Shiga Toxin‒Producing Escherichia coli Diagnoses from Health Practitioners, Queensland, Australia.

In Queensland, Australia, 31 of 96 Shiga toxin‒producing Escherichia coli cases during 2020-2022 were reported by a specialty pathology laboratory servicing alternative health practitioners. Those new cases were more likely to be asymptomatic or paucisymptomatic, prompting a review of the standard public health response.

Novel CRTC1::MRTFB(MKL2) Gene Fusion Detected in Myxoid Mesenchymal Neoplasms With Myogenic Differentiation Involving Bone and Soft Tissues.

Appropriate classification of fusion-driven bone and soft tissue neoplasms continues to evolve, often relying on the careful integration of morphologic findings with immunohistochemical, molecular, and clinical data. Herein, we present 3 cases of a morphologically distinct myxoid mesenchymal neoplasm with myogenic differentiation and novel CRTC1::MRTFB (formerly MKL2) gene fusion. Three tumors occurred in 1 male and 2 female patients with a median age of 72 years (range: 28-78). Tumors involved the left iliac bone, the right thigh, and the left perianal region with a median size of 4.0 cm (4.0-7.6 cm). Although 1 tumor presented as an incidental finding, the other 2 tumors were noted, given their persistent growth. At the time of the last follow-up, 1 patient was alive with unresected disease at 6 months, 1 patient was alive without evidence of disease at 12 months after surgery, and 1 patient died of disease 24 months after diagnosis. On histologic sections, the tumors showed multinodular growth and were composed of variably cellular spindle to round-shaped cells with distinct brightly eosinophilic cytoplasm embedded within a myxoid stroma. One tumor showed overt smooth muscle differentiation. Cytologic atypia and mitotic activity ranged from minimal (2 cases) to high (1 case). By immunohistochemistry, the neoplastic cells expressed focal smooth muscle actin, h-caldesmon, and desmin in all tested cases. Skeletal muscle markers were negative. Next-generation sequencing detected nearly identical CRTC1::MRTFB gene fusions in all cases. We suggest that myxoid mesenchymal tumors with myogenic differentiation harboring a CRTC1::MRTFB fusion may represent a previously unrecognized, distinctive entity that involves soft tissue and bone. Continued identification of these novel myxoid neoplasms with myogenic differentiation will be important in determining appropriate classification, understanding biologic potential, and creating treatment paradigms.

Indwelling stents cause obstruction and induce ureteral injury and fibrosis in a porcine model.

OBJECTIVES: To investigate global changes in ureters at the transcriptional, translational and functional levels, both while stents are indwelling and after removal and recovery, and to study the effects of targeting pathways that play a potential role. METHODS: Pig ureters were stented for varying amounts of time (48 h, 72 h, 14 days) and the impact on peristalsis, dilatation and hydronephrosis were assessed. RNAseq, proteomic, histological and smooth muscle (SM) function analyses were performed on ureteric and kidney tissues to assess changes induced by stenting and recovery. Pathway analysis was performed using Ingenuity Pathway Analysis software. To study the impact of possible interventions, the effects of erythropoeitin (EPO) and a Gli1 inhibitor were assessed. RESULTS: Stenting triggers massive ureteric dilatation, aperistalsis and moderate hydronephrosis within 48 h. Pathways associated with obstruction, fibrosis and kidney injury were upregulated by stenting. Increased expression of GLI1, clusterin-α (a kidney injury marker) and collagen 4A2 (a fibrosis marker) was found in stented vs contralateral unstented ureters. EPO did not improve peristalsis or contraction force but did decrease non-purposeful spasming seen exclusively in stented ureters. Tamsulosin administration increased contractility but not rate of peristalsis in stented ureters. CONCLUSIONS: Ureters respond to stents similarly to how they respond to an obstruction, that is, with activation of pathways associated with hydronephrosis, fibrosis and kidney injury. This is driven by significant dilatation and associated ureteric SM dysfunction. EPO and tamsulosin induced mild favourable changes in SM physiology, suggesting that targeting specific pathways has potential to address stent-induced complications.

