MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis.

SUMMARY: Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) has emerged as a promising liquid biopsy technology to detect cancers and monitor treatments. While several bioinformatics tools for DNA methylation analysis have been adapted for cfMeDIP-seq data, an end-to-end pipeline and quality control framework specifically for this data type is still lacking. Here, we present the MEDIPIPE, which provides a one-stop solution for cfMeDIP-seq data quality control, methylation quantification, and sample aggregation. The major advantages of MEDIPIPE are: (i) ease of implementation and reproducibility with Snakemake containerized execution environments that will be automatically deployed via Conda; (ii) flexibility to handle different experimental settings with a single configuration file; and (iii) computationally efficiency for large-scale cfMeDIP-seq profiling data analysis and aggregation. AVAILABILITY AND IMPLEMENTATION: This pipeline is an open-source software under the MIT license and it is freely available at https://github.com/pughlab/MEDIPIPE.

Direct Experimental Observations of Ion Distributions during Overcharging at the Muscovite-Water Interface by Adsorption of Rb+ and Halides (Cl- , Br- , I- ) at High Salinity.

Classical electric double layer (EDL) models have been widely used to describe ion distributions at charged solid-water interfaces in dilute electrolytes. However, the chemistry of EDLs remains poorly constrained at high ionic strength where ion-ion correlations control non-classical behavior such as overcharging, i. e., the accumulation of counter-ions in amounts exceeding the substrate's surface charge. Here, we provide direct experimental observations of correlated cation and anion distributions adsorbed at the muscovite (001)-aqueous electrolyte interface as a function of dissolved RbBr concentration ([RbBr]=0.01-5.8 M) using resonant anomalous X-ray reflectivity. Our results show alternating cation-anion layers in the EDL when [RbBr]≳100 mM, whose spatial extension (i. e., ~20 Šfrom the surface) far exceeds the dimension of the classical Stern layer. Comparison to RbCl and RbI electrolytes indicates that these behaviors are sensitive to the choice of co-ion. This new in-depth molecular-scale understanding of the EDL structure during transition from classical to non-classical regimes supports the development of realistic EDL models for technologies operating at high salinity such as water purification applications or modern electrochemical storage.

Direct Experimental Observations of Ion Distributions during Overcharging at the Muscovite-Water Interface by Adsorption of Rb+ and Halides (Cl- , Br- , I- ) at High Salinity.

The front cover artwork is provided by Argonne National Laboratory. The image shows the arrangement of correlated cations and anions at a charged solid surface in contact with highly concentrated electrolyte solutions. Read the full text of the Research Article at 10.1002/cphc.202300545.

EUS-Guided Biliary Drainage Versus ERCP in Malignant Biliary Obstruction Before Hepatobiliary Surgery: An International Multicenter Comparative Study.

INTRODUCTION: Endoscopic ultrasound-guided biliary drainage (EUS-BD) is the procedure of choice for patients who cannot undergo endoscopic retrograde cholangiopancreatography (ERCP). The outcomes of patients undergoing surgery after EUS-BD for malignancy are unknown. METHODS: We conducted an international, multicenter retrospective comparative study of patients who underwent hepatobiliary surgery after having undergone EUS-BD or ERCP from 6 tertiary care centers. Patient demographics, procedural data, and follow-up care were collected in a registry. RESULTS: One hundred forty-five patients were included: EUS-BD n=58 (mean age 66, 45% male), ERCP n=87 (mean age 68, 53% male). The majority of patients had pancreatic cancer, cholangiocarcinoma, or gallbladder malignancy. In the EUS-BD group, 29 patients had hepaticogastrostomy, 24 had choledochoduodenostomy, and 5 had rendezvous technique done. The most common surgery was Whipple in both groups (n=41 EUS-BD, n=56 ERCP) followed by partial hepatectomy (n=7 EUS-BD, n=14 ERCP) and cholecystectomy (n=2 EUS-BD, n=2 ERCP). Endoscopy clinical success was comparable in both groups (98% EUS-BD, 94% ERCP). Adverse event rates were similar in both groups: EUS-BD (n=10, 17%) and ERCP (n=23, 26%). Surgery technical success and clinical success were significantly higher in the EUS-BD group compared with the ERCP group (97% vs. 83%, 97% vs. 75%). Total Hospital stay from surgery to discharge was significantly higher in the ERCP group (19 d vs. 10 d, P =0.0082). DISCUSSION: Undergoing EUS-BD versus ERCP before hepatobiliary surgery is associated with fewer repeat endoscopic interventions, shorter duration between endoscopy and surgical intervention, higher rates of surgical clinical success, and shorter length of hospital stay after surgery.

