Literature mining discerns latent disease-gene relationships.

MOTIVATION: Dysregulation of a gene's function, either due to mutations or impairments in regulatory networks, often triggers pathological states in the affected tissue. Comprehensive mapping of these apparent gene-pathology relationships is an ever-daunting task, primarily due to genetic pleiotropy and lack of suitable computational approaches. With the advent of high throughput genomics platforms and community scale initiatives such as the Human Cell Landscape project, researchers have been able to create gene expression portraits of healthy tissues resolved at the level of single cells. However, a similar wealth of knowledge is currently not at our finger-tip when it comes to diseases. This is because the genetic manifestation of a disease is often quite diverse and is confounded by several clinical and demographic covariates. RESULTS: To circumvent this, we mined ∼18 million PubMed abstracts published till May 2019 and automatically selected ∼4.5 million of them that describe roles of particular genes in disease pathogenesis. Further, we fine-tuned the pretrained bidirectional encoder representations from transformers (BERT) for language modeling from the domain of natural language processing to learn vector representation of entities such as genes, diseases, tissues, cell-types, etc., in a way such that their relationship is preserved in a vector space. The repurposed BERT predicted disease-gene associations that are not cited in the training data, thereby highlighting the feasibility of in silico synthesis of hypotheses linking different biological entities such as genes and conditions. AVAILABILITY AND IMPLEMENTATION: PathoBERT pretrained model: https://github.com/Priyadarshini-Rai/Pathomap-Model. BioSentVec-based abstract classification model: https://github.com/Priyadarshini-Rai/Pathomap-Model. Pathomap R package: https://github.com/Priyadarshini-Rai/Pathomap.

Assessing the performance of farm soil-based and hybrid biofilters for methane abatement.

Mitigating methane (CH4) emissions using methanotrophs (methane-oxidizing bacteria, MOB), is a simple, energy efficient and cheap technology. The abundance and distribution of MOB in the environmental samples is critical for efficient removal of emitted CH4 from any source. This study evaluated the performance of farm soils without and with cheap, easily accessible bulking materials as sustainable hybrid biofilter media. Soil-only biofilters removed up to 865 ± 19 g CH4 m-3 d-1 with well-drained organic carbon-rich soils compared with 264 ± 14 g CH4 m-3 d-1 for poorly drained soil. The removal efficiency decreased with increasing flow rate (0.16→0.24 L min-1) and subsequent priming could not return soil biofilters to their previous removal rate.Hybrid biofilters using organic, carbon-rich soils and compost removed up to 2698 g CH4 m-3 d-1 (flow rate 0.35 L min-1). Increasing CH4 flow rates also reduced their efficiency, but the hybrid biofilters with compost quickly regained most of their efficiency and removed up to 2262 g CH4 m-3 d-1 (flow rate 0.3 L min-1) after remixing of biofilter media. These results show that hybrid biofilters removed higher CH4 than soil-only biofilters and were also more resilient. The MOB gene abundance results complement the CH4 removal capacity of both soil-only and hybrid biofilter materials used. The more aerobic, carbon-rich soils had more abundant MOB than the poorly drained soil. The most porous hybrid biofilter with compost and more available nutrients to sustain bacterial growth and activity had the highest MOB abundance and removed the most CH4.

Site-selective ring opening of bicyclo[n.1.0]alkanols: an Fe(II)-catalyzed 1,6-conjugate addition to p-quinone methides.

Herein, we report an efficient synthetic strategy for an Fe(ii)-catalyzed site-selective ring opening of bicyclo[n.1.0]alkanols and their concomitant 1,6-conjugate addition to p-quinone methides. Access to tertiary carbon centers with appendaged carbocycles of distinct sizes and functional groups are achieved, under a substrate-controlled bond scission of the fused cyclopropanols. Synthetic derivatizations further enhance the utility of the protocol.

Regiocontrol via Electronics: Insights into a Ru-Catalyzed, Cu-Mediated Site-Selective Alkylation of Isoquinolones via a C-C Bond Activation of Cyclopropanols.

