IBRAP: integrated benchmarking single-cell RNA-sequencing analytical pipeline.

Single-cell ribonucleic acid (RNA)-sequencing (scRNA-seq) is a powerful tool to study cellular heterogeneity. The high dimensional data generated from this technology are complex and require specialized expertise for analysis and interpretation. The core of scRNA-seq data analysis contains several key analytical steps, which include pre-processing, quality control, normalization, dimensionality reduction, integration and clustering. Each step often has many algorithms developed with varied underlying assumptions and implications. With such a diverse choice of tools available, benchmarking analyses have compared their performances and demonstrated that tools operate differentially according to the data types and complexity. Here, we present Integrated Benchmarking scRNA-seq Analytical Pipeline (IBRAP), which contains a suite of analytical components that can be interchanged throughout the pipeline alongside multiple benchmarking metrics that enable users to compare results and determine the optimal pipeline combinations for their data. We apply IBRAP to single- and multi-sample integration analysis using primary pancreatic tissue, cancer cell line and simulated data accompanied with ground truth cell labels, demonstrating the interchangeable and benchmarking functionality of IBRAP. Our results confirm that the optimal pipelines are dependent on individual samples and studies, further supporting the rationale and necessity of our tool. We then compare reference-based cell annotation with unsupervised analysis, both included in IBRAP, and demonstrate the superiority of the reference-based method in identifying robust major and minor cell types. Thus, IBRAP presents a valuable tool to integrate multiple samples and studies to create reference maps of normal and diseased tissues, facilitating novel biological discovery using the vast volume of scRNA-seq data available.

A new G-quadruplex-specific photosensitizer inducing genome instability in cancer cells by triggering oxidative DNA damage and impeding replication fork progression.

Photodynamic therapy (PDT) ideally relies on the administration, selective accumulation and photoactivation of a photosensitizer (PS) into diseased tissues. In this context, we report a new heavy-atom-free fluorescent G-quadruplex (G4) DNA-binding PS, named DBI. We reveal by fluorescence microscopy that DBI preferentially localizes in intraluminal vesicles (ILVs), precursors of exosomes, which are key components of cancer cell proliferation. Moreover, purified exosomal DNA was recognized by a G4-specific antibody, thus highlighting the presence of such G4-forming sequences in the vesicles. Despite the absence of fluorescence signal from DBI in nuclei, light-irradiated DBI-treated cells generated reactive oxygen species (ROS), triggering a 3-fold increase of nuclear G4 foci, slowing fork progression and elevated levels of both DNA base damage, 8-oxoguanine, and double-stranded DNA breaks. Consequently, DBI was found to exert significant phototoxic effects (at nanomolar scale) toward cancer cell lines and tumor organoids. Furthermore, in vivo testing reveals that photoactivation of DBI induces not only G4 formation and DNA damage but also apoptosis in zebrafish, specifically in the area where DBI had accumulated. Collectively, this approach shows significant promise for image-guided PDT.

Computational chromatography: A machine learning strategy for demixing individual chemical components in complex mixtures.

Surface-enhanced Raman spectroscopy (SERS) holds exceptional promise as a streamlined chemical detection strategy for biological and environmental contaminants compared with current laboratory methods. Priority pollutants such as polycyclic aromatic hydrocarbons (PAHs), detectable in water and soil worldwide and known to induce multiple adverse health effects upon human exposure, are typically found in multicomponent mixtures. By combining the molecular fingerprinting capabilities of SERS with the signal separation and detection capabilities of machine learning (ML), we examine whether individual PAHs can be identified through an analysis of the SERS spectra of multicomponent PAH mixtures. We have developed an unsupervised ML method we call Characteristic Peak Extraction, a dimensionality reduction algorithm that extracts characteristic SERS peaks based on counts of detected peaks of the mixture. By analyzing the SERS spectra of two-component and four-component PAH mixtures where the concentration ratios of the various components vary, this algorithm is able to extract the spectra of each unknown component in the mixture of unknowns, which is then subsequently identified against a SERS spectral library of PAHs. Combining the molecular fingerprinting capabilities of SERS with the signal separation and detection capabilities of ML, this effort is a step toward the computational demixing of unknown chemical components occurring in complex multicomponent mixtures.

