ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry

Gas chromatography–mass spectrometry (GC–MS) acquisitions routinely yield hundreds to thousands of Electron Ionization (EI) mass spectra. The chemical identification of these spectra typically involves a search protocol that seeks an exact match to a reference spectrum. Reference spectra are found in comprehensive libraries of small molecule EI spectra curated by commercial and public entities. We developed ARISTO (Automatic Reduction of Ion Spectra To Ontology), a webtool, which provides information regarding the general chemical nature of the compound underlying an input EI mass spectrum. Importantly, ARISTO can provide such annotation without necessitating an exact match to a specific compound. ARISTO provides assignments to a subset of the ChEBI (Chemical Entities of Biological Interest) dictionary, an ontology, which aims to cover biologically relevant small molecules. Our system takes as input a mass spectrum represented as a series of mass and intensity pairs; the system returns a graphical representation of the supported ontology as well as a detailed table of suggested annotations along with their associated statistical evidence. ARISTO is accessible at this URL: http://www.ionspectra.org/aristo. The system is free, open to all and does not require registration of any sort

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in a cellular environment. Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental evidence. We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative-molecular interaction standards. In this manuscript, we introduce these two algorithms and provide community access to the tool suite, describe examples of how these tools are useful to selectively present molecular interaction data and demonstrate a case where the algorithms were successfully used to identify a systematic error in an existing dataset

ClanTox: a classifier of short animal toxins

Toxins are detected in sporadic species along the evolutionary tree of the animal kingdom. Venomous animals include scorpions, snakes, bees, wasps, frogs and numerous animals living in the sea such as the stonefish, snail, jellyfish, hydra and more. Interestingly, proteins that share a common scaffold with animal toxins also exist in non-venomous species. However, due to their short length and primary sequence diversity, these, toxin-like proteins remain undetected by classical search engines and genome annotation tools. We construct a toxin classification machine and web server called ClanTox (Classifier of Animal Toxins) that is based on the extraction of sequence-driven features from the primary protein sequence followed by the application of a classification system trained on known animal toxins. For a given input list of sequences, from venomous or non-venomous settings, the ClanTox system predicts whether each sequence is toxin-like. ClanTox provides a ranked list of positively predicted candidates according to statistical confidence. For each protein, additional information is presented including the presence of a signal peptide, the number of cysteine residues and the associated functional annotations. ClanTox is a discovery-prediction tool for a relatively overlooked niche of toxin-like cell modulators, many of which are therapeutic agent candidates. The ClanTox web server is freely accessible at http://www.clantox.cs.huji.ac.il

Programs and processes for advancing pediatric acute kidney support therapy in hospitalized and critically ill children: A report from the 26th Acute Disease Quality Initiative (ADQI) consensus conference

Pediatric acute kidney support therapy (paKST) programs aim to reliably provide safe, effective, and timely extracorporeal supportive care for acutely and critically ill pediatric patients with acute kidney injury (AKI), fluid and electrolyte derangements, and/or toxin accumulation with a goal of improving both hospital-based and lifelong outcomes. Little is known about optimal ways to configure paKST teams and programs, pediatric-specific aspects of delivering high-quality paKST, strategies for transitioning from acute continuous modes of paKST to facilitate rehabilitation, or providing effective short- and long-term follow-up. As part of the 26th Acute Disease Quality Initiative Conference, the first to focus on a pediatric population, we summarize here the current state of knowledge in paKST programs and technology, identify key knowledge gaps in the field, and propose a framework for current best practices and future research in paKST

A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes

Motivation: Animal toxins operate by binding to receptors and ion channels. These proteins are short and vary in sequence, structure and function. Sporadic discoveries have also revealed endogenous toxin-like proteins in non-venomous organisms. Viral proteins are the largest group of quickly evolving proteomes. We tested the hypothesis that toxin-like proteins exist in viruses and that they act to modulate functions of their hosts

Pediatric Health-Related Quality of Life: Feasibility, Reliability and Validity of the PedsQL™ Transplant Module

The measurement properties of the newly developed Pediatric Quality of Life Inventory™ (PedsQL™) 3.0 Transplant Module in pediatric solid organ transplant recipients were evaluated. Participants included pediatric recipients of liver, kidney, heart and small bowel transplantation who were cared for at seven medical centers across the United States and their parents. Three hundred and thirty-eight parents of children ages 2–18 and 274 children ages 5–18 completed both the PedsQL™ 4.0 Generic Core Scales and the Transplant Module. Findings suggest that child self-report and parent proxy-report scales on the Transplant Module demonstrated excellent reliability (total scale score for child self-report α= 0.93; total scale score for parent proxy-report α= 0.94). Transplant-specific symptoms or problems were significantly correlated with lower generic HRQOL, supporting construct validity. Children with solid organ transplants and their parents reported statistically significant lower generic HRQOL than healthy children. Parent and child reports showed moderate to good agreement across the scales. In conclusion, the PedsQL™ Transplant Module demonstrated excellent initial feasibility, reliability and construct validity in pediatric patients with solid organ transplants.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79306/1/j.1600-6143.2010.03149.x.pd