Endoscopic Ultrasound-Directed Transgastric ERCP (EDGE) Utilization of Trends Among Interventional Endoscopists.

BACKGROUND: Endoscopic ultrasound-directed transgastric ERCP (EDGE) has become standard-of-care therapy at many centers for pancreaticobiliary disease in patients with Roux-en-Y Gastric Bypass. In this study, we aimed to evaluate the opinions and practices of endoscopists who perform EDGE. METHODS: A 22-question utilization of EDGE survey was sent to 36 advanced endoscopists at tertiary care centers in the United States. The two-section survey included questions regarding advanced endoscopy volume and training at the respective facilities, and questions on specific details of EDGE utilization. RESULTS: Among 36 interventional endoscopists (IE) surveyed, 14 (39%) reported performing > 1000 ERCPs annually. Thirty (83%) offered EDGE as an option for Roux-en-Y gastric bypass patients with previous cholecystectomy. Other options offered included: 19 (53%) offered Laparoscopy-assisted ERCP (LA-ERCP), 7 (19%) offered Single-Balloon ERCP (SBE), and 10 (28%) offered percutaneous drainage (PTC). Twenty (56%) IE performed 10 or less EDGE procedures, while 16 (44%) performed 11 or more. Single-session EDGE was performed by 7 (19%) IE, while 15 (42%) performed dual session, and 13 (36%) performed both. 19 (53%) actively closed fistulas while 17 (47%) let them close spontaneously. Thirty one (86%) reported a technical success rate of 91% to 100%. The most frequently reported immediate adverse event post-procedurally was abdominal pain, reported by 17 IE (47%). Weight gain was reported by 2 IE (6%). CONCLUSION: EDGE continues to gain in popularity as an option for Roux-en-Y gastric bypass patients requiring pancreaticobiliary interventions, with 24/36 IE (67%) believing that it should be the new standard. In addition, most report a low frequency of post-procedural weight gain. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov Identifier NCT05041608.

Inflammatory diseases in hematology: a review.

Hematopoietic cells are instrumental in generating and propagating protective inflammatory responses to infection or injury. However, excessive inflammation contributes to many diseases of the blood, bone marrow, and lymphatic system. We review three clinical categories of hematological inflammatory diseases in which recent clinical and translational advances have been made. The first category is monogenic inflammatory diseases. Genotype-driven research has revealed that previously mysterious diseases with protean manifestations are characterized by mutations that may be germline (e.g., deficiency of ADA2 or GATA2 deficiency) or somatic [e.g., vacuoles, enzyme E1, X-linked, autoinflammatory, somatic (VEXAS) syndrome]. The second category is the cytokine storm syndromes, including hemophagocytic lymphohistiocytosis, and Castleman disease. Cytokine storm syndromes are characterized by excessive production of inflammatory cytokines including interleukin-6 and interferon-γ, causing end-organ damage and high mortality. Finally, we review disorders associated with monoclonal and polyclonal hypergammaglobulinemia. The serum protein electrophoresis (SPEP) is typically ordered to screen for common diseases such as myeloma and humoral immunodeficiency. However, monoclonal and polyclonal hypergammaglobulinemia on SPEP can also provide important information in rare inflammatory diseases. For example, the autoinflammatory disease Schnitzler syndrome is notoriously difficult to diagnose. Although this orphan disease has eluded precise genetic or histological characterization, the presence of a monoclonal paraprotein, typically IgM, is an obligate diagnostic criterion. Likewise, polyclonal hypergammaglobulinemia may be an important early, noninvasive diagnostic clue for patients presenting with rare neoplastic diseases such as Rosai-Dorfman disease and angioimmunoblastic T-cell lymphoma. Applying these three categories to patients with unexplained inflammatory syndromes can facilitate the diagnosis of rare and underrecognized diseases.

CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer.

Tumors from individuals with cancer are frequently genetically profiled for information about the driving forces behind the disease. We present the CancerMine resource, a text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer. All data are available online ( http://bionlp.bcgsc.ca/cancermine ) and downloadable under a Creative Commons Zero license for ease of use.

Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments.

