GPCR-IPL score: multilevel featurization of GPCR-ligand interaction patterns and prediction of ligand functions from selectivity to biased activation.

G-protein-coupled receptors (GPCRs) mediate diverse cell signaling cascades after recognizing extracellular ligands. Despite the successful history of known GPCR drugs, a lack of mechanistic insight into GPCR challenges both the deorphanization of some GPCRs and optimization of the structure-activity relationship of their ligands. Notably, replacing a small substituent on a GPCR ligand can significantly alter extracellular GPCR-ligand interaction patterns and motion of transmembrane helices in turn to occur post-binding events of the ligand. In this study, we designed 3D multilevel features to describe the extracellular interaction patterns. Subsequently, these 3D features were utilized to predict the post-binding events that result from conformational dynamics from the extracellular to intracellular areas. To understand the adaptability of GPCR ligands, we collected the conformational information of flexible residues during binding and performed molecular featurization on a broad range of GPCR-ligand complexes. As a result, we developed GPCR-ligand interaction patterns, binding pockets, and ligand features as score (GPCR-IPL score) for predicting the functional selectivity of GPCR ligands (agonism versus antagonism), using the multilevel features of (1) zoomed-out 'residue level' (for flexible transmembrane helices of GPCRs), (2) zoomed-in 'pocket level' (for sophisticated mode of action) and (3) 'atom level' (for the conformational adaptability of GPCR ligands). GPCR-IPL score demonstrated reliable performance, achieving area under the receiver operating characteristic of 0.938 and area under the precision-recall curve of 0.907 (available in gpcr-ipl-score.onrender.com). Furthermore, we used the molecular features to predict the biased activation of downstream signaling (Gi/o, Gq/11, Gs and ß-arrestin) as well as the functional selectivity. The resulting models are interpreted and applied to out-of-set validation with three scenarios including the identification of a new MRGPRX antagonist.

Clinico-epidemiological presentations and management of Nipah virus infection during the outbreak in Kozhikode district, Kerala state, India 2023.

India experienced its sixth Nipah virus (NiV) outbreak in September 2023 in the Kozhikode district of Kerala state. The NiV is primarily transmitted by spillover events from infected bats followed by human-to-human transmission. The clinical specimens were screened using real-time RT-PCR, and positive specimens were further characterized using next-generation sequencing. We describe here an in-depth clinical presentation and management of NiV-confirmed cases and outbreak containment activities. The current outbreak reported a total of six cases with two deaths, with a case fatality ratio of 33.33%. The cases had a mixed presentation of acute respiratory distress syndrome and encephalitis syndrome. Fever was a persistent presentation in all the cases. The Nipah viral RNA was detected in clinical specimens until the post-onset day of illness (POD) 14, with viral load in the range of 1.7-3.3 × 104 viral RNA copies/mL. The genomic analysis showed that the sequences from the current outbreak clustered into the Indian clade similar to the 2018 and 2019 outbreaks. This study highlights the vigilance of the health system to detect and effectively manage the clustering of cases with clinical presentations similar to NiV, which led to early detection and containment activities.

Sociodemographic determinants of high tobacco use in Gond tribe of central India.

Background The prevalence of tobacco use is high in rural India, but limited information on tobacco use among the tribal population is available. We assessed the prevalence of tobacco use and type of tobacco use in the Gond tribal population. Methods We did a cross-sectional survey among the Gond tribal population residing in the Kundam block of Jabalpur district in Madhya Pradesh state in India. The study was carried out among persons aged 6 years and above during February-May 2017. Pre-tested interview schedules were used by trained field investigators to collect information on tobacco use. Results A total of 3351 individuals were included in this study, of which 58% were using some form of tobacco. The prevalence of tobacco use was higher among men compared to women, and it increased significantly from age 6 to 25 in both men and women. Tobacco use was significantly associated with age, gender and educational status of the respondents. Conclusion The study highlights a high tobacco use in the Gond tribe population. The high prevalence of tobacco use in younger ages is a matter of serious concern. The study establishes a need for information, education and communication and behavioural change communication activities; health camps focusing on the harmful effects of tobacco use and tobacco control campaign among tribal communities, tribal schools and ashrams.

