Antibacterial and Antibiofilm Activity of Croton urticifolius Lam. Essential Oil Via Membrane Disruption.

Antimicrobial resistance is a global health issue, in which microorganisms develop resistance to antimicrobial drugs, making infections more difficult to treat. This threatens the effectiveness of standard medical treatments and necessitates the urgent development of new strategies to combat resistant microbes. Studies have increasingly explored natural sources of new antimicrobial agents that harness the rich diversity of compounds found in plant species. This pursuit holds promise for the discovery of novel treatments for combating antimicrobial resistance. In this context, the chemical composition, antibacterial, and antibiofilm activities of the essential oil from Croton urticifolius Lam. leaves (CuEO) were evaluated. CuEO was extracted via hydrodistillation, and its chemical constituents were identified via gas chromatography-mass spectrometry (GC/MS). The antibacterial activity of CuEO was evaluated in a 96-well plate via the microdilution method, and the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values were determined. The effect of CuEO on biofilm formation was assessed by quantifying the biomass using crystal violet staining and viable cell counting. In addition, alterations in the cellular morphology of biofilms treated with CuEO were examined using scanning electron microscopy (SEM) and laser confocal microscopy. GC/MS analysis identified 26 compounds, with elemicine (39.72%); eucalyptol (19.03%), E-caryophyllene (5.36%), and methyleugenol (4.12%) as the major compounds. In terms of antibacterial activity, CuEO showed bacteriostatic effects against Staphylococcus aureus ATCC 700698, S. aureus ATCC 25923, Staphylococcus epidermidis ATCC 12228, and Escherichia coli ATCC 11303, and bactericidal activity against S. aureus ATCC 700698. In addition, CuEO significantly inhibited bacterial biofilm formation. Microscopic analysis showed that CuEO damaged the bacterial membrane by leaching out the cytoplasmic content. Therefore, the results of this study show that the essential oil of C. urticifolius may be a promising natural alternative for preventing infections caused by bacterial biofilms. This study is the first to report the antibiofilm activity of C. urticifolius essential oil.

Sex-dependent adipose glucose partitioning by the mitochondrial pyruvate carrier.

Objective: The mitochondrial pyruvate carrier (MPC) occupies a critical node in intermediary metabolism, prompting interest in its utility as a therapeutic target for the treatment of obesity and cardiometabolic disease. Dysregulated nutrient metabolism in adipose tissue is a prominent feature of obesity pathophysiology, yet the functional role of adipose MPC has not been explored. We investigated whether the MPC shapes the adaptation of adipose tissue to dietary stress in female and male mice. Methods: The impact of pharmacological and genetic disruption of the MPC on mitochondrial pathways of triglyceride assembly (lipogenesis and glyceroneogenesis) was assessed in 3T3L1 adipocytes and murine adipose explants, combined with analyses of adipose MPC expression in metabolically compromised humans. Whole-body and adipose-specific glucose metabolism were subsequently investigated in male and female mice lacking adipocyte MPC1 (Mpc1AD-/-) and fed either standard chow, high-fat western style, or high-sucrose lipid restricted diets for 24 weeks, using a combination of radiolabeled tracers and GC/MS metabolomics. Results: Treatment with UK5099 or siMPC1 impaired the synthesis of lipids and glycerol-3-phosphate from pyruvate and blunted triglyceride accumulation in 3T3L1 adipocytes, whilst MPC expression in human adipose tissue was negatively correlated with indices of whole-body and adipose tissue metabolic dysfunction. Mature adipose explants from Mpc1AD-/- mice were intrinsically incapable of incorporating pyruvate into triglycerides. In vivo, MPC deletion restricted the incorporation of circulating glucose into adipose triglycerides, but only in female mice fed a zero fat diet, and this associated with sex-specific reductions in tricarboxylic acid cycle pool sizes and compensatory transcriptional changes in lipogenic and glycerol metabolism pathways. However, whole-body adiposity and metabolic health were preserved in Mpc1AD-/- mice regardless of sex, even under conditions of zero dietary fat. Conclusion: These findings highlight the greater capacity for mitochondrially driven triglyceride assembly in adipose from female versus male mice and expose a reliance upon MPC-gated metabolism for glucose partitioning in female adipose under conditions of dietary lipid restriction.

Implementation of the Fast-track Protocol for Total Hip Arthroplasty in a Public Hospital in the State of São Paulo - Brazil.

