) million life-years and avert almost 106 (91.0 males and 15.5 females) thousand deaths between 2025 and 2049. Public health gains decline by 43% to 59,748 SVADs averted when the switching rate is reduced by half and by 24.3% (92,806 SVADs averted) with a 25% ENDS risk level from that of cigarettes but increased by 24.3% (121,375 SVADs averted) with the 5% ENDS risk. Conclusions: Mexico SAVM suggests that greater access to ENDS and a more permissive ENDS regulation, simultaneous with strong cigarette policies, would reduce smoking prevalence and decrease smoking-related mortality. The unanticipated effects of an ENDS ban merit closer scrutiny, with further consideration of how specific ENDS restrictions may maximize public health benefits.

Deep learning for the PSIPRED Protein Analysis Workbench.

The PSIRED Workbench is a long established and popular bioinformatics web service offering a wide range of machine learning based analyses for characterizing protein structure and function. In this paper we provide an update of the recent additions and developments to the webserver, with a focus on new Deep Learning based methods. We briefly discuss some trends in server usage since the publication of AlphaFold2 and we give an overview of some upcoming developments for the service. The PSIPRED Workbench is available at http://bioinf.cs.ucl.ac.uk/psipred.

Comparison of 3T MR arthrography and 3T MRI in intra-articular hip pathology: a cost-analysis.

BACKGROUND: MR arthrography (MRA) has previously been the radiological gold standard for investigating labral and chondral lesions of the hip joint. In recent years, 3T MRI has demonstrated comparable accuracy, being adopted as the first-line imaging investigation in many institutions. AIMS: We compare the associated increased cost and radiation dose of the fluoroscopic component of the MRA compared to MRI. METHODS: In this retrospective review over 2 years, 120 patients (mean age 27.3 years ± 13.2, range 8-67) underwent 3T MRA or non-contrast 3T MRI. Three musculoskeletal radiologists reported the data independently. Primary objectives included cost-comparison between each and radiation dose of the fluoroscopic component of the MRA. Secondary objectives included comparing detection of pathology involving the acetabular labrum, femoral cartilage, and acetabular cartilage. RESULTS: Then, 58 (48%) underwent 3T MRA and 62 (52%) patients underwent 3T MRI. The added cost of the fluoroscopic injection prior to MRA was €116.31/patient, equating to €7211.22 savings/year. MRA was associated with a small radiation dose of 0.003 mSv. CONCLUSIONS: Transitioning from 3T MRA to 3T MRI in the investigation of intra-articular hip pathology increases cost savings and reduces radiation dose.

DNA methylation signatures of youth-onset type 2 diabetes and exposure to maternal diabetes.

OBJECTIVE: Youth-onset type 2 diabetes (T2D) is physiologically distinct from adult-onset, but it is not clear how the two diseases differ at a molecular level. In utero exposure to maternal type 2 diabetes (T2D) is known to be a specific risk factor for youth-onset T2D. DNA methylation (DNAm) changes associated with T2D but which differ between youth- and adult-onset might delineate the impacts of T2D development at different ages and could also determine the contribution of exposure to in utero diabetes. METHODS: We performed an epigenome-wide analysis of DNAm on whole blood from 218 youth with T2D and 77 normoglycemic controls from the iCARE (improving renal Complications in Adolescents with type 2 diabetes through REsearch) cohort. Associations were tested using multiple linear regression models while adjusting for maternal diabetes, sex, age, BMI, smoking status, second-hand smoking exposure, cell-type proportions and genetic ancestry. RESULTS: We identified 3830 differentially methylated sites associated with youth T2D onset, of which 3794 were moderately (adjusted p-value < 0.05 and effect size estimate > 0.01) associated and 36 were strongly (adjusted p-value < 0.05 and effect size estimate > 0.05) associated. A total of 3725 of these sites were not previously reported in the EWAS Atlas as associated with T2D, adult obesity or youth obesity. Moreover, three CpGs associated with youth-onset T2D in the PFKFB3 gene were also associated with maternal T2D exposure (FDR < 0.05 and effect size > 0.01). This is the first study to link PFKFB3 and T2D in youth. CONCLUSION: Our findings support that T2D in youth has different impacts on DNAm than adult-onset, and suggests that changes in DNAm could provide an important link between in utero exposure to maternal diabetes and the onset of T2D.

Bile Spillage as a Prognostic Factor for Gall Bladder Cancer: A Systematic Review and Meta-analysis.

