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https://www.readbyqxmd.com/read/28448963/paradoxical-aging-in-hiv-immune-senescence-of-b-cells-is-most-prominent-in-young-age
#1
Stefano Rinaldi, Suresh Pallikkuth, Varghese K George, Lesley R de Armas, Rajendra Pahwa, Celeste M Sanchez, Maria Fernanda Pallin, Li Pan, Nicola Cotugno, Gordon Dickinson, Allan Rodriguez, Margaret Fischl, Maria Alcaide, Louis Gonzalez, Paolo Palma, Savita Pahwa
Combination antiretroviral therapies (cART)can lead to normal life expectancy in HIV-infected persons, and people aged >50 yrs represent the fastest growing HIV group. Although HIV and aging are independently associated with impaired humoral immunity, immune status in people aging with HIV is relatively unexplored. In this study influenza vaccination was used to probe age associated perturbations in the B cell compartment of HIV-negative "healthy controls" (HC) and virologically controlled HIV-infected participants on cART (HIV) (n=124), grouped by age as young (<40 yrs), middle-aged (40-59yrs) or old (>60 yrs)...
April 27, 2017: Aging
https://www.readbyqxmd.com/read/28425388/lower-bound-on-estimation-variance-of-the-ultrasonic-attenuation-coefficient-using-the-spectral-difference-reference-phantom-method
#2
Kayvan Samimi, Tomy Varghese
Ultrasonic attenuation is one of the primary parameters of interest in Quantitative Ultrasound (QUS). Non-invasive monitoring of tissue attenuation can provide valuable diagnostic and prognostic information to the physician. The Reference Phantom Method (RPM) was introduced as a way of mitigating some of the system-related effects and biases to facilitate clinical QUS applications. In this paper, under the assumption of diffuse scattering, a probabilistic model of the backscattered signal spectrum is used to derive a theoretical lower bound on the estimation variance of the attenuation coefficient using the Spectral-Difference RPM...
May 2017: Ultrasonic Imaging
https://www.readbyqxmd.com/read/28424988/overcoming-chemotherapy-drug-resistance-by-targeting-inhibitors-of-apoptosis-proteins-iaps
#3
REVIEW
Rama Rathore, Jennifer E McCallum, Elizabeth Varghese, Ana-Maria Florea, Dietrich Büsselberg
Inhibitors of apoptosis (IAPs) are a family of proteins that play a significant role in the control of programmed cell death (PCD). PCD is essential to maintain healthy cell turnover within tissue but also to fight disease or infection. Uninhibited, IAPs can suppress apoptosis and promote cell cycle progression. Therefore, it is unsurprising that cancer cells demonstrate significantly elevated expression levels of IAPs, resulting in improved cell survival, enhanced tumor growth and subsequent metastasis. Therapies to target IAPs in cancer has garnered substantial scientific interest and as resistance to anti-cancer agents becomes more prevalent, targeting IAPs has become an increasingly attractive strategy to re-sensitize cancer cells to chemotherapies, antibody based-therapies and TRAIL therapy...
April 19, 2017: Apoptosis: An International Journal on Programmed Cell Death
https://www.readbyqxmd.com/read/28412611/hypermethylation-of-death-associated-protein-kinase-dapk1-and-its-association-with-oral-carcinogenesis-an-experimental-and-meta-analysis-study
#4
Chinchu Jayaprakash, Vinay Koshy Varghese, Ravishankara Bellampalli, Raghu Radhakrishnan, Satadru Ray, Shama Prasada Kabekkodu, Kapaettu Satyamoorthy
OBJECTIVES: The value of abnormal DNA methylation of DAPK1 promoter and its association with various cancers have been suggested in the literature. To establish the significance of DNA methylation of DAPK1 promoter in oral squamous cell carcinoma (OSCC), we a) performed a case-control study, b) evaluated published data for its utility in the diagnosis and prognosis of OSCC and c) identified the association of DAPK1 gene expression with promoter DNA methylation status. DESIGN: Bisulfite gene sequencing of DAPK1 promoter region was performed on non-malignant and malignant oral samples...