Study of Correlation of CD4, CD8 Count with Tuberculous Pneumonia and Non Tuberculous Bacterial Pneumonia in Type 2 Diabetes Mellitu.

AIM: Type-2 DM patients are susceptible for various types of infections. Long standing Type2 DM patients have strong predilection for tuberculosis as seen in various studies. Here, we aimed to study susceptibility of tuberculosis as compared to other non tuberculous pneumonia in type-2 DM on the basis of CD markers. MATERIAL AND METHODS: A case control study on 150 subjects was conducted in S.P. Medical College and Associated Group of P.B.M. Hospitals, Bikaner. Subjects were divided into 3 groups each of 50 type-2 diabetic patients having tuberculous pneumonia, of 50 type-2 diabetic patients having non tuberculous pneumonia and 50 patients of type 2 diabetes as a control group attending Medical Outdoor and those Admitted in Hospital IPD Wards. All participants were subjected to detailed clinical examination and relevant investigations. Flow cytometry was used for CD4 and CD8 count. RESULTS: Diabetic patients with tuberculous pneumonia have significantly (p-value <0.05) elevated numbers of CD4 and CD8 cell count in comparison of both controls and nontuberculous pneumonia. Diabetic patients with non tuberculous pneumonia have significantly (p-value <0.05) lower CD4 and CD8 cell count in comparison of diabetic controls and diabetic patients with tuberculous pneumonia. CONCLUSION: DM is associated with an alteration in the immune response to tuberculosis, leading to a induction of CD4 and CD8 mediated cellular responses and likely contributing to increased immune pathology in M. tuberculosis infection. Our study also provides an impetus to perform longitudinal studies examining the role of immunological biomarkers in the development of tuberculosis in diabetic patients.

In silico identification of prolyl hydroxylase inhibitor by per-residue energy decomposition-based pharmacophore approach.

Hypoxia is an effective preconditioning stimulus and many cellular responses to hypoxia are mediated through a transcription control complex termed the hypoxia-inducible factor (HIF). The stability and activation of HIF are governed by HIF prolyl-4-hydroxylases 2 (PHD2). Hence, the development of a small molecule inhibitor for prolyl hydroxylase has been suggested as a potentially useful therapeutic strategy for the treatment of oxidative/ischemic stress conditions. Thus, to unveil a novel human PHD2 inhibitor, a custom-based virtual screening was carried out to identify the potential inhibitors against PHD2 based on; (1) the per-residue energy decomposition (PRED)-based pharmacophore model, (2) molecular docking, and (3) MD approaches. The PRED analysis was performed to identify the common interaction pattern of HIF fragment (5L9B) and crystallized ligand (4JZR) to develop a relevant accurate allosteric pharmacophore model. The custom pharmacophore model (AAARR) was developed and further used to screen multiple databases. The docking was performed as a secondary strategy for screening the pharmacophore hits. Furthermore, the docked complexes were screened by molecular dynamics (MD) simulation and molecular mechanics/generalized Born surface area (MM-GBSA) based binding free energy calculations to determine the binding energy of the inhibitors and to identify crucial interaction energy fingerprint. One hit has demonstrated good binding free energy and a better binding affinity for PHD2 compared to the other four selected ligands. Thus, the results obtained from pharmacophore, docking, and MD simulations depicted that linker length and metal binding in the scaffold could be effectively used as a potent inhibitor toward human PHD2 in AD therapeutics.

Cyclooxygenase 2 and vascular endothelial growth factor-potential targets to manage lepra reactions: A case-control study.

Reactions in leprosy have an immune mediated pathogenesis. While type 1 reactions are delayed hypersensitivity phenomenon, type 2 reactions are immune complex mediated. Key molecules which mediate the immune insult in lepra reactions require evaluation in order to tailor their therapy and prevent disability. The objective of the study was to evaluate expressions of Cyclooxygenase 2 and Vascular Endothelial Growth Factor in skin biopsies from leprosy patients and correlate their expression with presence of either type 1 or type 2 lepra reactions. This was a case control study. Cyclooxygenase 2 and Vascular Endothelial Growth Factor expression in dermal macrophages and vascular endothelium was assessed immunohistochemically. Biopsies from patients with Non-reactive leprosy and healthy controls were used for comparison. SPSS software was used for statistical analysis. A total of 147 skin biopsies were evaluated, including 18 with Type 1 reaction, 39 Type 2 reaction, 81 non-reactive leprosy and 9 healthy controls. Both Cyclooxygenase 2 and Vascular Endothelial Growth Factor expression were significantly higher in type 1 followed by type 2 reaction as compared to controls. These results may guide us regarding use of Cyclooxygenase 2 and Vascular Endothelial Growth Factor inhibitor drugs which may be a major step in treating reactive leprosy patients and preventing nerve damage and disability.

