at home and 30.2% at work. However, there is no estimate of the economic burden of any kind from SHS exposure in India. This study used a prevalence-based attributable risk approach combined with a PSM technique to estimate excess healthcare utilization for SHS exposed non-smokers and the annual direct economic costs of SHS in India. Annual direct SHS-attributable costs in India is INR 566.7 billion (USD 8.7 billion) SHS costs constituted 0.33% of GDP and 8.1% of healthcare expenditures in India.

Previous studies have reported differing clinical outcomes among hospitalised heart failure (HF) patients admitted under cardiology and general medicine (GM) without consideration of patients’ frailty.

To explore outcomes in patients admitted under the two specialities after taking into account their frailty and other characteristics.

This retrospective-study included all HF patients ≥18 years admitted between 1 January, 2013-31 December 2019 at two Australian tertiary-hospitals. Frailty was determined by use of the Hospital-Frailty-Risk-Score (HFRS) and patients with HFRS ≥5 were classified as frail. Propensity-score-matching (PSM) was used to match 11 variables between the two specialities. The primary outcomes included the days-alive-and-out-of-hospital (DAOH90) at 90 days of discharge, 30-day mortality and readmissions.

Of 4913 HF patients, mean age 76.2 (14.1) years, 51% males, 2653 (54%) were admitted under cardiology compared to 2260 (46%) under GM. Patients admitted under GM were more likely to be older females, with a higher Charlson-index and poor renal function than those admitted under cardiology. Overall, 23.8% patients were frail and frail patients were more likely to be admitted under GM than cardiology (33.6% vs. 15.3%, P < 0.001). PSM created 1532 well-matched patients in each group. After PSM, the DAOH90 was not significantly different among patients admitted in GM when compared to cardiology (Coefficient -5.36, 95% CI -11.73-1.01, P = 0.099). Other clinical outcomes were also similar between the two specialities.

Clinical characteristics of HF patients differ between GM and cardiology, however, clinical outcomes were not significantly different after taking into account frailty and other variables.

Clinical characteristics of HF patients differ between GM and cardiology, however, clinical outcomes were not significantly different after taking into account frailty and other variables.

Ribociclib, a CDK4/6 inhibitor, demonstrates preclinical antitumor activity in combination with taxanes. We evaluated the safety and efficacy of ribociclib plus docetaxel in a phase Ib/II study in metastatic castration-resistant prostate cancer (mCRPC).

Patients had chemotherapy-naïve mCRPC with progression on ≥ 1 androgen receptor signaling inhibitor (ARSI). The phase II primary endpoint was 6-month radiographic progression-free survival (rPFS) rate, with an alternative hypothesis of 55% versus 35% historical control. Circulating tumor cells (CTC) were collected at baseline and genomically profiled.

Forty-three patients were enrolled (N = 30 in phase II). Two dose-limiting toxicities were observed (grade 4 neutropenia and febrile neutropenia). The recommended phase II dose (RP2D) and schedule was docetaxel 60 mg/m2 every 21 days plus ribociclib 400 mg/day on days 1-4 and 8-15 with filgrastim on days 5-7. At the RP2D, neutropenia was the most common grade ≥ 3 adverse event (37%); however, no cases of febrile neutropenia were observed. The primary endpoint was met; the 6-month rPFS rate was 65.8% [95% confidence interval (CI) 50.6%-85.5%; P = 0.005] and median rPFS was 8.1 months (95% CI, 6.0-10.0 months). Thirty-two percent of evaluable patients achieved a PSA50 response. Nonamplified MYC in baseline CTCs was associated with longer rPFS (P = 0.052).

The combination of intermittent ribociclib plus every-3-weeks docetaxel demonstrated acceptable toxicity and encouraging efficacy in ARSI-pretreated mCRPC. Genomic profiling of CTCs may enrich for those most likely to derive benefit. Further evaluation in a randomized clinical trial is warranted.

The combination of intermittent ribociclib plus every-3-weeks docetaxel demonstrated acceptable toxicity and encouraging efficacy in ARSI-pretreated mCRPC. Genomic profiling of CTCs may enrich for those most likely to derive benefit. Further evaluation in a randomized clinical trial is warranted.Crown roots (CRs) are major components of the rice root system. They form at the basal node of the shoot, and their development is greatly influenced by environmental factors. Ammonium nitrogen is known to impact plant root development through ammonium transporters (AMTs), but it remains unclear whether ammonium and AMTs play roles in rice CR formation. In this study, we revealed a significant role of ammonium, rather than nitrate, in regulating rice CR development. High ammonium supply increases CR formation but inhibits CR elongation. Genetic evidence showed that ammonium regulation of CR development relies on ammonium uptake mediated jointly by ammonium transporters OsAMT1;1, OsAMT1;2; OsAMT1;3, and OsAMT2;1, but not on root acidification which was the result of ammonium uptake. OsAMTs are also needed for glutamine-induced CR formation. Furthermore, we showed that polar auxin transport dependent on the PIN auxin efflux carriers acts downstream of ammonium uptake and assimilation to activate local auxin signaling at CR primordia, in turn promoting CR formation. Taken together, our results highlight a critical role for OsAMTs in cooperatively regulating CR formation through regulating auxin transport under nitrogen-rich conditions.

Racial and ethnic variations in attribution of cervical precancer and cancer to human papillomavirus (HPV) types may result in different HPV vaccine protection, screening test coverage, and clinical management.

Pooling data from 7 US studies, we calculated the proportional attribution of precancers and cancers to HPV types using HPV DNA typing from diagnosis. All statistical tests were 2-sided.