Hydrogen-Bonded Water-Aminium Assemblies for Synthesis of Zeotypes with Ordered Heteroatoms.

Water plays a central role in the crystallization of a variety of organic, inorganic, biological, and hybrid materials. This is also true for zeolites and zeolite-like materials, an important class of industrial catalysts and adsorbents. Water is always present during their hydrothermal synthesis, either with or without organic species as structure-directing agents. Apart from its role as a solvent or a catalyst, structure direction by water in zeolite synthesis has never been clearly elucidated. Here, we report the crystallization of phosphate-based molecular sieves using rationally designed, hydrogen-bonded water-aminium assemblies, resulting in molecular sieves exhibiting the crystallographic ordering of heteroatoms. We demonstrate that a 1:1 assembly of water and diprotonated N,N-dimethyl-1,2-ethanediamine acts as a structure-directing agent in the synthesis of a silicoaluminophosphate material with phillipsite (PHI) topology, using SMARTER crystallography, which combines single-crystal X-ray diffraction and nuclear magnetic resonance spectroscopy, as well as ab initio molecular dynamics simulations. The molecular arrangement of the hydrogen-bonded assembly matches well with the shape and size of subunits in the PHI structure, and their charge distributions result in the strict ordering of framework tetrahedral atoms. This concept of structure direction by water-containing supramolecular assemblies should be applicable to the synthesis of many classes of porous materials.

Xanthogranulomatous epithelial tumors and keratin-positive giant cell-rich soft tissue tumors: two aspects of a single entity with frequent HMGA2-NCOR2 fusions.

Xanthogranulomatous epithelial tumor (XGET) and keratin-positive giant cell-rich soft tissue tumor with HMGA2-NCOR2 fusion (KPGCT) are two recently described neoplasms with both distinct and overlapping clinical and histopathologic features. We hypothesized that XGET and KPGCT may be related and represent a histologic spectrum of a single entity. To test this, we sought to characterize the clinical, radiographic, immunohistochemical, ultrastructural and molecular features of additional tumors with features of XGET and/or KPGCT, which we refer to descriptively as keratin-positive xanthogranulomatous/giant cell-rich tumors (KPXG/GCT). The archives were searched for potential cases of KPXG/GCT. Clinical and imaging features were noted. Slides were assessed for histologic and immunohistochemical findings. Ultrastructural and next generation RNA sequencing-based analysis were also performed. Nine cases were identified arising in seven women and two men [median age of 33 years (range: 12-87)]. Median tumor size was 4 cm (range: 2.4-14.0 cm) and tumors presented in the thigh (2), buttock (1), forearm (2), groin (1), cranial fossa (1), ilium (1), and tibia (1). Morphologically, tumors were most frequently characterized by a fibrous capsule, with associated lymphoid reaction, enclosing a polymorphous proliferation of histiocytes, giant cells (Touton and osteoclast-types), mixed inflammatory infiltrate, hemorrhage and hemosiderin deposition, which imparted a variably xanthogranulomatous to giant cell tumor-like appearance. One case clearly showed mononuclear cells with eosinophilic cytoplasm characteristic of XGET. All cases expressed keratin and 7 of 9 were found to harbor HMGA2-NCOR2 fusions including cases with xanthogranulomatous appearance. One patient developed local recurrence and multifocal pulmonary lesions, which were radiographically suspicious for metastases. Shared clinical, histologic and immunohistochemical features, and the shared presence of HMGA2-NCOR2 fusions supports interpretation of KPXG/GCT as a single entity which includes XGET and KPGCT. Given limited clinical follow-up to date and rare cases with apparently aggressive findings, we provisionally regard these tumors as having uncertain biologic potential.