INTRODUCTION: Biliary spillage (BS) is a common complication following initial cholecystectomy for gall bladder cancer (GBC). Few studies have explored the importance of BS as a long-term prognostic factor. We perform a meta-analysis of the association between BS and survival in GBC. METHODS: A systematic literature search was performed in February 2023. Studies evaluating the incidence of BS and its association with long-term outcomes in patients undergoing initial laparoscopic or open cholecystectomy for either incidental or resectable GBC were included. Overall survival (OS), disease-free survival (DFS), and rate of peritoneal carcinomatosis (RPC) were the primary end points. Forest plot analyses were used to calculate the pooled hazard ratios (HRs) of OS, DFS, and RPC. Metaregression was used to evaluate study-level association between BS and perioperative risk factors. RESULTS: Of 181 published articles, 11 met inclusion criteria with a sample size of 1116 patients. The rate of BS ranged between 9% and 67%. On pooled analysis, BS was associated with worse OS (HR = 1.68, 95% confidence interval [CI] = 1.32-2.14), DFS (pooled HR= 2.19, 95% CI = 1.30-3.68), and higher RPC (odds ratio = 9.37, 95% CI = 3.49-25.2). The rate of BS was not associated with higher T stage, lymph node metastasis, higher grade, positive margin status, reresection, or conversion rates. CONCLUSIONS: Our meta-analysis shows that BS is a predictor of higher peritoneal recurrence and poor survival in GBC. BS was not associated with tumor characteristics or conversion rates. Further research is needed to identify other potential risk factors for BS and investigate the ideal treatment schedule to improve survival.

The intrinsic substrate specificity of the human tyrosine kinome.

Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth1. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome1-3. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood4-7. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.

Steps towards operationalizing One Health approaches.

One Health recognizes the health of humans, agriculture, wildlife, and the environment are interrelated. The concept has been embraced by international health and environmental authorities such as WHO, WOAH, FAO, and UNEP, but One Health approaches have been more practiced by researchers than national or international authorities. To identify priorities for operationalizing One Health beyond research contexts, we conducted 41 semi-structured interviews with professionals across One Health sectors (public health, environment, agriculture, wildlife) and institutional contexts, who focus on national-scale and international applications. We identify important challenges, solutions, and priorities for delivering the One Health agenda through government action. Participants said One Health has made progress with motivating stakeholders to attempt One Health approaches, but achieving implementation needs more guidance (action plans for how to leverage or change current government infrastructure to accommodate cross-sector policy and strategic mission planning) and facilitation (behavioral change, dedicated personnel, new training model).

Changes in management of head and neck malignancies during the COVID-19 pandemic.

Objective: Despite multiple studies from high-income countries, reports from low- and middle-income countries on the impact of COVID-19 on head and neck cancer care remain sparse. This study aimed to assess the effects of the COVID-19 pandemic on head and neck cancer patients at a tertiary reference centre in Bosnia and Herzegovina. Methods: We included 228 patients with malignant head and neck tumours evaluated and treated between January 1, 2019, and December 31, 2021. Patient demographics, histological characteristics, and treatment modalities were retrospectively obtained and compared between the pre-pandemic period (pre-COVID-19 group) and the period after the implementation of COVID-19 restrictive measures (COVID-19 group). Results: Patients were significantly older during the COVID-19 pandemic. In particular, 63 patients (44.7%) were under 65 and 78 (55.3%) were 65 or older, while in the pre-COVID-19 period, 53 patients (60.9%) were under 65 and 34 (39.1%) were 65 or older (p = 0.017). The pre-COVID-19 and COVID-19 groups did not significantly differ regarding other patient- and tumour characteristics, or primary treatment modalities. Conclusions: During the COVID-19 pandemic, significantly fewer patients were under 65 at the time of initial work-up, potentially reflecting the more enhanced disease-related anxiety of the younger population. Future studies are warranted to address this population's specific educational and psychological needs to ensure appropriate cancer care.

Characterization of an Algorithm for Autonomous, Closed-Loop Neuromodulation During Motor Rehabilitation.

BACKGROUND: Recent evidence demonstrates that manually triggered vagus nerve stimulation (VNS) combined with rehabilitation leads to increased recovery of upper limb motor function after stroke. This approach is premised on studies demonstrating that the timing of stimulation relative to movements is a key determinant in the effectiveness of this approach. OBJECTIVE: The overall goal of the study was to identify an algorithm that could be used to automatically trigger VNS on the best movements during rehabilitative exercises while maintaining a desired interval between stimulations to reduce the burden of manual stimulation triggering. METHODS: To develop the algorithm, we analyzed movement data collected from patients with a history of neurological injury. We applied 3 different algorithms to the signal, analyzed their triggering choices, and then validated the best algorithm by comparing triggering choices to those selected by a therapist delivering VNS therapy. RESULTS: The dynamic algorithm triggered above the 95th percentile of maximum movement at a rate of 5.09 (interquartile range [IQR] = 0.74) triggers per minute. The periodic algorithm produces stimulation at set intervals but low movement selectivity (34.05%, IQR = 7.47), while the static threshold algorithm produces long interstimulus intervals (27.16 ± 2.01 seconds) with selectivity of 64.49% (IQR = 25.38). On average, the dynamic algorithm selects movements that are 54 ± 3% larger than therapist-selected movements. CONCLUSIONS: This study shows that a dynamic algorithm is an effective strategy to trigger VNS during the best movements at a reliable triggering rate.