Acute Kidney Injury in Neonatal Encephalopathy: An Evaluation of the AWAKEN Database

Background: Acute kidney injury (AKI) is common in neonatal encephalopathy (NE) and is associated with worse outcomes. Our objectives were to determine the incidence, risk factors, and outcomes of AKI in infants with NE. Methods: We performed a retrospective analysis of infants ≥ 34 weeks' gestational age with a diagnosis of NE from the Analysis of Worldwide Acute Kidney injury Epidemiology in Neonates (AWAKEN) database. AKI was defined using the modified Kidney Disease Improving Global Outcomes criteria. Perinatal and postnatal factors were evaluated. Multivariate logistic and linear regressions were performed. Results: One hundred and thirteen patients with NE were included. 41.6% (47) developed AKI. Being born outside the admitting institution (OR 4.3; 95% CI 1.2-14.8; p = 0.02), intrauterine growth restriction (OR 10.3, 95% CI 1.1-100.5; p = 0.04), and meconium at delivery (OR 2.8, 95% CI 1.04-7.7; p = 0.04) conferred increased odds of AKI. After controlling for confounders, infants with AKI stayed in the hospital an average of 8.5 days longer than infants without AKI (95% CI 0.79-16.2 days; p = 0.03). Conclusions: In this multi-national analysis, several important perinatal factors were associated with AKI and infants with both NE and AKI had longer length of stay than NE alone. Future research aimed at early AKI detection, renoprotective management strategies, and understanding the long-term renal consequences is warranted in this high-risk group of patients

Acute kidney injury in critically Ill children and young adults with suspected SARS-CoV2 infection

This article is made available for unrestricted research re-use and secondary analysis in any form or be any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Background: We aimed to study the association of suspected versus confirmed infection with the novel SARS-CoV2 virus with the prevalence of acute kidney injury (AKI) in critically ill children. Methods: Sequential point-prevalence study of children and young adults aged 7 days to 25 years admitted to intensive care units under investigation for SARS-CoV2 infection. AKI was staged in the first 14 days of enrollment using KDIGO creatinine-based staging. SARS-CoV2 positive (CONFIRMED) were compared to SUSPECTED (negative or unknown). Outcome data was censored at 28-days. Results: In 331 patients of both sexes, 179 (54.1%) were CONFIRMED, 4.2% (14) died. AKI occurred in 124 (37.5%) and severe AKI occurred in 63 (19.0%). Incidence of AKI in CONFIRMED was 74/179 (41.3%) versus 50/152 (32.9%) for SUSPECTED; severe AKI occurred in 35 (19.6%) of CONFIRMED and 28 (18.4%) of SUSPECTED. Mortality was 6.2% (n = 11) in CONFIRMED, but 9.5% (n = 7) in those CONFIRMED with AKI. On multivariable analysis, only Hispanic ethnicity (relative risk 0.5, 95% CI 0.3-0.9) was associated with less AKI development among those CONFIRMED. Conclusions: AKI and severe AKI occur commonly in critically ill children with SARS-CoV2 infection, more than double the historical standard. Further investigation is needed during this continuing pandemic to describe and refine the understanding of pediatric AKI epidemiology and outcomes. Trial registration: NCT01987921. Impact: What is the key message of the article? AKI occurs in children exposed to the novel SARS-CoV2 virus at high prevalence (~40% with some form of AKI and 20% with severe AKI). What does it add to the existing literature? Acute kidney injury (AKI) occurs commonly in adult patients with SARS-CoV2 (COVID), very little data describes the epidemiology of AKI in children exposed to the virus. What is the impact? A pediatric vaccine is not available; thus, the pandemic is not over for children. Pediatricians will need to manage significant end-organ ramifications of the novel SARS-CoV2 virus including AKI

Advances in understanding ischemic acute kidney injury

Acute kidney injury (AKI) is independently associated with increased morbidity and mortality. Ischemia is the leading cause of AKI, and short of supportive measures, no currently available therapy can effectively treat or prevent ischemic AKI. This paper discusses recent developments in the understanding of ischemic AKI pathophysiology, the emerging relationship between ischemic AKI and development of progressive chronic kidney disease, and promising novel therapies currently under investigation. On the basis of recent breakthroughs in understanding the pathophysiology of ischemic AKI, therapies that can treat or even prevent ischemic AKI may become a reality in the near future