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Community detection is an important area of research in social media mining. Numerous algorithms have been developed to detect disjoint, overlapping, and dynamic communities in a network. However, most of the existing algorithms do not consider the influence of each node in a group, which may be different and can affect the result of community detection. In this paper, we have proposed a novel Louvain-based algorithm named “NI-Louvain,” which considers the influence of each node in a group that not only detects community but also most influential nodes in the community. The proposed algorithm works in three steps. First, the input graph is processed to reduce its density. This is done by calculating cliques from the graph. In second step, Louvain's multilevel algorithm is applied to this clique graph. The resultant community obtained has a better modularity value than the communities obtained from existing algorithms like edge betweenness, label propagation, leading eigen, Louvain, fast greedy, walktrap, and infomap. In the third step, the nodes of resultant communities are transformed back to the nodes of the original graph. This step is beneficial in detecting overlapping communities, fuzzy membership of each node, most influential node in each community formed, and outlier nodes.

Regulatory T cells (Treg) are conventionally viewed to suppress endogenous and therapyinduced anti-tumor immunity; however, their role in modulating responses to immune checkpoint blockade (ICB) is unclear. In this study, we integrated single-cell RNAseq/TCRseq of >73,000 tumor-infiltrating Treg(TIL-Treg) from anti-PD-1-treated and treatment naive non-small cell lung cancers (NSCLC) with single cell analysis of tumor-associated antigen (TAA)-specific Tregderived from a murine tumor model. We identified 10 subsets of human TIL-Treg, most of which have high concordance with murine TIL-Tregsubsets. Notably, one subset selectively expresses high levels of OX40 and GITR, whose engangement by cognate ligand mediated proliferative programs and NF-kB activation, as well as multiple genes involved in Tregsuppression, in particular LAG3. Functionally, the OX40hiGITRhisubset in the most highly suppressiveex vivoand Tregexpression of OX40, GITR and LAG3, correlated with resistance to PD-1 blockade. Surprisingly, in the murine tumor model, we found that virtually all TIL-Tregexpressing T cell receptors that are specific for TAA fully develop a distinct Th1-like signature over a two-week period after entry into the tumor, down-regulating FoxP3 and up-regulating expression ofTBX21 (Tbet), IFNγ and certain pro-inflammatory granzymes. Application of a gene score from the murine TAA-specific Th1-like Tregsubset to the human single-cell dataset revealed a highly analogous subcluster that was enriched in anti-PD-1 responding tumors. These findings demonstrate that TIL-Tregpartition into multiple distinct transcriptionally-defined subsets with potentially opposing effects on ICB-induced anti-tumor immunity and suggest that TAA-specific TIL-Tregmay positively contribute to anti-tumor responses.One-Sentence SummaryWe define 10 subsets of lung cancer-infiltrating regulatory T cells, one of which is highly suppressive and enriched in anti-PD-1 non-responders and the other is Th1-like and is enriched in PD-1 responders.

Mesothelioma is a rare and fatal cancer with limited therapeutic options until the recent approval of combination immune checkpoint blockade. Here we report the results of the phase 2 PrE0505 trial (NCT02899195) of the anti-PD-L1 antibody durvalumab plus platinum-pemetrexed chemotherapy for 55 patients with previously untreated, unresectable pleural mesothelioma. The primary endpoint was overall survival compared to historical control with cisplatin and pemetrexed chemotherapy; secondary and exploratory endpoints included safety, progression-free survival and biomarkers of response. The combination of durvalumab with chemotherapy met the pre-specified primary endpoint, reaching a median survival of 20.4 months versus 12.1 months with historical control. Treatment-emergent adverse events were consistent with known side effects of chemotherapy, and all adverse events due to immunotherapy were grade 2 or lower. Integrated genomic and immune cell repertoire analyses revealed that a higher immunogenic mutation burden coupled with a more diverse T cell repertoire was linked to favorable clinical outcome. Structural genome-wide analyses showed a higher degree of genomic instability in responding tumors of epithelioid histology. Patients with germline alterations in cancer predisposing genes, especially those involved in DNA repair, were more likely to achieve long-term survival. Our findings indicate that concurrent durvalumab with platinum-based chemotherapy has promising clinical activity and that responses are driven by the complex genomic background of malignant pleural mesothelioma., In a phase 2 trial, the combination of chemotherapy with durvalumab, an anti-PD-L1 antibody, exhibited promising clinical activity in patients with previously untreated, unresectable mesothelioma, with additional analyses providing insights into genomic and immunologic features potentially associated with response.