Ligand-based pharmacophore modeling and docking studies on vitamin D receptor inhibitors.

In recent years, pharmacophore modeling and molecular docking approaches have been extensively used to characterize the structural requirements and explore the conformational space of a ligand in the binding pocket of the selected target protein. Herein, we report a pharmacophore modeling and molecular docking of 45 compounds comprising of the indole scaffold as vitamin D receptor (VDR) inhibitors. Based on the selected best hypothesis (DRRRR.61), an atom-based three-dimensional quantitative structure-activity relationships model was developed to rationalize the structural requirement of biological activity modulating components. The developed model predicted the binding affinity for the training set and test set with R2(training) = 0.8869 and R2(test) = 0.8139, respectively. Furthermore, molecular docking and dynamics simulation were performed to understand the underpinning of binding interaction and stability of selected VDR inhibitors in the binding pocket. In conclusion, the results presented here, in the form of functional and structural data, agreed well with the proposed pharmacophores and provide further insights into the development of novel VDR inhibitors with better activity.

Profiling the transcriptome response of Atlantic salmon head kidney to formalin-killed Renibacterium salmoninarum.

Renibacterium salmoninarum is a Gram-positive, intracellular bacterial pathogen that causes Bacterial Kidney Disease (BKD) in Atlantic salmon (Salmo salar). The host transcriptomic response to this immune-suppressive pathogen remains poorly understood. To identify R. salmoninarum-responsive genes, Atlantic salmon were intraperitoneally injected with a low (5 × 105 cells/kg, Low-Rs) or high (5 × 107 cells/kg; High-Rs) dose of formalin-killed R. salmoninarum bacterin or phosphate-buffered saline (PBS control); head kidney samples were collected before and 24 h after injection. Using 44K microarray analysis, we identified 107 and 345 differentially expressed probes in response to R. salmoninarum bacterin (i.e. High-Rs vs. PBS control) by Significance Analysis of Microarrays (SAM) and Rank Products (RP), respectively. Twenty-two microarray-identified genes were subjected to qPCR assays, and 17 genes were confirmed as being significantly responsive to the bacterin. There was an up-regulation in expression of genes playing putative roles as immune receptors and antimicrobial effectors. Genes with putative roles as pathogen recognition (e.g. clec12b and tlr5) or immunoregulatory (e.g. tnfrsf6b and tnfrsf11b) receptors were up-regulated in response to R.salmoninarum bacterin. Also, chemokines and a chemokine receptor showed opposite regulation [up-regulation of effectors (i.e. ccl13 and ccl) and down-regulation of cxcr1] in response to the bacterin. The present study identified and validated novel biomarker genes (e.g. ctsl1, lipe, cldn4, ccny) that can be used to assess Atlantic salmon response to R. salmoninarum, and will be valuable in the development of tools to combat BKD.

Transcriptomic Profiling in Fins of Atlantic Salmon Parasitized with Sea Lice: Evidence for an Early Imbalance Between Chalimus-Induced Immunomodulation and the Host's Defense Response.