For all racial and ethnic groups, most cases of cervical intraepithelial neoplasia grade 3 (CIN3) (84.2%-90.8% of 5526) and squamous cell carcinoma (SCC) (90.4%-93.8% of 1138) were attributed to types targeted by the 9-valent vaccine. A higher proportion of CIN3s were attributed to nonvaccine HPV types among non-Hispanic Black women (15.8%) compared with non-Hispanic Asian or Pacific Islander (9.7%; P = .002), non-Hispanic White (9.2%; P < .001), and Hispanic (11.3%; P = .004) women. The proportion of SCCs attributed to 9-valent types was similar by race and ethnicity (P = .80). A higher proportion of CIN3s weof CIN3s and SCCs, with greater potential impact for CIN3s among Black women. HPV screening tests target high-risk HPV types, including HPV35. Future genotyping triage strategies could consider the importance of HPV35- and other HPV16-related types.Carbon and water are two main factors limiting leaf expansion. Restriction of leaf growth by low availability of carbon or water is among the earliest visible effects of potassium (K) deficiency. It is not known how K is involved in regulating the rhythmic supply of these two substrates, which differ remarkably across the day-night cycle, affecting leaf expansion. We investigated the effects of different K regimes on the time courses of leaf expansion, carbon assimilation, carbohydrates, and hydraulic properties of Brassica napus. Potassium supply increased leaf area, predominantly by promoting night-time leaf expansion (>60%), which was mainly associated with increased availability of carbohydrates from photosynthetic carbon fixation and import from old leaves rather than improvement of leaf hydraulics. However, sufficient K improved leaf hydraulic conductance to balance diurnal evaporative water loss and increase the osmotic contribution of water-soluble carbohydrates, thereby maintaining leaf turgor and increasing the daytime expansion rate. The results also indicated an ontogenetic role of K in modifying the amplitude of circadian expansion; almost 80% of the increase in leaf area occurred before the area reached 66.9% of the mature size. Our data provide mechanistic insight into K-mediated diel coordination of rhythmic carbon supply and water balance in leaf expansion.

Residues of polar pesticides cannot be determined by QuEChERS-based multiresidue extractions because of their non-amenability to reverse-phase chromatographic separation and poor recoveries. On the other hand, single-residue methods pose limitations because of the various requirements of sample preparation and LC-MS/MS conditions. A new multiresidue method is thus warranted for rapid and simultaneous analysis of polar pesticides.

The study developed a multiresidue method for the simultaneous analysis of glyphosate and its metabolite (aminomethylphosphonic acid, AMPA), glufosinate and its metabolites (3-methylphosphinicopropionic acid and N-acetyl-glufosinate), ethephon, fosetyl-aluminum and its metabolite (phosphonic acid), and trimesium in grape and pomegranate by LC-MS/MS.

The homogenized samples (10 g) were extracted with acidified methanol (20 mL). An aliquot of the extract was diluted with acetonitrile (1 + 1) and measured by LC-MS/MS using a Torus DEA column. The performance of a hydrophilic interth the SANTE/12682/2019 validation guidelines and EU-MRLs, the method can be recommended for regulatory testing purposes.

A high-throughput residue analysis method targeting nine polar and ionic compounds in grape and pomegranate involved a single multiresidue extraction, followed by direct analysis using LC-MS/MS. A satisfactory method performance was achieved through intra- and inter-laboratory validation. The method sensitivity met the EU-MRLs and the SANTE/12682/2019 analytical quality control criteria.

A high-throughput residue analysis method targeting nine polar and ionic compounds in grape and pomegranate involved a single multiresidue extraction, followed by direct analysis using LC-MS/MS. A satisfactory method performance was achieved through intra- and inter-laboratory validation. The method sensitivity met the EU-MRLs and the SANTE/12682/2019 analytical quality control criteria.

Grandparents are key resources in grandchildren care globally. However, mixed findings indicated that multiple role engagement may enhance well-being and bring demands on grandparent caregivers in different contexts. This systematic review examines the association between the intensity of grandparent caregiving and their health and well-being (i.e., physical, mental, cognitive, and life satisfaction) by continent and country/region.

Systematic searches were conducted in four databases. Peer-reviewed articles with quantitative designs published between 1990 and November 2021 were identified. A rigorous selection process was followed using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The studies were critically appraised, and their results were narratively synthesized.

Sixty-five articles from 29 countries/regions were included. Findings suggested a concave curvilinear relationship between the intensity of grandparent caregiving and their health and well-being, with tcknowledging the bidirectional relationship between well-being and grandparents’ capacity for providing care, the well-being as outcome is a limitation. Despite so, this systematic review calls for culturally-tailored family programs to support grandparent caregiving.

Metformin hydrochloride is the first-choice antihyperglycemic agent and its several fixed-dose combinations (FDCs) with pioglitazone hydrochloride, sitagliptin phosphate, and gliclazide are used for the management of type II diabetes. Numerous reversed-phase HPLC (RP-HPLC) and HPTLC methods have been reported for estimation of FDCs of metformin but each FDC needs separate and dedicated chromatographic conditions for analysis. No RP-HPLC method has been reported yet which promotes synchronous estimation of FDC products of metformin to save time, resources, cost, and organic solvent for analysis.

Hence, an economical and eco-friendly RP-HPLC method was developed for the synchronous estimation of FDCs of metformin hydrochloride using an enhanced analytical quality by design (AQbD) approach.