AAV-mediated expression of galactose-1-phosphate uridyltransferase corrects defects of galactose metabolism in classic galactosemia patient fibroblasts.

Classic galactosemia (CG) is a rare disorder of autosomal recessive inheritance. It is caused predominantly by point mutations as well as deletions in the gene encoding the enzyme galactose-1-phosphate uridyltransferase (GALT). The majority of the more than 350 mutations identified in the GALT gene cause a significant reduction in GALT enzyme activity resulting in the toxic buildup of galactose metabolites that in turn is associated with cellular stress and injury. Consequently, developing a therapeutic strategy that reverses both the oxidative and ER stress in CG cells may be helpful in combating this disease. Recombinant adeno-associated virus (AAV)-mediated gene therapy to restore GALT activity offers the potential to address the unmet medical needs of galactosemia patients. Here, utilizing fibroblasts derived from CG patients we demonstrated that AAV-mediated augmentation of GALT protein and activity resulted in the prevention of ER and oxidative stress. We also demonstrate that these CG patient fibroblasts exhibit reduced CD109 and TGFßRII protein levels and that these effectors of cellular homeostasis could be restored following AAV-mediated expression of GALT. Finally, we show initial in vivo proof-of-concept restoration of galactose metabolism in a GALT knockout mouse model following treatment with AAV-GALT.

Inappropriate use of clinical practices in Canada: a systematic review.

BACKGROUND: Inappropriate health care leads to negative patient experiences, poor health outcomes and inefficient use of resources. We aimed to conduct a systematic review of inappropriately used clinical practices in Canada. METHODS: We searched multiple bibliometric databases and grey literature to identify inappropriately used clinical practices in Canada between 2007 and 2021. Two team members independently screened citations, extracted data and assessed methodological quality. Findings were synthesized in 2 categories: diagnostics and therapeutics. We reported ranges of proportions of inappropriate use for all practices. Medians and interquartile ranges (IQRs), based on the percentage of patients not receiving recommended practices (underuse) or receiving practices not recommended (overuse), were calculated. All statistics are at the study summary level. RESULTS: We included 174 studies, representing 228 clinical practices and 28 900 762 patients. The median proportion of inappropriate care, as assessed in the studies, was 30.0% (IQR 12.0%-56.6%). Underuse (median 43.9%, IQR 23.8%-66.3%) was more frequent than overuse (median 13.6%, IQR 3.2%-30.7%). The most frequently investigated diagnostics were glycated hemoglobin (underused, range 18.0%-85.7%, n = 9) and thyroid-stimulating hormone (overused, range 3.0%-35.1%, n = 5). The most frequently investigated therapeutics were statin medications (underused, range 18.5%-71.0%, n = 6) and potentially inappropriate medications (overused, range 13.5%-97.3%, n = 9). INTERPRETATION: We have provided a summary of inappropriately used clinical practices in Canadian health care systems. Our findings can be used to support health care professionals and quality agencies to improve patient care and safety in Canada.

Formation of 6H-Ba3Ce0.75Mn2.25O9 during Thermochemical Reduction of 12R-Ba4CeMn3O12: Identification of a Polytype in the Ba(Ce,Mn)O3 Family.

The resurgence of interest in a hydrogen economy and the development of hydrogen-related technologies has initiated numerous research and development efforts aimed at making the generation, storage, and transportation of hydrogen more efficient and affordable. Solar thermochemical hydrogen production (STCH) is a process that potentially exhibits numerous benefits such as high reaction efficiencies, tunable thermodynamics, and continued performance over extended cycling. Although CeO2 has been the de facto standard STCH material for many years, more recently 12R-Ba4CeMn3O12 (BCM) has demonstrated enhanced hydrogen production at intermediate H2/H2O conditions compared to CeO2, making it a contender for large-scale hydrogen production. However, the thermo-reduction stability of 12R-BCM dictates the oxygen partial pressure (pO2) and temperature conditions optimal for cycling. In this study, we identify the formation of a 6H-BCM polytype at high temperature and reducing conditions, experimentally and computationally, as a mechanism and pathway for 12R-BCM decomposition. 12R-BCM was synthesized with high purity and then controllably reduced using thermogravimetric analysis (TGA). Synchrotron X-ray diffraction (XRD) data is used to identify the formation of a 6H-Ba3Ce0.75Mn2.25O9 (6H-BCM) polytype that is formed at 1350 °C under strongly reducing pO2. Density functional theory (DFT) total energy and defect calculations show a window of thermodynamic stability for the 6H-polytype consistent with the XRD results. These data provide the first evidence of the 6H-BCM polytype and could provide a mechanistic explanation for the superior water-splitting behaviors of 12R-BCM.