Objective Evaluate the results of the implementation of the Fast Track Protocol (FTP), a medical practice based on scientific evidence, for elective total hip arthroplasty surgery, mainly comparing the National Average Hospital Admission Rate of 7.1 days. Methods 98 patients who underwent elective total hip arthroplasty surgery via the direct anterior approach, anterolateral approach and posterior approach were included in the FTP from December 2018 to March 2020, being followed up preoperatively, intraoperatively and immediately postoperatively. Results The average length of hospital stay was 2.8 days, being 2.1 days for the direct anterior approach, 3.0 days for the anterolateral access approach and 4.1 days for the posterior access approach. The average surgery time was 90 minutes, 19 (19.39%) of the patients were referred to the ICU in the postoperative period, however, none of them underwent surgery using the direct anterior approach. We had no cases of deep vein thrombosis (DVT), pulmonary embolism (PTE) or neurological injury, 19 (19.39%) patients had postoperative bleeding requiring dressing change, 4 (4.08%) needed blood transfusion, 2 (2.04%) patients had implant instability, 1 (1.02%) patient had a fracture during surgery and 1 (1.02%) patient died of cardiac complications. Conclusion FTP may be a viable alternative to reduce the length of stay and immediate postoperative complications for elective total hip arthroplasty surgery decreasing the length of stay of patients by 2 to 3 times when compared to the national average of 7.1 days.

Kinin B1 receptor modulates glucose homeostasis and physical exercise capacity by altering adrenal catecholamine synthesis and secretion.

Our group has shown in several papers that kinin B1 receptor (B1R) is involved in metabolic adaptations, mediating glucose homeostasis and interfering in leptin and insulin signaling. Since catecholamines are involved with metabolism management, we sought to evaluate B1R role in catecholamine synthesis/secretion. Using B1R global knockout mice, we observed increased basal epinephrine content, accompanied by decreased hepatic glycogen content and increased glucosuria. When these mice were challenged with maximal intensity exercise, they showed decreased epinephrine and norepinephrine response, accompanied by disturbed glycemic responses to effort and poor performance. This phenotype was related to alterations in adrenal catecholamine synthesis: increased basal epinephrine concentration and reduced norepinephrine content in response to exercise, as well decreased gene expression and protein content of tyrosine hydroxylase and decreased gene expression of dopamine beta hydroxylase and kinin B2 receptor. We conclude that the global absence of B1R impairs catecholamine synthesis, interfering with glucose metabolism at rest and during maximal exercise.

Kinin B1 receptor controls maternal adiponectin levels and influences offspring weight gain.

Given the importance of the kinin B1 receptor in insulin and leptin hormonal regulation, which in turn is crucial in maternal adaptations to ensure nutrient supply to the fetus, we investigated the role of this receptor in maternal metabolism and fetoplacental development. Wild-type and kinin B1 receptor-deficient (B1KO) female mice were mated with male mice of the opposite genotype. Consequently, the entire litter was heterozygous for kinin B1 receptor, ensuring that there would be no influence of offspring genotype on the maternal phenotype. Maternal kinin B1 receptor blockade reduces adiponectin secretion by adipose tissue ex vivo, consistent with lower adiponectin levels in pregnant B1KO mice. Furthermore, fasting insulinemia also increased, which was associated with placental insulin resistance, reduced placental glycogen accumulation, and heavier offspring. Therefore, we propose the combination of chronic hyperinsulinemia and reduced adiponectin secretion in B1KO female mice create a maternal obesogenic environment that results in heavier pups.

Drug resistance prediction for Mycobacterium tuberculosis with reference graphs.

