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Shyamashree Banerjee, Parth Sarthi Sen Gupta, Arnab Nayek, Sunit Das, Vishma Pratap Sur, Pratyay Seth, Rifat Nawaz Ul Islam, Amal K Bandyopadhyay
UNLABELLED: Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution (PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized outputs in excel format along with detailed methodology...
2015: Bioinformation
Leena Sathe, Cheryl Bolinger, M Amin-ul Mannan, Thomas E Dever, Madhusudan Dey
The Hac1 transcription factor in yeast up-regulates a collection of genes that control protein homeostasis. Base-pairing interactions between sequences in the intron and the 5'-untranslated region (5' UTR) of the HAC1 mRNA represses Hac1 protein production under basal conditions, whereas cytoplasmic splicing of the intron by the Ire1 kinase-endonuclease, activated under endoplasmic reticulum stress conditions, relieves the inhibition and enables Hac1 synthesis. Using a random mutational screen as well as site-directed mutagenesis, we identify point mutations within the 5' UTR-intron interaction site that derepress translation of the unspliced HAC1 mRNA...
September 4, 2015: Journal of Biological Chemistry
Mufti Rana Farrukh, Ul-Ashraf Nissar, Peerzada J Kaiser, Quadri Afnan, Praduman R Sharma, Shashi Bhushan, Sheikh A Tasduq
BACKGROUND: Previously we have reported that generation of reactive oxygen species is the prime event responsible for calcium mediated activation of PERK-eIF2α-CHOP pathway and apoptosis in UV-B irradiated human skin fibroblasts (Hs68). We have also reported that glycyrrhizic acid (GA) mediates potent photoprotective activity against UV-B - irradiation-induced photodamage in human skin fibroblast. OBJECTIVE: In the present study, we aimed to investigate the role of GA in preventing oxidative stress mediated unfolded protein response (UPR) and mitogen activated protein kinases (MAPK) pathway...
July 2015: Journal of Photochemistry and Photobiology. B, Biology
Marlene S Jarosch, Christine Gebhardt, Silvia Fano, Christine Huchzermeyer, Rizwan Ul Haq, Christoph J Behrens, Uwe Heinemann
We investigated the effects of hypoxia on sharp wave-ripple complex (SPW-R) activity and recurrent epileptiform discharges in rat hippocampal slices, and the mechanisms underlying block of this activity. Oxygen levels were measured using Clark-style oxygen sensor microelectrodes. In contrast to recurrent epileptiform discharges, oxygen consumption was negligible during SPW-R activity. These network activities were reversibly blocked when oxygen levels were reduced to 20% or less for 3 min. The prolongation of hypoxic periods to 6 min caused reversible block of SPW-Rs during 20% oxygen and irreversible block when 0% oxygen (anoxia) was applied...
July 2015: European Journal of Neuroscience
Khalid Hussain Janbaz, Tashfeen Akhtar, Fatima Saqib, Imran Imran, Muhammad Zia-Ul-Haq, Chaweeewan Jansakul, Vincenzo De Feo, Marius Moga
BACKGROUND: Solena heterophylla Lour. has traditionally been used in the management of diseases pertaining to gastrointestinal, respiratory and vascular system and present study was undertaken to validate its traditional uses. METHODS: The aqueous ethanolic extract of Solena heterophylla Lour (Sh.Cr) was tested in-vitro on isolated rabbit jejunum, tracheal and aorta preparations. The responses of tissues were recorded using isotonic transducers coupled with PowerLab data acquisition system...
2015: Journal of Translational Medicine
Khalid Hussain Janbaz, Muhammad Zaeem Ahsan, Fatima Saqib, Imran Imran, Muhammad Zia-Ul-Haq, Muhammad Abid Rashid, Hawa Z E Jaafar, Marius Moga
BACKGROUND: Pyrus pashia Buch.-Ham. ex D. Don. has been used conventionally by many communities in the Himalayan region for the management of gastrointestinal, respiratory, and vascular complications. Set against this background, this study was carried out to justify the scientific basis to validate folkloric uses of fruits of Pyrus pashia Buch.-Ham. ex D. Don. (Pp.Cr) in traditional systems of medicine. METHODS: The crude ethanol extract of fruits of Pyrus pashia Buch...
2015: PloS One
K H Janbaz, A Qayyum, F Saqib, I Imran, M Zia-Ul-Haq, V de Feo
Cymbopogon martinii (Cm.Cr) is traditionally used in south Asian communities for the management of multiple ailments including gastrointestinal, respiratory and vascular disorders and the present study was undertaken to validate these folkloric uses. The application of a methanol extract of the plant (Cm.Cr) to isolated rabbit jejunum preparation exhibited relaxation through decrease in magnitude and frequency of spontaneous contractions. The Cm.Cr also exerted relaxant effect on high K(+) (80 mM) induced contractions in isolated rabbit jejunum preparations...
