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Context: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the central system in epigenomic exploration. Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is an important technology to identify the genome-wide location of DNA-binding proteins such as histones proteins, transcription factors, RNA polymerase, or any protein of interest. ChIP-seq has been used to study the binding sites and efficacy of drugs in cancer cell lines etc. Aims: In current research, breast cancer cell line data have been used to study the effect PADI2 (peptidyl arginine deiminase) gene in the progression of breast cancer. Further, this ChIP-seq data have also been used to study the binding site of Amanitin drug in breast cancer. Settings and Design: Breast cancer ChIP-seq data have been retrieved from the European Nucleotide Archive database with project Id PRJNA415426 short read archive. Four samples of FASTQ files were used and analyzed for the genome-wide analysis. Materials and Methods: Galaxy server (https://usegalaxy.org/) was used for complete ChIP-seq data analysis; different tools such as fast-quality control (QC), multi-QC, Bowtie2, model-based analysis of ChIP-sequencing, and ChIPseeker tools were used for motif enrichment and functional analysis. Motif analysis was done through the Multiple Expectation maximizations for Motif Elicitation database (https://meme-suite.org/meme/db/motifs). Results: Computational investigation demonstrates the binding sequences of the T47-D breast cancer cell line as TTTTGTATTTTTAGT, and this motif occurs 2123 times in the Homo Sapiens reference genome that is hg19. Conclusions: This research classifies the binding site and affinity of the T47-D human breast cancer cell line. Further, wet laboratory studies are required to verify the function of the predicted motifs and their importance in drug development or research in breast cancer.

Cutaneous squamous cell carcinoma (cSCC) comprises 20% of cases of nonmelanoma skin cancers in the United States. In total, 3% to 5% of squamous cell carcinoma (SCC) are metastatic at the time of presentation, associated with significant mortality due to a lack of standardized treatment options. In total, 95% of these tumors are amenable to the initial standard of treatment, which is surgical resection. However, a small percentage of them require systemic therapy as they are either locally advanced to regional lymph nodes or have distant metastasis. The common sites of presentation of cSCC are the scalp and the face with predictable spread to the intra-parotid, upper jugular, and perifacial lymph nodes. In our case report, however, our patient had a large lump lesion on the upper back, an unusual site of presentation of cSCC, with locally advanced metastasis to the left axillary lymph nodes. Subsequently, the tumor marker study revealed a positive SMARCA4 variant (the essential ATPase subunit of the Switch (SWI)/Sucrose Nonfermenting (SNF) chromatin-remodeling complex) that is even rarer in the context of cSCC. Furthermore, abnormalities in SWI/SNF chromatin-remodeling complex subunits have shown promising results as a target therapy for immune checkpoint inhibitor (ICI) therapy. We present an atypical presentation site of locally advanced rare variant SMARCA4-positive cSCC in a patient who received treatment with chemoradiation and systemic therapy with ICI after primary surgical resection. To date, only 2 cases of SMARCA4-positive cSCC were found in the literature with no details of the treatment received. Our case is unique in its atypical site of presentation as well as showing partial response to radiotherapy (RT) and systemic therapy with ICI.

OBJECTIVES/GOALS: Scholarly activity is a key component of most residency programs. To establish fundamental research skills and fill gaps within training curricula, we developed an online, asynchronous set of modules to introduce trainees to various topics that are germane to the conduct of research and evaluated its effectiveness in resident research education. METHODS/STUDY POPULATION: Research 101 was utilized by residents at the Brookdale Hospital Medical Center in Brooklyn, NY. Resident knowledge, confidence, and satisfaction were assessed using pre- and post-module surveys with 5-point Likert scaled questions, open-ended text responses, and a final quiz. RESULTS/ANTICIPATED RESULTS: Pre-module survey results indicated that residents were most confident with the Aligning expectations, Introduction to research, and Study design and data analysis basics modules and least confident with the Submitting an Institutional Review Board (IRB) protocol at UC and Presenting your summer research modules. Post-module survey responses increased significantly compared to pre-module results for all modules and learning objectives (p

SARS-CoV-2 serosurveys help estimate the extent of transmission and guide the allocation of COVID-19 vaccines. We measured SARS-CoV-2 seroprevalence among women attending ANC clinics to assess exposure trends over time in Zambia. We conducted repeated cross-sectional SARS-CoV-2 seroprevalence surveys among pregnant women aged 15-49 years attending their first ANC visits in four districts of Zambia (two urban and two rural) during September 2021-September 2022. Serologic testing was done using a multiplex bead assay which detects IgG antibodies to the nucleocapsid protein and the spike protein receptor-binding domain (RBD). We calculated monthly SARS-CoV-2 seroprevalence by district. We also categorized seropositive results as infection alone, infection and vaccination, or vaccination alone based on anti-RBD and anti-nucleocapsid test results and self-reported COVID-19 vaccination status (vaccinated was having received ≥1 dose). Among 8,304 participants, 5,296 (63.8%) were cumulatively seropositive for SARS-CoV-2 antibodies from September 2021 through September 2022. SARS-CoV-2 seroprevalence primarily increased from September 2021 to September 2022 in three districts (Lusaka: 61.8-100.0%, Chongwe: 39.6-94.7%, Chipata: 56.5-95.0%), but in Chadiza, seroprevalence increased from 27.8% in September 2021 to 77.2% in April 2022 before gradually dropping to 56.6% in July 2022. Among 5,906 participants with a valid COVID-19 vaccination status, infection alone accounted for antibody responses in 77.7% (4,590) of participants. Most women attending ANC had evidence of prior SARS-CoV-2 infection and most SARS-CoV-2 seropositivity was infection-induced. Capturing COVID-19 vaccination status and using a multiplex bead assay with anti-nucleocapsid and anti-RBD targets facilitated distinguishing infection-induced versus vaccine-induced antibody responses during a period of increasing COVID-19 vaccine coverage in Zambia. Declining seroprevalence in Chadiza may indicate waning antibodies and a need for booster vaccines. ANC clinics have a potential role in ongoing SARS-CoV-2 serosurveillance and can continue to provide insights into SARS-CoV-2 antibody dynamics to inform near real-time public health responses.