Robust deep learning object recognition models rely on low frequency information in natural images.

Machine learning models have difficulty generalizing to data outside of the distribution they were trained on. In particular, vision models are usually vulnerable to adversarial attacks or common corruptions, to which the human visual system is robust. Recent studies have found that regularizing machine learning models to favor brain-like representations can improve model robustness, but it is unclear why. We hypothesize that the increased model robustness is partly due to the low spatial frequency preference inherited from the neural representation. We tested this simple hypothesis with several frequency-oriented analyses, including the design and use of hybrid images to probe model frequency sensitivity directly. We also examined many other publicly available robust models that were trained on adversarial images or with data augmentation, and found that all these robust models showed a greater preference to low spatial frequency information. We show that preprocessing by blurring can serve as a defense mechanism against both adversarial attacks and common corruptions, further confirming our hypothesis and demonstrating the utility of low spatial frequency information in robust object recognition.

How does sleeve gastrectomy impact long-term eating-related symptoms, distress, and behavior? A cross-sectional study using the BODY-Q patient-reported outcome measures.

BACKGROUND: Patients undergoing sleeve gastrectomy (SG) experience transformative changes in eating-related experiences that include eating-related symptoms, emotions, and habits. Long-term assessment of these endpoints with rigorous patient-reported outcome measures (PROMs) is limited. We assessed patients undergoing SG with the Body-Q Eating Module PROMs. METHODS: All patients evaluated at the Emory Bariatric Center were given the Body-Q Eating Modules questionnaire at preoperative/postoperative clinic visits. Rasch scores and prevalence of relevant endpoints were assessed across six time-points of interest: preoperatively, post-operative months 0-6, 7-12, 12-24, 24-36, and over 36. Student's t-test and Chi-square test were used for analysis. RESULTS: Overall, 1,352 questionnaires were completed pre-operatively and 493 postoperatively. Survey compliance was 81%. Compared to the pre-operative group, the post-operative group had lower BMI (39.7 vs. 46.4, p < 0.001) and higher age (46.3 vs. 44.9, p = 0.019). Beginning one year after SG, patients experience more frequent eating-related pain, nausea and constipation compared to pre-operative baseline (p < 0.05). They also more frequently experience eating-related regurgitation and dumping syndrome-related symptoms beginning post-operative year two (p < 0.05). In the first year after SG, patients more rarely feel eating-related embarrassment, guilt, and disappointment compared to pre-operative baseline (p < 0.05). These improvements disappear one year after SG, after which patients more frequently experience feeling out of control, unhappy, like a failure, disappointed, and guilty (p < 0.05). In the first year after SG, patients experience an increased frequency in positive eating behaviors (ate healthy foods, showed self-control, stopped before full; (p < 0.05). Only two eating-related behavior improvements persist long-term: feeling in control and eating the right amount (p < 0.05). CONCLUSIONS: Patients undergoing SG may experience more frequent eating-related symptoms, distress, and behavior in the long-term. These findings can enhance the pre-operative informed consent and guide development of a more tailored approach to postoperative clinical management such as more frequent visits with the dietician.

In silico dynamics of COVID-19 phenotypes for optimizing clinical management.

Understanding the underlying mechanisms of COVID-19 progression and the impact of various pharmaceutical interventions is crucial for the clinical management of the disease. We developed a comprehensive mathematical framework based on the known mechanisms of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, incorporating the renin-angiotensin system and ACE2, which the virus exploits for cellular entry, key elements of the innate and adaptive immune responses, the role of inflammatory cytokines, and the coagulation cascade for thrombus formation. The model predicts the evolution of viral load, immune cells, cytokines, thrombosis, and oxygen saturation based on patient baseline condition and the presence of comorbidities. Model predictions were validated with clinical data from healthy people and COVID-19 patients, and the results were used to gain insight into identified risk factors of disease progression including older age; comorbidities such as obesity, diabetes, and hypertension; and dysregulated immune response. We then simulated treatment with various drug classes to identify optimal therapeutic protocols. We found that the outcome of any treatment depends on the sustained response rate of activated CD8+ T cells and sufficient control of the innate immune response. Furthermore, the best treatment-or combination of treatments-depends on the preinfection health status of the patient. Our mathematical framework provides important insight into SARS-CoV-2 pathogenesis and could be used as the basis for personalized, optimal management of COVID-19.