Identifying neoepitopes that elicit an adaptive immune response is a major bottleneck to developing personalized cancer vaccines. Experimental validation of candidate neoepitopes is extremely resource intensive, and the vast majority of candidates are non-immunogenic, making their identification a needle-in-a-haystack problem. To address this challenge, we present computational methods for predicting MHC-I epitopes and identifying immunogenic neoepitopes with improved precision. The BigMHC method comprises an ensemble of seven pan-allelic deep neural networks trained on peptide-MHC eluted ligand data from mass spectrometry assays and transfer learned on data from assays of antigen-specific immune response. Compared with four state-of-the-art classifiers, BigMHC significantly improves the prediction of epitope presentation on a test set of 45,409 MHC ligands among 900,592 random negatives (AUROC=0.9733, AUPRC=0.8779). After transfer learning on immunogenicity data, BigMHC yields significantly higher precision than seven state-of-the-art models in identifying immunogenic neoepitopes, making BigMHC effective in clinical settings. All data and code are freely available athttps://github.com/KarchinLab/bigmhc.

Community detection is a dominant research field in social media mining. Numerous algorithms have been developed to detect community structure in network. Each of them focuses on different characte...

Every method used to quantify biomolecular interactions has its own strengths and limitations. To quantify protein‐DNA binding affinities, nitrocellulose filter binding assays with (32)P‐labeled DNA quantify K (d) values from 10(−12) to 10(−8) M but have several technical limitations. Here, we considered the suitability of biolayer interferometry (BLI), which monitors association and dissociation of a soluble macromolecule to an immobilized species; the ratio k (off)/k (on) determines K (d). However, for lactose repressor protein (LacI) and an engineered repressor protein (“LLhF”) binding immobilized DNA, complicated kinetic curves precluded this analysis. Thus, we determined whether the amplitude of the BLI signal at equilibrium related linearly to the fraction of protein bound to DNA. A key question was the effective concentration of immobilized DNA. Equilibrium titration experiments with DNA concentrations below K (d) (equilibrium binding regime) must be analyzed differently than those with DNA near or above K (d) (stoichiometric binding regime). For ForteBio streptavidin tips, the most frequent effective DNA concentration was ~2 × 10(−9) M. Although variation occurred among different lots of sensor tips, binding events with K (d) ≥ 10(−8) M should reliably be in the equilibrium binding regime. We also observed effects from multi‐valent interactions: Tetrameric LacI bound two immobilized DNAs whereas dimeric LLhF did not. We next used BLI to quantify the amount of inducer sugars required to allosterically diminish protein‐DNA binding and to assess the affinity of fructose‐1‐kinase for the DNA‐LLhF complex. Overall, when experimental design corresponded with appropriate data interpretation, BLI was convenient and reliable for monitoring equilibrium titrations and thereby quantifying a variety of binding interactions.

BACKGROUND: Recent studies have reported T cell immunity to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in unexposed donors, possibly due to crossrecognition by T cells specific for common cold coronaviruses (CCCs). True T cell crossreactivity, defined as the recognition by a single TCR of more than one distinct peptide-MHC ligand, has never been shown in the context of SARS-CoV-2. METHODS: We used the viral functional expansion of specific T cells (ViraFEST) platform to identify T cell responses crossreactive for the spike (S) glycoproteins of SARS-CoV-2 and CCCs at the T cell receptor (TCR) clonotype level in convalescent COVID-19 patients (CCPs) and SARS-CoV-2–unexposed donors. Confirmation of SARS-CoV-2/CCC crossreactivity and assessments of functional avidity were performed using a TCR cloning and transfection system. RESULTS: Memory CD4(+) T cell clonotypes that crossrecognized the S proteins of SARS-CoV-2 and at least one other CCC were detected in 65% of CCPs and unexposed donors. Several of these TCRs were shared among multiple donors. Crossreactive T cells demonstrated significantly impaired SARS-CoV-2–specific proliferation in vitro relative to monospecific CD4(+) T cells, which was consistent with lower functional avidity of their TCRs for SARS-CoV-2 relative to CCC. CONCLUSIONS: Our data confirm, for what we believe is the first time, the existence of unique memory CD4(+) T cell clonotypes crossrecognizing SARS-CoV-2 and CCCs. The lower avidity of crossreactive TCRs for SARS-CoV-2 may be the result of antigenic imprinting, such that preexisting CCC-specific memory T cells have reduced expansive capacity upon SARS-CoV-2 infection. Further studies are needed to determine how these crossreactive T cell responses affect clinical outcomes in COVID-19 patients. FUNDING: NIH funding (U54CA260492, P30CA006973, P41EB028239, R01AI153349, R01AI145435-A1, R21AI149760, and U19A1088791) was provided by the National Institute of Allergy and Infectious Diseases, the National Cancer Institute, and the National Institute of Biomedical Imaging and Bioengineering. The Bloomberg~Kimmel Institute for Cancer Immunotherapy, The Johns Hopkins University Provost, and The Bill and Melinda Gates Foundation provided funding for this study.

