Epidemiologic Characteristics of Mpox among People Experiencing Homelessness, Los Angeles County, California, USA, 2022.

In Los Angeles County, California, USA, public health surveillance identified 118 mpox cases among persons experiencing homelessness (PEH) during July-September 2022. Age and sex were similar for mpox case-patients among PEH and in the general population. Seventy-one (60%) PEH mpox case-patients were living with HIV, 35 (49%) of them virally suppressed. Hospitalization was required for 21% of case-patients because of severe disease. Sexual contact was likely the primary mode of transmission; 84% of patients reported sexual contact <3 weeks before symptom onset. PEH case-patients lived in shelters, encampments, cars, or on the street, or stayed briefly with friends or family (couch surfed). Some case-patients stayed at multiple locations during the 3-week incubation period. Public health follow-up and contact tracing detected no secondary mpox cases among PEH in congregate shelters or encampments. Equitable efforts should continue to identify, treat, and prevent mpox among PEH, who often experience severe disease.

Transcriptome analysis provides insights into the stress response in cultivated peanut (Arachis hypogaea L.) subjected to drought-stress.

BACKGROUND: Peanut (Arachis hypogaea L.) is one of the valuable oilseed crops grown in drought-prone areas worldwide. Drought severely limits peanut production and productivity significantly. METHOD AND RESULTS: In order to decipher the drought tolerance mechanism in peanut under drought stress, RNA sequencing was performed in TAG - 24 (drought tolerant genotype) and JL-24 (drought susceptible genotype). Approximately 51 million raw reads were generated from four different libraries of two genotypes subjected to drought stress exerted by 20% PEG 6000 stress and control conditions, of which ~ 41 million (80.87%) filtered reads were mapped to the Arachis hypogaea L. reference genome. The transcriptome analysis detected 1,629 differentially expressed genes (DEGs), 186 genes encoding transcription factors (TFs) and 30,199 SSR among the identified DEGs. Among the differentially expressed TF encoding genes, the highest number of genes were WRKY followed by bZIP, C2H2, and MYB during drought stress. The comparative analysis between the two genotypes revealed that TAG-24 exhibits activation of certain key genes and transcriptional factors that are involved in essential biological processes. Specifically, TAG-24 showed activation of genes involved in the plant hormone signaling pathway such as PYL9, Auxin response receptor gene, and ABA. Additionally, genes related to water deprivation such as LEA protein and those involved in combating oxidative damage such as Glutathione reductase were also found to be activated in TAG-24. CONCLUSION: This genome-wide transcription map, therefore, provides a valuable tool for future transcript profiling under drought stress and enriches the genetic resources available for this important oilseed crop.

Evaluation of the Homeless Management Information System for COVID-19 Surveillance Among People Experiencing Homelessness.

BACKGROUND: Variable and incomplete reporting of housing status creates challenges in the surveillance of coronavirus disease 2019 (COVID-19) among the homeless population in Los Angeles County (LA County) and nationwide. METHODS: We developed standard investigation procedures to assess the housing status of LA County COVID-19 patients. Using data sharing procedures, we matched COVID-19 patients to Homeless Management Information System (HMIS) client profiles and supplemented with additional data sources for contributory data points and to further housing status ascertainment. RESULTS: We identified 10 586 COVID-19 patients among people experiencing homelessness (PEH) between 30 March 2020 and 30 December 2021; 2801 (26.5%) patients were first identified from HMIS profile matches, 1877 (17.7%) from quarantine/isolation housing intake rosters, 573 (5.4%) from hospital records, 749 (7.1%) from case and contact interviews, 3659 (34.6%) directly from PEH medical and service providers, and 927 (8.8%) had unknown sources. Among COVID-19 patients matched to HMIS profiles, 5351 (42.5%) were confirmed to be PEH at the time of COVID-19 diagnosis. CONCLUSIONS: Interoperability between public health data, HMIS, and external partners have been critical components in evaluating the impact of COVID-19 among the LA County homeless population. No one data source was complete for COVID-19 surveillance in this population.

Rothia santali sp. nov., endophytic bacteria isolated from sandalwood (Santalum album L.) seedling.