A New Community-to-Hospital Specialist Otology Pathway Using Telemedicine: A Pilot Study of 50 Patients.

INTRODUCTION: Pathway innovation using smartphone otoscopy and tablet-based audiometry technologies to deliver ear and hearing services via trained audiologists may improve efficiency of the service. An ENT-integrated-community-ear service (ENTICES-combining community audiology management, remote ENT review and novel technologies) was piloted. We aimed to assess the efficiency and safety of ENTICES. METHOD: ENTICES was a community-based and audiologist-led pathway. Patients with otological symptoms were self-referred to this service. Smartphone otoscopy and tablet-based audiograms were performed. Two otologists reviewed all decisions made in the community by audiologists based on video-otoscopy, hearing tests and chart reviews. Data on the first 50 consecutive new patients attending either consultant-led hospital otology clinics (HOC), audiologist-led hospital advanced audiology diagnostics (AAD) or ENTICES clinics were collected between 1 August 2021 and 31 December 2021. Data were collected through chart reviews and questionnaires to compare the three pathways with respect to efficiency, patient satisfaction, technology utility and safety. RESULTS: No audiology-led ENTICES decisions were amended by hospital otologists following remote review. Remote review of video-otoscopy with history was sufficient for a diagnosis in 80% of cases. Adding hearing tests and standardised history increased the diagnostic yield to 98%. Patient satisfaction scores showed 100% service recommendation. The cost per patient, per visit, was £83.36, £99.07 and £69.72 for AAD, HOC or ENTICES, respectively. CONCLUSION: ENTICES provides a safe ear and hearing service that patients rated highly. Thirty-two per cent of hospital otology patients were eligible for this service. For those patients, ENTICES is 20% more cost-effective and can reduce the number of clinic visits by up to 60% compared with HOC.

Multimodal Intralesional Therapy for Reshaping the Myeloid Compartment of Tumors Resistant to Anti-PD-L1 Therapy via IRF8 Expression.

Intralesional therapy is a promising approach for remodeling the immunosuppressive tumor microenvironment while minimizing systemic toxicities. A combinatorial in situ immunomodulation (ISIM) regimen with intratumoral administration of Fms-like tyrosine kinase 3 ligand (Flt3L), local irradiation, and TLR3/CD40 stimulation induces and activates conventional type 1 dendritic cells in the tumor microenvironment and elicits de novo adaptive T cell immunity in poorly T cell-inflamed tumors. However, the impact of ISIM on myeloid-derived suppressor cells (MDSCs), which may promote treatment resistance, remains unknown. In this study, we examined changes in the frequencies and heterogeneity of CD11b+Ly-6CloLy-6G+ polymorphonuclear (PMN)-MDSCs and CD11b+Ly-6ChiLy-6G- monocytic (M)-MDSCs in ISIM-treated tumors using mouse models of triple-negative breast cancer. We found that ISIM treatment decreased intratumoral PMN-MDSCs, but not M-MDSCs. Although the frequency of M-MDSCs remained unchanged, ISIM caused a substantial reduction of CX3CR1+ M-MDSCs that express F4/80. Importantly, these ISIM-induced changes in tumor-residing MDSCs were not observed in Batf3-/- mice. ISIM upregulated PD-L1 expression in both M-MDSCs and PMN-MDSCs and synergized with anti-PD-L1 therapy. Furthermore, ISIM increased the expression of IFN regulatory factor 8 (IRF8) in myeloid cells, a known negative regulator of MDSCs, indicating a potential mechanism by which ISIM decreases PMN-MDSC levels. Accordingly, ISIM-mediated reduction of PMN-MDSCs was not observed in mice with conditional deletion of IRF8 in myeloid cells. Altogether, these findings suggest that ISIM holds promise as a multimodal intralesional therapy to alter both lymphoid and myeloid compartments of highly aggressive poorly T cell-inflamed, myeloid-enriched tumors resistant to anti-PD-L1 therapy.