PD-1 blockade unleashes CD8 T cells1, including those specific for mutation-associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit these T cell responses. Single-cell transcriptomics have revealed global T cell dysfunction programs in tumour-infiltrating lymphocytes (TIL). However, the majority of TIL do not recognize tumour antigens2, and little is known about transcriptional programs of MANA-specific TIL. Here, we identify MANA-specific T cell clones using the MANA functional expansion of specific T cells assay3 in neoadjuvant anti-PD-1-treated non-small cell lung cancers (NSCLC). We use their T cell receptors as a ‘barcode’ to track and analyse their transcriptional programs in the tumour microenvironment using coupled single-cell RNA sequencing and T cell receptor sequencing. We find both MANA- and virus-specific clones in TIL, regardless of response, and MANA-, influenza- and Epstein–Barr virus-specific TIL each have unique transcriptional programs. Despite exposure to cognate antigen, MANA-specific TIL express an incompletely activated cytolytic program. MANA-specific CD8 T cells have hallmark transcriptional programs of tissue-resident memory (TRM) cells, but low levels of interleukin-7 receptor (IL-7R) and are functionally less responsive to interleukin-7 (IL-7) compared with influenza-specific TRM cells. Compared with those from responding tumours, MANA-specific clones from non-responding tumours express T cell receptors with markedly lower ligand-dependent signalling, are largely confined to HOBIThigh TRM subsets, and coordinately upregulate checkpoints, killer inhibitory receptors and inhibitors of T cell activation. These findings provide important insights for overcoming resistance to PD-1 blockade., Single-cell RNA sequencing and T cell receptor sequencing are combined to identify transcriptional programs specific to mutation-associated neoantigen-specific T cells in non-small cell lung cancers treated with anti-PD-1, providing insights into resistance to PD-1 blockade.

Big data is affecting every walk of life right from mobile maps, GPS, online shopping, wearable gadgets to our day-to-day activities. Data generated are in terabytes which if collected and mined properly can infer important results for decision making and planning in business, education, health care, etc. So, big data analytics are in demand. Big data analytics require a tool for data analysis and a platform for parallel computing. R is one of the most robust languages for data science, whereas Hadoop is distributed computing framework to handle big data processing. R and Hadoop integration seems to be a perfect combination for data analytics. In this paper, we have explored major big data technologies available and also compared major data analytics languages being used nowadays. We have discussed procedures for combining R and Hadoop to get best of the two in analysing big data. This paper will be beneficial for researchers who are working in the area of big data analysis.

It has been 23 years since the initial version of R was launched. In this duration R has been modified several times, and now it has evolved as a giant in the field of data analysis. Nowadays R is one of the best known tool for data mining, statistics and machine learning. Today R is enjoying a vast community that provides quick response and support. With over 10000 packages available to download as per our requirement, R appears as complete solution for all data science related task .In this paper we have discussed brief history of R project. We have also described the present status of R and distinguish features of R. We have tried to explain why R is the first choice for data analysis by comparing it with other languages available for data science. We have also discussed its limitations and solutions to deal with these. This paper will be beneficial for researchers to gain an insight of R, who are going to work on data analysis related project.