Tuberculosis is a global pandemic disease with a rising burden of antimicrobial resistance. As a result, the World Health Organization (WHO) has a goal of enabling universal access to drug susceptibility testing (DST). Given the slowness of and infrastructure requirements for phenotypic DST, whole-genome sequencing, followed by genotype-based prediction of DST, now provides a route to achieving this. Since a central component of genotypic DST is to detect the presence of any known resistance-causing mutations, a natural approach is to use a reference graph that allows encoding of known variation. We have developed DrPRG (Drug resistance Prediction with Reference Graphs) using the bacterial reference graph method Pandora. First, we outline the construction of a Mycobacterium tuberculosis drug resistance reference graph. The graph is built from a global dataset of isolates with varying drug susceptibility profiles, thus capturing common and rare resistance- and susceptible-associated haplotypes. We benchmark DrPRG against the existing graph-based tool Mykrobe and the haplotype-based approach of TBProfiler using 44 709 and 138 publicly available Illumina and Nanopore samples with associated phenotypes. We find that DrPRG has significantly improved sensitivity and specificity for some drugs compared to these tools, with no significant decreases. It uses significantly less computational memory than both tools, and provides significantly faster runtimes, except when runtime is compared to Mykrobe with Nanopore data. We discover and discuss novel insights into resistance-conferring variation for M. tuberculosis - including deletion of genes katG and pncA - and suggest mutations that may warrant reclassification as associated with resistance.

Antimicrobial Activity the Essential Oil from Croton pluriglandulosus Carn. Leaves against Microorganisms of Clinical Interest.

Multiresistant pathogens pose a serious threat to human health. The genus Candida is one class of human pathogenic yeasts responsible for infections affecting healthy and immunocompromised patients. In this context, plant essential oils emerged as a future natural alternative to control the diseases caused by these pathogens. Based on that, the present study aimed to evaluate the antimicrobial potential of essential oil from C. pluriglandulosus and understand the mechanism of action. Here, it highlighted antimicrobial activity and the mechanisms of action of the essential oil extracted from C. pluriglandulosus Carn.-Torres & Riina (CpEO) leaves on human pathogenic microorganisms in planktonic and biofilm lifestyles. In addition, for the first time, the oil composition was revealed by GC-MS analysis and the toxicity to human red blood cells (HRBC). Twenty-six chemical compounds were identified in CpEO, elemicin, bicyclogermacrene, caryophyllene, brevifolin, and 2,4,6-trimethoxy-styrene. Through hemolytic assay, it was shown that CpEO has no toxicity to human RBCs. At the concentration of 50 µg mL-1, CpEO did not show great antibacterial potential. However, promising data were found for C. krusei and C. parapsilosis inhibiting by 89.3% and 80.7% of planktonic cell growth and 83.5% and 77.9% the biofilm formation, respectively. Furthermore, the mechanisms of action CpEO were elucidated by fluorescence. Scanning electron microscopy revealed damage to the cell membrane and pore formation, ROS overproduction, and induction of apoptosis in candida cells. Our results reinforce the potential of CpEO as an effective alternative molecule of pharmaceutical interest.

NDB-UFES: An oral cancer and leukoplakia dataset composed of histopathological images and patient data.

The gold standard for the diagnosis of oral cancer is the microscopic analysis of specimens removed preferentially through incisional biopsies of oral mucosa with a clinically detected suspicious lesion. This dataset contains captured histopathological images of oral squamous cell carcinoma and leukoplakia. A total of 237 images were captured, 89 leukoplakia with dysplasia images, 57 leukoplakia without dysplasia images and 91 carcinoma images. The images were captured with an optical light microscope, using 10x and 40x objectives, attached to a microscope camera and visualized through a software. The images were saved in PNG format at 2048 × 1536 size pixels and they refer to hematoxylin-eosin stained histopathologic slides from biopsies performed between 2010 and 2021 in patients managed at the Oral Diagnosis project (NDB) of the Federal University of Espírito Santo (UFES). Oral leukoplakias were represented by samples with and without epithelial dysplasia. Since the diagnosis considers socio-demographic data (gender, age and skin color) as well as clinical data (tobacco use, alcohol consumption, sun exposure, fundamental lesion, type of biopsy, lesion color, lesion surface and lesion diagnosis), this information was also collected. So, our aim by releasing this dataset NDB-UFES is to provide a new dataset to be used by researchers in Artificial Intelligence (machine and deep learning) to develop tools to assist clinicians and pathologists in the automated diagnosis of oral potentially malignant disorders and oral squamous cell carcinoma.

Subacute high-refined carbohydrate diet leads to abnormal reproductive control of the hypothalamic-pituitary axis in female rats.