Design, synthesis and biological evaluation of novel pyrazolo-pyrimidin-amines as potent and selective BTK inhibitors.

To discover the best-in-class Bruton's Tyrosine Kinase (BTK) inhibitors, for th treatment of autoimmune disorders like cancer (B-Cell Lymphoma (BCL)) and rheumatoid arthritis (RA), in the present investigation, novel structural optimizations were carried out. Introduction of novel bicyclic amine linkers and aromatic backbone led to series of compounds 9a-h and 14a-u. Compound 14b was found to be potent, orally bioavailable, selective and irreversible BTK inhibitor. In vitro, 14b showed IC50 of 1.0 nM and 0.8 nM, in BTK and TMD8 assays, respectively. In vivo,14b displayed robust efficacy in collagen-induced arthritis (CIA) and TMD8 xenograft models, which could be correlated with its improved oral bioavailability. In the repeated dose acute toxicity study, 14b showed no adverse changes, indicating that the BTK inhibitor 14b could be viable therapeutic option for the treatment of autoimmune disorders.

Does the use of a suction calibration system (SCS) reduce stapler load firings and operative time? A randomized controlled trial comparing use of endoscopic calibration vs. SCS in laparoscopic sleeve gastrectomy.

BACKGROUND: It is critical to ensure appropriate and consistent sleeve size and orientation during laparoscopic sleeve gastrectomy (LSG). Various devices are used to achieve this, including weighted rubber bougies, esophagogastroduodenoscopy (EGD), and suction calibration systems (SCS). Prior reports suggest that SCSs may decrease operative time and stapler load firings but are limited by single-surgeon experience and retrospective design. We performed the first randomized controlled trial comparing SCS against EGD in patients undergoing LSG to investigate whether the SCS decreases the number of stapler load firings. METHODS: This was a randomized, non-blinded study from a single MBSAQIP-accredited academic center. Appropriate LSG candidates ≥ 18 years of age were randomized to EGD or SCS calibration. Exclusion criteria included prior gastric or bariatric surgery, detection of hiatal hernia before surgery, and intraoperative hiatal hernia repair. A randomized block design was employed controlling for body mass index, gender, and race. Seven surgeons employed a standardized LSG operative technique. The primary endpoint was the number of stapler load firings. Secondary endpoints were operative duration, reflux symptoms, and change in total body weight (TBW). Endpoints were analyzed via t-test. RESULTS: A total of 125 LSG patients (84% female) underwent study enrollment, with an average age of 44 ± 12 years and average BMI of 49 ± 8 kg/m2. Overall, 117 patients were randomized to receive EGD (n = 59) or SCS (n = 58) calibration. No significant differences in baseline characteristics were identified. The mean number of stapler load firings for EGD and SCS groups were 5.43 ± 0.89 and 5.31 ± 0.81, respectively (p = 0.463). The mean operative times for EGD and SCS groups were 94.4 ± 36.5 and 93.1 ± 27.9 min, respectively (p = 0.83). There were no significant differences in post-operative reflux, TBW loss, or complications. CONCLUSION: Use of EGD and SCS resulted in a similar number of LSG stapler load firings and operative duration. Additional research is needed to compare LSG calibration devices in different patients and settings to optimize surgical technique.

Robotic versus laparoscopic gastrectomy for adenocarcinoma in the US: a propensity score-matching analysis of 11,173 patients on oncological adequacy.