Glioblastoma multiforme (GBM) is the most deadly brain tumor, and currently lacks effective treatment options. Brain tumor-initiating cells (BTICs) and orthotopic xenografts are widely used in investigating GBM biology and new therapies for this aggressive disease. However, the genomic characteristics and molecular resemblance of these models to GBM tumors remain undetermined. We used massively parallel sequencing technology to decode the genomes and transcriptomes of BTICs and xenografts and their matched tumors in order to delineate the potential impacts of the distinct growth environments. Using data generated from whole-genome sequencing of 201 samples and RNA sequencing of 118 samples, we show that BTICs and xenografts resemble their parental tumor at the genomic level but differ at the mRNA expression and epigenomic levels, likely due to the different growth environment for each sample type. These findings suggest that a comprehensive genomic understanding of in vitro and in vivo GBM model systems is crucial for interpreting data from drug screens, and can help control for biases introduced by cell-culture conditions and the microenvironment in mouse models. We also found that lack of MGMT expression in pretreated GBM is linked to hypermutation, which in turn contributes to increased genomic heterogeneity and requires new strategies for GBM treatment.

Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma.

Although generally curable with intensive chemotherapy in resource-rich settings, Burkitt lymphoma (BL) remains a deadly disease in older patients and in sub-Saharan Africa. Epstein-Barr virus (EBV) positivity is a feature in more than 90% of cases in malaria-endemic regions, and up to 30% elsewhere. However, the molecular features of BL have not been comprehensively evaluated when taking into account tumor EBV status or geographic origin. Through an integrative analysis of whole-genome and transcriptome data, we show a striking genome-wide increase in aberrant somatic hypermutation in EBV-positive tumors, supporting a link between EBV and activation-induced cytidine deaminase (AICDA) activity. In addition to identifying novel candidate BL genes such as SIN3A, USP7, and CHD8, we demonstrate that EBV-positive tumors had significantly fewer driver mutations, especially among genes with roles in apoptosis. We also found immunoglobulin variable region genes that were disproportionally used to encode clonal B-cell receptors (BCRs) in the tumors. These include IGHV4-34, known to produce autoreactive antibodies, and IGKV3-20, a feature described in other B-cell malignancies but not yet in BL. Our results suggest that tumor EBV status defines a specific BL phenotype irrespective of geographic origin, with particular molecular properties and distinct pathogenic mechanisms. The novel mutation patterns identified here imply rational use of DNA-damaging chemotherapy in some patients with BL and targeted agents such as the CDK4/6 inhibitor palbociclib in others, whereas the importance of BCR signaling in BL strengthens the potential benefit of inhibitors for PI3K, Syk, and Src family kinases among these patients.

Photoacoustic Imaging Quantifies Drug Release from Nanocarriers via Redox Chemistry of Dye-Labeled Cargo.

We report a new approach to monitor drug release from nanocarriers via a paclitaxel-methylene blue conjugate (PTX-MB) with redox activity. This construct is in a photoacoustically silent reduced state inside poly(lactic-co-glycolic acid) (PLGA) nanoparticles (PTX-MB@PLGA NPs). During release, PTX-MB is spontaneously oxidized to produce a concentration-dependent photoacoustic signal. An in vitro drug-release study showed an initial burst release (25 %) between 0-24 h and a sustained release between 24-120 h with a cumulative release of 40.6 % and a 670-fold increase in photoacoustic signal. An in vivo murine drug release showed a photoacoustic signal enhancement of up to 649 % after 10 hours. PTX-MB@PLGA NPs showed an IC50 of 78 µg mL-1 and 44.7±4.8 % decrease of tumor burden in an orthotopic model of colon cancer via luciferase-positive CT26 cells.

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma.

Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32% of DLBCL and 89% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4% and 13.4% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis.

Scientific Overview: CSCI-CITAC Annual General Meeting and Young Investigators' Forum 2015.