We previously reported that female rats placed on a diet containing refined carbohydrates (HCD) resulted in obesity and reproductive abnormalities, such as high serum LH concentration and abnormal ovarian function. However, the impacts at the hypothalamic-pituitary (HP) function, specifically regarding pathways linked to reproductive axis modulation are unknown. In this study, we assessed whether subacute feeding with HCD results in abnormal reproductive control in the HP axis. Female rats were fed with HCD for 15 days and reproductive HP axis morphophysiology was assessed. HCD reduced hypothalamic mRNA expression (Kiss1, Lepr, and Amhr2) and increased pituitary LHß+ cells. These changes likely contribute to the increase in serum LH concentration observed in HCD. Blunted estrogen negative feedback was observed in HCD, with increased kisspeptin protein expression in the arcuate nucleus of the hypothalamus (ARH), lower LHß+ cells and LH concentration in ovariectomized (OVX)+HCD rats. Thus, these data suggest that HCD feeding led to female abnormal reproductive control of HP axis.

Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.

Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections makes it effectively impossible to search these data using tools such as BLAST and its successors. Here, we present a technique called phylogenetic compression, which uses evolutionary history to guide compression and efficiently search large collections of microbial genomes using existing algorithms and data structures. We show that, when applied to modern diverse collections approaching millions of genomes, lossless phylogenetic compression improves the compression ratios of assemblies, de Bruijn graphs, and k-mer indexes by one to two orders of magnitude. Additionally, we develop a pipeline for a BLAST-like search over these phylogeny-compressed reference data, and demonstrate it can align genes, plasmids, or entire sequencing experiments against all sequenced bacteria until 2019 on ordinary desktop computers within a few hours. Phylogenetic compression has broad applications in computational biology and may provide a fundamental design principle for future genomics infrastructure.

GPR160 is not a receptor of anorexigenic cocaine- and amphetamine-regulated transcript peptide.

Cocaine- and amphetamine-regulated transcript peptide (CARTp) is an anorexigenic neuropeptide whose receptor is undisclosed. Previously, we reported the specific binding of CART(61-102) to pheochromocytoma PC12 cells, where CART(61-102) affinity and the number of binding sites per cell corresponded to ligand-receptor binding. Recently, Yosten et al. designated orphan GPR160 as the CARTp receptor, because the GPR160 antibody abolished neuropathic pain and anorexigenic effects induced by CART(55-102) and exogenous CART(55-102) coimmunoprecipitated with GPR160 in KATOIII cells. As no direct evidence that CARTp is a ligand for GPR160 has been described, we decided to verify this hypothesis by testing CARTp affinity to the GPR160 receptor. We investigated the GPR160 expression in PC12 cells since it is cell line known to specifically bind CARTp. Moreover, we examined the specific CARTp binding in THP1 cells, with high endogenous GPR160 expression and GPR160-transfected cell lines U2OS and U-251 MG. In PC12 cells, the GPR160 antibody did not compete for specific binding with 125I-CART(61-102) or with 125I-CART(55-102), and GPR160 mRNA expression and GPR160 immunoreactivity were not detected. Moreover, THP1 cells did not show any 125I-CART(61-102) or 125I-CART(55-102) specific binding despite GPR160 detection by fluorescent immunocytochemistry (ICC). Finally, no 125I-CART(61-102) or 125I-CART(55-102) specific binding in the GPR160-transfected cell lines U2OS and U-251 MG, selected due to their negligible endogenous expression of GPR160, was detected, despite the detection of GPR160 by fluorescent ICC. Our binding studies clearly demonstrated that GPR160 cannot be a receptor for CARTp. Further studies are needed to identify true CARTp receptors.

Smoking induces increased apoptosis in osteoblasts: changes in bone matrix organic components.

Clinical studies demonstrate the impact of smoking on bone tissue fragility and higher incidence of fractures. However, it is not totally understood which physiological mechanisms could be involved in these events. Previously, we showed important changes in bone tissue components in experimental model of cigarette smoke (CS) exposure. CS exposure induces worsening in bone mineralization and a decrease in collagen type I deposition, leading to bone fragility. Considering that the majority of clinical studies described bone structural changes by radiographic images, in this study we performed analyses "in situ" using tissue samples from smokers, former smokers and non-smokers to better understand how the increase in inflammatory mediators induced by smoking exposure could interfere in bone cells activity leading bone structural changes. We observed increased levels of IL-1ß, IL-6 and TNF-α in bone tissue homogenates with a concomitant increase in osteoblast apoptosis in smokers and former smokers compared with non-smokers. Histological changes in both smokers and former smokers were characterized by reduction in collagen type I. Only in smokers, it was observed decrease in trabecular area, suggesting increased bone resorption and increase in collagen type V. These results showed that osteoblasts apoptosis in association with increased bone resorption leads bone structural changes in smokers.