A novel, mustard yellow-pigmented aerobic bacterial strain designated AR01T was isolated from hypocotyl tissue of a sandalwood seedling from Bangalore, India. The 16S rRNA gene of strain AR01T had the highest 98.97% sequence similarity with Rothia halotolerans YIM 90716T (KCTC 19172) followed by Rothia kristinae PM 129T (NBRC 15354T) (97.31%) and Rothia koreensis P31T (JCM 15915) (97.11%), respectively. The strain AR01T was coccoid-shaped, non-motile, non-spore forming, oxidase negative and catalase positive. The strain AR01T has a genome size of 3.31 Mb containing 2993 protein-coding genes including 48 tRNA and 10 rRNAs spread across 84 contigs. The genomic DNA G + C content was 71.77 mol%. The calculated dDDH was 31.10% and the OrthoANI value was 85.27% when compared with its closest related type strain Rothia halotolerans YIM 90716T. The predominant cellular fatty acids were C16:0 iso, C15:0 anteiso and C17:0 anteiso. The strain AR01T contains major polar lipids including diphosphatidylglycerol and phosphatidylglycerol. The distinct physiological, biochemical characteristics and genotypic relatedness indicated that AR01T represents a novel species of the genus Rothia, for which the name Rothia santali sp. nov. (Type strain AR01T = MCC 4800T = JCM 35593T) is proposed.

Retraction Note to: Environmental impact of plantations in and around the petroleum refinery: a case study.

This article [1] has been retracted at the request of the Editor-in-Chief. Significant sections of the article show a similarity with the author's own article published previously [2]. All the authors agree with the retraction.

Wavelet Based Analytical Expressions to Steady State Biofilm Model Arising in Biochemical Engineering.

In this paper, we have developed an efficient wavelet based approximation method to biofilm model under steady state arising in enzyme kinetics. Chebyshev wavelet based approximation method is successfully introduced in solving nonlinear steady state biofilm reaction model. To the best of our knowledge, until now there is no rigorous wavelet based solution has been addressed for the proposed model. Analytical solutions for substrate concentration have been derived for all values of the parameters δ and SL. The power of the manageable method is confirmed. Some numerical examples are presented to demonstrate the validity and applicability of the wavelet method. Moreover the use of Chebyshev wavelets is found to be simple, efficient, flexible, convenient, small computation costs and computationally attractive.

Antigenotoxic and Antimutagenic Activities of Probiotic Lactobacillus rhamnosus Vc against N-Methyl-N'-Nitro-N-Nitrosoguanidine.

The present study provides experimental evidence of in vivo reduction of genotoxic and mutagenic activities of potent carcinogen N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) by the strain Lactobacillus rhamnosus Vc. In vitro studies revealed that coincubation of MNNG with viable cells of L. rhamnosus Vc resulted in the detoxification of the parent compound accompanied with reduction in genotoxicity (69%) and mutagenicity (61%) as evaluated by SOS-Chromotest and Ames test, respectively. Oral feeding of probiotic bacteria L. rhamnosus Vc (10(9) cfu) to Gallus gallus (chicks) for 30 days provided protection against MNNG-induced damage as evidenced from the significant decrease (P = 0.009) in glutathione S-transferase activity in the L. rhamnosus Vc+MNNG-treated chicks in comparison to the MNNG-treated chicks. Histopathology of colon and liver showed intact cells and mild inflammation in the L. rhamnosus Vc+MNNG-treated chicks, whereas heavy inflammation and degenerative changes were observed in MNNG-treated chicks. The results indicate that the probiotic L. rhamnosus Vc provided in vivo protection against MNNG-induced colon damage by detoxification of MNNG to less toxic metabolites.

Effects of unregulated anthropogenic activities on mixing ratios of volatile organic air pollutants--A case study.