INTRODUCTION: Surgery remains the cornerstone treatment for gastric cancer. Previous studies have reported better lymphadenectomy with minimally invasive approaches. There is a paucity of data comparing robotic and laparoscopic gastrectomy in the US. Herein, we examined whether oncological adequacy differs between laparoscopic and robotic approaches. METHODS: The National Cancer Database was utilized to identify patients who underwent gastrectomy for adenocarcinoma between 2010 and 2019. A propensity score-matching analysis between robotic gastrectomy (RG) versus laparoscopic gastrectomy (LG) was performed. The primary outcomes were lymphadenectomy ≥ 16 nodes and surgical margins. RESULTS: A total of 11,173 patients underwent minimally invasive surgery for gastric adenocarcinoma between 2010 and 2019. Of those 8320 underwent LG and 2853 RG. Comparing the unmatched cohorts, RG was associated with a higher rate of adequate lymphadenectomy (63.5% vs 57.1%, p < .0.0001), higher rate of negative margins (93.8% vs 91.9%, p < 0.001), lower rate of prolonged length of stay (26.0% vs 29.6%, p < .0.001), lower 90-day mortality (3.7% vs 5.0%, p < 0.0001), and a better 5-year overall survival (OS) (56% vs 54%, p = 0.03). A propensity score-matching cohort with a 1:1 ratio was created utilizing the variables associated with lymphadenectomy ≥ 16 nodes. The matched analysis revealed that the rate of adequate lymphadenectomy was significantly higher for RG compared to LG, 63.5% vs 60.4% (p = 0.01), respectively. There was no longer a significant difference between RG and LG regarding the rate of negative margins, prolonged length of stay, 90-day mortality, rate of receipt of postoperative chemotherapy, and OS. CONCLUSIONS: This propensity score-matching analysis with a large US cohort shows that RG was associated with a higher rate of adequate lymphadenectomy compared to LR. RG and LG had a similar rate of negative margins, prolonged length of stay, receipt of postoperative chemotherapy, 90-day mortality, and OS, suggesting that RG is a comparable surgical approach, if not superior to LG.

S136-operationalizing an enhanced recovery protocol after bariatric surgery: single institutional pilot experience forging data-driven standard work.

BACKGROUND: Enhanced recovery protocols (ERPs) after metabolic and bariatric surgery (MBS) may help decrease length of stay (LOS) and postoperative nausea/vomiting but implementation is often fraught with challenges. The primary aim of this pilot study was to standardize a MBS ERP with a real-time data support dashboard and checklist and assess impact on global and individual element compliance. The secondary aim was to evaluate 30 day outcomes including LOS, hospital readmissions, and re-operations. METHODS AND PROCEDURES: An ERP, paper checklist, and virtual dashboard aligned on MBS patient care elements for pre-, intra-, and post-operative phases of care were developed and sequentially deployed. The dashboard includes surgical volumes, operative times, ERP compliance, and 30 day outcomes over a rolling 18 month period. Overall and individual element ERP compliance and outcomes were compared pre- and post-implementation via two-tailed Student's t-tests. RESULTS: Overall, 471 patients were identified (pre-implementation: 193; post-implementation: 278). Baseline monthly average compliance rates for all patient care elements were 1.7%, 3.7%, and 6.2% for pre-, intra-, and post-operative phases, respectively. Following ERP integration with dashboard and checklist, the intra-operative phase achieved the highest overall monthly average compliance at 31.3% (P < 0.01). Following the intervention, pre-operative acetaminophen administration had the highest monthly mean compliance at ≥ 99.1%. Overall TAP block use increased 3.2-fold from a baseline mean rate of 25.4-80.8% post-implementation (P < 0.01). A significant decrease in average intra-operative monthly morphine milligram equivalents use was noted with a 56% drop pre- vs. post-implementation. Average LOS decreased from 2.0 to 1.7 days post-implementation with no impact on post-operative outcomes. CONCLUSION: Implementation of a checklist and dashboard facilitated ERP integration and adoption of process measures with many improvements in compliance but no impact on 30 day outcomes. Further research is required to understand how clinical support tools can impact ERP adoption among MBS patients.

Integrin α5 Is Regulated by miR-218-5p in Endothelial Progenitor Cells.