Assessment of Gualaxo do Norte River water quality (Minas Gerais, Brazil) affected by the dam breach of Fundão utilizing exploratory multivariate techniques.

At the end of 2015, the Fundão dam belonging to the Samarco S.A. mining company was ruptured, releasing a flood of mud into the Gualaxo do Norte River, which advanced into the Doce River. The aim of the present study was to apply exploratory multivariate approaches to water quality data obtained during sampling campaigns at the Gualaxo do Norte River during the dry and rainy seasons, between July 2016 and June 2017. A total of 27 locations along the river were sampled, covering unaffected areas and regions influenced by the tailings waste from the dam. Determinations of chemical, physical, and microbiological water quality parameters were performed. Application of principal component analysis (PCA) resulted in the first two components together explaining 39.49% and 37.91% of the total variance for the dry and rainy season data, respectively. In both cases, the PCA groups were related to variables such as turbidity and total solids, which both presented higher values in regions affected by the mud flow. These results are in agreement with those obtained by the Kohonen neural network method, where two-dimensional maps confirmed the samples according to the affected and unaffected area by the disaster.

Essential Oil from Croton blanchetianus Leaves: Anticandidal Potential and Mechanisms of Action.

Antimicrobial drugs are becoming ineffective given the resistance acquired by microorganisms. As such, it is imperative to seek new antimicrobial molecules that could provide a basis for the development of new drugs. Therefore, this work aimed to evaluate the antimicrobial potential and the mechanisms of action of the essential oil extracted from leaves of Croton blanchetianus (named CbEO) on different fungi and bacteria of clinical importance in both planktonic and biofilm lifestyles. GC-MS/MS analysis revealed the presence of twenty-two different compounds in the CbEO, which were identified using the Kovats retention index. Among these, the most abundant were amorphene (20.03%), spathulenol (5%), bicyclogermacrene (1.49%), caryophyllene oxide (4.55%), and eucalyptol (5.62%). CbOE (50 µg mL-1) barely inhibited the growth of Bacillus subtilis (23%), Pseudomonas aeruginosa (27%), and Salmonella enterica (28%), and no inhibition was obtained against Enterobacter aerogenes and Klebsiella pneumoniae. Additionally, no activity against bacterial biofilm was detected. In contrast, CbEO was active against Candida species. C. albicans and C. parapsilosis were inhibited by 78 and 75%, respectively. The antibiofilm potential also was favorable against C. albicans and C. parapsilosis, inhibiting 44 and 74% of biofilm formation and reducing around 41 and 27% of the preformed biofilm, respectively. CbOE caused membrane damage and pore formation, overproduction of ROS, and apoptosis on C. albicans and C. parapsilosis cells, as well as not inducing hemolysis in human red cells. The results obtained in this work raise the possibility of using the essential oil of C. blanchetianus leaves as an alternative to fight infections caused by C. albicans and C. parapsilosis.

Kinin B1 receptor modulates mitochondrial activity responsivity in fasting and voluntary exercise.

The Kallikrein-Kinin System (KKS) plays an important role in energy metabolism. We have previously described the importance of the kinin B1 receptor (B1R) in metabolism regulation. Considering that the liver manages the different energy demands of different body tissues, we combined two stressful conditions - fasting and voluntary exercise - to address how B1R may affect liver metabolism, focusing on mitochondrial function. AIMS: To investigate how the kinin B1 receptor (B1R) modulates mitochondrial activity under stress conditions, focusing on the rate of energy expenditure and shift in metabolism. MAIN METHODS: Wild-type and B1R-knockout (B1KO) male mice remained in a calorimetric cage with a wheel for 7 days; 48 h before euthanasia, half of the animals from both groups were submitted to fasting conditions. Mitochondrial activity, ketone bodies, and gene expression involving mitochondrial activity were evaluated. KEY FINDINGS: B1R modulates the mitochondrial activity under fasting and voluntary exercise, reducing the VO2 expenditure and HEAT. B1KO animals who exercised and underwent fasting did not have increased glucose levels, suggesting a preference for lipids as an energy source. Moreover, these animals displayed RER around 0.8, which indicates a ß-oxidation increment. Interestingly, the lack of B1R did not induce mitochondrial activity and biogenesis, suggesting interference in metabolism responsivity, a condition modulated by sirtuins under PGC-1α control. SIGNIFICANCE: B1R modulates mitochondrial respiratory control ratios, which suggests metabolic suppression, influencing hepatic metabolism and, consequently, energy homeostasis.