The AQbD approach was implemented using analytical-failure modes critical effects analysis (FMCEA) as per International council for harmonisation (ICH) Q8 and Q9 guidelines. The analytical-FMCEA was applied by identificultiple combined pharmaceutical dosage forms of metformin hydrochloride. The method was developed by the implementation of the AFMCEA-based AQbD approach as per the regulatory requirements of ICH.

The multipurpose RP-HPLC method has been developed and validated for the synchronous estimation of multiple combined pharmaceutical dosage forms of metformin hydrochloride. The method was developed by the implementation of the AFMCEA-based AQbD approach as per the regulatory requirements of ICH.Significant improvements in genome sequencing and assembly technology have led to increasing numbers of high-quality genomes, revealing complex evolutionary scenarios such as multiple whole-genome duplication events, which hinders ancestral genome reconstruction via the currently available computational frameworks. Here, we present the Inferring Ancestor Genome Structure (IAGS) framework, a novel block/endpoint matching optimization strategy with single-cut-or-join distance, to allow ancestral genome reconstruction under both simple (single-copy ancestor) and complex (multicopy ancestor) scenarios. We evaluated IAGS with two simulated data sets and applied it to four different real evolutionary scenarios to demonstrate its performance and general applicability. IAGS is available at https//github.com/xjtu-omics/IAGS.The mechanisms that coordinate cellular gene expression are highly complex and intricately interconnected. Thus, it is necessary to move beyond a fully reductionist approach to understanding genetic information flow and begin focusing on the networked connections between genes that organize cellular function. Continued advancements in computational hardware, coupled with the development of gene correlation network algorithms, provide the capacity to study networked interactions between genes rather than their isolated functions. For example, gene coexpression networks are used to construct gene relationship networks using linear metrics such as Spearman or Pearson correlation. Recently, there have been tools designed to deepen these analyses by differentiating between intrinsic vs extrinsic noise within gene expression values, identifying different modules based on tissue phenotype, and capturing potential nonlinear relationships. In this report, we introduce an algorithm with a novel application of image-based segmentation modalities utilizing blob detection techniques applied for detecting bigenic edges in a gene expression matrix. We applied this algorithm called EdgeCrafting to a bulk RNA-sequencing gene expression matrix comprised of a healthy kidney and cancerous kidney data. We then compared EdgeCrafting against 4 other RNA expression analysis techniques Weighted Gene Correlation Network Analysis, Knowledge Independent Network Construction, NetExtractor, and Differential gene expression analysis.Assessing central carbon metabolism in plants can be challenging due to the dynamic range in pool sizes, with low levels of important phosphorylated sugars relative to more abundant sugars and organic acids. Here, we report a sensitive liquid chromatography-mass spectrometry (LC-MS) method for analyzing central metabolites on a hybrid column, where both anion-exchange and hydrophilic interaction chromatography (HILIC) ligands are embedded in the stationary phase. The LC method was developed for enhanced selectivity of 27 central metabolites in a single run with sensitivity at femtomole levels observed for most phosphorylated sugars. The method resolved phosphorylated hexose, pentose, and triose isomers that are otherwise challenging. Compared to a standard HILIC approach, these metabolites had improved peak areas using our approach due to ion-enhancement or low ion-suppression in the biological sample matrix. The approach was applied to investigate metabolism in high lipid-producing tobacco leaves that exhibited increased levels of the acetyl-CoA, a precursor for oil biosynthesis. The application of the method to isotopologue detection and quantification was considered through evaluating 13C-labeled seeds from Camelina sativa. The method provides a means to analyze intermediates more comprehensively in central metabolism of plant tissues.The combination of chemotherapy and immune therapies still promises to synergize for prolonged tumor control. However, the quest for optimal combinations tailored for tumor histology remains ongoing. A recent study provides evidence on the feasibility of the trabectedin/durvalumab combination and reports on interesting preliminary efficacy. See related article by Toulmonde et al., p. 1765.Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software have proven to be successful in designing and modifying proteins, they can also be overly sensitive to small conformational differences between structures of the same protein. To cope with this, we introduce here pyFoldX, a python library that allows the integrative analysis of structures of the same protein using FoldX, an established forcefield and modeling software. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module, and an easy integration with the data analysis ecosystem of the python programming language.

pyFoldX rely on the FoldX software for energy calculations and modelling, which can be downloaded upon registration in http//foldxsuite.crg.eu/ and its licence is free of charge for academics. The pyFoldX library is open-source. Full details on installation, tutorials covering the library functionality, and the scripts used to generate the data and figures presented in this paper are available at https//github.com/leandroradusky/pyFoldX.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.Acoustic emission analysis is promising to investigate the physiological events leading to drought-induced injury and mortality. However, their nature and source are not fully understood, making this technique difficult to use as a direct measure of the loss of xylem hydraulic conductance. Acoustic emissions were recorded during severe dehydration in lavender plants (Lavandula angustifolia) and compared with the dynamics of embolism development and cell damage. The timing and characteristics of acoustic signals from two independent recording systems were compared by principal component analysis (PCA). Changes in water potential, branch diameter, loss of hydraulic conductance, and cellular damage were also measured to quantify drought-induced damages. Two distinct phases of acoustic emissions were observed during dehydration the first one associated with a rapid loss of diameter and a significant increase in loss of xylem conductance (90%), and the second with slower changes in diameter and a significant increase in cellular damage. Based on PCA, a developed algorithm discriminated hydraulic-related acoustic signals from other sources, proposing a reconstruction of hydraulic vulnerability curves. Cellular damage preceded by hydraulic failure seems to lead to a lack of recovery. The second acoustic phase would allow detection of plant mortality.The ubiquitin-proteasome system is associated with various phenomena including learning and memory. In this study, we report that E3 ubiquitin ligase homologs and proteasome function are involved in taste avoidance learning, a type of associative learning between starvation and salt concentrations, in Caenorhabditis elegans. Pharmacological inhibition of proteasome function using bortezomib causes severe defects in taste avoidance learning. Among 9 HECT-type ubiquitin ligase genes, loss-of-function mutations of 6 ubiquitin ligase genes cause significant abnormalities in taste avoidance learning. Double mutations of those genes cause lethality or enhanced defects in taste avoidance learning, suggesting that the HECT-type ubiquitin ligases act in multiple pathways in the processes of learning. Furthermore, mutations of the ubiquitin ligase genes cause additive effects on taste avoidance learning defects of the insulin-like signaling mutants. Our findings unveil the consequences of aberrant functions of the proteasome and ubiquitin systems in learning behavior of Caenorhabditis elegans.