BACKGROUND: Endothelial cell injury is a common nidus of renal injury in patients and consistent with the high prevalence of AKI reported during the coronavirus disease 2019 pandemic. This cell type expresses integrin α5 (ITGA5), which is essential to the Tie2 signaling pathway. The microRNA miR-218-5p is upregulated in endothelial progenitor cells (EPCs) after hypoxia, but microRNA regulation of Tie2 in the EPC lineage is unclear. METHODS: We isolated human kidney-derived EPCs (hkEPCs) and surveyed microRNA target transcripts. A preclinical model of ischemic kidney injury was used to evaluate the effect of hkEPCs on capillary repair. We used a genetic knockout model to evaluate the effect of deleting endogenous expression of miR-218 specifically in angioblasts. RESULTS: After ischemic in vitro preconditioning, miR-218-5p was elevated in hkEPCs. We found miR-218-5p bound to ITGA5 mRNA transcript and decreased ITGA5 protein expression. Phosphorylation of 42/44 MAPK decreased by 73.6% in hkEPCs treated with miR-218-5p. Cells supplemented with miR-218-5p downregulated ITGA5 synthesis and decreased 42/44 MAPK phosphorylation. In a CD309-Cre/miR-218-2-LoxP mammalian model (a conditional knockout mouse model designed to delete pre-miR-218-2 exclusively in CD309+ cells), homozygotes at e18.5 contained avascular glomeruli, whereas heterozygote adults showed susceptibility to kidney injury. Isolated EPCs from the mouse kidney contained high amounts of ITGA5 and showed decreased migratory capacity in three-dimensional cell culture. CONCLUSIONS: These results demonstrate the critical regulatory role of miR-218-5p in kidney EPC migration, a finding that may inform efforts to treat microvascular kidney injury via therapeutic cell delivery.

Use of tranexamic acid-soaked NasoPore® in the emergency department, to reduce epistaxis admissions.

OBJECTIVES: The aim of this study was to assess the efficacy of a new emergency department (ED) intervention for the management of non-traumatic, anterior epistaxis in adult patients, aiming to reduce epistaxis admissions. DESIGN: A new epistaxis pathway was introduced for use by ED practitioners. This was disseminated in ED through an educational campaign by the ear, nose and throat team. A tranexamic acid (500 mg/5 mL)-soaked NasoPore® packing step was introduced for epistaxis which did not terminate following 10 min of simple first aid. The pathway was utilised for adult patients presenting with non-traumatic, anterior epistaxis. Pre- and post-implementation periods were defined, and all adults attending ED with non-traumatic, anterior epistaxis were included. Pre- and post-implementation epistaxis treatment interventions, admission rates and re-attendance rates were recorded by retrospective audit and compared. RESULTS: In the post-implementation group, epistaxis admissions were 51.7% (p < .05) lower than in the pre-implementation group, as a proportion of the total number attending ED with epistaxis during these periods. CONCLUSIONS: The significant reduction in epistaxis admissions demonstrates that this ED intervention is beneficial for patient outcomes.

High RAD51 gene expression is associated with aggressive biology and with poor survival in breast cancer.

PURPOSE: Although the DNA repair mechanism is important in preventing carcinogenesis, its activation in established cancer cells may support their proliferation and aggravate cancer progression. RAD51 cooperates with BRCA2 and is essential in the homologous recombination of DNA repair. To this end, we hypothesized that RAD51 gene expression is associated with cancer cell proliferation and poor prognosis of breast cancer (BC) patients. METHODS: A total of 8515 primary BC patients with transcriptome and clinical data from 17 independent cohorts were analyzed. The median value was used to divide each cohort into high and low RAD51 expression groups. RESULTS: High RAD51 expression enriched the DNA repair gene set and was correlated with DNA repair-related genes. Nottingham histological grade, Ki67 expression and cell proliferation-related gene sets (E2F Targets, G2M Checkpoint and Myc Targets) were all significantly associated with the high RAD51 BC group. RAD51 expression was positively correlated with Homologous Recombination Deficiency, as well as both mutational burden and neoantigens that accompanied a higher infiltration of immune cells. Primary BC with lymph node metastases was associated with high expression of RAD51 in two cohorts. There was no strong correlation between RAD51 expression and drug sensitivity in cell lines, and RAD51 expression was lower after the neoadjuvant chemotherapy compared to before the treatment. High RAD51 BC was associated with poor prognosis consistently in three independent cohorts. CONCLUSION: RAD51 gene expression is associated with aggressive cancer biology, cancer cell proliferation, and poor survival in breast cancer.