UNLABELLED: During the months of October to November, many important festivals are celebrated in India. Celebration of these festivals are marked by extensive use of fireworks or pyrotechnics, bonfire, incense burning, open air community cooking, and temporary eateries using crude fuel such as coal, wood, kerosene, cow dung, burning of raw/semiwood, and coconut shells. The present study deals with the influence of these unregulated anthropogenic activities on ambient mixing level of volatile organic compounds (VOCs), especially some carbonyl compounds. The study was undertaken in the metropolitan city of Kolkata, India, with very high population density, which is even higher during festival period. The average total carbonyl level at different sites in Kolkata varied from 134.8 to 516.5 µg m(-3) in pre-festival season, whereas in post-festival season the same varied from 252.2 to 589.3 µg m(-3). Formaldehyde to acetaldehyde ratio altered from 0.62 in pre-festival season to 1.78 in post-festival season. Diurnal variation also altered, indicating variation in source composition of carbonyls. The total ozone forming potential calculated for all 14 carbonyls in pre-festival season increased by 35% in post-festival season. The effect of anthropogenic activities typical to the event of Diwali night characterized by intense execution of pyrotechnics resulted in significantly high level of carbonyl VOCs. Principal component analysis study for the event of Diwali shows clear contribution of the event on certain carbonyl VOCs. The results indicate elevated primary emissions of these pollutants and also their effect on formation of secondary pollutants. The study emphasizes the need of generating awareness among the communities in society as well as need for regulations to minimize the emissions and related hazards to the extent possible. IMPLICATIONS: Altered anthropogenic activities typical of festival season including extensive use of pyrotechnics affect ambient level of volatile organic compounds, especially some carbonyls. Such activities have considerable effect on interspecies ratio and diurnal variation. They also affect formation of secondary pollutants such as tropospheric ozone. Principal component analysis (PCA) study shows clear contribution of the pyrotechnics execution on certain carbonyl VOCs. The findings emphasize the need of generating awareness in society and need for regulations to minimize the emissions.

Emission, speciation, and evaluation of impacts of non-methane volatile organic compounds from open dump site.

Surface emission from Dhapa, the only garbage disposal ground in Kolkata, is a matter of concern to the local environment and also fuels the issues of occupational and environmental health. Surface emission of the Dhapa landfill site was studied using a flux chamber measurement for nonmethane volatile organic compounds (NMVOCs). Eighteen noncarbonyl volatile organic compounds (VOCs) and 14 carbonyl VOCs, including suspected and known carcinogens, were found in appreciable concentrations. The concentrations of the target species in the flux chamber were found to be significantly higher for most of the species in summer than winter. Surface emission rate of landfill gas was estimated by using two different approaches to assess the applicability for an open landfill site. It was found that the emissions predicted using the model Land GEM version 3.02 is one to two orders less than the emission rate calculated from flux chamber measurement for the target species. Tropospheric ozone formation has a serious impact for NMVOC emission. The total ozone-forming potential (OFP) of the Dhapa dumping ground considering all target NMVOCs was estimated to be 4.9E+04 and 1.2E+05 g/day in winter and summer, respectively. Also, it was found that carbonyl VOCs play a more important role than noncarbonyl VOCs for tropospheric ozone formation. Cumulative cancer risk estimated for all the carcinogenic species was found to be 2792 for 1 million population, while the total noncancer hazard index (HI) was estimated to be 246 for the occupational exposure to different compounds from surface emission to the dump-site workers at Dhapa. Implications: This paper describes the real-time surface emission of NMVOCs from an open municipal solid waste (MSW) dump site studied using a flux chamber. Our study findings indicate that while planning for new landfill site in tropical meteorology, real-time emission data must be considered, rather than relying on modeled data. The formation of tropospheric ozone from emitted NMVOC has also been studied. Our result shows how an open landfill site acts as a source and adds to the tropospheric ozone for the airshed of a metropolitan city.

Source identification study of heavy metal contamination in the industrial hub of Unnao, India.