A comprehensive study of a 29-capsid AAV library in a non-human primate central nervous system.

Non-human primates (NHPs) are a preferred animal model for optimizing adeno-associated virus (AAV)-mediated CNS gene delivery protocols before clinical trials. In spite of its inherent appeal, it is challenging to compare different serotypes, delivery routes, and disease indications in a well-powered, comprehensive, multigroup NHP experiment. Here, a multiplex barcode recombinant AAV (rAAV) vector-tracing strategy has been applied to a systemic analysis of 29 distinct, wild-type (WT), AAV natural isolates and engineered capsids in the CNS of eight macaques. The report describes distribution of each capsid in 15 areas of the macaques' CNS after intraparenchymal (putamen) injection, or cerebrospinal fluid (CSF)-mediated administration routes (intracisternal, intrathecal, or intracerebroventricular). To trace the vector biodistribution (viral DNA) and targeted tissues transduction (viral mRNA) of each capsid in each of the analyzed CNS areas, quantitative next-generation sequencing analysis, assisted by the digital-droplet PCR technology, was used. The report describes the most efficient AAV capsid variants targeting specific CNS areas after each route of administration using the direct side-by-side comparison of WT AAV isolates and a new generation of rationally designed capsids. The newly developed bioinformatics and visualization algorithms, applicable to the comparative analysis of several mammalian brain models, have been developed and made available in the public domain.

Considerations When Developing Blood-Brain Barrier Crossing Drug Delivery Technology.

Efficient therapeutic transport across the neurovasculature remains a challenge for developing medicine to treat central nervous system (CNS) disorders (Bell and Ehlers, Neuron 81:1-3, 2014). This chapter is meant to provide some insight and key considerations for developing and evaluating various technologies and approaches to CNS drug delivery. First, a brief review of various biological barriers, including the immune system, cellular and protein components of the blood-brain barrier (BBB), and clearance mechanisms in peripheral organs is provided. Next, a few examples and learnings from existing BBB-crossing modalities will be reviewed. Insight from "BBBomic" databases and thoughts on basic requirements for successful in vivo validation studies are discussed. Finally, an additional engineering barrier, namely manufacturing and product scalability, is highlighted as it relates to clinical translation and feasibility for developing BBB-crossing delivery technologies. A goal of this chapter is to provide an overview of the many barriers to the successful delivery of medicines into the brain. An emphasis will be placed on biotherapeutic and gene therapy applications for the treatment of neurological and neurodegenerative disorders.

G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress.