Melanoma trials that defined surgical management: Brief overview of current/upcoming adjuvant/neoadjuvant trials.

Adjuvant systemic therapy for cutaneous melanoma has experienced practice-changing shifts over the last decade. The successful results of immunotherapies and targeted therapies in the metastatic setting have allowed for investigative trials of the same therapies in the adjuvant and now neoadjuvant setting, with the potential for improved clinical outcomes in patients with high risk resected Stage III and IV melanoma.

miR-218 Expressed in Endothelial Progenitor Cells Contributes to the Development and Repair of the Kidney Microvasculature.

Ischemia due to hypoperfusion is one of the most common forms of acute kidney injury. We hypothesized that kidney hypoxia initiates the up-regulation of miR-218 expression in endothelial progenitor cells (EPCs) to guide endocapillary repair. Murine renal artery-derived EPCs (CD34+/CD105-) showed down-regulation of mmu-Mir218-5p/U6 RNA ratio after ischemic injury, while in human renal arteries, MIR218-5p expression was up-regulated after ischemic injury. MIR218 expression was clarified in cell culture experiments in which increases in both SLIT3 and MIR218-2-5p expressions were observed after 5 minutes of hypoxia. ROBO1 transcript, a downstream target of MIR218-2-5p, showed inverse expression to MIR218-2-5p. EPCs transfected with a MIR218-5p inhibitor in three-dimensional normoxic culture showed premature capillary formation. Organized progenitor cell movement was reconstituted when cells were co-transfected with Dicer siRNA and low-dose Mir218-5p mimic. A Mir218-2 knockout was generated to assess the significance of miR-218-2 in a mammalian model. Mir218-2-5p expression was decreased in Mir218-2-/- embryos at E16.5. Mir218-2-/- decreased CD34+ angioblasts in the ureteric bud at E16.5 and were nonviable. Mir218-2+/- decreased peritubular capillary density at postnatal day 14 and increased serum creatinine after ischemia in adult mice. Systemic injection of miR-218-5p decreased serum creatinine after injury. These experiments demonstrate that miR-218 expression can be triggered by hypoxia and modulates EPC migration in the kidney.

Discovery of novel, potent and orally efficacious inhibitor of neutral amino acid transporter B0AT1 (SLC6A19).

Amino acid restriction by inhibition of neutral amino acid transporter, B0AT1 (SLC6A19) activity has been recently shown to improve glyceamic control by upregulating glucagon like peptide (GLP1) and fibroblast growth factor (FGF21) in mice. Hence, pharmacological inhibition of B0AT1 is expected to treat type-2 diabetes and related disorder. In this study, rationally designed trifluoromethyl sulfonyl derivatives were identified as novel, potent and orally bioavailable B0AT1 inhibitors. Compound 39 was found to be nanomolar potent (IC50: 0.035 µM) B0AT1 inhibitor with excellent pharmacokinetic profile (%F: 66) in mice and efficacious in vivo in diet induced obese (DIO) mice model.

Etiological profile of diarrhea in solid organ transplant recipients at a tertiary care center in Southern India.