March 31, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28408900/the-thrombopoietin-receptor-structural-basis-of-traffic-and-activation-by-ligand-mutations-agonists-and-mutated-calreticulin
#5
REVIEW
Leila N Varghese, Jean-Philippe Defour, Christian Pecquet, Stefan N Constantinescu
A well-functioning hematopoietic system requires a certain robustness and flexibility to maintain appropriate quantities of functional mature blood cells, such as red blood cells and platelets. This review focuses on the cytokine receptor that plays a significant role in thrombopoiesis: the receptor for thrombopoietin (TPO-R; also known as MPL). Here, we survey the work to date to understand how this receptor functions at a molecular level throughout its lifecycle, from traffic to the cell surface, dimerization and binding cognate cytokine via its extracellular domain, through to its subsequent activation of associated Janus kinases and initiation of downstream signaling pathways, as well as the regulation of these processes...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/28404010/risk-stratification-of-barrett-s-oesophagus-using-a-non-endoscopic-sampling-method-coupled-with-a-biomarker-panel-a-cohort-study
#6
Caryn S Ross-Innes, Hamza Chettouh, Achilleas Achilleos, Nuria Galeano-Dalmau, Irene Debiram-Beecham, Shona MacRae, Petros Fessas, Elaine Walker, Sibu Varghese, Theodore Evan, Pierre S Lao-Sirieix, Maria O'Donovan, Shalini Malhotra, Marco Novelli, Babett Disep, Phillip V Kaye, Laurence B Lovat, Rehan Haidry, Michael Griffin, Krish Ragunath, Pradeep Bhandari, Adam Haycock, Danielle Morris, Stephen Attwood, Anjan Dhar, Colin Rees, Matt D Rutter, Richard Ostler, Benoit Aigret, Peter D Sasieni, Rebecca C Fitzgerald
BACKGROUND: Barrett's oesophagus predisposes to adenocarcinoma. However, most patients with Barrett's oesophagus will not progress and endoscopic surveillance is invasive, expensive, and fraught by issues of sampling bias and the subjective assessment of dysplasia. We investigated whether a non-endoscopic device, the Cytosponge, could be coupled with clinical and molecular biomarkers to identify a group of patients with low risk of progression suitable for non-endoscopic follow-up. METHODS: In this multicentre cohort study (BEST2), patients with Barrett's oesophagus underwent the Cytosponge test before their surveillance endoscopy...
January 2017: Lancet. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28365230/mutational-correlates-of-virological-failure-in-individuals-receiving-a-who-recommended-tenofovir-containing-first-line-regimen-an-international-collaboration
#7
Soo-Yon Rhee, Vici Varghese, Susan P Holmes, Gert U Van Zyl, Kim Steegen, Mark A Boyd, David A Cooper, Sabin Nsanzimana, Shanmugam Saravanan, Charlotte Charpentier, Tulio de Oliveira, Mary-Ann A Etiebet, Federico Garcia, Dominique Goedhals, Perpetua Gomes, Huldrych F Günthard, Raph L Hamers, Christopher J Hoffmann, Gillian Hunt, Awachana Jiamsakul, Pontiano Kaleebu, Phyllis Kanki, Rami Kantor, Bernhard Kerschberger, Vincent C Marconi, Jean D'amour Ndahimana, Nicaise Ndembi, Nicole Ngo-Giang-Huong, Casper Rokx, Maria M Santoro, Jonathan M Schapiro, Daniel Schmidt, Lillian Seu, Kim C E Sigaloff, Sunee Sirivichayakul, Lindiwe Skhosana, Henry Sunpath, Michele Tang, Chunfu Yang, Sergio Carmona, Ravindra K Gupta, Robert W Shafer
Tenofovir disoproxil fumarate (TDF) genotypic resistance defined by K65R/N and/or K70E/Q/G occurs in 20% to 60% of individuals with virological failure (VF) on a WHO-recommended TDF-containing first-line regimen. However, the full spectrum of reverse transcriptase (RT) mutations selected in individuals with VF on such a regimen is not known. To identify TDF regimen-associated mutations (TRAMs), we compared the proportion of each RT mutation in 2873 individuals with VF on a WHO-recommended first-line TDF-containing regimen to its proportion in a cohort of 50,803 antiretroviral-naïve individuals...
March 19, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28360473/recurrent-endobronchial-actinomycosis-following-an-interventional-procedure
#8
Arjun Padmanabhan, Abin Varghese Thomas
Actinomycosis is an indolent, slowly progressive infection caused by anaerobic or microaerophilic bacteria, primarily from the genus Actinomyces. Thoracic involvement is observed in approximately 15% of cases of infection with actinomycosis. Here, we present a case of a 61-year-old male who presented with recurrent endobronchial actinomycosis. The case is being presented because of its rarity on three counts - endobronchial involvement, which is uncommon, recurrence in different sites in the bronchial tree, which is even rarer and development of the disease following an endobronchial procedure...