Protein-protein interactions (PPIs) play a key role in diverse biological processes but only a small subset of the interactions have been experimentally identified. Additionally, high-throughput experimental techniques that detect PPIs are known to suffer various limitations such as exaggerated false positives and negatives rates. The semantic similarity derived from the Gene Ontology (GO) annotation is regarded as one of the most powerful indicators for protein interactions. However, while computational approaches for prediction of PPIs have gained popularity in recent years, most methods fail to capture the specificity of GO terms.

We propose TransformerGO, a model that is capable of capturing the semantic similarity between gene ontology sets dynamically using an attention mechanism. We generate dense graph embeddings for GO terms using an algorithmic framework for learning continuous representations of nodes in networks called node2vec. TransformerGO learns deep semantic relations between annotated terms and can distinguish between negative and positive interactions with high accuracy. TransformerGO outperforms classic semantic similarity measures on gold standard PPI datasets and state-of-the-art machine learning-based approaches on large datasets from S. cerevisiae and H. sapiens. We show how the neural attention mechanism embedded in the transformer architecture detects relevant functional terms when predicting interactions.

https//github.com/Ieremie/TransformerGO.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

Inferring an accurate gene regulatory network (GRN) has long been a key goal in the field of systems biology. In order to do this, it is important to find a suitable balance between the maximum number of true positive and the minimum number of false positive interactions. Another key feature is that the inference method can handle the large size of modern experimental data, meaning the method needs to be both fast and accurate. The LSCO (Least Squares Cut-Off) method can fulfill both these criteria, however as it is based on least squares it is vulnerable to known issues of amplifying extreme values, small or large. In GRN this manifests itself with genes that are erroneously hyper-connected to a large fraction of all genes due to extremely low value fold changes.

We developed a GRN inference method called LSCON (Least Squares Cut-Off with Normalization) that tackles this problem. LSCON extends the LSCO algorithm by regularization to avoid hyper-connected genes and thereby reduce false positives. The regularization employed is based on normalization, which removes effects of extreme values on the fit. We benchmarked LSCON and compared it to Genie3, LASSO, LSCO, and Ridge regression, in terms of accuracy, speed, and tendency to predict hyper-connected genes. The results show that LSCON achieves better or equal accuracy compared to LASSO, the best existing method, especially for data with extreme values. Thanks to the speed of least squares regression, LSCON does this an order of magnitude faster than LASSO.

Data https//bitbucket.org/sonnhammergrni/lscon; Code https//bitbucket.org/sonnhammergrni/genespider.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

Testing safety of Delta24-RGD (DNX-2401), an oncolytic adenovirus, locally delivered by convection enhanced delivery (CED) in tumor and surrounding brain of patients with recurrent glioblastoma.

Dose-escalation phase I study with 3+3 cohorts, dosing 107 to 1 × 1011 viral particles (vp) in 20 patients. Besides clinical parameters, adverse events, and radiologic findings, blood, cerebrospinal fluid (CSF), brain interstitial fluid, and excreta were sampled over time and analyzed for presence of immune response, viral replication, distribution, and shedding.

Of 20 enrolled patients, 19 received the oncolytic adenovirus Delta24-RGD, which was found to be safe and feasible. Four patients demonstrated tumor response on MRI, one with complete regression and still alive after 8 years. Most serious adverse events were attributed to increased intracranial pressure caused by either an inflammatory reaction responding to steroid treatment or viral meningitis being transient and self-limiting. Often viral DNA concentrations in CSF increased over time, peaking after 2 to 4 weeks and remaining up to 3 months. Concomitantly Th1- and Th2-associated cytokine levels and numbers of CD3+ T and natural killer cells increased. Posttreatment tumor specimens revealed increased numbers of macrophages and CD4+ and CD8+ T cells. No evidence of viral shedding in excreta was observed.

CED of Delta24-RGD not only in the tumor but also in surrounding brain is safe, induces a local inflammatory reaction, and shows promising clinical responses.

CED of Delta24-RGD not only in the tumor but also in surrounding brain is safe, induces a local inflammatory reaction, and shows promising clinical responses.

Correctly annotating individual cell’s type is an important initial step in single cell RNA sequencing (scRNA-seq) data analysis. Here, we present NeuCA web server, a neural network-based scRNA-seq cell annotation tool with web-app portal and graphical user interface, for automatically assigning cell labels. NeuCA algorithm is accurate and exhaustive, maximizing the usage of measured cells for downstream analysis. NeuCA web server provides over 20 ready-to-use pre-trained classifiers for commonly used tissue types. As the first web-app tool with neural-network infrastructure implemented, NeuCA web will facilitate the research community in analyzing and annotating scRNA-seq data.