Scholarly activity is a key component of most residency programmes. To establish fundamental research skills and fill gaps within training curricula, we developed an online, asynchronous set of modules called Research 101 to introduce trainees to various topics that are germane to the conduct of research and evaluated its effectiveness in resident research education. Research 101 was utilised by residents at One Brooklyn Health in Brooklyn, NY. Resident knowledge, confidence, and satisfaction were assessed using pre- and post-module surveys with 5-point Likert scaled questions, open-ended text responses, and a multiple-choice quiz. Pre-module survey results indicated that residents were most confident with the Aligning expectations, Introduction to research, and Study design and data analysis basics modules and least confident with the Submitting an Institutional Review Board protocol and Presenting your summer research modules. Post-module survey responses demonstrated increased learning compared to pre-module results for all modules and learning objectives (p < 0.0001). “This module met my needs” was endorsed 91.4% of the time. The median score for the final quiz that consisted of 25 multiple-choice questions was 23. Thematic analysis of open-ended post-module survey responses identified multiple strengths and opportunities for improvement in course content and instructional methods. These data demonstrate that residents benefit from completion of Research 101, as post-module survey scores were significantly higher than pre-module survey scores for all modules and questions, final quiz scores were high, and open-ended responses highlighted opportunities for additional resident learning.

In the present research, a few well-known artificial intelligence tools were explored for efficient hit selection which could be further utilized for the discovery of CaMK-II inhibitors for the Treatment of arrhythmia. To achieve the desired goals pharmacophore modelling, database retrieval, molecular docking studies, and toxicity prediction were performed. Pharmacophore modelling was performed with the Pharmit open-source database which gave the features viz. Hydrogen Bond Donor, Hydrogen Bond Acceptor, and Hydrophobic. This pharmacophore is generated with the aid of the protein of CaMK-II (PDB ID: 2WEL) and co-crystallized ligand K88. Further, this generated pharmacophore was screened through the various Pharmit databases which include CHEMBL30, ChemDiv, ChemSpace, MCULE, MolPort, NCI Open Chemical Repository, Lab Network, and ZINC. Further, the top two hits from each database that has maximum similarity with the pharmacophore have been selected for the molecular docking and ADMET studies. Among, all the hits CHEMBL 1952032 showed good binding interactions with CaMK-II. Also, it was found to be non-toxic upon evaluation through the OSIRIS property explorer. In the future, it can be explored against the CaMK-II for the development of novel CaMK-II inhibitors which can be used for the mitigation of arrhythmia.

Background: Breast cancer (BC) is one of the most common cancers in women worldwide, including an estimated 570,000 deaths in 2015. More than 1.5 million women (25% of all women with cancer) are diagnosed with BC every year worldwide. BC is a metastatic cancer and usually spreads to distant organs such as bone, liver, lungs and the brain. Early detection of the disease can lead to better prognosis and higher survival rates. After genome sequencing, DNA microarray analysis has become the most widely used source of genome scale data in life sciences. Microarray's definition studies produce a large number of genetic expression and other genomics performance data, which promises to provide key information on genetic functioning and interaction within and within metabolic pathways. Aim: Prediction and functional enrichment of significant genes expressed in Breast Cancer. Materials and Methods: Microarray data for this study were downloaded from NCBI gene expression omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo), with accession number of GSE157737. It includes four different kind sets of samples, i.e., healthy control neutrophils, healthy donor monocytes, metastatic BC patient G-myeloid-derived suppressor cell (G-MDSCs) and sepsis patient G-MDSCs. The statistical method was applied to identify the differentially expressed gene (DEGs) using Limma package and significant analysis of microarray (SAM) test. Results: The top ten DEGs were identified between different sample sets using Limma package. Out of 32,321 genes, 93 genes were identified to be the significant genes through SAM test. The functional annotation of significant genes was done using different databases such as gene ontology, Kyoto Encyclopedia of Genes and Genomes and Database for Annotation, Visualisation and Integrated Discovery. Significant genes were found to be enriched in haematopoietic cell lineage pathway and the cancer-causing pathway. Conclusions: This research identifies the important genes that have function in BC and regulation of such genes and pathway can be a potential treatment for the BC and prevent the tumour growth.