Background: Recent data indicate that one in five women undergo caesarean section (CS). In the last decade, there has been a dramatic increase in the caesarean section rate worldwide, which now exceeds 30% in some regions. Thus, the increasing rate of caesarean section became a matter of international public health concern. Our study aimed to classify the CS-based on Robson ten group classification system (RTGCS) criteria which will subsequently enable us to standardise the indication of CS and establish protocols to reduce the number of CS in our set up.Method: A retrospective study was conducted in ESI Hospital, New Delhi wherein Robson TGCS was used to classify CS for 15 months (January 2019 to April 2020).Results: Overall CS rate in our hospital over the specified period was 34.5%. All women with one or more previous cesareans (group V) had the maximum number of cesareans, 37%, followed by nulliparous, single, cephalic, term pregnancy (induced) i.e group II, 22.1% and nulliparous women more than 37 weeks in spontaneous labour (group I), 9.5%.Conclusions: RTGCS is easy to comprehend and reproduce. All deliveries and cesareans should be universally categorized by the Robsons TGCS. An attempt should be made to evaluate the group contributing most to the CS rate and interventions should be made accordingly.

A cornual gestation is one of the most hazardous and life-threatening type of ectopic pregnancy with a mortality rate of 2-5 times higher than other ectopic pregnancies. Because of the myometrium stretch ability, they usually present late around 7-12 weeks of gestation. Thus, the diagnosis and treatment of such cases become challenging. In the case of ruptured cornual ectopic pregnancy, the patient usually presents with hemodynamic instability. Presenting a case report of a 28-year-old female who presented to the labour room of ESI hospital, Okhla, New Delhi at 12 weeks of pregnancy in a state of shock. A provisional diagnosis of ruptured cornual ectopic was made based on clinical examination and ultrasound report. Resuscitation followed by emergency laparotomy done as a life-saving procedure for the patient. Ruptured cornual ectopic needs urgent intervention and multidisciplinary approach. However, with the advancement and expertise in the field of radiology and early diagnosis can be made which can contribute towards more conservative management of such cases.

Acute puerperal inversion is rare but potentially fatal obstetric emergency and prompt recognition will enable immediate repositioning of uterus before it becomes edematous and incarcerated. Manual repositioning along with use of uterine balloon tamponade is simple and effective way for repositioning of inverted uterus as well as prevention of recurrence.

Shigellosis is an endemic disease prevalent in developing and poor countries due to fecal-oral transmission resulting a significant morbidity and mortality rate. Emergence of multidrug resistant (MDR) in Shigella sp. reveals the inefficacy towards the first line antibiotics like quinolones, cotrimoxazole and ampicillin against it. There is continuous need to monitor the characteristics and antibiotic resistance patterns of this pathogen regarding the identification of new potential therapeutic drug targets. Availability of complete protein of different Shigella species viz flexneri, body, dysentery and son has made it possible to carry out the Insilico analysis of its protein for the identification of potential vaccine and drug targets. Subtractive proteomics approach is being used to mine the list of proteins present in different Shigella species which are non-homologous to human and essential for the survival of the pathogen. The metabolic chokepoint analysis also enriches the list of essential protein and adds those proteins in the list which are uniquely found in pathogenic pathway, catalyzed by single enzyme and involved in multi pathways. Screening of essential proteins against human gut flora and approved drug targets revealed the targets which are non-homologous to human gut flora and homologous to the approved drug targets. Broad spectrum drug targets screening revealed a list of highly conserved proteins of various pathogens including different Shigella species. Probably the drug developed against these targets may be useful in treating multiple diseases or diseases which results due to co-infection of different pathogens. Subcellular localization prediction revealed a list protein, which could be potential vaccine targets in different Shigella species. Virtual screening against these identified targets might be useful in the discovery of novel Drug against MDR Shigella species.

Hippocampal pyramidal neurons have characteristic dendrite asymmetry, characterized by structurally and functionally distinct apical and basolateral dendrites. The ability of the neuron to generate and maintain dendrite asymmetry is vital, since synaptic inputs received are critically dependent on dendrite architecture. Little is known about the role of neuronal activity in guiding maintainance of dendrite asymmetry. Our data indicate that dendrite asymmetry is established and maintained early during development. Further, our results indicate that cell intrinsic and global alterations of neuronal activity have differential effects on net extension of apical and basolateral dendrites. Thus, apical and basolateral dendrite extension may be independently regulated by cell intrinsic and network neuronal activity during development, suggesting that individual dendrites may have autonomous control over net extension. We propose that regulated individual dendrite extension in response to cell intrinsic and neuronal network activity may allow temporal control of synapse specificity in the developing hippocampus.