NeuCA web server is implemented with R Shiny application online at https//statbioinfo.shinyapps.io/NeuCA/.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.T-cell receptors (TCR) recognize intracellular and extracellular cancer antigens, allowing T cells to target many tumor antigens. To sustain proliferation and persistence, T cells require not only signaling through the TCR (signal 1), but also costimulatory (signal 2) and cytokine (signal 3) signaling. Because most cancer cells lack costimulatory molecules, TCR engagement at the tumor site results in incomplete T-cell activation and transient antitumor effects. To overcome this lack of signal 2, we genetically modified tumor-specific T cells with a costimulatory chimeric antigen receptor (CoCAR). Like classical CARs, CoCARs combine the antigen-binding domain of an antibody with costimulatory endodomains to trigger T-cell proliferation, but CoCARs lack the cytotoxic CD3ζ chain to avoid toxicity to normal tissues. We first tested a CD19-targeting CoCAR in combination with an HLA-A*0201-restricted, survivin-specific transgenic TCR (sTCR) in serial cocultures with leukemia cells coexpressing the cognate peptide-HLA complex (signal 1) and CD19 (signal 2). The CoCAR enabled sTCR+ T cells to kill tumors over a median of four additional tumor challenges. CoCAR activity depended on CD19 but was maintained in tumors with heterogeneous CD19 expression. In a murine tumor model, sTCR+CoCAR+ T cells improved tumor control and prolonged survival compared with sTCR+ T cells. We further evaluated the CoCAR in Epstein-Barr virus-specific T cells (EBVST). CoCAR-expressing EBVSTs expanded more rapidly than nontransduced EBVSTs and delayed tumor progression in an EBV+ murine lymphoma model. Overall, we demonstrated that the CoCAR can increase the activity of T cells expressing both native and transgenic TCRs and enhance antitumor responses.

The detection of somatic mutations in genes of myeloid cells in asymptomatic patients – defining clonal hematopoiesis of indeterminate potential (CHIP) – predisposes to cardiovascular events (CVE) in the general population. We aimed to determine whether CHIP was associated with CVE in SLE patients.

The study is an ancillary study of the randomized, double-blind, placebo-controlled, multicenter trial PLUS study conducted from June 2007 through August 2010 at 37 centers in France involving 573 SLE patients. The search for somatic mutations by high-throughput sequencing of 53 genes involved in clonal hematopoiesis was performed on genomic DNA collected at PLUS inclusion. The CHIP prevalence was assessed in SLE and in a retrospective cohort of 479 patients free of hematological malignancy. The primary outcome was the incident CVE in SLE.

Screening for CHIP was performed in 438 SLE patients (38 [29-47] years, 91·8% female). Overall, 63 somatic mutations were identified in 47 patients defining a CHIP prevalence of 10·7% in SLE. Most SLE patients (78·7%) carried a single mutation. Most variants (62·5%) were located in the DNMT3A gene. CHIP was associated with age, age at SLE diagnosis and a lower frequency of antiphospholipid antibodies. CHIP occurred more than 20-years earlier (p < 0·00001) in SLE than in controls. The detection of CHIP at inclusion was not associated with the occurrence of CVE during follow up (HR = 0·42 (0·06 – 3·21), p = 0·406).

The prevalence of CHIP is high in SLE with respect to age but was not associated with incident CVE.

ClinicalTrials.gov, https//clinicaltrials.gov, NCT05146414.

ClinicalTrials.gov, https//clinicaltrials.gov, NCT05146414.In this issue of Blood Cancer Discovery, Umeda and colleagues identify and comprehensively analyze a novel recurrent UBTF mutation (tandem duplications) in pediatric acute myeloid leukemia. Acute myeloid leukemia cases with UBTF tandem duplications display distinctive biologic features, including association with FLT3-ITD and WT1 mutations and high-risk disease, and appear to represent a new genetic subtype of acute myeloid leukemia. See related article by Umeda et al., p. 194 (7).Translation is essential for megakaryocyte (MK) maturation and platelet production. However, how the translational pathways are regulated in this process remains unknown. In this study, we found that MK/platelet-specific lactate dehydrogenase A (LdhA) knockout mice exhibited an increased number of platelets with remarkably accelerated MK maturation and proplatelet formation. Interestingly, the role of LDHA in MK maturation and platelet formation did not depend on lactate content, which was the major product of LDHA. Mechanism studies revealed that LDHA interacted with eukaryotic elongation factor 2 (eEF2) in the cytoplasm, controlling the participation of eEF2 in translation at the ribosome. Furthermore, the interaction of LDHA and eEF2 was dependent on nicotinamide adenine dinucleotide (NADH), a coenzyme of LDHA. NADH-competitive inhibitors of LDHA could release eEF2 from the LDHA pool, upregulate translation, and enhance MK maturation in vitro. Among LDHA inhibitors, stiripentol significantly promoted the production of platelets in vivo under a physiological state and in the immune thrombocytopenia model. Moreover, stiripentol could promote platelet production from human cord blood mononuclear cell-derived MKs and also have a superposed effect with romiplostim. In short, this study shows a novel nonclassical function of LDHA in translation that may serve as a potential target for thrombocytopenia therapy.