Parasitic sea lice (e.g., Lepeophtheirus salmonis) cause costly outbreaks in salmon farming. Molecular insights into parasite-induced host responses will provide the basis for improved management strategies. We investigated the early transcriptomic responses in pelvic fins of Atlantic salmon parasitized with chalimus I stage sea lice. Fin samples collected from non-infected (i.e. pre-infected) control (PRE) and at chalimus-attachment sites (ATT) and adjacent to chalimus-attachment sites (ADJ) from infected fish were used in profiling global gene expression using 44 K microarrays. We identified 6568 differentially expressed probes (DEPs, FDR < 5%) that included 1928 shared DEPs between ATT and ADJ compared to PRE. The ATT versus ADJ comparison revealed 90 DEPs, all of which were upregulated in ATT samples. Gene ontology/pathway term network analyses revealed profound changes in physiological processes, including extracellular matrix (ECM) degradation, tissue repair/remodeling and wound healing, immunity and defense, chemotaxis and signaling, antiviral response, and redox homeostasis in infected fins. The QPCR analysis of 37 microarray-identified transcripts representing these functional themes served to confirm the microarray results with a significant positive correlation (p < 0.0001). Most immune/defense-relevant transcripts were downregulated in both ATT and ADJ sites compared to PRE, suggesting that chalimus exerts immunosuppressive effects in the salmon's fins. The comparison between ATT and ADJ sites demonstrated the upregulation of a suite of immune-relevant transcripts, evidencing the salmon's attempt to mount an anti-lice response. We hypothesize that an imbalance between immunomodulation caused by chalimus during the early phase of infection and weak defense response manifested by Atlantic salmon makes it a susceptible host for L. salmonis.

Associations between clinical symptoms, plasma norepinephrine and deregulated immune gene networks in subgroups of adolescent with Chronic Fatigue Syndrome.

BACKGROUND: Chronic Fatigue Syndrome (CFS) is one of the most important causes of disability among adolescents while limited knowledge exists on genetic determinants underlying disease pathophysiology. METHODS: We analyzed deregulated immune-gene modules using Pathifier software on whole blood gene expression data (29 CFS patients, 18 controls). Deconvolution of immune cell subtypes based on gene expression profile was performed using CIBERSORT. Supervised consensus clustering on pathway deregulation score (PDS) was used to define CFS subgroups. Associations between PDS and immune, neuroendocrine/autonomic and clinical markers were examined. The impact of plasma norepinephrine level on clinical markers over time was assessed in a larger cohort (91 patients). RESULTS: A group of 29 immune-gene sets was shown to differ patients from controls and detect subgroups within CFS. Group 1P (high PDS, low norepinephrine, low naïve CD4+ composition) had strong association with levels of serum C-reactive protein and Transforming Growth Factor-beta. Group 2P (low PDS, high norepinephrine, high naïve CD4+ composition) had strong associations with neuroendocrine/autonomic markers. The corresponding plasma norepinephrine level delineated 91 patients into two subgroups with significant differences in fatigue score. CONCLUSION: We identified 29 immune-gene sets linked to plasma norepinephrine level that could delineate CFS subgroups. Plasma norepinephrine stratification revealed that lower levels of norepinephrine were associated with higher fatigue. Our data suggests potential involvement of neuro-immune dysregulation and genetic stratification in CFS.

A Study of Correlation between Apolipoprotein B and Dyslipidemia in Type 2 Diabetes Patients and its Relation with Proteinuria- A Tertiary Care Hospital Based Study.

OBJECTIVES: Individual with diabetes may have several from of Dyslipidemia. Dyslipidemia has been considered to be factor that plays a risk in progression of micro vascular disease, especially in diabetes.1 The present study is intended to Study of correlation between Apolipoprotein B and Dyslipidemia in type 2 diabetes patients and prevalence of dyslipidemia in type 2 diabetic patients. MATERIAL AND METHODS: Prospective cross- sectional study conducted on 100 cases of type 2 diabetes mellitus. Groups are divided according to A/C ratio and association of dyslipidemia was seen. Serum Apolipoprotein B was measured using immunoturbidimetric method. RESULTS: Pearson's correlation analysis of Apo B with lipid parameters in diabetic patients showed that, LDL, TC and Tg were positively correlated with Apo- B. There was a positive and linear correlation between LDL and Tg. Apo- B was negatively correlated with HDL-C. CONCLUSION: The majority of patients studied had low HDL-C, elevated non HDL- C, elevated total cholesterol, elevated triglycerides, elevated LDL -C and elevated apo B. Apolipoprotein B had a positive linear correlation with total cholesterol, triglycerides, LDL-C, non-HDL-C. The strongest positive correlation was with nonHDL-C. Patients with low HDL-C had high apo B levels.

Alteration in lipid composition differentiates breast cancer tissues: a 1H HRMAS NMR metabolomic study.