A site-selective C(3)/C(4)-alkylation of N-pyridylisoquinolones is achieved by employing C-C bond activation of cyclopropanols under Ru(II)-catalyzed/Cu(II)-mediated conditions. The regioisomeric ratios of the products follow directly from the electronic nature of the cyclopropanols and isoquinolones used, with electron-withdrawing groups yielding predominantly the C(3)-alkylated products, whereas the electron-donating groups primarily generate the C(4)-alkylated isomers. Density functional theory calculations and detailed mechanistic investigations suggest the simultaneous existence of the singlet and triplet pathways for the C(3)- and C(4)-product formation. Further transformations of the products evolve the utility of the methodology thereby yielding scaffolds of synthetic relevance.

Small RNA sequencing and identification of papaya (Carica papaya L.) miRNAs with potential cross-kingdom human gene targets.

Several studies have demonstrated potential role of plant-derived miRNAs in cross-kingdom species relationships by transferring into non-plant host cells to regulate certain host cellular functions. How nutrient-rich plants regulate host cellular functions, which in turn alleviate physiological and disease conditions in the host remains to be explored in detail. This computational study explores the potential targets, putative role, and functional implications of miRNAs derived from Carica papaya L., one of the most cultivated tropical crops in the world and a rich source of phytochemicals and enzymes, in human diet. Using the next-generation sequencing, -Illumina HiSeq2500, ~ 30 million small RNA sequence reads were generated from C. papaya young leaves, resulting in the identification of a total of 1798 known and 49 novel miRNAs. Selected novel C. papaya miRNAs were predicted to regulate certain human targets, and subsequent annotation of gene functions indicated a probable role in various biological processes and pathways, such as MAPK, WNT, and GPCR signaling pathways, and platelet activation. These presumptive target gene in humans were predominantly linked to various diseases, including cancer, diabetes, mental illness, and platelet disorder. The computational finding of this study provides insights into how C. papaya-derived miRNAs may regulate certain conditions of human disease and provide a new perspective on human health. However, the therapeutic potential of C. papaya miRNA can be further explored through experimental studies.

Iridium(III)-Catalyzed C(3)-H Alkylation of Isoquinolines via Metal Carbene Migratory Insertion.

An Ir(III)-catalyzed C(3)-H alkylation of N-acetyl-1,2-dihydroisoquinolines with diverse acceptor-acceptor diazo compounds has been achieved under a single catalytic system via metal carbene migratory insertion. Moreover, further synthetic transformations of the alkylated products such as aromatization, selective decarboxylation, and decarbonylation lead to the formation of several synthetically viable isoquinoline derivatives having immense potentials.

Transition-Metal-Catalyzed C-H Bond Functionalization of Arenes/Heteroarenes via Tandem C-H Activation and Subsequent Carbene Migratory Insertion Strategy.

The past decade has witnessed tremendous developments in transition-metal-catalyzed C-H bond activation and subsequent carbene migratory insertion reactions, thus assisting in the construction of diverse arene/heteroarene scaffolds. Various transition-metal catalysts serve this purpose and provide efficient pathways for an easy access to substituted heterocycles. A brief introduction to metal-carbenes has been provided along with key mechanistic pathways underlying the coupling reactions. The purpose of this review is to provide a concise knowledge about diverse directing group-assisted coupling of varied arenes/heteroarenes and acceptor-acceptor/donor-acceptor diazo compounds. The review also highlights the synthesis of various carbocycles and fused heterocycles through diazo insertion pathways, via C-C, C-N and C-O bond forming reactions. The mechanism usually involves a C-H activation process, followed by diazo insertion leading to subsequent coupling.

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.

Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.

Geographical Landscape and Transmission Dynamics of SARS-CoV-2 Variants Across India: A Longitudinal Perspective.

Globally, SARS-CoV-2 has moved from one tide to another with ebbs in between. Genomic surveillance has greatly aided the detection and tracking of the virus and the identification of the variants of concern (VOC). The knowledge and understanding from genomic surveillance is important for a populous country like India for public health and healthcare officials for advance planning. An integrative analysis of the publicly available datasets in GISAID from India reveals the differential distribution of clades, lineages, gender, and age over a year (Apr 2020-Mar 2021). The significant insights include the early evidence towards B.1.617 and B.1.1.7 lineages in the specific states of India. Pan-India longitudinal data highlighted that B.1.36* was the predominant clade in India until January-February 2021 after which it has gradually been replaced by the B.1.617.1 lineage, from December 2020 onward. Regional analysis of the spread of SARS-CoV-2 indicated that B.1.617.3 was first seen in India in the month of October in the state of Maharashtra, while the now most prevalent strain B.1.617.2 was first seen in Bihar and subsequently spread to the states of Maharashtra, Gujarat, and West Bengal. To enable a real time understanding of the transmission and evolution of the SARS-CoV-2 genomes, we built a transmission map available on https://covid19-indiana.soic.iupui.edu/India/EmergingLineages/April2020/to/March2021. Based on our analysis, the rate estimate for divergence in our dataset was 9.48 e-4 substitutions per site/year for SARS-CoV-2. This would enable pandemic preparedness with the addition of future sequencing data from India available in the public repositories for tracking and monitoring the VOCs and variants of interest (VOI). This would help aid decision making from the public health perspective.