Background: India is one of the most severely affected countries due to the COVID-19 pandemic. A higher risk of severe illness and complications from COVID-19 had been observed in pregnant women as compared to nonpregnant women. The government of India on July 2, 2021, provided approval for the vaccination of pregnant women against COVID-19. A little data regarding the safety or harm during pregnancy of vaccination were available that time. Lack of safety data, fear, mistrust, underestimation of efficacy of vaccine, and chaos due to pandemic makes indecisive surrounding for pregnant women and this causes hesitancy with decision making about the COVID-19 vaccination. Aims and Objectives: This study aims to analyze the willingness and hesitancy of pregnant women to get vaccinated against COVID-19. Materials and Methods: This prospective study was conducted in a tertiary care institute in Northern India. Five hundred antenatal women who were eligible for COVID-19 vaccination were included in this study. Informed consent has been taken and data were analyzed after filling face to face questionnaire regarding vaccine acceptance or hesitancy. Results: The present study revealed low acceptance of COVID-19 vaccination in pregnancy. Prime reasons for the same are no allowance by the family and the possibility of vaccine harming the baby. Conclusion: Specific efforts should be directed toward high-risk populations including pregnant women and those who are planning for pregnancy. This will promote vaccination rates by increasing people’s trust in immunization and the health-care system.

IntroductionWhile cystic fibrosis (CF) lung disease is characterized by persistent inflammation and infections and chronic inflammatory diseases are often accompanied by autoimmunity, autoimmune reactivity in CF has not been studied in depth.MethodsIn this work we undertook an unbiased approach to explore the systemic autoantibody repertoire in CF using autoantibody microarrays.Results and discussionOur results show higher levels of several new autoantibodies in the blood of people with CF (PwCF) compared to control subjects. Some of these are IgA autoantibodies targeting neutrophil components or autoantigens linked to neutrophil-mediated tissue damage in CF. We also found that people with CF with higher systemic IgM autoantibody levels have lower prevalence of S. aureus infection. On the other hand, IgM autoantibody levels in S. aureus-infected PwCF correlate with lung disease severity. Diabetic PwCF have significantly higher levels of IgA autoantibodies in their circulation compared to nondiabetic PwCF and several of their IgM autoantibodies associate with worse lung disease. In contrast, in nondiabetic PwCF blood levels of IgA autoantibodies correlate with lung disease. We have also identified other autoantibodies in CF that associate with P. aeruginosa airway infection. In summary, we have identified several new autoantibodies and associations of autoantibody signatures with specific clinical features in CF.

Nodular amyloidoma in the lungs is a rare entity, also the occurrence of extramedullary plasmacytoma (EMP) in the lungs is rare. To have concomitant EMP and amyloidoma presented as a single lung mass is even rarer. There was only one similar case reported in the abstract form previously. Our case did not respond to many novel chemotherapy agents, suggesting that this combination of amyloidoma and plasmacytoma belonged to a poor prognosis entity, requiring different treatment modalities, such as early bone marrow transplantation or CART (chimeric antigen receptors T) therapy.

SMARCA4-deficient undifferentiated tumors (SMARCA4-dUT) are infrequently occurring aggressive neoplasms found predominantly in young male smokers. These tumors are distinguished by the loss of expression of Brahma-related gene 1 (BRG1) due to a deactivating mutation of SMARCA4. Immunophenotype can be variable but characteristically lack the expression of BRG1. SMARCA4-dUT has a poor prognosis and generally progresses or recurs. The median survival is around 6 months. Here, we report a case of a 36-year-old male smoker who presents with multiple right-sided lung masses. The patient was found to have a loss of SMARAC4 and SMARCA2 along with the absence of markers of vascular, melanocytic, lymphoid, keratin, or myogenic origin. Tumor size was reduced significantly after 3 cycles of carboplatin and 1 cycle of pembrolizumab. From reviewing the literature and the clinical course in our case, we suggest combination chemotherapy plus immune checkpoint inhibitor (ICI) therapy to be the first choice of therapy for treating SMARCA4-dUT of lungs. Further research and studies are needed to evaluate the response to ICI therapy alone or combination therapy (chemotherapy plus ICI).

Abstract Rationale Transbronchial cryobiopsy has been increasingly used to diagnose interstitial lung diseases. However, there is uncertainty regarding its accuracy and risks, mainly due to a paucity of prospective or randomized trials comparing cryobiopsy to surgical biopsy. Objectives To evaluate the diagnostic yield and complications of cryobiopsy in patients selected by multidisciplinary discussion. Methods This was a prospective cohort from 2017 to 2019. We included consecutive patients with suspected interstitial lung diseases being considered for lung biopsy presented at our multidisciplinary meeting. Measurements and main results Of 112 patients, we recommended no biopsy in 31, transbronchial forceps biopsy in 16, cryobiopsy in 54 and surgical biopsy in 11. By the end of the study, 34 patients had had cryobiopsy and 24 patients, surgical biopsy. Overall pathologic and multidisciplinary diagnostic yield of cryobiopsy was 47.1% and 61.8%, respectively. The yield increased over time for both pathologic (year 1: 28.6%, year 2: 54.5%, year 3: 66.7%, p = 0.161) and multidisciplinary (year 1: 50%, year 2: 63.6%, year 3: 77.8%, p = 0.412) diagnosis. Overall rate of grade 4 bleeding after cryobiopsy was 11.8%. Cryobiopsy required less chest tube placement (11.8% vs 100%, p

Cystic fibrosis (CF) lung disease begins early in childhood and is characterized by neutrophilic inflammation of the airways. Neutrophil extracellular traps (NETs) represent one mechanism by which neutrophils contribute to lung damage. The enzyme peptidylarginine deiminase 4 (PAD4) is required for NET formation. Our overall concept is that NET formation delivers PAD4 outside the neutrophil resulting in autoantibody generation, and this autoimmunity may be a novel mechanism contributing to CF lung disease progression. The aim of this study was to investigate clinical predictors of serum anti-PAD4 autoantibody (PAD4 Ab) levels in CF subjects with a wide range of ages from early childhood through middle age. We measured PAD4 Ab levels in sera from 104 CF subjects. PAD4 Abs were detectable among CF children as young as one year of age and elevated compared to paediatric healthy controls. PAD4 Ab levels increased significantly with age (r = 0.584, p