A Report of Salaries of Academic Cardiothoracic Surgeons Based on Race and Ethnicity.

BACKGROUND: Diversity in the physician workforce improves patient care, physician well-being, and innovation. Workforce diversity is dependent on fair compensation that is unbiased by race or ethnicity. The purpose of our study was to determine if a disparity of representation and salary based on race/ethnicity exists in academic cardiothoracic surgery. METHODS: We performed a cross-sectional analysis of data collected by the Accreditation Council of Graduate Medical Education (ACGME) and Association of American Medical Colleges (AAMC) Faculty Data for U.S. Medical School Faculty 2021 and 2022. Salary data was not available if an academic rank and race/ethnicity had fewer than 6 cardiothoracic surgeons. We performed a descriptive analysis of the number of faculty and compared median and mean salaries according to academic rank using paired t-test. RESULTS: Of the 758 academic cardiothoracic surgeons, 64.9% were white, 25.2% Asian, 3.3% Black/African American, 4.9% Hispanic/Latino, and 1.7% other race/ethnicity. Cardiothoracic surgeons at the academic rank of professor were 74.6% White, 17.7% Asian, 3.4% Black/African American, 3.9% Hispanic/Latino, and 0.4% other races. Asian faculty earned 89-171%, Black/African American faculty earned 59-94%, and Hispanic/Latino earned 84-165% of the median salary earned by White faculty. Black/African American faculty consistently and significantly (p = .002) earned lower median salaries compared to White faculty at each academic rank measured. CONCLUSIONS: The academic cardiothoracic surgery workforce lacks diversity, especially at the highest academic ranks. Salary equity among races/ethnicities is complex, requiring additional study. However, Black/African American cardiothoracic surgeons experience low representation and salary disparity at every academic rank measured.

Phylogenomics and genetic analysis of solvent-producing Clostridium species.

The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.

Evidence-Based Review of Nonsurgical Treatments for Knee and Hip Osteoarthritis.

Knee and hip osteoarthritis (OA) are highly prevalent joint diseases that lead to chronic pain, disability, and increased mortality. In this review, we provide a summary of nonsurgical treatments available for knee and hip OA that have evidence to support their use. We also provide a summary of the treatments available for knee and hip OA that do not have sufficient evidence to support their use. Treatments covered in this review include pharmacologic and nonpharmacologic modalities. Cite this article as: Misra D, Felson DT. Evidence-based review of nonsurgical treatments for knee and hip osteoarthritis. Eur J Rheumatol. Published online March 25, 2024. doi: 10.5152/ eurjrheum.2024.22096.

What is the definition of stone dust and how does it compare with clinically insignificant residual fragments? A comprehensive review.

PURPOSE: During endoscopic stone surgery, Holmium:YAG (Ho:YAG) and Thulium Fiber Laser (TFL) technologies allow to pulverize urinary stones into fine particles, ie DUST. Yet, currently there is no consensus on the exact definition of DUST. This review aimed to define stone DUST and Clinically Insignificant Residual Fragments (CIRF). METHODS: Embase, MEDLINE (PubMed) and Cochrane databases were searched for both in vitro and in vivo articles relating to DUST and CIRF definitions, in November 2023, using keyword combinations: "dust", "stones", "urinary calculi", "urolithiasis", "residual fragments", "dusting", "fragments", "lasers" and "clinical insignificant residual fragments". RESULTS: DUST relates to the fine pulverization of urinary stones, defined in vitro as particles spontaneously floating with a sedimentation duration ≥ 2 sec and suited for aspiration through a 3.6Fr-working channel (WC) of a flexible ureteroscope (FURS). Generally, an upper size limit of 250 µm seems to agree with the definition of DUST. Ho:YAG with and without "Moses Technology", TFL and the recent pulsed-Thulium:YAG (pTm:YAG) can produce DUST, but no perioperative technology can currently measure DUST size. The TFL and pTm:YAG achieve better dusting compared to Ho:YAG. CIRF relates to residual fragments (RF) that are not associated with imminent stone-related events: loin pain, acute renal colic, medical or interventional retreatment. CIRF size definition has decreased from older studies based on Shock Wave Lithotripsy (SWL) (≤ 4 mm) to more recent studies based on FURS (≤ 2 mm) and Percutaneous Nephrolithotomy(PCNL) (≤ 4 mm). RF ≤ 2 mm are associated with lower stone recurrence, regrowth and clinical events rates. While CIRF should be evaluated postoperatively using Non-Contrast Computed Tomography(NCCT), there is no consensus on the best diagnostic modality to assess the presence and quantity of DUST. CONCLUSION: DUST and CIRF refer to independent entities. DUST is defined in vitro by a stone particle size criteria of 250 µm, translating clinically as particles able to be fully aspirated through a 3.6Fr-WC without blockage. CIRF relates to ≤ 2 RF on postoperative NCCT.