Vaccine Breakthrough Infections by SARS-CoV-2 Variants after ChAdOx1 nCoV-19 Vaccination in Healthcare Workers.

This study elucidated the clinical, humoral immune response and genomic analysis of vaccine breakthrough (VBT) infections after ChAdOx1 nCoV-19/Covishield vaccine in healthcare workers (HCWs). Amongst 1858 HCWs, 1639 had received either two doses (1346) or a single dose (293) of ChAdOx1 nCoV-19 vaccine. SARS-CoV-2 IgG antibodies and neutralizing antibodies were measured in the vaccinated group and the development of SARS-CoV-2 infection was monitored.Forty-six RT-PCR positive samples from the 203 positive samples were subjected to whole genome sequencing (WGS). Of the 203 (10.92%) infected HCWs, 21.46% (47/219) were non-vaccinated, which was significantly more than 9.52% (156/1639) who were vaccinated and infection was higher in doctors and nurses. Unvaccinated HCWs had 1.57 times higher risk compared to partially vaccinated HCWs and 2.49 times higher risk than those who were fully vaccinated.The partially vaccinated were at higher risk than the fully vaccinated (RR 1.58). Antibody non-response was seen in 3.44% (4/116), low antibody levels in 15.51% (18/116) and medium levels were found in 81.03% (94/116). Fully vaccinated HCWs had a higher antibody response at day 42 than those who were partially vaccinated (8.96 + 4.00 vs. 7.17 + 3.82). Whole genome sequencing of 46 samples revealed that the Delta variant (B.1.617.2) was predominant (69.5%). HCWs who had received two doses of vaccine showed better protection from mild, moderate, or severe infection, with a higher humoral immune response than those who had received a single dose. The genomic analysis revealed the predominance of the Delta variant (B.1.617.2) in the VBT infections.

Predicting the impact of patient and private provider behavior on diagnostic delay for pulmonary tuberculosis patients in India: A simulation modeling study.

BACKGROUND: Tuberculosis (TB) incidence in India continues to be high due, in large part, to long delays experienced by patients before successful diagnosis and treatment initiation, especially in the private sector. This diagnostic delay is driven by patients' inclination to switch between different types of providers and providers' inclination to delay ordering of accurate diagnostic tests relevant to TB. Our objective is to quantify the impact of changes in these behavioral characteristics of providers and patients on diagnostic delay experienced by pulmonary TB patients. METHODS AND FINDINGS: We developed a discrete event simulation model of patients' diagnostic pathways that captures key behavioral characteristics of providers (time to order a test) and patients (time to switch to another provider). We used an expectation-maximization algorithm to estimate the parameters underlying these behavioral characteristics, with quantitative data encoded from detailed interviews of 76 and 64 pulmonary TB patients in the 2 Indian cities of Mumbai and Patna, respectively, which were conducted between April and August 2014. We employed the estimated model to simulate different counterfactual scenarios of diagnostic pathways under altered behavioral characteristics of providers and patients to predict their potential impact on the diagnostic delay. Private healthcare providers including chemists were the first point of contact for the majority of TB patients in Mumbai (70%) and Patna (94%). In Mumbai, 45% of TB patients first approached less-than-fully-qualified providers (LTFQs), who take 28.71 days on average for diagnosis. About 61% of these patients switched to other providers without a diagnosis. Our model estimates that immediate testing for TB by LTFQs at the first visit (at the current level of diagnostic accuracy) could reduce the average diagnostic delay from 35.53 days (95% CI: 34.60, 36.46) to 18.72 days (95% CI: 18.01, 19.43). In Patna, 61% of TB patients first approached fully qualified providers (FQs), who take 9.74 days on average for diagnosis. Similarly, immediate testing by FQs at the first visit (at the current level of diagnostic accuracy) could reduce the average diagnostic delay from 23.39 days (95% CI: 22.77, 24.02) to 11.16 days (95% CI: 10.52, 11.81). Improving the diagnostic accuracy of providers per se, without reducing the time to testing, was not predicted to lead to any reduction in diagnostic delay. Our study was limited because of its restricted geographic scope, small sample size, and possible recall bias, which are typically associated with studies of patient pathways using patient interviews. CONCLUSIONS: In this study, we found that encouraging private providers to order definitive TB diagnostic tests earlier during patient consultation may have substantial impact on reducing diagnostic delay in these urban Indian settings. These results should be combined with disease transmission models to predict the impact of changes in provider behavior on TB incidence.