Acinetobacter baumannii is a bacterial pathogen that is commonly associated with hospital-acquired illnesses. Antimicrobial drug resistance in A. baumannii includes several penicillin classes, first and second-generation cephalosporins, cephamycins, most aminoglycosides, chloramphenicol, and tetracyclines. The recent rise in multidrug-resistant A. baumannii strains has resulted in an increase in pneumoniae associated with ventilators, urinary tract infections associated with the catheter, and bloodstream infections, all of which have increased complications in treatment, cost of treatment, and death. Small compounds known as antimicrobial peptides (AMPs) are known to have damaging effects on pathogenic bacteria. To determine their antimicrobial activity, AMPs are created from proteins acquired from various sources and evaluated in vitro. In the last phase of lytic cycle, bacteriophages release hydrolytic enzymes called endolysins that cleave the host’s cell wall. Due to their superior potency and specificity compared to antibiotics, lysins are used as antibacterial agents. In the present study, different types of endolysin from phages of A. baumannii were selected based on an extensive literature survey. From the PhaLP database, the sequences of the selected lysins were retrieved in FASTA format and antimicrobial peptides were found among them. With the help of available bioinformatic tools, the anti-biofilm property, anti-fungal property, cell-penetrating property, and cellular toxicity of the antimicrobial peptides were determined. Out of the fourteen antimicrobial peptides found from the eight selected endolysins of A. baumannii specific phage, eight of them has anti-biofilm property, nine of them has anti-fungal property, five of them has cell-penetrating property and all of them are non-toxic.

Introduction: Buruli Ulcer (BU) is caused due to mycobacteria, namely Mycobacterium ulcerans. Buruli ulcer is caused by the mycolactones that are secreted by the Mycobacterium ulcerans which results into the tissue necrosis. Metagenomics is a branch of genomics that deals with the study of uncultured microbial genomes present in natural samples like human body parts, environmental samples, food and dairy, disease conditions. Metagenomics branch has enabled us to explore and elucidate the importance of microbial genomes in healthy and infected samples. Aim: To evaluate metagenomic and microbial analysis of buruli and non buruli ulcer skin wound samples along with structural and functional analysis of MUL_3720 protein. Materials and Methods: The present analytical study was conducted from May 2021 to January 2022 at Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India. European Nucleotide Archive (ENA) database was used to retrieve metagenome data of BU and non BU skin lesions with the project id PRJEB14948. Galaxy server was used for the metagenomics analysis from quality control to identification and classification of microbial community in the samples. Different tools from the Galaxy like FASTQC, Trim Galore, KRAKEN2, convert kraken, Krona pie chart tools were used for metagenomic analysis and for taxonomic classification of microbes. Finally, Krona pie chart was generated that gives an elaborate understanding of the different microbes and their percentage in the BU. Complete annotation like protein structure prediction, domain analysis of MUL_3720 protein of Mycobacterium ulcerans was also done as potential drug target against BU. Statistical analysis was done using Krona pie chart generation and prediction. Results: Metagenomic analysis shows that there is difference in microbiome of BU and non BU samples. Differential microbes identified were Mycobacteriacae 1-2%, Sporomusa species 18-22% and Desulfovibrio halophillus 24-25%. Bacteria which were present in both the samples are Actiniidae, Desulfovibrio halophillus, Sphingomonas, and Mycobacteriacae. Structural and functional annotation of MUL_3720 protein of Mycobacterium ulcerans shows that MUL_3720 protein can be potential drug target for drug discovery. Conclusion: This study highlights the metagenome of Buruli Ulcer skin wound and can be used to identify potential drug targets for Buruli Ulcer. Metagenomic analysis of BU and non BU skin wound shows that there is difference in microbial community hence this information can be used in proper diagnostic and medication to combat Buruli Ulcer disease.

Abstract COVID-19 has emerged as global pandemic with largest damage to the public health, economy and human psyche.The genome sequence data obtained during the ongoing pandemic are valuable to understand the virus evolutionary patterns and spread across the globe. Increased availability of genome information of circulating SARS-CoV-2 strains in India will enable the scientific community to understand the emergence of new variants and their impact on human health. The first case of COVID-19 was detected in Chambal region of Madhya Pradesh state in mid of March 2020 followed by multiple introduction events and expansion of cases within next three months. More than 5000 COVID-19 suspected samples referred to Defence Research and Development Establishment, Gwalior, Madhya Pradesh were analyzed during the nation -wide lockdown and unlock period. A total of 136 cases were found positive over a span of three months that included virus introduction to the region and its further spread. Whole genome sequences employing Oxford nanopore technology were generated for 26 SARS-CoV-2 circulating in 10 different districts in Madhya Pradesh state of India. This period witnessed index cases with multiple travel histories responsible for introduction of COVID-19 followed by remarkable expansion of virus. The genome wide substitutions including in important viral proteins were identified. The detailed phylogenetic analysis revealed the circulating SARS-CoV-2 clustered in multiple clades including A2a, A4 and B. The cluster-wise segregation was observed, suggesting multiple introduction links and subsequent evolution of virus in the region. This is the first comprehensive whole genome sequence analysis from central India, which revealed the emergence and evolution of SARS-CoV-2 during thenation-wide lockdown and unlock.