December 2014: Journal of Physiology and Pharmacology: An Official Journal of the Polish Physiological Society
Syed Mudasir Ahmad, Farooz Ahmad Bhat, Masood-Ul Hassan Balkhi, Bilal Ahmad Bhat
Despite numerous studies on the taxonomy of a highly complex group of schizothoracine (snow trouts), with over five recognized species from Kashmir, India (Schizothorax niger, Schizothorax esocinus, Schizothorax plagiostomus, Schizothorax curvifrons and Schizothorax labiatus) based on traditional morphological data, the relationships between these species is poorly understood and the taxonomic validity is still under debate. To resolve the evolutionary relationships among these species, we sequenced mitochondrial fragments, including 16Sr RNA, Cytb and the D-loop...
December 2014: Genetica
Long-Chao Zhang, Na Li, Xin Liu, Jing Liang, Hua Yan, Ke-Bin Zhao, Lei Pu, Hui-Bi Shi, Yue-Bo Zhang, Li-Gang Wang, Li-Xian Wang
BACKGROUND: In pig, limb bone length influences ham yield and body height to a great extent and has important economic implications for pig industry. In this study, an intercross population was constructed between the indigenous Chinese Minzhu pig breed and the western commercial Large White pig breed to examine the genetic basis for variation in limb bone length. The aim of this study was to detect potential genetic variants associated with porcine limb bone length. METHODS: A total of 571 F2 individuals from a Large White and Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip, and phenotyped for femur length (FL), humerus length (HL), hipbone length (HIPL), scapula length (SL), tibia length (TL), and ulna length (UL)...
2014: Genetics, Selection, Evolution: GSE
Jonathan Wiesen, Gustavo Heresi, Wayne Tsuang
Critical Care Case Report Posters IISESSION TYPE: Affiliate Case Report PosterPRESENTED ON: Tuesday, October 28, 2014 at 01:30 PM - 02:30 PMINTRODUCTION: Severe pulmonary hypertension can result in pulmonary artery (PA) dilatation with resultant mechanical complications, such as pulmonary valve insufficiency, PA rupture and, rarely, compression of nearby anatomical structures.CASE PRESENTATION: A 53-year-old male with a known history of severe, inoperable, chronic thromboembolic pulmonary hypertension (CTEPH), presented with hypotension and hypoxic respiratory failure...
October 1, 2014: Chest
Jun Hwan Choi, Eun Young Han, Bo Ryun Kim, Sun Mi Kim, Sang Hee Im, So Young Lee, Chul Woong Hyun
OBJECTIVE: To investigate the effectiveness of commercial gaming-based virtual reality (VR) therapy on the recovery of paretic upper extremity in subacute stroke patients. METHODS: Twenty patients with the first-onset subacute stroke were enrolled and randomly assigned to the case group (n=10) and the control group (n=10). Primary outcome was measured by the upper limb score through the Fugl-Meyer Assessment (FMA-UL) for the motor function of both upper extremities...
August 2014: Annals of Rehabilitation Medicine
Soon-Cheol Chung, Mi-Hyun Choi, Hyung-Sik Kim, Na-Rae You, Sang-Pyo Hong, Jung-Chul Lee, Sung-Jun Park, Ji-Hye Baek, Ul-Ho Jeong, Ji-Hye You, Dae-Woon Lim, Hyun-Jun Kim
This study investigated neuronal activation differences under two conditions: driving only and distracted driving. Driving and distraction tasks were performed using a Magnetic Resonance (MR)-compatible driving simulator with a driving wheel and pedal. The experiment consisted of three blocks, and each block had both a Rest phase (1 min) and a Driving phase (2 min). During the Rest phase, drivers were instructed to simply look at the stop screen without performing any driving tasks. During the Driving phase, each driver was required to drive at 110 km/h under two conditions: driving only and driving while performing additional distraction tasks...
2014: Bio-medical Materials and Engineering
Quratulain Merchant, Naveed Ur Rehman Siddiqui, Amina Rehmat, Muneer Amanullah, Anwar Ul Haq, Babar Hasan
BACKGROUND: Hypokalaemia is frequently encountered in the daily clinical practices of a paediatric cardiac intensive care unit (PCICU). It is a strong independent predictor of mortality in patients with heart failure. Thus, prompt potassium replacement therapy holds pivotal importance in therapy for hypokalaemia. Although intravenous potassium replacement (IVPR) in hypokalaemia is the preferred route in most intensive care settings, it is associated with known safety risks and can lead to arrhythmias, cardiac arrest and death if inappropriately administered...