Computational identification of miRNA and their cross kingdom targets from expressed sequence tags of Ocimum basilicum.

MicroRNAs (miRNAs) are conserved small non coding RNAs, which are typically 22-24 nucleotides long and play an important role in post transcription regulation andin various biological processes in both animals and plants. Ocimum basilicum is an important medicinal plant having different bioactive compounds eugenol and essential oils that possess numerous therapeutic properties. However, only a few miRNAs of Ocimum basilicum and its function have been studied till date. The present study focusses on the identification of miRNA from expressed sequenced tags by carrying out computational approaches based on the homology search method. A total of 10 potential miRNAs with 8 different families were predicted in O.basilicum. Furthermore, the psRNA target server was used to predict cross kingdom target genes on human transcriptome for identification ofpotential miRNAs. Eight miRNA families were found to modulate the 87 human target genes which were associated with RAS/MAPK signalling cascade, cardiomyopathy, HIV, breast cancer, lung cancer, Alzheimer's diseases and several neurological disorders. Moreover, O.basilicum miRNAs regulate the key human target genes having significance in various diseases and important biological networks with 10 hub nodes interactions. Thus this study gives the pave for further studies to explore the potential of miRNA mediated cross kingdom regulation and treatment of various diseases including cancer.

Anti-pathogenic potential of a classical ayurvedic Triphala formulation.

A classical ayurvedic polyherbal formulation namely Triphala was assessed for its anti-pathogenic potential against five different pathogenic bacteria. Virulence of four of them towards the model host Caenorhabditis elegans was attenuated (by 18-45%) owing to pre-treatment with Triphala (≤20 µg/ml). Triphala could also exert significant therapeutic effect on worms already infected with Chromobacterium violaceum, Serratia marcescens or Staphylococcus aureus. Prophylactic use of Triphala allowed worms to score 14-41% better survival in face of subsequent pathogen challenge. Repeated exposure to this formulation induced resistance in S. marcescens, but not in P. aeruginosa. It also exerted a post-extract effect (PEE) on three of the test pathogens. Triphala was able to modulate production of quorum sensing (QS)-regulated pigments in three of the multidrug-resistant gram-negative test bacteria. Haemolytic activity of S. aureus was heavily inhibited under the influence of this formulation. P. aeruginosa's lysozyme-susceptibility was found to increase by ~25-43% upon Triphala-pretreatment. These results validate therapeutic potential of one of the most widely used polyherbal ayurvedic formulations called Triphala.

Sirolimus as a potential radiosensitizer in squamous cell cancer of the head and neck.

BACKGROUND: An estimated 34,000 cases of squamous cell carcinomas of the head and neck (HNSCC) will be diagnosed in 2007 with 7500 estimated deaths. Radiation is commonly used to treat these patients. Preclinical studies have suggested that sirolimus may be an effective radiosensitizer in HNSCC. METHODS: The present case report describes a patient, status post liver transplant, who was switched to sirolimus for immunosupression. The patient subsequently underwent radiation therapy for a T2N0M0 SCC of the larynx. RESULTS: The patient had an unusually early response to radiation, with a clinical complete response after 7 fractions of radiation. However, the patients also had toxicity earlier than expected and required a break from radiation after 11 fractions. CONCLUSIONS: To the authors' knowledge, this is the first observation to suggest that sirolimus is an effective radiosensitizer in patients with HNSCC. We hope that our results will create interest in future clinical studies.