Background: Gene expression information can be decoded to identify not only differentially expressed genes but also co-expressed genes that can give insight into protein interaction network. Current research has been done for the prediction of genes associated with Neurodevelopmental process using Microarray data and to construct the network of coexpressed genes and their functional annotation. Methods: Mesenchymal stem cells (MSCs) were exposed with Resveratrol (RV), Nerve Growth Factor (NGF) and RV+NGF to study the effect of neuroprotective role of RV (Data submitted NCBI's Gene Expression Omnibus (GEO Series accession number GSE121261). Bioinformatics software's, tools and databases like R and Bioconductor, Affy package, CoExpress 1.0b software, Metascape tool and Gene Ontology database was used prediction and functional enrichment of coexpressed genes. Normalization was done using RMA (Robust Multi-array Average) as implemented in Affy package and co-expressed genes were identified using CoExpress 1.0b with default parameters. Results: Co- expression result shows that total 135 genes have same gene expression across microarray chip these genes have function in different biological processes like, developmental processes, MAPK TRK pathway, muscle structure development etc. Total fifteen were identified that have function in nervous system development. Conclusions: This study identifies the list of co-expressed that were expressed in neurodevelopmental stage. These genes can be used further as neuronal markers, neuronal injury identification and diagnosis prospective at the developmental stage. Further verification methods are required for these predicted proteins for their applicability in drug development process.

Although extracellular host DNA (ecDNA) levels in CF airways were linked to airflow obstruction and recombinant DNAse therapy is beneficial for CF patients, it remains incompletely understood whether ecDNA also leads to an autoimmune response. Here we hypothesized that chronic presence of DNA in CF airways triggers the production of autoantibodies targeting host human DNA. We measured the levels of IgA autoantibodies recognising host double-stranded (ds) DNA in the blood and sputum samples of CF patients and only sera of controls subjects and patients suffering from rheumatoid arthritis and systemic lupus erythematosus (SLE) that served as non-CF, autoimmune disease cohorts. We found that concentrations of anti-dsDNA IgA, but not IgG, autoantibodies in the circulation were significantly elevated in adult CF patients compared to age-matched, control subjects. Systemic levels of anti-dsDNA IgA antibodies negatively correlated with FEV1% predicted, a measure of lung function, in CF patients. Anti-dsDNA IgA autoantibodies were also detected in CF sputa but sputum levels did not correlate with the degree of airway obstruction or sputum levels of DNA. We also found elevated autoantibody levels in CF children as 76.5% of CF patients younger than 10 years and 87.5% of CF patients 10–21 years had higher blood anti-dsDNA IgA levels than the highest value found in healthy control adults. Overall, our results detect elevated systemic anti-dsDNA IgA autoantibody levels in CF adults, teenagers and young children. We speculate that the appearance of an autoimmune response against host DNA in CF is an early event potentially contributing to disease pathogenesis.Highlights CF serum contains elevated levels of anti-dsDNA IgA, but not anti-dsDNA IgG, autoantibodies Anti-dsDNA IgA autoantibody levels in serum correlate with airflow obstruction in CF Anti-dsDNA IgA autoantibodies are detected in CF sputum but do not correlate with airflow obstruction Anti-dsDNA IgA autoantibodies are also elevated in the blood of the majority of CF toddlers and youth

Abstract Background Prednisone has been shown to reverse lung function declines in hypersensitivity pneumonitis patients without established fibrosis. Second line immunosuppressants like azathioprine and mycophenolate mofetil have a steroid sparing effect and improve DLCO. There is no published literature on the use of leflunomide in such patients. Methods We reviewed our experience with leflunomide for treatment of chronic hypersensitivity pneumonitis in 40 patients. We stratified patients according to the presence or absence of significant (> 20%) fibrosis. We studied the effect of leflunomide on FVC and DLCO trajectory and reported the changes at 12 months. Results Treatment with leflunomide tended to improve the estimated FVC slope from 0.18 ± 1.90% (SEM) of predicted per year to 4.62 ± 1.65% of predicted (NS, p = 0.118). It significantly improved the FVC at 12 months of treatment by 4.4% of predicted (p = 0.02). DLCO continued to increase at 1.45 ± 1.44% (SEM) of predicted per year. Non-fibrotic cHP patients had the largest gain in pulmonary function. Their FVC increased by 8.3% (p = 0.001) and DLCO by 4.8% (p = 0.011). Patients with fibrotic cHP did not improve. Leflunomide treatment was associated with significant gastrointestinal and other adverse effects leading 40% of patients to discontinue therapy. It had a significant steroid sparing effect with half the patients weaned off prednisone entirely. Conclusions Leflunomide appears to be a fairly well tolerated steroid sparing immunosuppressant that improves pulmonary function in cHP patients. It is most effective in patients without significant fibrosis.

Among thoracic tumors, these include subsets of a relatively newly described and yet to be fully characterized tumor entity: SMARCA4-deficient Undifferentiated Tumor (SMARCA4-dUT). Mutations of SMARCA4 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4) gene and loss of BRG1 (Brahma-related gene-1) is the underlying molecular hallmark of SMARCA4-dUT. They mostly involved the mediastinum, lung, and/or pleura showing undifferentiated round cell or rhabdoid morphology associated with aggressive clinical behavior. The pathogenesis of these tumors is still not clear. Morphologically, SMARAC4-dUT is differentiated from SMARCA4-dNSCLC by the presence of squamous and solid components in the latter. Immunohistochemically SMARC4-dUT has characteristic loss of SMARCA4 and SMARCA2 and strong expression of SOX2, CD34, and SALL4. Common sites of metastasis include lymph nodes, bones, and adrenal glands but rarely brain metastasis. We present a unique and rare case of a 76-year-old male with a right lung mass with documented pathology of SMARCA4-dUT and was found to have multiple brain metastases.