India's Unnao region is home to many leather-treatment facilities and related industries. Industrial and agricultural waste leads to heavy metal contamination that infiltrates groundwater and leads to human health hazards. This work measured the amount of heavy metal in groundwater at specific sites near the industrial facilities in Unnao and identified potential sources of contamination as anthropogenic or lithogenic. Groundwater samples were taken from 10 bore well sites chosen for depth and proximity to industry. Data obtained from sample sites was interpreted using a multivariate statistical analytical approach, i.e., principal component analysis, clustering analysis, and correlation analysis. The results of the multivariate analysis showed that cadmium, copper, manganese, nickel, lead, and zinc were correlated with anthropogenic sources, while iron and chromium were associated with lithogenic sources. These findings provide information on the possible sources of heavy metal contamination and could be a model for assessing and monitoring heavy metal pollution in groundwater in other locales. This study analyzed a selection of heavy metals chosen on the basis of industries located in the study area, which might not provide a complete range of information about the sources and availability of all heavy metals. Therefore, an extended investigation on heavy metal fractions will be developed in further studies.

Draft genome sequence of 'Candidatus Phytoplasma asteris,' strain SW86 associated with sandal spike disease (SSD).

The sandal spike disease (SSD), related to 'Ca. Phytoplasma asteris' (Aster Yellows group), poses a significant threat to Indian sandalwood (Santalum album L.), making it the second most expensive wood globally due to declining population density. The epidemiology of SSD and the nature of the pathogen remain poorly understood. The SW86 isolate, collected from the Marayoor Sandalwood Reserve, was chosen for genome sequencing subsequent to confirming its titer and enriching phytoplasma DNA. Genome sequencing, utilizing Illumina and Oxford Nanopore Technology platforms, enabled a targeted hybrid metagenomic assembly resulting in 20 scaffolds totaling 554,025 bp, housing 436 protein-coding genes, 27 tRNA, and 1 rRNA operon. The genome analysis highlighted specific gene distributions, emphasizing translation, ribosomal structure, and biogenesis, with 352 genes assigned to 18 functional categories. Additionally, 322 proteins received functional assignments in the KEGG database, emphasizing 'Genetic Information Processing' and 'Environmental Information Processing'. Key potential pathogenicity factors, including signal peptide proteins and virulence proteins, were identified. Noteworthy findings include homologs of effectors genes like SAP11 and SAP05 and pathogenesis-related proteins, such as hemolysin III and SodA genes, in the SW86 genome. The duplicated cation-transporting P-type ATPase in the SW86 genome suggests a role in enhancing adaptability and contributing to the severity of SSD symptoms. This genome analysis provides crucial insights into the genomic features and potential virulence factors of 'Ca. Phytoplasma asteris' strain SW86, advancing our understanding of pathogenicity mechanisms and offering avenues for future disease management strategies in Indian sandalwood. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-03952-5.

Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer.

Breast cancers (BRCA) exhibit substantial transcriptional heterogeneity, posing a significant clinical challenge. The global transcriptional changes in a disease context, however, are likely mediated by few key genes which reflect disease etiology better than the differentially expressed genes (DEGs). We apply our network-based tool PathExt to 1,059 BRCA tumors across 4 subtypes to identify key mediator genes in each subtype. Compared to conventional differential expression analysis, PathExt-identified genes exhibit greater concordance across tumors, revealing shared and subtype-specific biological processes; better recapitulate BRCA-associated genes in multiple benchmarks, and are more essential in BRCA subtype-specific cell lines. Single-cell transcriptomic analysis reveals a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target key genes potentially mediating drug resistance.

A quality improvement initiative to reduce the time to initial maternal visit in the neonatal intensive care unit.

OBJECTIVE: We aimed to reduce the time interval between an infant's admission to the Neonatal Intensive Care Unit (NICU) and first maternal interaction. METHODS: We identified three key drivers: 1. Collaboration with Labor and Delivery, 2. Education of staff and parents, and 3. Improved documentation of maternal presence. We measured the time interval from NICU admission to the initial maternal presence. We followed length of stay as a balancing measure to assay whether use of remote televisitation impeded efficient parental teaching and delayed discharge. RESULTS: We reduced the time interval from an average of 19.7 h in February 2020 to 12.3 h in June 2021. We expanded an already existing televisitation program as a surrogate to in-person interaction during COVID-19 pandemic. Televisitation did not affect in-person parental presence or LOS. CONCLUSION: Our multidisciplinary efforts resulted in a significantly accelerated time to initial maternal presence and did not prolong LOS.

Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in Triple Negative Breast Cancer.