2014: BMJ Open
Muhammad Tahir Ul Qamar, Arooj Mumtaz, Rabbia Naseem, Amna Ali, Tabeer Fatima, Tehreem Jabbar, Zubair Ahmad, Usman Ali Ashfaq
Dengue infection has turned into a serious health concern globally due to its high morbidity rate and a high possibility of increase in its mortality rate on the account of unavailability of any proper treatment for severe dengue infection. The situation demands an urgent development of efficient and practicable treatment to deal with Dengue virus (DENV). Flavonoids, a class of phytochemicals present in medicinal plants, possess anti-viral activity and can be strong drug candidates against viruses. NS1 glycoprotein of Dengue virus is involved in its RNA replication and can be a strong target for screening of drugs against this virus...
2014: Bioinformation
Mudasir Ahmad Syed, Farooz Ahmad Bhat, Masood-ul Hassan Balkhi, Bilal Ahmad Bhat
Schizothoracine fish commonly called snow trouts inhibit the entire network of snow and spring fed cool waters of Kashmir, India. Over 10 species reported earlier, only five species have been found, these include Schizothorax niger, Schizothorax esocinus, Schizothorax plagiostomus, Schizothorax curvifrons and Schizothorax labiatus. The relationship between these species is contradicting. To understand the evolutionary relation of these species, we examined the sequence information of mitochondrial D-loop of 25 individuals representing five species...
2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Mohd Lateef Wani, Abdul Gani Ahangar, Shyam Singh, Ifat Irshad, Nayeem Ul-Hassan, Shadab Nabi Wani, Farooq Ahmad Ganie, Mohd Akbar Bhat
BACKGROUND: The interest in beating heart surgery is growing since better results can be obtained with this procedure compared to conventional myocardial protection techniques using cardioplegic solutions. This led us to consider mitral valve replacement with beating heart. OBJECTIVES: This study aimed to determine the safety and efficacy of beating heart mitral valve replacement without cross clamp. METHODS: This prospective study was conducted on the patients with isolated mitral valve disease requiring mitral valve replacement according to ACC / AHA guidelines...
April 2014: International Cardiovascular Research Journal
Farit M Afendi, Naoaki Ono, Yukiko Nakamura, Kensuke Nakamura, Latifah K Darusman, Nelson Kibinge, Aki Hirai Morita, Ken Tanaka, Hisayuki Horai, Md Altaf-Ul-Amin, Shigehiko Kanaya
Molecular biological data has rapidly increased with the recent progress of the Omics fields, e.g., genomics, transcriptomics, proteomics and metabolomics that necessitates the development of databases and methods for efficient storage, retrieval, integration and analysis of massive data. The present study reviews the usage of KNApSAcK Family DB in metabolomics and related area, discusses several statistical methods for handling multivariate data and shows their application on Indonesian blended herbal medicines (Jamu) as a case study...
2013: Computational and Structural Biotechnology Journal
Parth Sarthi Sen Gupta, Shyamashree Banerjee, Rifat Nawaz Ul Islam, Sudipta Mondal, Buddhadev Mondal, Amal K Bandyopadhyay
UNLABELLED: In the genomic and proteomic era, efficient and automated analyses of sequence properties of protein have become an important task in bioinformatics. There are general public licensed (GPL) software tools to perform a part of the job. However, computations of mean properties of large number of orthologous sequences are not possible from the above mentioned GPL sets. Further, there is no GPL software or server which can calculate window dependent sequence properties for a large number of sequences in a single run...
2014: Bioinformation
Mamoona Yasin, Khalid Hussain Janbaz, Imran Imran, Anwar-ul-Hassan Gilani, Samra Bashir
This study evaluated the antispasmodic, bronchodilator and anti-platelet activities of Abies webbiana to rationalize some of its folk uses in gut and airways disorders and inflammation. The crude extract of A. webbiana (Aw.Cr) caused a complete relaxation of both spontaneous and K(+) (80 mM)-induced contractions in isolated rabbit jejunum in a concentration-dependent manner. Aw.Cr shifted the Ca(++) concentration-response curves (CRCs) to the right, in a fashion similar to verapamil, confirming its Ca(++) channel blocking (CCB) effect...
August 2014: Phytotherapy Research: PTR
Raghu Lingam, Pallavi Gupta, Shamsa Zafar, Zelee Hill, Aisha Yousafzai, Sharad Iyengar, Siham Sikander, Zaeem ul Haq, Shilpa Mehta, Jolene Skordis-Worrel, Atif Rahman, Betty Kirkwood
Undernutrition and inadequate stimulation both negatively influence child health and development and have a long-term impact on school attainment and income. This paper reports data from India and Pakistan looking at how families interact, play with, and feed children; their expectations of growth and development; and the perceived benefits, consequences, opportunities, and barriers of adopting recommended feeding and developmental behaviors. These data were collected as part of formative research for the Sustainable Program Incorporating Nutrition and Games (SPRING) trial...
January 2014: Annals of the New York Academy of Sciences
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