March 2017: Lung India: Official Organ of Indian Chest Society
https://www.readbyqxmd.com/read/28351298/aberrant-gene-specific-dna-methylation-signature-analysis-in-cervical-cancer
#9
Samatha Bhat, Shama Prasada Kabekkodu, Vinay Koshy Varghese, Sanjiban Chakrabarty, Sandeep P Mallya, Harish Rotti, Deeksha Pandey, Pralhad Kushtagi, Kapaettu Satyamoorthy
Multicomponent molecular modifications such as DNA methylation may offer sensitive and specific cervical intraepithelial neoplasia and cervical cancer biomarkers. In this study, we tested cervical tissues at various stages of tumor progression for 5-methylcytosine and 5-hydroxymethylcytosine levels and also DNA promoter methylation profile of a panel of genes for its diagnostic potential. In total, 5-methylcytosine, 5-hydroxymethylcytosine, and promoter methylation of 33 genes were evaluated by reversed-phase high-performance liquid chromatography, enzyme-linked immunosorbent assay based technique, and bisulfate-based next generation sequencing...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28351035/resting-state-functional-connectivity-changes-associated-with-visuospatial-cognitive-deficits-in-patients-with-mild-alzheimer-disease
#10
Rakesh Balachandar, Srikala Bharath, John P John, Himanshu Joshi, Shilpa Sadanand, Jitender Saini, Keshav J Kumar, Mathew Varghese
BACKGROUND/AIMS: Alzheimer disease (AD) is a neurodegenerative disorder characterized by progressive disconnection of various brain networks leading to neuropsychological impairment. Pathology in the visual association areas has been documented in presymptomatic AD and therefore we aimed at examining the relationship between brain connectivity and visuospatial (VS) cognitive deficits in early AD. METHODS: Tests for VS working memory, episodic memory and construction were used to classify patients with AD (n = 48) as having severe VS deficits (n = 12, female = 4) or mild deficits (n = 11, female = 4)...
March 29, 2017: Dementia and Geriatric Cognitive Disorders
https://www.readbyqxmd.com/read/28348879/absence-of-genome-reduction-in-diverse-facultative-endohyphal-bacteria
#11
David A Baltrus, Kevin Dougherty, Kayla R Arendt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T B K Reddy, Chew Yee Ngan, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, A Elizabeth Arnold
Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all...
February 2017: Microbial Genomics
https://www.readbyqxmd.com/read/28348474/malignant-hepatic-epithelioid-hemangioendothelioma-with-villaret-syndrome
#12
Hanchanale Pavan, Joy Varghese, Kavya Harika, Mukul Vij, Venkataraman Jayanthi, Mohamed Rela
Malignant hepatic epithelioid hemangioendothelioma is a rare, vascular tumor of the liver with peak incidence in the middle age with a female preponderance and of unknown etiology. Majority of the tumors are asymptomatic. The gold standard for diagnosis of the tumor is liver histology showing presence of epithelioid tumor cells on a background of a hyaline stroma. Immunohistochemical positivity for CD31, CD34, Factor VIII, and Podoplanin (D2-40) is confirmatory. The treatment of choice is liver transplantation...
March 2017: Journal of Clinical and Experimental Hepatology
https://www.readbyqxmd.com/read/28346697/car-t-cell-therapy-for-pancreatic-cancer
#13
REVIEW
Carl J DeSelm, Zachary E Tano, Anna M Varghese, Prasad S Adusumilli
Chimeric antigen receptor (CAR) T-cell therapy utilizes genetic engineering to redirect a patient's own T cells to target cancer cells. The remarkable results in hematological malignancies prompted investigating this approach in solid tumors such as pancreatic cancer. The complex tumor microenvironment, stromal hindrance in limiting immune response, and expression of checkpoint blockade on T cells pose hurdles. Herein, we summarize the opportunities, challenges, and state of knowledge in targeting pancreatic cancer with CAR T-cell therapy...
March 27, 2017: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28346405/structural-and-functional-insight-into-human-o-glcnacase
#14
Christian Roth, Sherry Chan, Wendy A Offen, Glyn R Hemsworth, Lianne I Willems, Dustin T King, Vimal Varghese, Robert Britton, David J Vocadlo, Gideon J Davies
O-GlcNAc hydrolase (OGA) removes O-linked N-acetylglucosamine (O-GlcNAc) from a myriad of nucleocytoplasmic proteins. Through co-expression and assembly of OGA fragments, we determined the three-dimensional structure of human OGA, revealing an unusual helix-exchanged dimer that lays a structural foundation for an improved understanding of substrate recognition and regulation of OGA. Structures of OGA in complex with a series of inhibitors define a precise blueprint for the design of inhibitors that have clinical value...
