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https://www.readbyqxmd.com/read/28227928/pca-criterion-for-svm-mlp-classifier-for-flavivirus-biomarker-from-salivary-sers-spectra-at-febrile-stage
#1
A R M Radzol, Khuan Y Lee, W Mansor, I S Omar, A R M Radzol, Khuan Y Lee, W Mansor, I S Omar, Khuan Y Lee, A R M Radzol, I S Omar, W Mansor
Non-structural protein (NS1) has been conceded as one of the biomarkers for flavivirus that causes diseases with life threatening consequences. NS1 is an antigen that allows detection of the illness at febrile stage, mostly from blood samples currently. Our work here intends to define an optimum model for PCA-SVM with MLP kernel for classification of flavivirus biomarker, NS1 molecule, from SERS spectra of saliva, which to the best of our knowledge has never been explored. Since performance of the model depends on the PCA criterion and MLP parameters, both are examined in tandem...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227691/understanding-the-cochlear-implant-environment-by-mapping-perilymph-proteomes-from-different-species
#2
Jonathan C Palmer, Megan S Lord, Jeremy L Pinyon, Andrew K Wise, Nigel H Lovell, Paul M Carter, Ya Lang Enke, Gary D Housley, Rylie A Green, Jonathan C Palmer, Megan S Lord, Jeremy L Pinyon, Andrew K Wise, Nigel H Lovell, Paul M Carter, Ya Lang Enke, Gary D Housley, Rylie A Green, Ya Lang Enke, Rylie A Green, Jonathan C Palmer, Nigel H Lovell, Paul M Carter, Jeremy L Pinyon, Gary D Housley, Andrew K Wise, Megan S Lord
Cochlear implants operate within a bony channel of the cochlea, bathed in a fluid known as the perilymph. The perilymph is a complex fluid containing ions and proteins, which are known to actively interact with metallic electrodes. To improve our understanding of how cochlear implant performance varies in preclinical in vivo studies in comparison to human trials and patient outcomes, the protein composition (or perilymph proteome) is needed. Samples of perilymph were gathered from feline and guinea pig subjects and analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS) to produce proteomes and compare against the recently published human proteome...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227256/binding-affinity-prediction-of-s-cerevisiae-14-3-3-and-gyf-peptide-recognition-domains-using-support-vector-regression
#3
Volkan Uslan, Huseyin Seker, Volkan Uslan, Huseyin Seker, Huseyin Seker, Volkan Uslan
Proteins interact with other proteins and bio-molecules to carry out biological processes in a cell. Computational models help understanding complex biochemical processes that happens throughout the life of a cell. Domain-mediated protein interaction to peptides one such complex problem in bioinformatics that requires computational predictive models to identify meaningful bindings. In this study, domain-peptide binding affinity prediction models are proposed based on support vector regression. Proposed models are applied to yeast bmh 14-3-3 and syh GYF peptide-recognition domains...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227171/structural-classification-of-protein-sequences-based-on-signal-processing-and-support-vector-machines
#4
Charalambos Chrysostomou, Huseyin Seker, Charalambos Chrysostomou, Huseyin Seker, Huseyin Seker, Charalambos Chrysostomou
The function of any protein depends directly on its secondary and tertiary structure. Proteins can fold into a three-dimensional shape, which is primarily depended on the arrangement of amino acids in the primary structure. In recent years, with the explosive sequencing of proteins, it is unfeasible to perform detailed experimental studies, as these methodologies are very expensive and time consuming. This leaves the structure of the majority of currently available protein sequences unknown. In this paper, a predictive model is therefore presented for the classification of protein sequence's secondary structures, namely alpha helix and beta sheet...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227013/pan-cancer-analysis-for-studying-cancer-stage-using-protein-and-gene-expression-data
#5
Sameer Mishra, Chanchala D Kaddi, May D Wang, Sameer Mishra, Chanchala D Kaddi, May D Wang, Sameer Mishra, Chanchala D Kaddi, May D Wang
Pan-cancer analyses attempt to discover similar features among multiple cancers to identify fundamental patterns common to cancer development and progression. A pan-cancer analysis integrating both protein expression and transcriptomic data is important because it can identify genes that are linked to proteins potentially responsible for a patient's status. This study aims to identify differentially expressed (DE) genes between early and advanced cases of multiple cancer types through the usage of RNA sequencing data...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226896/evaluation-of-biofouling-for-implantable-micro-dialysis-system
#6
T Ota, N To, Y Kanno, N Miki, T Ota, N To, Y Kanno, N Miki, T Ota, Y Kanno, N Miki, N To
Implantable artificial kidney can drastically improve the quality of life of the renal disease patients. In previous study, our group has developed a multi-layered micro dialysis device which is composed of micro stainless steel channels and nano-porous polyethersulfone (PES) membranes. The device conducts hemofiltration without dialysis fluids, which is advantageous in miniaturization. We investigated the water-permeability of the PES membrane through in vivo experiments using rat model of renal disease for 5 hours and verified the effectiveness of the device...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226776/an-in-silico-model-of-the-effects-of-vitamin-d3-on-mycobacterium-infected-macrophage