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes.

There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).

Top-down projections of the prefrontal cortex to the ventral tegmental area, laterodorsal tegmental nucleus, and median raphe nucleus.

Anatomical and functional evidence suggests that the PFC is fairly unique among all cortical regions, as it not only receives input from, but also robustly projects back to mesopontine monoaminergic and cholinergic cell groups. Thus, the PFC is in position to exert a powerful top-down control over several state-setting modulatory transmitter systems that are critically involved in the domains of arousal, motivation, reward/aversion, working memory, mood regulation, and stress processing. Regarding this scenario, the origin of cortical afferents to the ventral tegmental area (VTA), laterodorsal tegmental nucleus (LDTg), and median raphe nucleus (MnR) was here compared in rats, using the retrograde tracer cholera toxin subunit b (CTb). CTb injections into VTA, LDTg, or MnR produced retrograde labeling in the cortical mantle, which was mostly confined to frontal polar, medial, orbital, and lateral PFC subdivisions, along with anterior- and mid-cingulate areas. Remarkably, in all of the three groups, retrograde labeling was densest in layer V pyramidal neurons of the infralimbic, prelimbic, medial/ventral orbital and frontal polar cortex. Moreover, a lambda-shaped region around the apex of the rostral pole of the nucleus accumbens stood out as heavily labeled, mainly after injections into the lateral VTA and LDTg. In general, retrograde PFC labeling was strongest following injections into MnR and weakest following injections into VTA. Altogether, our findings reveal a fairly similar set of prefrontal afferents to VTA, LDTg, and MnR, further supporting an eminent functional role of the PFC as a controller of major state-setting mesopontine modulatory transmitter systems.

CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS.

MOTIVATION: Genome-wide association studies (GWAS), aiming to find genetic variants associated with a trait, have widely been used on bacteria to identify genetic determinants of drug resistance or hypervirulence. Recent bacterial GWAS methods usually rely on k-mers, whose presence in a genome can denote variants ranging from single-nucleotide polymorphisms to mobile genetic elements. This approach does not require a reference genome, making it easier to account for accessory genes. However, a same gene can exist in slightly different versions across different strains, leading to diluted effects. RESULTS: Here, we overcome this issue by testing covariates built from closed connected subgraphs (CCSs) of the de Bruijn graph defined over genomic k-mers. These covariates capture polymorphic genes as a single entity, improving k-mer-based GWAS both in terms of power and interpretability. However, a method naively testing all possible subgraphs would be powerless due to multiple testing corrections, and the mere exploration of these subgraphs would quickly become computationally intractable. The concept of testable hypothesis has successfully been used to address both problems in similar contexts. We leverage this concept to test all CCSs by proposing a novel enumeration scheme for these objects which fully exploits the pruning opportunity offered by testability, resulting in drastic improvements in computational efficiency. Our method integrates with existing visual tools to facilitate interpretation. AVAILABILITY AND IMPLEMENTATION: We provide an implementation of our method, as well as code to reproduce all results at https://github.com/HectorRDB/Caldera_ISMB. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines.

Answer ALS is a biological and clinical resource of patient-derived, induced pluripotent stem (iPS) cell lines, multi-omic data derived from iPS neurons and longitudinal clinical and smartphone data from over 1,000 patients with ALS. This resource provides population-level biological and clinical data that may be employed to identify clinical-molecular-biochemical subtypes of amyotrophic lateral sclerosis (ALS). A unique smartphone-based system was employed to collect deep clinical data, including fine motor activity, speech, breathing and linguistics/cognition. The iPS spinal neurons were blood derived from each patient and these cells underwent multi-omic analytics including whole-genome sequencing, RNA transcriptomics, ATAC-sequencing and proteomics. The intent of these data is for the generation of integrated clinical and biological signatures using bioinformatics, statistics and computational biology to establish patterns that may lead to a better understanding of the underlying mechanisms of disease, including subgroup identification. A web portal for open-source sharing of all data was developed for widespread community-based data analytics.