Cells limit energy-consuming mRNA translation during stress to maintain metabolic homeostasis. Sequestration of mRNAs by RNA binding proteins (RBPs) into RNA granules reduces their translation, but it remains unclear whether RBPs also function in partitioning of specific transcripts to polysomes (PSs) to guide selective translation and stress adaptation in cancer. To study transcript partitioning under cell stress, we catalogued mRNAs enriched in prostate carcinoma PC-3 cell PSs, as defined by polysome fractionation and RNA sequencing (RNAseq), and compared them to mRNAs complexed with the known SG-nucleator protein, G3BP1, as defined by spatially-restricted enzymatic tagging and RNAseq. By comparing these compartments before and after short-term arsenite-induced oxidative stress, we identified three major categories of transcripts, namely those that were G3BP1-associated and PS-depleted, G3BP1-dissociated and PS-enriched, and G3BP1-associated but also PS-enriched. Oxidative stress profoundly altered the partitioning of transcripts between these compartments. Under arsenite stress, G3BP1-associated and PS-depleted transcripts correlated with reduced expression of encoded mitochondrial proteins, PS-enriched transcripts that disassociated from G3BP1 encoded cell cycle and cytoprotective proteins whose expression increased, while transcripts that were both G3BP1-associated and PS-enriched encoded proteins involved in diverse stress response pathways. Therefore, G3BP1 guides transcript partitioning to reprogram mRNA translation and support stress adaptation.

Conservative Media Use and Childhood COVID-19 Vaccine Information: A Test of the Contradictory Health Information Processing Model.

The Contradictory Health Information Processing (CHIP) model explains individuals' processing of conflicting health claims. Tests of the model, while highly supportive, have been experimental and have relied upon low-familiar topics. Accordingly, a survey of parents with a child aged <12 years (N = 510) was conducted to test the application of the CHIP model to the controversial issue of childhood COVID-19 vaccination; such a vaccine had not yet been approved for this age group at the time of the survey. As hypothesized, reliance upon conservative news was associated with the perception that media information contradicted official guidance to vaccinate children, which led to issue uncertainty. Issue uncertainty prompted negative appraisals and decision uncertainty. Specifically, decision uncertainty partially mediated the effect of issue uncertainty on negative appraisals of vaccination, which in turn aroused threat emotions. However, threat emotions did not predict information-seeking, as specified in the model. This result may have been due to respondents having already decided to vaccinate their child, or not - a reflection of the partisan nature of the topic and the extensive coverage it had received. Theoretical and practical implications are discussed.

Patterns of myocardial injury in recovered troponin-positive COVID-19 patients assessed by cardiovascular magnetic resonance.

BACKGROUND: Troponin elevation is common in hospitalized COVID-19 patients, but underlying aetiologies are ill-defined. We used multi-parametric cardiovascular magnetic resonance (CMR) to assess myocardial injury in recovered COVID-19 patients. METHODS AND RESULTS: One hundred and forty-eight patients (64 ± 12 years, 70% male) with severe COVID-19 infection [all requiring hospital admission, 48 (32%) requiring ventilatory support] and troponin elevation discharged from six hospitals underwent convalescent CMR (including adenosine stress perfusion if indicated) at median 68 days. Left ventricular (LV) function was normal in 89% (ejection fraction 67% ± 11%). Late gadolinium enhancement and/or ischaemia was found in 54% (80/148). This comprised myocarditis-like scar in 26% (39/148), infarction and/or ischaemia in 22% (32/148) and dual pathology in 6% (9/148). Myocarditis-like injury was limited to three or less myocardial segments in 88% (35/40) of cases with no associated LV dysfunction; of these, 30% had active myocarditis. Myocardial infarction was found in 19% (28/148) and inducible ischaemia in 26% (20/76) of those undergoing stress perfusion (including 7 with both infarction and ischaemia). Of patients with ischaemic injury pattern, 66% (27/41) had no past history of coronary disease. There was no evidence of diffuse fibrosis or oedema in the remote myocardium (T1: COVID-19 patients 1033 ± 41 ms vs. matched controls 1028 ± 35 ms; T2: COVID-19 46 ± 3 ms vs. matched controls 47 ± 3 ms). CONCLUSIONS: During convalescence after severe COVID-19 infection with troponin elevation, myocarditis-like injury can be encountered, with limited extent and minimal functional consequence. In a proportion of patients, there is evidence of possible ongoing localized inflammation. A quarter of patients had ischaemic heart disease, of which two-thirds had no previous history. Whether these observed findings represent pre-existing clinically silent disease or de novo COVID-19-related changes remain undetermined. Diffuse oedema or fibrosis was not detected.