March 27, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28339605/uniparental-chicken-offsprings-derived-from-oogenesis-of-chicken-primordial-germ-cells-zz-%C3%A2
#15
Chunhai Liu, Il-Kuk Chang, Kamal A Khazanehdari, Shruti Thomas, Preetha Varghese, Vijaya Baskar, Razan Alkhatib, Wenhai Li, Jörg Kinne, Michael J McGrew, Ulrich Wernery
Cloning (somatic cell nuclear transfer) in avian species has proven unachievable due to the physical structure of the avian oocyte. Here, the sexual differentiation of primordial germ cells with genetic sex ZZ (ZZ PGCs) was investigated in female germline chimeric chicken hosts with the aim to produce uniparental offspring. ZZ PGCs were expanded in culture and transplanted into the same and opposite sex chicken embryos which were partially sterilized using irradiation. All tested chimeric roosters (ZZ/ZZ) showed germline transmission with transmission rates of 3...
March 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28336937/results-of-the-randomized-phase-iib-arctic-trial-of-low-dose-rituximab-in-previously-untreated-cll
#16
D R Howard, T Munir, L McParland, A C Rawstron, D Milligan, A Schuh, A Hockaday, D J Allsup, S Marshall, A S Duncombe, J L O'Dwyer, A F Smith, R Longo, A Varghese, P Hillmen
ARCTIC was a multi-center, randomized-controlled, open, phase IIB non-inferiority trial in previously untreated Chronic Lymphocytic Leukemia (CLL). Conventional frontline therapy in fit patients is fludarabine, cyclophosphamide and rituximab (FCR). The trial hypothesized that including mitoxantrone with low-dose rituximab (FCM-miniR) would be non-inferior to FCR. 200 patients were recruited to assess the primary endpoint of complete remission (CR) rates according to IWCLL criteria. Secondary endpoints were progression-free survival (PFS), overall survival (OS), overall response rate, minimal residual disease (MRD) negativity, safety and cost-effectiveness...
March 24, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28334134/a-compilation-of-web-based-research-tools-for-mirna-analysis
#17
Vaibhav Shukla, Vinay Koshy Varghese, Shama Prasada Kabekkodu, Sandeep Mallya, Kapaettu Satyamoorthy
Since the discovery of microRNAs (miRNAs), a class of noncoding RNAs that regulate the gene expression posttranscriptionally in sequence-specific manner, there has been a release of number of tools useful for both basic and advanced applications. This is because of the significance of miRNAs in many pathophysiological conditions including cancer. Numerous bioinformatics tools that have been developed for miRNA analysis have their utility for detection, expression, function, target prediction and many other related features...
February 25, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28331271/adenoid-cystic-carcinoma-of-trachea
#18
Ashish Varghese, Swati Suneha, John C Watkinson
Adenoid cystic carcinoma (ACC) is the second most common primary malignant tumor of the trachea, after squamous cell carcinoma. Patients present with upper airway obstructive symptoms and signs including dyspnoea, cough, haemoptysis, and stridor which are often insidious, delaying diagnosis and optimal management. Described here is an unusual case of primary ACC cervical trachea with concomitant micropapillary thyroid carcinoma (microPTC) in a middle-aged lady presenting with cough and breathing difficulty since 3 months...
February 2017: Indian Journal of Surgery
https://www.readbyqxmd.com/read/28304057/topography-preserved-microwave-plasma-etching-for-top-down-layer-engineering-in-mos2-and-other-van-der-waals-materials
#19
Abin Varghese, Chithra H Sharma, Madhu Thalakulam
A generic and universal layer engineering strategy for van der Waals (vW) materials, scalable and compatible with the current semiconductor technology, is of paramount importance in realizing all-two-dimensional logic circuits and to move beyond the silicon scaling limit. In this letter, we demonstrate a scalable and highly controllable microwave plasma based layer engineering strategy for MoS2 and other vW materials. Using this technique we etch MoS2 flakes layer-by-layer starting from an arbitrary thickness and area down to the mono- or the few-layer limit...
March 17, 2017: Nanoscale
https://www.readbyqxmd.com/read/28302769/complete-genome-sequence-of-nitrosomonas-cryotolerans-atcc-49181-a-phylogenetically-distinct-ammonia-oxidizing-bacterium-isolated-from-arctic-waters
#20
Marlen C Rice, Jeanette M Norton, Lisa Y Stein, Jessica Kozlowski, Annette Bollmann, Martin G Klotz, Luis Sayavedra-Soto, Nicole Shapiro, Lynne A Goodwin, Marcel Huntemann, Alicia Clum, Manoj Pillay, Neha Varghese, Natalia Mikhailova, Krishna Palaniappan, Natalia Ivanova, Supratim Mukherjee, T B K Reddy, Chew Yee Ngan, Chris Daum, Nikos Kyrpides, Tanja Woyke
Nitrosomonas cryotolerans ATCC 49181 is a cold-tolerant marine ammonia-oxidizing bacterium isolated from seawater collected in the Gulf of Alaska. The high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO2 fixation were identified.
March 16, 2017: Genome Announcements
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