Stiff person syndrome (SPS) is a rare autoimmune disease caused by lack of inhibition to excitatory neurotransmitters in the central nervous system (CNS) leading to inappropriate motor unit firing. The pathophysiology is incompletely understood; however, high titers of antiglutamic acid decarboxylase antibody (anti-GAD Ab) are strongly associated with this disease. We present a 50-year-old woman with a history of ongoing gait and balance issues for 5 years with multiple negative workups. She recently had an acute exacerbation which left her bedbound, unable to move her legs or turn from side to side. After a negative workup at an outside hospital, the patient was discharged to a subacute rehabilitation facility. She then presented to our institution due to worsening of her condition and was ultimately diagnosed with SPS which was successfully treated. We review the case presentation and treatment options in the context of a severe disabling disease presentation.

Abstract Background Insecticidal fabrics are important personal protective measures against mosquitoes, ticks and other disease vectors. In the absence of internationally accepted guidelines, bioefficacy tests have been carried out using continuous exposure and three minutes exposure bioassay methods. Recently, we have reported an improved method for bioefficacy testing of insecticidal fabrics, which involves continuous exposure of mosquitoes to the test fabrics. The present paper reports the comparative evaluation of the outcomes of the continuous exposure bioassay and the three minutes bioassay on the same fabric samples. Methods Permethrin content in the treated fabric samples was determined through HPLC analysis and NMR studies were performed to establish the stability of the analyte. Bioefficacy tests were carried out against dengue vector Aedes aegypti and malaria vector Anopheles stephensi as per the improved test method and the three minutes bioassay method. Results The permethrin doses in the fabric samples ranged from 60 to 3000 mg/m2 and 36.2% of permethrin was retained after 10 washings. The extraction and chromatographic analysis were not found to affect the stability of permethrin. In continuous exposure, all fabric samples showed bioefficacy, as the mean complete knockdown time for both Ae. aegypti (10.5–34.5 min) and An. stephensi (14.5–36.8 min) was ≤ 71.5 min. The same samples were found to be not effective when tested using the three minutes bioassay method, since the knockdown and mortality percentages were well below the required bioefficacy values. The bioefficacy of the fabric samples in terms of complete knockdown time was significantly higher against Ae. aegypti in comparison to An. stephensi. The mean complete knockdown time of Ae. aegypti increased to 48.3 min after 10 washings indicating a significant reduction in bioefficacy. Conclusions Bioefficacy testing of the insecticidal fabrics using the improved method resulted in outcomes, which could be correlated better with the permethrin content in the fabric samples. The improved method is more appropriate for the testing of insecticidal fabrics than the three minutes bioassay method. Further evaluation of the improved method using different test arthropods could help in the formulation of specific guidelines for the bioefficacy testing of insecticidal fabrics.

Objective: Parasites of the genus Plasmodium cause a great deal of morbidity and mortality worldwide, largely in regions with limited access and indication to the tools necessary to control mosquito populations and to treat human infections of malaria. Five species of this class of eukaryotic pathogens cause different human diseases, with Plasmodium falciparum alone infecting approximately 500 million people per year and resulting in approximately one million deaths. Materials and Methods: The two genes encoding the Shewanella-like protein phosphatases of P. falciparum, SHLP1 and SHLP2, are conserved among members of Plasmodiidae family. SHLP is frequently found in asexual blood stages and expressed at all stages of the life cycle of parasite. SHLP deletion results in a reduction in microneme formation, ookinetes (zygote) development, and complete ablation of oocyst formation, thereby blocking transmission of parasite. Structure modeling of SHLP protein can be helpful in understanding the active site and binding site information and hence can be used for drug designing and for therapeutics against malaria. Study of SHLP and its variants was carried out using UniProtKB database. Homology modeling was performed using Schrödinger software, and the modeled structure was verified using Ramachandran plot. Ten antioxidants were searched in PubChem database for docking and comparative analysis. Docking was carried out against SHLP-modeled protein, and the ligand–protein interaction map was analyzed. Effective role of resveratrol was studied against SHLP protein using docking method to identify protein–ligand interaction scheme and bond formation. Results: SHLP protein was modeled and docking was carried out to identify the binding sites and interaction with the SHLP protein. Docking study suggested that resveratrol has a strong interaction with SHLP protein and can be used as a potential ligand for drug designing. Conclusion: SHLP plays a crucial role in ookinetes and microneme development in Plasmodium; hence ligand, which can interact and inhibit SHLP protein, can be a potential drug against malarial parasite development. We studied the binding of antioxidant, such as resveratrol, with this protein-using docking method and it was found that resveratrol as an antioxidant can bind with the target SHLP protein.

The use of electronic cigarettes, or “vaping,” has garnered significant popularity and attention in recent years. Its pulmonary and systemic effects have yet to be fully studied and quantified, and recent reports of vaping-related illnesses and deaths have brought the clinical consequences of vaping into the public spotlight. This report describes the case of a 34 year old woman who presented to clinic with new-onset cough and dyspnea, shortly after beginning to use electronic cigarettes. Imaging demonstrated new micronodular opacities and mediastinal lymphadenopathy, while pathology confirmed granulomatous disease. After she received counseling and successfully quit vaping, her symptoms resolved and repeat imaging demonstrated resolution of parenchymal findings and lymphadenopathy. This case report therefore presents a longitudinal narrative of reversible vaping-related pulmonary granulomatous disease.