Emerging single-cell RNA sequencing (scRNA-seq) technology empowers biological research at cellular level. One of the most crucial scRNA-seq data analyses is clustering single cells into subpopulations. However, the high variability, high sparsity, and high dimensionality of scRNA-seq data pose lots of challenges for clustering analysis. Although many single-cell clustering methods have been recently developed, few of them fully exploit latent relationship among cells, thus leading to suboptimal clustering results.

Here, we propose a novel unsupervised clustering method, scGAC (single-cell Graph Attentional Clustering), for scRNA-seq data. scGAC firstly constructs a cell graph and refines it by network denoising. Then it learns clustering-friendly representation of cells through a graph attentional autoencoder, which propagates information across cells with different weights and captures latent relationship among cells. Finally, scGAC adopts a self-optimizing method to obtain the cell clusters. Experiments on 16 real scRNA-seq datasets show that scGAC achieves excellent performance and outperforms existing state-of-art single-cell clustering methods.

Python implementation of scGAC is available at Github (https//github.com/Joye9285/scGAC) and Figshare (https//figshare.com/articles/software/scGAC/19091348).

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.The genetics of relapsed pediatric acute myeloid leukemia (AML) has yet to be comprehensively defined. Here, we present the spectrum of genomic alterations in 136 relapsed pediatric AMLs. We identified recurrent exon 13 tandem duplications (TD) in upstream binding transcription factor (UBTF) in 9% of relapsed AML cases. UBTF-TD AMLs commonly have normal karyotype or trisomy 8 with cooccurring WT1 mutations or FLT3-ITD but not other known oncogenic fusions. These UBTF-TD events are stable during disease progression and are present in the founding clone. In addition, we observed that UBTF-TD AMLs account for approximately 4% of all de novo pediatric AMLs, are less common in adults, and are associated with poor outcomes and MRD positivity. Expression of UBTF-TD in primary hematopoietic cells is sufficient to enhance serial clonogenic activity and to drive a similar transcriptional program to UBTF-TD AMLs. Collectively, these clinical, genomic, and functional data establish UBTF-TD as a new recurrent mutation in AML.

We defined the spectrum of mutations in relapsed pediatric AML and identified UBTF-TDs as a new recurrent genetic alteration. These duplications are more common in children and define a group of AMLs with intermediate-risk cytogenetic abnormalities, FLT3-ITD and WT1 alterations, and are associated with poor outcomes. See related commentary by Hasserjian and Nardi, p. 173. This article is highlighted in the In This Issue feature, p. 171.

We defined the spectrum of mutations in relapsed pediatric AML and identified UBTF-TDs as a new recurrent genetic alteration. These duplications are more common in children and define a group of AMLs with intermediate-risk cytogenetic abnormalities, FLT3-ITD and WT1 alterations, and are associated with poor outcomes. See related commentary by Hasserjian and Nardi, p. 173. This article is highlighted in the In This Issue feature, p. 171.

CALGB/SWOG 80405 was a randomized phase III trial in first-line patients with metastatic colorectal cancer treated with bevacizumab, cetuximab, or both, plus chemotherapy. We tested the effect of tumor immune features on overall survival (OS).

Primary tumors (N = 554) were profiled by RNA sequencing. Immune signatures of macrophages, lymphocytes, TGFβ, IFNγ, wound healing, and cytotoxicity were measured. CIBERSORTx scores of naive and memory B cells, plasma cells, CD8+ T cells, resting and activated memory CD4+ T cells, M0 and M2 macrophages, and activated mast cells were measured.

Increased M2 macrophage score [HR, 6.30; 95% confidence interval (CI), 3.0-12.15] and TGFβ signature expression (HR, 1.35; 95% CI, 1.05-1.77) were associated with shorter OS. Increased scores of plasma cells (HR, 0.55; 95% CI, 0.38-0.87) and activated memory CD4+ T cells (HR, 0.34; 95% CI, 0.16-0.65) were associated with longer OS. Using optimal cutoffs from these four features, patients were categorized as having either 4, 3, 2, or 0-1 beneficial features associated with longer OS, and the median (95% CI) OS decreased from 42.5 (35.8-47.8) to 31.0 (28.8-34.4), 25.2 (20.6-27.9), and 17.7 (13.5-20.4) months respectively (P = 3.48e-11).

New immune features can be further evaluated to improve patient response. They provide the rationale for more effective immunotherapy strategies.

New immune features can be further evaluated to improve patient response. They provide the rationale for more effective immunotherapy strategies.

Polypharmacy is the combined use of drugs for the treatment of diseases. However, it often shows a high risk of side effects. Due to unnecessary interactions of combined drugs, the side effects of polypharmacy increase the risk of disease and even lead to death. Thus, obtaining abundant and comprehensive information on the side effects of polypharmacy is a vital task in the healthcare industry. Early traditional methods employed machine learning techniques to predict side effects. However, they often make costly efforts to extract features of drugs for prediction. Later, several methods based on knowledge graphs are proposed. They are reported to outperform traditional methods. However, they still show limited performance by failing to model complex relations of side effects among drugs.

To resolve the above problems, we propose a novel model by further incorporating complex relations of side effects into knowledge graph embeddings. Our model can translate and transmit multidirectional semantics with fewer parameters, leading to better scalability in large-scale knowledge graphs. Experimental evaluation shows that our model outperforms state-of-the-art models in terms of the average area under the ROC and precision-recall curves.

Code and data are available at https//github.com/galaxysunwen/MSTE-master.

Code and data are available at https//github.com/galaxysunwen/MSTE-master.