Breast cancers exhibit substantial transcriptional heterogeneity, posing a significant challenge to the prediction of treatment response and prognostication of outcomes. Especially, translation of TNBC subtypes to the clinic remains a work in progress, in part because of a lack of clear transcriptional signatures distinguishing the subtypes. Our recent network-based approach, PathExt, demonstrates that global transcriptional changes in a disease context are likely mediated by a small number of key genes, and these mediators may better reflect functional or translationally relevant heterogeneity. We apply PathExt to 1059 BRCA tumors and 112 healthy control samples across 4 subtypes to identify frequent, key-mediator genes in each BRCA subtype. Compared to conventional differential expression analysis, PathExt-identified genes (1) exhibit greater concordance across tumors, revealing shared as well as BRCA subtype-specific biological processes, (2) better recapitulate BRCA-associated genes in multiple benchmarks, and (3) exhibit greater dependency scores in BRCA subtype-specific cancer cell lines. Single cell transcriptomes of BRCA subtype tumors reveal a subtype-specific distribution of PathExt-identified genes in multiple cell types from the tumor microenvironment. Application of PathExt to a TNBC chemotherapy response dataset identified TNBC subtype-specific key genes and biological processes associated with resistance. We described putative drugs that target top novel genes potentially mediating drug resistance. Overall, PathExt applied to breast cancer refines previous views of gene expression heterogeneity and identifies potential mediators of TNBC subtypes, including potential therapeutic targets.

Charting the transcriptomic landscape of primary and metastatic cancers in relation to their origin and target normal tissues.

Metastasis is a leading cause of cancer-related deaths, yet understanding how metastatic tumors adapt from their origin to target tissues is challenging. To address this, we assessed whether primary and metastatic tumors resemble their tissue of origin or target tissue in terms of gene expression. We analyzed gene expression profiles from various cancer types, including single-cell and bulk RNA-seq data, in both paired and unpaired primary and metastatic patient cohorts. We quantified the transcriptomic distances between tumor samples and their normal tissues, revealing that primary tumors are more similar to their tissue of origin, while metastases shift towards the target tissue. Pathway-level analysis highlighted critical transcriptomic changes during metastasis. Notably, primary cancers exhibited higher activity in cancer hallmarks, including Activating Invasion and Metastasis , compared to metastatic cancers. This comprehensive landscape analysis provides insight into how cancer tumors adapt to their metastatic environments, providing a transcriptome-wide view of the processes involved.

Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome.

BACKGROUND: Precision oncology is gradually advancing into mainstream clinical practice, demonstrating significant survival benefits. However, eligibility and response rates remain limited in many cases, calling for better predictive biomarkers. METHODS: We present ENLIGHT, a transcriptomics-based computational approach that identifies clinically relevant genetic interactions and uses them to predict a patient's response to a variety of therapies in multiple cancer types without training on previous treatment response data. We study ENLIGHT in two translationally oriented scenarios: personalized oncology (PO), aimed at prioritizing treatments for a single patient, and clinical trial design (CTD), selecting the most likely responders in a patient cohort. FINDINGS: Evaluating ENLIGHT's performance on 21 blinded clinical trial datasets in the PO setting, we show that it can effectively predict a patient's treatment response across multiple therapies and cancer types. Its prediction accuracy is better than previously published transcriptomics-based signatures and is comparable with that of supervised predictors developed for specific indications and drugs. In combination with the interferon-γ signature, ENLIGHT achieves an odds ratio larger than 4 in predicting response to immune checkpoint therapy. In the CTD scenario, ENLIGHT can potentially enhance clinical trial success for immunotherapies and other monoclonal antibodies by excluding non-responders while overall achieving more than 90% of the response rate attainable under an optimal exclusion strategy. CONCLUSIONS: ENLIGHT demonstrably enhances the ability to predict therapeutic response across multiple cancer types from the bulk tumor transcriptome. FUNDING: This research was supported in part by the Intramural Research Program, NIH and by the Israeli Innovation Authority.

Cushing disease with pregnancy.