The 2015 Annual General Meeting of The Canadian Society of Clinician Investigators (CSCI) and Clinician Investigator Trainee Association of Canada/Association des Cliniciens-Chercheurs en Formation du Canada (CITAC/ACCFC) was held in Toronto November 23-25, 2015, in conjunction with The University of Toronto Clinician Investigator Program Research Day. The theme for this year's meeting was "It takes a village" and the focus was the various support systems necessary to train a successful clinician scientist. The meeting featured an opening presentation by Dr. Vincent Dumez and workshops by Dr. Peter Nickerson, Dr. Jane Aubin, Dr. Kelly Warmington and Dr. Norman Rosenblum, and MD/PhD trainees Nardin Samuel, Kevin Wang and Kirill Zaslavsky. The keynote speakers were Dr. David Malkin (Hospital for Sick Children) who received the CSCI-RCPSC Henry Friesen Award, Dr. Brent Richards (McGill University) who received the Joe Doupe Award and Ernesto Shiffrin (Lady Davis Institute) who received the Distinguished Scientist Award. As always, the conference showcased outstanding scientific presentations from clinician investigator trainees from across the country at the Young Investigators' Forum. The research topics, which ranged from basic sciences to clinical medicine and translational work, are summarized in this review. Over 90 abstracts were presented at this year's meeting during two poster sessions, with several of the outstanding abstracts selected for oral presentations.

Scientific overview: CSCI-CITAC Annual General Meeting and Young Investigators' Forum 2014.

The Canadian Society of Clinician Investigators (CSCI) and Clinical Investigator Trainee Association of Canada/Association des cliniciens-chercheurs en formation du Canada (CITAC/ACCFC) annual general meeting (AGM) was held in Toronto during November 21-24, 2015 for the first time in conjunction with the University of Toronto Clinician-Investigator Program Research Day. The overall theme for this year's meeting was the role of mentorship in career development, with presentations from Dr. Chaim Bell (University of Toronto), Dr. Shurjeel Choudhri (Bayer Healthcare), Dr. Ken Croitoru (University of Toronto), Dr. Astrid Guttman (University of Toronto), Dr. Prabhat Jha (University of Toronto) and Dr. Sheila Singh (McMaster University). The keynote speakers of the 2014 AGM included Dr. Qutayba Hamid, who was presented with the Distinguished Scientist Award, Dr. Ravi Retnakaran, who was presented with the Joe Doupe Award, and Dr. Lorne Babiuk, who was the CSCI-RCPSC Henry Friesen Award winner. The highlight of the conference was, once again, the outstanding scientific presentations from the numerous clinician investigator (CI) trainees from across the country who presented at the Young Investigators' Forum. Their research topics spanned the diverse fields of science and medicine, ranging from basic science to cutting-edge translational research, and their work has been summarized in this review. Over 120 abstracts were presented at this year's meeting. This work was presented during two poster sessions, with the six most outstanding submitted abstracts presented in the form of oral presentations during the President's Forum.

Multiplexed neurochemical sensing with sub-nM sensitivity across 2.25 mm2 area.

Multichannel arrays capable of real-time sensing of neuromodulators in the brain are crucial for gaining insights into new aspects of neural communication. However, measuring neurochemicals, such as dopamine, at low concentrations over large areas has proven challenging. In this research, we demonstrate a novel approach that leverages the scalability and processing power offered by microelectrode array devices integrated with a functionalized, high-density microwire bundle, enabling electrochemical sensing at an unprecedented scale and spatial resolution. The sensors demonstrate outstanding selective molecular recognition by incorporating a selective polymeric membrane. By combining cutting-edge commercial multiplexing, digitization, and data acquisition hardware with a bio-compatible and highly sensitive neurochemical interface array, we establish a powerful platform for neurochemical analysis. This multichannel array has been successfully utilized in vitro and ex vivo systems. Notably, our results show a sensing area of 2.25 mm2 with an impressive detection limit of 820 pM for dopamine. This new approach paves the way for investigating complex neurochemical processes and holds promise for advancing our understanding of brain function and neurological disorders.

NeuroRoots, a bio-inspired, seamless brain machine interface for long-term recording in delicate brain regions.

Scalable electronic brain implants with long-term stability and low biological perturbation are crucial technologies for high-quality brain-machine interfaces that can seamlessly access delicate and hard-to-reach regions of the brain. Here, we created "NeuroRoots," a biomimetic multi-channel implant with similar dimensions (7 µm wide and 1.5 µm thick), mechanical compliance, and spatial distribution as axons in the brain. Unlike planar shank implants, these devices consist of a number of individual electrode "roots," each tendril independent from the other. A simple microscale delivery approach based on commercially available apparatus minimally perturbs existing neural architectures during surgery. NeuroRoots enables high density single unit recording from the cerebellum in vitro and in vivo. NeuroRoots also reliably recorded action potentials in various brain regions for at least 7 weeks during behavioral experiments in freely-moving rats, without adjustment of electrode position. This minimally invasive axon-like implant design is an important step toward improving the integration and stability of brain-machine interfacing.