We determined the efficacy of self-administered subcutaneous mini-dose glucagon (MDG) to treat fasting-induced hypoglycemia in type 1 diabetes (T1D).

This was a 4-week randomized, controlled crossover trial of 2-week MDG or 2-week oral glucose tablets (OG, control) involving 17 adults with T1D during Ramadan.

Compared with OG, MDG demonstrated a significant higher change in blood glucose from baseline to 30 min (Δt30, P < 0.001) and 1 h (Δt60, P = 0.02). The efficacy of MDG was preserved following ≥8 h fasting with significantly higher Δt30 in MDG (P = 0.01). Over the entire 2 weeks, MDG period had increased time in 70-180 mg/dL (P = 0.009) and less time <70 mg/dL (P = 0.04). MDG use resulted in higher completion of fasts compared with OG (P < 0.001).

MDG administration is an effective alternative to OG for prevention and treatment of fasting-induced hypoglycemia, offering improved glycemic control and promoting successful completion of prolonged fasts.

MDG administration is an effective alternative to OG for prevention and treatment of fasting-induced hypoglycemia, offering improved glycemic control and promoting successful completion of prolonged fasts.

Nailfold videocapillaroscopy (NVC) plays a well-established role in differentiating primary from secondary Raynaud’s phenomenon due to systemic sclerosis (SSc). However, the association of NVC with novel severe organ involvement/progression in SSc has never been evaluated in a multicentre, multinational study, which we now perform for the first time.

Follow-up data from 334 SSc patients (265 women; 18 LSSc/203 LcSSc/113 DcSSc) registered between November 2008 and January 2016 by seven tertiary centres in the EUSTAR-database, were analysed. Novel severe organ involvement/progression was defined as new/progressive involvement of the peripheral vasculature, lungs, heart, skin, gastrointestinal tract, kidneys, musculoskeletal system, or death, at 12- or 24-month follow-up. NVC images at enrolment were quantitatively and qualitatively evaluated according to the standardised definitions of the EULAR Study Group on Microcirculation in Rheumatic Diseases. Uni- and multivariable logistic regression modelling (ULR,spite the participation of tertiary centres, which follow their patients in a standardised way, we were underpowered to detect associations with infrequent severe organ involvement/progression.

Cross-sectional analyses of primary cancer genomes have identified regions of recurrent somatic copy-number alteration, many of which result from positive selection during cancer formation and contain driver genes. However, no effective approach exists for identifying genomic loci under significantly different degrees of selection in cancers of different subtypes, anatomic sites, or disease stages.

CNGPLD is a new tool for performing case-control somatic copy-number analysis that facilitates the discovery of differentially amplified or deleted copy-number aberrations in a case group of cancer compared to a control group of cancer. This tool uses a Gaussian process statistical framework in order to account for the covariance structure of copy-number data along genomic coordinates and to control the false discovery rate at the region level.

CNGPLD is freely available at https//bitbucket.org/djhshih/cngpld as an R package.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

RNA-binding proteins (RBPs) play crucial roles in post-transcriptional regulation. Accurate identification of RBPs helps understand gene expression, regulation, etc. In recent years, some computational methods were proposed to identify RBPs. However, these methods fail to accurately identify RBPs from some specific species with limited data, such as bacteria.

In this study, we introduce a computational method called PreRBP-TL for identifying species-specific RBPs based on transfer learning. The weights of the prediction model were initialized by pre-training with the large general RBP dataset and then fine-tuned with the small species-specific RPB dataset by using transfer learning. The experimental results show that the PreRBP-TL achieves better performance for identifying the species-specific RBPs from Human, Arabidopsis, Escherichia coli, and Salmonella, outperforming eight state-of-the-art computational methods. It is anticipated PreRBP-TL will become a useful method for identifying RBPs.

For the convenience of researchers to identify RBPs, the web server of PreRBP-TL was established, freely available at http//bliulab.net/PreRBP-TL.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.DNA methylation signatures in tumors could serve as reliable biomarkers that are accessible in archival tissues for tracking the epigenetic dynamics shaped by both cancer cells and the tumor microenvironment. However, given the ultrahigh dimensionality and noncollapsible nature of the data, it remains challenging to screen all CpG sites to identify the most promising marker panels. In this article, we introduce the concept of tumor-based expression quantitative trait methylation (eQTM) for the prioritization and systematic mining of predictive biomarkers. In melanoma as a disease model, eQTM CpGs and genes represent new and efficient candidate targets to be investigated for both prognostic and immune status monitoring purposes. Three cis-eQTM CpGs (cg07786657, cg12446199, and cg00027570) were strongly associated with and can serve as surrogate biomarkers for the tumor immune cytolytic activity score (CYT). In addition, multiple eQTM genes could be further exploited for predicting immunoregulatory phenotypes. A targeted gene panel analysis identified one eQTM in TCF7 (cg25947408) as a novel candidate biomarker for uncoupling overall T-cell differentiation and exhaustion status in a tumor. The prognostic significance of this eQTM as an independent signature to CYT was validated by both The Cancer Genome Atlas and Moffitt melanoma cohort data. Overall, eQTMs represent a mechanistically distinct class of potential biomarkers that can be used to predict patient prognosis and immune status.

This study provides a novel and promising approach to identify targeted epigenetic biomarkers in cancer and will spur further analysis in tumor immune phenotyping.