INTRODUCTION: Breast cancer is the most frequent diagnosed cancer among women with a mortality rate of 15% of all cancer related deaths in women. Breast cancer is heterogeneous in nature and produces plethora of metabolites allowing its early detection using molecular diagnostic techniques like magnetic resonance spectroscopy. OBJECTIVES: To evaluate the variation in metabolic profile of breast cancer focusing on lipids as triglycerides (TG) and free fatty acids (FFA) that may alter in malignant breast tissues and lymph nodes from adjacent benign breast tissues by HRMAS 1H NMR spectroscopy. METHODS: The 1H NMR spectra recorded on 173 tissue specimens comprising of breast tumor tissues, adjacent tissues, few lymph nodes and overlying skin tissues obtained from 67 patients suffering from breast cancer. Multivariate statistical analysis was employed to identify metabolites acting as major confounders for differentiation of malignancy. RESULT: Reduction in lipid content were observed in malignant breast tissues along with a higher fraction of FFA. Four small molecule metabolites e.g., choline containing compounds (Chocc), taurine, glycine, and glutamate were also identified as major confounders. The test set for prediction provided sensitivity and specificity of more than 90% excluding the lymph nodes and skin tissues. CONCLUSION: Fatty acids composition in breast cancer using in vivo magnetic resonance spectroscopy (MRS) is gaining its importance in clinical settings (Coum et al. in Magn Reson Mater Phys Biol Med 29:1-4, 2016). The present study may help in future for precise evaluation of lipid classification including small molecules as a source of early diagnosis of invasive ductal carcinoma by employing in vivo magnetic resonance spectroscopic methods.

Non-peptide-based new class of platelet aggregation inhibitors: Design, synthesis, bioevaluation, SAR, and in silico studies.

A series of 2-oxo-2-phenylethylidene linked 2-oxo-benzo[1,4]oxazine analogues 17a-x and 18a-o, incorporated with a variety of electron-withdrawing as well as electron-donating groups at ring A and ring C, were synthesized under greener conditions in excellent yields (up to 98%). These analogues 17a-x and 18a-o were evaluated for their arachidonic acid (AA)-induced platelet aggregation inhibitory activities in comparison with the standard reference aspirin (IC50 = 21.34 ± 1.09 µg/mL). Among all the screened compounds, eight analogues, 17i, 17x, 18f, 18g, 18h, 18i, 18l, and 18o, were identified as promising platelet aggregation inhibitors as compared to aspirin. In addition, cytotoxic studies in 3T3 fibroblast cell lines by MTT assay of the promising compounds (17i, 17x, 18f-18i, 18l, and 18o) were also performed and the compounds were found to be non-toxic in nature. Furthermore, the results on the AA-induced platelet aggregation inhibitory activities of these compounds (17i, 17x, 18f-18i, 18l, and 18o) were validated via in silico molecular docking simulation studies. To the best of our knowledge, this is the first report of the identification of non-peptide-based functionalized 2-oxo-benzo[1,4]oxazines as platelet aggregation inhibitors.

Study of Correlation between Diabetic Pulmonopathy with Serum Adiponectin Levels in Patients of Type 2 Diabetes Mellitus.

Diabetes mellitus a disease with various macro and micro vascular complications due to its various metabolic dysregulations, is well known to involve lungs in long run in both type 1 and 2 diabetes mellitus, causing tremendous burden on health care system. Common simple lung function tests alone are likely to underestimate the prevalence and degree of lung dysfunction in diabetes, but newer noninvasive tests of lung mechanical function provide a more sensitive assessment of peripheral airway function, hence by establishing a marker and risk factors for pulmonary involvement in diabetic individuals, cases with high risk for pulmonary involvement can be found before hand and proper medical therapy can be started for primary prophylaxis of same, Hence in this study we tried to find out any correlation between serum adiponectin levels and pulmonary dysfunction in patients of type 2 diabetes mellitus, which shows a significant role of adiponectin as early marker of the disease with p value of 0.04, the decrease in serum adiponectin level is also associated with more severe disease, hence adiponectin levels can be used as early markers of pulmonary dysfunction in diabetic patients.

Clinical and Etiological Profile of Fever with Thrombocytopenia - A Tertiary Care Hospital Based Study.