Impact of Metabolic Syndrome on Early Postoperative Outcomes After Cervical Disk Replacement: A Propensity-matched Analysis.

STUDY DESIGN: Retrospective cohort study. OBJECTIVE: To compare the demographics, perioperative variables, and complication rates following cervical disk replacement (CDR) among patients with and without metabolic syndrome (MetS). SUMMARY OF BACKGROUND DATA: The prevalence of MetS-involving concurrent obesity, insulin resistance, hypertension, and hyperlipidemia-has increased in the United States over the last 2 decades. Little is known about the impact of MetS on early postoperative outcomes and complications following CDR. METHODS: The 2005-2020 National Surgical Quality Improvement Program was queried for patients who underwent primary 1- or 2-level CDR. Patients with and without MetS were divided into 2 cohorts. MetS was defined, according to other National Surgical Quality Improvement Program studies, as concurrent diabetes mellitus, hypertension requiring medication, and body mass index ≥30 kg/m 2 . Rates of 30-day readmission, reoperation, complications, length of hospital stay, and discharge disposition were compared using χ 2 and Fisher exact tests. One to 2 propensity-matching was performed, matching for demographics, comorbidities, and number of operative levels. RESULTS: A total of 5395 patients were included for unmatched analysis. Two hundred thirty-six had MetS, and 5159 did not. The MetS cohort had greater rates of 30-day readmission (2.5% vs. 0.9%; P =0.023), morbidity (2.5% vs. 0.9%; P =0.032), nonhome discharges (3% vs. 0.6%; P =0.002), and longer hospital stays (1.35±4.04 vs. 1±1.48 days; P =0.029). After propensity-matching, 699 patients were included. All differences reported above lost significance ( P >0.05) except for 30-day morbidity (superficial wound infections), which remained higher for the MetS cohort (2.5% vs. 0.4%, P =0.02). CONCLUSIONS: We identified MetS as an independent predictor of 30-day morbidity in the form of superficial wound infections following single-level CDR. Although MetS patients experienced greater rates of 30-day readmission, nonhome discharge, and longer lengths of stay, MetS did not independently predict these outcomes after controlling for baseline differences in patient characteristics. LEVEL OF EVIDENCE: Level III.

Psoas Muscle Health is Correlated With Time to Achieve MCID in Patients With Predominant Axial Back Pain Following Decompression Surgery: Early Results.

STUDY DESIGN: Retrospective cohort study. OBJECTIVE: To determine the impact of psoas muscle health [cross-sectional area (CSA)] on achieving minimal clinically important differences (MCID) in patient-reported outcome measures (PROMs) following laminectomy for patients with predominant back pain (PBP) and leg pain (PLP). SUMMARY OF BACKGROUND DATA: Psoas muscle health is linked to postoperative outcomes in decompression patients, with MRI-based grading of psoas CSA correlating with these outcomes. However, evidence on its impact on symptomatic recovery, measured by PROMs, is lacking. METHODS: One hundred six patients with PBP (VAS back > VAS leg) and 139 patients with PLP (VAS leg > VAS back) who underwent laminectomy from 2017 to 2021 were included. Axial T2 MRI images were analyzed for psoas CSA using a validated method. Based on the lowest-quartile normalized total psoas area (NTPA) thresholds, patients were divided into "good" and "poor" muscle health groups. The correlation analyses were performed between the psoas CSA and changes in PROMs. Kaplan-Meier survival analysis was conducted to determine the probability of achieving MCID as a function of time. RESULTS: Of 106 patients with PBP, 83 (78.3%) had good muscle health, and 23 (21.6%) had poor muscle health. Of 139 patients with PLP, 54 (38.8%) had good muscle health, and 85 (61.1%) had poor muscle health. In the PBP group, older age was associated with poor muscle health (69.70±9.26 vs . 59.92±15.01, P =0.0002). For both cohorts, there were no differences in the rate of MCID achievement for any PROMs between the good and poor muscle health groups. In the PBP group, Kaplan-Meier analysis showed patients with good psoas health achieved MCID-VAS back and Oswestry Disability Index (ODI) in median times of 14 and 42 days ( P =0.045 and 0.015), respectively. CONCLUSION: Good psoas muscle health is linked to faster attainment of MCID, especially in patients with PBP compared with PLP after decompression surgery. LEVEL OF EVIDENCE: III.