Correlation between body mass index and prostate volume in benign prostatic hyperplasia patients undergoing holmium enucleation of the prostate surgery.

BACKGROUND: Benign prostatic obstruction (BPO) due to benign prostatic hyperplasia (BPH) is a leading cause of morbidity in men over the age of 40. This study examined whether there was an association between body mass index (BMI) and pre-operative prostate volume and whether expression of two genes, alpha-2-macroglobulin (A2M) and transforming growth factor beta 3 (TGFB3), was correlated with BMI, pre-operative prostate volume, and age at surgery. METHODS: Medical records of patients who underwent holmium enucleation of the prostate surgery for treatment of BPO were retrospectively reviewed. Surgical specimens were obtained from formalin-fixed paraffin-embedded blocks, and expression of the targeted genes was quantified using a real time PCR approach. Linear regression analysis was performed to assess association between BMI and prostate volume adjusting for demographic characteristics and co-morbidity. Spearman's correlation was used to examine whether gene expression was correlated with BMI, prostate volume, and age at surgery. RESULTS: A total of 278 patients were identified, including 62.9% European Americans (n = 175) and 27.7% Hispanic Americans (n = 77). BMI was significantly correlated with prostate volume (Spearman's rho = 0.123, P = 0.045). In linear regression analysis, BMI was positively associated with prostate volume (ß = 0.01, P = 0.004), while hyperlipidemia was negatively associated with prostate volume (ß = -0.08, P = 0.02). A trend for a positive association was also observed for diabetes (ß = 0.07, P = 0.099). In the race/ethnicity stratified analysis, age at surgery showed a trend for significantly positive association with prostate volume in European Americans (ß = 0.005, P = 0.08), but not in Hispanic Americans. Expression of the A2M gene in the stroma was negatively correlated with age at surgery (P = 0.006). A2M expression in the gland was positively correlated with prostate volume among older men (Age ≥ 70, P = 0.01) and overweight men (BMI 25-30, P = 0.04). TGFB3 expression in the gland was positively correlated with BMI (P = 0.007) among older men. CONCLUSIONS: This study demonstrated the positive correlation between BMI and prostate volume. Expression of TGFB3 and A2M was correlated with BMI, prostate volume, and age at surgery.

Narratives of Prevention and Affliction in Type 2 Diabetes: Mechanisms of Influence in a Sample of Middle-aged Women.

Research suggests that readers identify more with a competent protagonist who acts to prevent diabetes than with a less competent protagonist whose inaction leads to disease. We sought a better understanding of the mediators of this protagonist competence effect. Middle-aged women (45-55) read a prevention narrative depicting a protagonist at risk for type 2 diabetes (T2D) who prevents diabetes through lifestyle changes or an affliction narrative in which protagonist inaction leads to disease (N = 315). The prevention narrative elicited more identification than the affliction narrative for participants at low risk of T2D, but less identification for higher risk participants. Identification's impact on intentions to adopt self-protective behaviors was partially mediated by self-referencing. Protagonist competence did not affect transportation, but transportation had a direct effect on behavioral intentions and an indirect effect on intentions mediated by self-referencing. Fear arousal predicted behavioral intentions and was highest among those who read the affliction narrative and rated self as at risk for T2D. Protagonist competence had an indirect effect on intentions mediated by attributions of trustworthiness in response to the affliction narrative. This study contributes to our understanding of how narratives work and underscores the importance of tailoring narratives to the risk profile of individuals.

When Media Health Stories Conflict: Test of the Contradictory Health Information Processing (CHIP) Model.