Objectives: Febrile thrombocytopenia is a condition commonly caused by infections. The present study is intended to know the underlying etiology of fever with thrombocytopenia, the various presentations and complications in our community. Material and Methods: A cross-sectional epidemiological study was conducted including 1217 patients aged more than 14 years with fever and thrombocytopenia admitted in the medical wards from October 2013 to September 2014. Detailed clinical examination and routine investigations were done; specific investigations like blood culture, widal test, antigen test for malaria, IgM ELISA leptospira, IgM ELISA dengue, bone marrow aspiration/biopsy etc. were done as and when indicated. The data are presented as percentage and numbers. Rates and ratios are computed. Results: Infection was the commonest cause of thrombocytopenia and dengue was the commonest of the infections followed by malaria. Bleeding manifestations were seen in 42.7% of patients. 91.40% of patients with bleeding tendencies had petechiae/purpura as the commonest bleeding manifestation, followed by spontaneous bleeding in 57%. Spontaneous bleeding was noted when platelet counts were less than 20,000. Petechiae/Purpura were seen more commonly when platelet count was in the range of less than or equal to 50,000. Good recovery was noted in 95%, while 5% had mortality. Septicemia accounted for 85.24% of deaths followed by malaria (6.55%) and dengue (5%). Conclusion: Fever with thrombocytopenia is an important clinical condition commonly caused by infections, particularly dengue and malaria. In majority of patients thrombocytopenia was transient and asymptomatic, but in significant number of cases there were bleeding manifestations. On treating the specific cause drastic improvement in platelet count was noted. Mortality in febrile thrombocytopenia is not directly associated with degree of thrombocytopenia but with concomitant involvement of other organs leading to multiorgan dysfunction.

SNP in KCNQ1 Gene is Associated with Susceptibility to Diabetic Nephropathy in Subjects with Type 2 Diabetes in India.

OBJECTIVE: Diabetic nephropathy (DN) remains the most common cause of end stage renal disease (ESRD) as the burden of diabetes increases worldwide. Only 25 to 40% of patients with type 2 diabetes mellitus (T2DM) develop diabetic nephropathy irrespective of glycemic control so there should be a specific genetic basis for the development of diabetic nephropathy. METHODS: We have collected venous blood samples from 50 cases (Diabetic nephropathy) and 20 controls (T2DM without nephropathy) diagnosed by spot urine albumin creatinine ratio (ACR). DNA was isolated from processed samples. PCR study and sequencing was done to detect polymorphism of rs2237897 in KCNQ1 gene. RESULTS: Statistically significant difference was found when the allelic frequencies between the two groups were compared (p=0.03), with the C allele having a 2.4 fold higher risk of having diabetic nephropathy (risk ratio, RR )= 1.16, 95%CI of RR = 1.01 to 1.3, Odds Ratio (OR) =2.4; 95% CI of OR =1.06 to 4.6). Chi-square analysis showed a significant difference in genotype frequency of rs2237897 (χ2 = 4.63, p=0.03) in Diabetic nephropathy subjects, compared with that of controls. CONCLUSIONS: This study suggested that, KCNQ1 being an established type 2 diabetes gene, genetic variation in this gene may contribute to susceptibility to diabetic nephropathy and the C allele is the risk allele for diabetic nephropathy, which is different from Japanese population where the T allele was the risk allele.

Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome.