Ecotin, first described in Escherichia coli, is a potent inhibitor of a broad range of serine proteases including those typically released by the innate immune system such as neutrophil elastase (NE). Here we describe the identification of ecotin orthologs in various Campylobacter species, including Campylobacter rectus and Campylobacter showae residing in the oral cavity and implicated in the development and progression of periodontal disease in humans. To investigate the function of these ecotins in vitro, the orthologs from C. rectus and C. showae were recombinantly expressed and purified from E. coli. Using CmeA degradation/protection assays, fluorescence resonance energy transfer and NE activity assays, we found that ecotins from C. rectus and C. showae inhibit NE, factor Xa and trypsin, but not the Campylobacter jejuni serine protease HtrA or its ortholog in E. coli, DegP. To further evaluate ecotin function in vivo, an E. coli ecotin-deficient mutant was complemented with the C. rectus and C. showae homologs. Using a neutrophil killing assay, we demonstrate that the low survival rate of the E. coli ecotin-deficient mutant can be rescued upon expression of ecotins from C. rectus and C. showae. In addition, the C. rectus and C. showae ecotins partially compensate for loss of N-glycosylation and increased protease susceptibility in the related pathogen, Campylobacter jejuni, thus implicating a similar role for these proteins in the native host to cope with the protease-rich environment of the oral cavity.

Cystic fibrosis (CF) airway disease is characterized by chronic microbial infections and infiltration of inflammatory polymorphonuclear (PMN) granulocytes. Staphylococcus aureus (S. aureus) is a major lung pathogen in CF that persists despite the presence of PMNs and has been associated with CF lung function decline. While PMNs represent the main mechanism of the immune system to kill S. aureus, it remains largely unknown why PMNs fail to eliminate S. aureus in CF. The goal of this study was to observe how the CF airway environment affects S. aureus killing by PMNs. PMNs were isolated from the blood of healthy volunteers and CF patients. Clinical isolates of S. aureus were obtained from the airways of CF patients. The results show that PMNs from healthy volunteers were able to kill all CF isolates and laboratory strains of S. aureus tested in vitro. The extent of killing varied among strains. When PMNs were pretreated with supernatants of CF sputum, S. aureus killing was significantly inhibited suggesting that the CF airway environment compromises PMN antibacterial functions. CF blood PMNs were capable of killing S. aureus. Although bacterial killing was inhibited with CF sputum, PMN binding and phagocytosis of S. aureus was not diminished. The S. aureus-induced respiratory burst and neutrophil extracellular trap release from PMNs also remained uninhibited by CF sputum. In summary, our data demonstrate that the CF airway environment limits killing of S. aureus by PMNs and provides a new in vitro experimental model to study this phenomenon and its mechanism.

Cicatricial organizing pneumonia is an uncommon form of organizing pneumonia, which may manifest as persisting linear opacities on computerized tomography (CT) scan mimicking a fibrosing interstitial pneumonia. It may also manifest with pulmonary ossification, which is a metaplastic bone formation within the lung tissue. The latter presentation could be either nodular or dendriform, both secondary to underlying lung disease and rarely idiopathic. Dendriform pulmonary ossification (DPO) has rarely been described as a cause of spontaneous pneumothorax. We present a case of a 55-year-old male with history of recurrent pneumothoraces and worsening dyspnea on exertion. A CT of the chest revealed progressive bilateral sub-pleural and peribronchovascular reticular opacities associated with densely ossified branching and nodular opacities. Video-assisted thoracoscopic biopsy of the lung demonstrated cicatricial organizing pneumonia with areas of marked diffuse DPO. The case highlights that dendriform pulmonary ossification arising from cicatricial organizing pneumonia should be considered in the differential diagnosis of recurrent pneumonias among patients with lower lobe sub-pleural reticular opacities. The case highlights that dendriform pulmonary ossification rarely can cause spontaneous pneumothorax and can be associated with cicatricial organizing pneumonia and reticular opacities on imaging.

Neuronal developmental disorder is a class of diseases in which there is impairment of the central nervous system and brain function. The brain in its developmental phase undergoes tremendous changes depending upon the stage and environmental factors. Neurodevelopmental disorders include abnormalities associated with cognitive, speech, reading, writing, linguistic, communication, and growth disorders with lifetime effects. Computational methods provide great potential for betterment of research and insight into the molecular mechanism of diseases. In this study, we have used four samples of microarray neuronal developmental data: control, RV (resveratrol), NGF (nerve growth factor), and RV + NGF. By using computational methods, we have identified genes that are expressed in the early stage of neuronal development and also involved in neuronal diseases. We have used MeV application to cluster the raw data using distance metric Pearson correlation coefficient. Finally, 60 genes were selected on the basis of coexpression analysis. Further pathway analysis was done using the Metascape tool, and the biological process was studied using gene ontology database. A total of 13 genes AKT1, BAD, BAX, BCL2, BDNF, CASP3, CASP8, CASP9, MYC, PIK3CD, MAPK1, MAPK10, and CYCS were identified that are common in all clusters. These genes are involved in neuronal developmental disorders and cancers like colorectal cancer, apoptosis, tuberculosis, amyotrophic lateral sclerosis (ALS), neuron death, and prostate cancer pathway. A protein-protein interaction study was done to identify proteins that belong to the same pathway. These genes can be used to design potential inhibitors against neurological disorders at the early stage of neuronal development. The microarray samples discussed in this publication are part of the data deposited in NCBI’s Gene Expression Omnibus (Yadav et al., 2018) and are accessible through GEO Series (accession number GSE121261).