Synaptic activity is intimately linked to neuronal structure and function. Stimulation of live cultured primary neurons, coupled with fluorescent indicator imaging, is a powerful technique to assess the impact of synaptic activity on neuronal protein trafficking and function. Current technology for neuronal stimulation in culture include chemical techniques or microelectrode or optogenetic based techniques. While technically powerful, chemical stimulation has limited spatial resolution and microelectrode and optogenetic techniques require specialized equipment and expertise. We report an optimized and improved technique for laser based photoconductive stimulation of live neurons using an inverted confocal microscope that overcomes these limitations. The advantages of this approach include its non-invasive nature and adaptability to temporal and spatial manipulation. We demonstrate that the technique can be manipulated to achieve spatially selective stimulation of live neurons. Coupled with live imaging of fluorescent indicators, this simple and efficient technique should allow for significant advances in neuronal cell biology.

Case report A 10 year old girl was admitted with a history of two episodes of seizures within a period of 6 months associated with tremors and weakness in the left upper and lower limbs. She was treated with phenytoin sodium and dexamethasone, both given orally. On examination, she was conscious, oriented and neurological examination revealed left hemiparesis with motor power grade of 5/6. Her blood investigations and ultrasonography of abdomen were normal. Computed tomography (CT) scan of the brain showed a porencephalic cyst communicating with the right ventricle with a marked midline shift (Figure 1). Magnetic resonance imaging (MRI) of brain showed a well-defined mass lesion 82 x 73 mm in axial, 67 x 68 mm in coronal and 78 x 70 mm in sagittal planes in right parietal basal ganglia area with mass effect and without perilesional vasogenic oedema and without restriction of diffused weighted imaging. Surgical removal of the cyst was done. The cyst ruptured during the course of surgery and for the prevention of anaphylactic reaction, injection chlorpheniramine maleate and injection hydrocortisone were given. The cyst with the contents was successfully removed. The diagnosis of hydatid cyst was established by histopathology.

δ-Catenin is a component of the cadherin-catenin cell adhesion complex and its loss has been implicated in the mental retardation associated with the Cri du chat syndrome. We have previously demonstrated that loss of δ-catenin in a murine model during development results in excessive spine and synaptic density and function. In order to examine the role of potential molecules that might cooperate with δ-catenin to regulate spine density, we focused on Mef2. Our data demonstrate that while loss of δ-catenin does not alter the expression levels of endogenous Mef2, expression of Mef2 in neurons that are knocked down for δ-catenin promotes spine elimination. These results establish a molecular mechanism by which excessive spines in the absence of δ-catenin may be eliminated and may point toward pharmacological therapy for the Cri du chat syndrome.

The ability to culture and maintain postnatal mouse hippocampal and cortical neurons is highly advantageous, particularly for studies on genetically engineered mouse models. Here we present a protocol to isolate and culture pyramidal neurons from the early postnatal (P0-P1) mouse hippocampus and cortex. These low-density dissociated cultures are grown on poly-L-lysine–coated glass substrates without feeder layers. Cultured neurons survive well, develop extensive axonal and dendritic arbors, express neuronal and synaptic markers, and form functional synaptic connections. Further, they are highly amenable to low- and high-efficiency transfection and time-lapse imaging. This optimized cell culture technique can be used to culture and maintain neurons for a variety of applications including immunocytochemistry, biochemical studies, shRNA-mediated knockdown and live imaging studies. The preparation of the glass substrate must begin 5 d before the culture. The dissection and plating out of neurons takes 3–4 h and neurons can be maintained in culture for up to 4 weeks.

Holocarboxylase synthetase (HCS) is a chromatin protein that is essential for mediating the covalent binding of biotin to histones. Biotinylation of histones plays crucial roles in the repression of genes and repeats in the human genome. We tested the feasibility of DNA adenine methyltransferase identification (DamID) technology to map HCS binding sites in human mammary cell lines. Full-length HCS was fused to DNA adenine methyltransferase (Dam) for subsequent transfection into breast cancer (MCF-7) and normal breast (MCF-10A) cells. HCS docking sites in chromatin were identified by using the unique adenine methylation sites established by Dam in the fusion construct; docking sites were unambiguously identified using methylation-sensitive digestion, cloning, and sequencing. In total, 15 novel HCS binding sites were identified in the two cell lines, and the following 4 of the 15 overlapped between MCF-7 and MCF-10A cells: inositol polyphosphate-5-phosphatase A, corticotropin hormone precursor, ribosome biogenesis regulatory protein, and leptin precursor. We conclude that DamID is a useful technology to map HCS binding sites in human chromatin and propose that the entire set of HCS binding sites could be mapped by combining DamID with microarray technology.