This study provides a novel and promising approach to identify targeted epigenetic biomarkers in cancer and will spur further analysis in tumor immune phenotyping.Inactivating mutations of von Hippel-Lindau (VHL) are highly prevalent in clear cell renal cell carcinoma (ccRCC). Improved understanding of the vulnerabilities of VHL-deficient ccRCC could lead to improved treatment strategies. The activity of DNA dioxygenase ten-eleven translocation (TET)2 is significantly reduced in multiple cancers by different mechanisms, but its role in ccRCC progression remains unclear. Here, we report that increased expression of TET2, but not TET1 and TET3, is negatively associated with tumor metastasis and advanced tumor stage and is positively associated with good prognosis uniquely in ccRCC among all 33 types of cancer in The Cancer Genome Atlas datasets. TET2 restrained glycolysis and pentose phosphate pathway metabolism in a VHL deficiency-dependent manner, thereby suppressing ccRCC progression. Notably, TET2 and VHL mutations tended to cooccur in ccRCC, providing genetic evidence that they cooperate to inhibit the progression of ccRCC. Mechanistically, TET2 was recruited by traC.Iron porphyrins are synthesized by systematically introducing electron withdrawing groups (EWGs) on pyrroles to evaluate the relationship between rate (k) and overpotential (η). The results indicate that while EWGs lead to a rise in the thermodynamic FeIII/II reduction potential (E0), the potential of the O2 reduction reaction (ORR) does not scale with E0. More importantly, the iron porphyrins with higher E0 show an order of magnitude higher rate of ORR than unsubstituted iron tetraphenyl porphyrin. This contests the scaling relationship often offered to predict rates of ORR by iron porphyrins based on their E0. Mechanistic investigations reveal that the rate-determining step (rds) of ORR change between these iron porphyrins with EWG’s, as the pKa and E0 of several key intermediate species likely change on altering the macrocycle. These results suggest that linear dependence of log(rate) on E0 or η may only be valid for complexes where the rds of ORR remains the same.Helicobacter pylori colonizes half of the global population and causes gastritis, peptic ulcer disease or gastric cancer. In this study, we were interested in human annexin (ANX), which comprises a protein family with diverse and partly unknown physiological functions, but with a potential role in microbial infections and possible involvement in gastric cancer. We demonstrate here for the first time that H. pylori is able to specifically bind ANXs. Binding studies with purified H. pylori LPS and specific H. pylori LPS mutant strains indicated binding of ANXA5 to lipid A, which was dependent on the lipid A phosphorylation status. Remarkably, ANXA5 binding almost completely inhibited LPS-mediated Toll-like receptor 4- (TLR4) signaling in a TLR4-specific reporter cell line. Furthermore, the interaction is relevant for gastric colonization, as a mouse-adapted H. pylori increased its ANXA5 binding capacity after gastric passage and its ANXA5 incubation in vitro interfered with TLR4 signaling. Moreover, both ANXA2 and ANXA5 levels were upregulated in H. pylori-infected human gastric tissue, and H. pylori can be found in close association with ANXs in the human stomach. Furthermore, an inhibitory effect of ANXA5 binding for CagA translocation could be confirmed. Taken together, our results highlight an adaptive ability of H. pylori to interact with the host cell factor ANX potentially dampening innate immune recognition.The continuous emergence of severe acute respiratory coronavirus 2 (SARS-CoV-2) variants and the increasing number of breakthrough infection cases among vaccinated people support the urgent need for research and development of antiviral drugs. Viral entry is an intriguing target for antiviral drug development. We found that diltiazem, a blocker of the L-type calcium channel Cav1.2 pore-forming subunit (Cav1.2 α1c) and an FDA-approved drug, inhibits the binding and internalization of SARS-CoV-2, and decreases SARS-CoV-2 infection in cells and mouse lung. Cav1.2 α1c interacts with SARS-CoV-2 spike protein and ACE2, and affects the attachment and internalization of SARS-CoV-2. Our finding suggests that diltiazem has potential as a drug against SARS-CoV-2 infection and that Cav1.2 α1c is a promising target for antiviral drug development for COVID-19.Clostridioides difficile infection (CDI) is the leading cause of nosocomial diarrhea and pseudomembranous colitis in the USA. In addition to these symptoms, patients with CDI can develop severe inflammation and tissue damage, resulting in life-threatening toxic megacolon. CDI is mediated by two large homologous protein toxins, TcdA and TcdB, that bind and hijack receptors to enter host cells where they use glucosyltransferase (GT) enzymes to inactivate Rho family GTPases. GT-dependent intoxication elicits cytopathic changes, cytokine production, and apoptosis. At higher concentrations TcdB induces GT-independent necrosis in cells and tissue by stimulating production of reactive oxygen species via recruitment of the NADPH oxidase complex. Although GT-independent necrosis has been observed in vitro, the relevance of this mechanism during CDI has remained an outstanding question in the field. In this study we generated novel C. difficile toxin mutants in the hypervirulent BI/NAP1/PCR-ribotype 027 R20291 strain to test the hypothesis that GT-independent epithelial damage occurs during CDI. Using the mouse model of CDI, we observed that epithelial damage occurs through a GT-independent process that does not involve immune cell influx. The GT-activity of either toxin was sufficient to cause severe edema and inflammation, yet GT activity of both toxins was necessary to produce severe watery diarrhea. These results demonstrate that both TcdA and TcdB contribute to disease pathogenesis when present. Further, while inactivating GT activity of C. difficile toxins may suppress diarrhea and deleterious GT-dependent immune responses, the potential of severe GT-independent epithelial damage merits consideration when developing toxin-based therapeutics against CDI.