Introduction: Late presentation has been observed as the hallmark of breast cancer, due to lack of awareness and non-existent breast cancer screening programmes. Breast cancer is the most common female cancer worldwide including India. The study was conducted to assess the awareness about breast cancer among the reproductive women and to find out the factors responsible for increased awareness. Methodology: A cross-sectional descriptive study was carried out among 250 reproductive age group females of rural and urban area of Etawah district. Information was collected under following broad headings:-Educational Status, socio-demographic profile and knowledge of various risk factors, preventive measures and screening. Result: Majority of the participants were illiterate (23%) and belong to upper lower (34%) and lower class (33%).Out of 250 participants 147(59%)were unaware about breast cancer. On comparing knowledge, rural females were more unaware about breast cancer, its warning symptoms, signs and its preventive measures. Also awareness of Self Breast Examination was very low in both urban and rural population. Conclusion: The present study hereby concludes that knowledge about breast cancer among reproductive females was low. In comparison to urban area this knowledge is very low in rural area.

Introduction: Acceptance of family planning is lagging behind even if community feels the need of restricting the fertility because of various socio-cultural factors, misconceptions and lack of knowledge. This study was aimed to study the prevalence of unmet need for family planningamong sexually active married women of reproductive age group in a rural area of Etawah and its co-relates. Methods: Cross sectional study was conducted in Community Development Block, Saifai, Etawah, UP on810 sexually active females of reproductive age group. Subjects were included in study from purposively selected 5 villages of Saifai. Results: The mean age of respondents was 29.19±6.7 years. The prevalence of unmet need for family planning was estimated to be 45.7% among study subjects. The prevalence of unmet need for family planning was found more among females of lower socioeconomic group, those with lower educational status and their partners as well, females having >2 children and females belonging to nuclear family and association of all these factors was found statistically significant with unmet need for family planning. Conclusion: There is urgent need to focus the efforts on family planning towards all the females in reproductive age group in general and towards those older age group, illiterate belong to nuclear family and lower socio-economic status.

Background: Mosquitoes are well known as vectors of several disease causing pathogens. The extensive use of synthetic insecticides in the mosquito control strategies resulted to the development of pesticide resistance and fos- tered environmental deterioration. Hence in recent years plants become alternative source of mosquito control agents. The present study assessed the larvicidal and oviposition altering activity of six different plants species- Alstonia scholaris, Callistemon viminalis, Hyptis suaveolens, Malvastrum coromandelianum, Prosopis juliflora, Vernonia cinerea against Aedes albopictus mosquito in laboratory. Methods: Leaf extracts of all the six plants species in five different solvents of various polarities were used in the range of 20–400ppm for larval bioassay and 50,100 and 200ppm for cage bioassay (for the study of oviposition be- havior) against Ae. albopictus. The larval mortality data were recorded after 24 h and subjected to Probit analysis to determine the lethal concentrations (LC50), while OAI (Oviposition activity index) was calculated for oviposition altering activity of the plant extracts. Results: Vernonia cinerea extract in acetone and C. viminalis extract in isopropanol were highly effective against Aedes albopictus larvae with LC50 value 64.57, 71.34ppm respectively. Acetone extract of P. juliflora found to be strong oviposition-deterrent which inhibited >2 fold egg laying (OAI-0.466) at 100ppm. Conclusion: Vernonia cinerea and C. viminallis leaf extracts have the potential to be used as larvicide and P.juliflora as an oviposition-deterrent for the control of Ae. albopictus mosquito.

We investigated two siblings with granulomatous histiocytosis prominent in the nasal area, mimicking rhinoscleroma and Rosai-Dorfman syndrome. Genome-wide linkage analysis and whole-exome sequencing identified a homozygous frameshift deletion in SLC29A3, which encodes human equilibrative nucleoside transporter-3 (hENT3). Germline mutations in SLC29A3 have been reported in rare patients with a wide range of overlapping clinical features and inherited disorders including H syndrome, pigmented hypertrichosis with insulin-dependent diabetes, and Faisalabad histiocytosis. With the exception of insulin-dependent diabetes and mild finger and toe contractures in one sibling, the two patients with nasal granulomatous histiocytosis studied here displayed none of the many SLC29A3-associated phenotypes. This mild clinical phenotype probably results from a remarkable genetic mechanism. The SLC29A3 frameshift deletion prevents the expression of the normally coding transcripts. It instead leads to the translation, expression, and function of an otherwise noncoding, out-of-frame mRNA splice variant lacking exon 3 that is eliminated by nonsense-mediated mRNA decay (NMD) in healthy individuals. The mutated isoform differs from the wild-type hENT3 by the modification of 20 residues in exon 2 and the removal of another 28 amino acids in exon 3, which include the second transmembrane domain. As a result, this new isoform displays some functional activity. This mechanism probably accounts for the narrow and mild clinical phenotype of the patients. This study highlights the 'rescue' role played by a normally noncoding mRNA splice variant of SLC29A3, uncovering a new mechanism by which frameshift mutations can be hypomorphic.