BACKGROUND: Breast cancer is a heterogeneous disease at the clinical and molecular level. In this study we integrate classifications extracted from five different molecular levels in order to identify integrated subtypes. METHODS: Tumor tissue from 425 patients with primary breast cancer from the Oslo2 study was cut and blended, and divided into fractions for DNA, RNA and protein isolation and metabolomics, allowing the acquisition of representative and comparable molecular data. Patients were stratified into groups based on their tumor characteristics from five different molecular levels, using various clustering methods. Finally, all previously identified and newly determined subgroups were combined in a multilevel classification using a "cluster-of-clusters" approach with consensus clustering. RESULTS: Based on DNA copy number data, tumors were categorized into three groups according to the complex arm aberration index. mRNA expression profiles divided tumors into five molecular subgroups according to PAM50 subtyping, and clustering based on microRNA expression revealed four subgroups. Reverse-phase protein array data divided tumors into five subgroups. Hierarchical clustering of tumor metabolic profiles revealed three clusters. Combining DNA copy number and mRNA expression classified tumors into seven clusters based on pathway activity levels, and tumors were classified into ten subtypes using integrative clustering. The final consensus clustering that incorporated all aforementioned subtypes revealed six major groups. Five corresponded well with the mRNA subtypes, while a sixth group resulted from a split of the luminal A subtype; these tumors belonged to distinct microRNA clusters. Gain-of-function studies using MCF-7 cells showed that microRNAs differentially expressed between the luminal A clusters were important for cancer cell survival. These microRNAs were used to validate the split in luminal A tumors in four independent breast cancer cohorts. In two cohorts the microRNAs divided tumors into subgroups with significantly different outcomes, and in another a trend was observed. CONCLUSIONS: The six integrated subtypes identified confirm the heterogeneity of breast cancer and show that finer subdivisions of subtypes are evident. Increasing knowledge of the heterogeneity of the luminal A subtype may add pivotal information to guide therapeutic choices, evidently bringing us closer to improved treatment for this largest subgroup of breast cancer.

Cerebral Air Embolism Secondary to Lung Laceration.

Cerebral air embolism is a rare clinical entity in day-to-day practice. The introduction of air into the venous or the arterial system can cause cerebral air embolism leading to severe neurological deficits. The common causes reported in the literature are iatrogenic; it can be caused by positive pressure maneuvers performed during cardiac resuscitation, lung biopsy, and the placement of venous catheters in the presence of a patent foramen ovale. We report a case of cerebral air embolism which has occurred secondary to lung laceration. The patient underwent intercostal drainage for hydro-pneumothorax and developed forceful cough and suddenly changed in consciousness. Air embolism was diagnosed by computed tomography brain and was managed by high-concentration oxygen therapy and other supportive measures and is being discharged in satisfactory condition.

Intraoperative low tidal volume ventilation strategy has no benefits during laparoscopic cholecystectomy.

BACKGROUND AND AIMS: Benefits of intraoperative low tidal volume ventilation during laparoscopic surgery are not conclusively proven, even though its advantages were seen in other situations with intraoperative respiratory compromise such as one-lung ventilation. The present study compared the efficacy of intraoperative low tidal volume ventilatory strategy (6 ml/kg along with positive end-expiratory pressure [PEEP] of 10 cmH2O) versus one with higher tidal volume (10 ml/kg with no PEEP) on various clinical parameters and plasma levels of interleukin (IL)-6 in patients undergoing laparoscopic cholecystectomy. MATERIAL AND METHODS: A total of 58 adult patients with American Society of Anesthesiologists physical status I or II, undergoing laparoscopic cholecystectomy were randomized to receive the low or higher tidal volume strategy as above (n = 29 each). The primary outcome measure was postoperative PaO2. Systemic levels of IL-6 along with clinical indices of intraoperative gas exchange, pulmonary mechanics, and hemodynamic consequences were measured as secondary outcome measures. RESULTS: There was no statistically significant difference in oxygenation; intraoperative dynamic compliance, peak airway pressures, or hemodynamic parameters, or the IL-6 levels between the two groups (P > 0.05). Low tidal volume strategy was associated with significantly higher mean airway pressure, lower airway resistance, greater respiratory rates, and albeit clinically similar, higher PaCO2and lower pH (P < 0.05). CONCLUSION: Strategy using 6 ml/kg tidal volume along with 10 cmH2O of PEEP was not associated with any significant improvement in gas exchange, hemodynamic parameters, or systemic inflammatory response over ventilation with 10 ml/kg volume without PEEP during laparoscopic cholecystectomy.

BLAST output visualization in the new sequencing era.

The Basic Local Alignment Search Tool (BLAST) algorithm remains one of the most widely used bioinformatic programs. For many projects, new sequencing technologies and increased database sizes will increase the BLAST output significantly. Frequently, this output is so large that it is no longer able to be processed manually. As BLAST users are increasingly recruited from mainstream biology without any bioinformatic background, user-friendly programs capable of BLAST output visualization, analysis and post-processing are in demand. In this review, freely available BLAST output processing programs are categorized as BLAST output interpreters, BLAST environments, BLAST output parsers or specialized tools. They are evaluated according to their user-friendliness, analysis features and high-throughput data processing capabilities.