BACKGROUND: Diarrhea is one of the common gastrointestinal (GI) adverse events after solid organ transplantation. Diarrhea may be caused by infectious or non-infectious etiology. The infectious etiology of diarrhea varies according to the location and duration of diarrhea. Non-infectious etiologies include drugs, inflammatory bowel disease, neoplasia. The objective of this study was to evaluate the etiological profile of diarrhea in solid organ transplant recipients presenting to a tertiary care center in Southern India. METHODS: This was a retrospective analysis of prospectively collected data of all solid organ transplantation recipients referred to the Department of Medical Gastroenterology for evaluation of diarrhea from April 2012 till May 2014. All patients had stool evaluated by wet mount examination, modified acid fast (AFB) stain, trichrome stain, culture, and Clostridium difficile toxin assay. EDTA plasma was collected for quantitative Cytomegalovirus (CMV) detection by real-time PCR. If the diarrhea was acute (<2 wk), and no etiological agent was identified, empirical antibiotic therapy was instituted and followed up. If persistent or chronic diarrhea (>2-4 wk), endoscopic evaluation (upper GI endoscopy and/or colonoscopy with biopsies), depending on the clinical type of diarrhea was done. If no specific etiological diagnosis was established after endoscopic evaluation, breath test for SIBO and celiac serology were done. If no specific etiology was identified after the above investigations, dose of immunosuppressive drugs was reduced. If diarrhea responded to dose reduction, it was considered to be drug related. RESULTS: Fifty-eight episodes of diarrhea occurred in 55 solid organ transplant recipients during the study period. Renal transplant recipients constituted the majority (70%). Most (79%) of patients included in the study had their transplant > 6 mo ago. Infective diarrhea was the etiology in 46%, drug-related diarrhea in 29.3%. No specific etiology was identified in 22.4% of patients. Parasites accounted for 69% of all infective diarrhea. Stool evaluation was the main investigation in establishing diagnosis in acute diarrhea. Endoscopic evaluation was required in two thirds of patients to establish diagnosis in chronic diarrhea. CONCLUSION: GI infections and drug-related diarrhea were the common causes of diarrhea in solid organ transplant recipients. Parasites were the most common infectious etiology of diarrhea. Step-wise evaluation was able to identify the etiology in ~ 77% of patients. Overall, 98% of diarrheal episodes resolved.

Domain-driven models yield better predictions at lower cost than reservoir computers in Lorenz systems.

Recent advances in computing algorithms and hardware have rekindled interest in developing high-accuracy, low-cost surrogate models for simulating physical systems. The idea is to replace expensive numerical integration of complex coupled partial differential equations at fine time scales performed on supercomputers, with machine-learned surrogates that efficiently and accurately forecast future system states using data sampled from the underlying system. One particularly popular technique being explored within the weather and climate modelling community is the echo state network (ESN), an attractive alternative to other well-known deep learning architectures. Using the classical Lorenz 63 system, and the three tier multi-scale Lorenz 96 system (Thornes T, Duben P, Palmer T. 2017 Q. J. R. Meteorol. Soc. 143, 897-908. (doi:10.1002/qj.2974)) as benchmarks, we realize that previously studied state-of-the-art ESNs operate in two distinct regimes, corresponding to low and high spectral radius (LSR/HSR) for the sparse, randomly generated, reservoir recurrence matrix. Using knowledge of the mathematical structure of the Lorenz systems along with systematic ablation and hyperparameter sensitivity analyses, we show that state-of-the-art LSR-ESNs reduce to a polynomial regression model which we call Domain-Driven Regularized Regression (D2R2). Interestingly, D2R2 is a generalization of the well-known SINDy algorithm (Brunton SL, Proctor JL, Kutz JN. 2016 Proc. Natl Acad. Sci. USA 113, 3932-3937. (doi:10.1073/pnas.1517384113)). We also show experimentally that LSR-ESNs (Chattopadhyay A, Hassanzadeh P, Subramanian D. 2019 (http://arxiv.org/abs/1906.08829)) outperform HSR ESNs (Pathak J, Hunt B, Girvan M, Lu Z, Ott E. 2018 Phys. Rev. Lett. 120, 024102. (doi:10.1103/PhysRevLett.120.024102)) while D2R2 dominates both approaches. A significant goal in constructing surrogates is to cope with barriers to scaling in weather prediction and simulation of dynamical systems that are imposed by time and energy consumption in supercomputers. Inexact computing has emerged as a novel approach to helping with scaling. In this paper, we evaluate the performance of three models (LSR-ESN, HSR-ESN and D2R2) by varying the precision or word size of the computation as our inexactness-controlling parameter. For precisions of 64, 32 and 16 bits, we show that, surprisingly, the least expensive D2R2 method yields the most robust results and the greatest savings compared to ESNs. Specifically, D2R2 achieves 68 × in computational savings, with an additional 2 × if precision reductions are also employed, outperforming ESN variants by a large margin. This article is part of the theme issue 'Machine learning for weather and climate modelling'.