Pregnancy occurs rarely in patients with Cushing syndrome (CS) due to hypercortisolism. So far, about 150 cases of CS in pregnancy have been reported in the literature. We describe a 22-year-old female who presented in pregnancy with clinical features of CS. She delivered at 34 weeks of gestation and baby had transient adrenal insufficiency in the neonatal period. Mother underwent transsphenoidal surgery 1 year postpartum and on follow up she is under remission. Neonatal hypoadrenalism should be anticipated in maternal CS.

Air quality status during Diwali festival of India: a case study.

The PM(2.5) and PM(10) samples were collected during Diwali celebration from study area and characterized for ionic concentration of four anions (NO(3) (-), NO(2) (-), Cl(-), SO(4) (2-)) and five cations (K(+), Mg(2+), NH(4) (+), Ca(2+), Na(+)). The results showed that the ionic concentrations were three times compared to those on pre and post Diwali days. Predominant ions for PM(2.5) were K(+) 33.7 µg/m(3), Mg(+) 31.6 µg/m(3), SO(4) (2-) 22.1 µg/m(3), NH(4) (+) 17.5 µg/m(3) and NO(3) (-) 18 µg/m(3) and for PM(10) the ionic concentrations were Mg(+) 29.6 µg/m(3), K(+) 26 µg/m(3), SO(4) (2-) 19.9 µg/m(3), NH(4) (+) 16.8 µg/m(3) and NO(3) (-) 16 µg/m(3). While concentration of SO(2) and NO(2) were 17.23, 70.33 µg/m(3) respectively.

Respiratory support strategies in the management of severe, longstanding bronchopulmonary dysplasia.

Despite efforts to minimize ventilator-induced lung injury, some preterm infants require positive pressure support after 36 weeks' post-menstrual age. Infants with severe BPD typically experience progressive mismatch of ventilation and perfusion, which manifests as respiratory distress, hypoxemia in room air, hypercarbia, and growth failure. Lung compliance varies, but lung resistance generally increases with prolonged exposure to positive pressure ventilation and other sources of inflammation. Serial lung radiographs reveal a heterogeneous pattern, with areas of both hyperinflation and atelectasis; in extreme cases, macrocystic changes may be noted. Efforts to wean the respiratory support are often unsuccessful, and trials of high frequency ventilation, exogenous corticosteroids, and diuretics are common. The incidence of pulmonary hypertension increases with the severity of BPD, as does the mortality rate. Therefore, periodic screening and efforts to mitigate the risk of PH is fundamental to the management of longstanding BPD. Failure of conventional, lung-protective strategies (e.g., high rate/low tidal-volume and/or high frequency ventilation) warrants consideration of ventilatory strategies individualized to the disease physiology. Non-invasive modes of respiratory support may be successful in infants with mild to moderate BPD phenotypes. However, infants with moderate to severe BPD phenotypes often require invasive respiratory support, and pressure-limited or volume-targeted conventional ventilation may be better suited to the physiology than high-frequency ventilation. The consistent provision of adequate support is fundamental to the management of longstanding BPD and is best achieved with a stepwise increase in ventilator support until comfortable spontaneous respirations are achieved. Adequately supported infants typically experience improvements in both oxygenation and ventilation, which, if sustained, may arrest and generally reverses the course of a potentially lethal lung disease. Care should be individualized to address the most likely pulmonary mechanics, including variable lung compliance, elevated airway resistance, and variable airway obstruction.

Cross-species identification of cancer resistance-associated genes that may mediate human cancer risk.

Cancer is a predominant disease across animals. We applied a comparative genomics approach to systematically characterize genes whose conservation levels correlate positively (PC) or negatively (NC) with cancer resistance estimates across 193 vertebrates. Pathway analysis reveals that NC genes are enriched for metabolic functions and PC genes in cell cycle regulation, DNA repair, and immune response, pointing to their corresponding roles in mediating cancer risk. We find that PC genes are less tolerant to loss-of-function (LoF) mutations, are enriched in cancer driver genes, and are associated with germline mutations that increase human cancer risk. Their relevance to cancer risk is further supported via the analysis of mouse functional genomics and cancer mortality of zoo mammals' data. In sum, our study describes a cross-species genomic analysis pointing to candidate genes that may mediate human cancer risk.