Guided by Uncertainty Management Theory, UMT, we tested a model that explicates how uncertainty arising from contradictory health information is managed through information seeking. In an online experiment, 763 U.S. adults were randomly assigned to one of three message conditions: contradictory, non-contradictory, or control. Participants in the contradictory and non-contradictory conditions answered questions about their perceptions of contradiction, issue and decision uncertainty, negative appraisals and emotions, and information-seeking intentions. They also completed measures of several moderator variables, including information overload, intolerance for uncertainty, and health self-efficacy. Baseline levels of issue and decision uncertainty were measured in the control condition. Model tenets were confirmed: perceptions of contradiction led to issue uncertainty which, in turn, prompted cognitive appraisals directly, and indirectly through increased decision uncertainty. The effects of issue and decision uncertainty on information-seeking intentions were mediated by negative appraisals and threat emotions. Individuals with high health self-efficacy and positive outcome expectations of information search were more likely to manage uncertainty through information seeking. These results support the use of the CHIP model when perceptions of contradiction and decision uncertainty need to be accounted for, while also validating UMT for its original purposes. Model refinements and implications are discussed.

From Network Positions to Language Use: Understanding the Effects of Brokerage and Closure Structures from a Linguistic Perspective.

We investigated cancer survivors' interactions on an online breast cancer support forum, focusing on how the network structures of brokerage and closure relate to the types of support received and to the language used in posts. Data came through the extraction of 1,443 forum members' online networks. Automated linguistic analysis was carried out on the 27,248 threads these survivors made and the 336,151 replies they received. Survivors' brokerage and closure levels were positively correlated with the use of positive affective words in their posts, a linguistic marker of well-being. Different network positions fostered different types of support in the community. Specifically, people bridging unconnected users (the broker role) were more likely to receive informational support whereas people in closely knit groups (the closure role) were more likely to receive emotional support. Theoretical, methodological, and practical implications are examined.

Alignment-free clustering of UMI tagged DNA molecules.

MOTIVATION: Next-Generation Sequencing has led to the availability of massive genomic datasets whose processing raises many challenges, including the handling of sequencing errors. This is especially pertinent in cancer genomics, e.g. for detecting low allele frequency variations from circulating tumor DNA. Barcode tagging of DNA molecules with unique molecular identifiers (UMI) attempts to mitigate sequencing errors; UMI tagged molecules are polymerase chain reaction (PCR) amplified, and the PCR copies of UMI tagged molecules are sequenced independently. However, the PCR and sequencing steps can generate errors in the sequenced reads that can be located in the barcode and/or the DNA sequence. Analyzing UMI tagged sequencing data requires an initial clustering step, with the aim of grouping reads sequenced from PCR duplicates of the same UMI tagged molecule into a single cluster, and the size of the current datasets requires this clustering process to be resource-efficient. RESULTS: We introduce Calib, a computational tool that clusters paired-end reads from UMI tagged sequencing experiments generated by substitution-error-dominant sequencing platforms such as Illumina. Calib clusters are defined as connected components of a graph whose edges are defined in terms of both barcode similarity and read sequence similarity. The graph is constructed efficiently using locality sensitive hashing and MinHashing techniques. Calib's default clustering parameters are optimized empirically, for different UMI and read lengths, using a simulation module that is packaged with Calib. Compared to other tools, Calib has the best accuracy on simulated data, while maintaining reasonable runtime and memory footprint. On a real dataset, Calib runs with far less resources than alignment-based methods, and its clusters reduce the number of tentative false positive in downstream variation calling. AVAILABILITY AND IMPLEMENTATION: Calib is implemented in C++ and its simulation module is implemented in Python. Calib is available at https://github.com/vpc-ccg/calib. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Acute cardiotoxicity associated with alemtuzumab infusion for multiple sclerosis.

Alemtuzumab infusion is rarely associated with serious cardiac toxicity. We report a case of acute troponin-negative chest pain with dynamic T-wave changes, immediately following first infusion of alemtuzumab in a patient with multiple sclerosis. The chest pain and ECG (electrocardiogram) changes improved with cessation of alemtuzumab and conservative management. The presumed cause was infusion-associated cytokine release, but the precise mechanism is unknown.