#7
Maya Gough, Elebeoba May, Maya Gough, Elebeoba May, Maya Gough, Elebeoba May
Mycobacterium tuberculosis is a global health concern, causing over one million deaths a year. Alveolar macrophages, as the primary host cell of this intracellular bacterium, play an important role in the course of disease. Vitamin D3 is known to have a potent effect on macrophage behavior during infection, modulating the production of pro- and anti-inflammatory cytokines and immune effector molecules. In a vitamin D3 deficient host, the immune systems response to infection is greatly impaired. We used a quantitative systems biology approach to model the intracellular effects of vitamin D3 and compared our simulation output to our in vitro model of mycobacterium infection of macrophages in the presence and absence of Vitamin D3...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226774/modeling-non-clinical-and-clinical-drug-tests-in-gaucher-disease
#8
Clyde F Phelix, Allen K Bourdon, Greg Villareal, Richard G LeBaron, Clyde F Phelix, Allen K Bourdon, Greg Villareal, Richard G LeBaron, Richard G LeBaron, Clyde F Phelix, Allen K Bourdon, Greg Villareal
There is need for modeling biological systems to accelerate drug pipelines for treating metabolic diseases. The eliglustat treatment for Gaucher disease is approved by the FDA with a companion genomic test. The Transcriptome-To-Metabolome™ biosimulation technology was used to model, in silico, a standard non-clinical eliglustat test with an in vitro canine kidney cell system over-expressing a human gene; and a clinical test using human fibroblasts from control and Gaucher disease subjects. Protein homology modeling and docking studies were included to gather affinity parameters for the kinetic metabolic model...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226772/computational-analysis-of-androgen-receptor-dependent-radiosensitivity-in-prostate-cancer
#9
Mengdi Qian, Alexandru Almasan, Evren Gurkan-Cavusoglu, Mengdi Qian, Alexandru Almasan, Evren Gurkan-Cavusoglu, Mengdi Qian, Evren Gurkan-Cavusoglu, Alexandru Almasan
In this study, we quantitatively analyze the mechanism by which androgen deprivation therapy (ADT) is enhancing radiosensitivity in prostate cancer (PCa) patients. It has been shown in laboratory experiments, as well as in patient data in the literature, that the androgen receptor (AR) reduces the effectiveness of ionizing radiation treatment by enhancing the non-homologous end joining (NHEJ) repair of radiation damage. The suppression of AR by ADT suppresses the activity of NHEJ that leads to radiosensitivity in PCa patients...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226455/the-effect-of-multiple-thin-film-coatings-of-protein-loaded-sol-gel-on-total-multi-electrode-array-thickness
#10
Matthew D McDermott, Kevin J Otto, Matthew D McDermott, Kevin J Otto, Matthew D McDermott, Kevin J Otto
Tetramethyl orthosilicate shows promise as a thin-film delivery vehicle for multi-electrode arrays for drug release and electrical performance; however, its effect upon device footprint has yet to be assessed. Using a previously established silicon wafer chip model, the thickness of one, two, and four protein doped coatings of sol-gel were analyzed via profilometry. Coating thickness was found to be 0.4μm, 1.1μm and 2.2μm on each side of the device. This addition to a native MEA is minimal when compared to other drug delivery paradigms currently associated with neural implants...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226322/chronic-administration-of-rosa-canina-hydro-alcoholic-extract-attenuates-depressive-like-behavior-and-recognition-memory-impairment-in-diabetic-mice-a-possible-role-of-oxidative-stress
#11
Ramin Farajpour, Saeed Sadigh-Eteghad, Nahid Ahmadian, Mohammad Farzipour, Javad Mahmoudi, Alireza Majdi
OBJECTIVE: This study was designed to evaluate whether or not chronic Rosa Canina (RC) extract administration could improve recognition memory and depressive-like behaviour in diabetic mice. MATERIALS AND METHODS: Seventy-five (75) male Albino mice (25-30 g) were randomly divided into five groups (15 in each group). A single intraperitoneal (ip) injection of 200 mg/kg streptozotocin (STZ) was administered to the mice to induce diabetes. The control group received normal saline, and the diabetic groups received normal saline or 50, 250 and 500 mg/kg of RC extract for 28 days...
February 22, 2017: Medical Principles and Practice: International Journal of the Kuwait University, Health Science Centre
https://www.readbyqxmd.com/read/28226265/alterations-of-ubiquitin-related-proteins-in-the-pathology-and-development-of-schizophrenia-evidence-from-human-and-animal-studies
#12
Jessica L Andrews, Frederic J Goodfellow, Natalie Matosin, Mollie K Snelling, Kelly A Newell, Xu-Feng Huang, Francesca Fernandez-Enright
Gene expression analyses in post-mortem schizophrenia brains suggest that a number of ubiquitin proteasome system (UPS) genes are associated with schizophrenia; however the status of UPS proteins in the schizophrenia brain is largely unknown. Ubiquitin related proteins are inherently involved in memory, neuronal survival and morphology, which are processes implicated in neurodevelopmental disorders such as schizophrenia. We examined levels of five UPS proteins (Protein Inhibitor of Activated STAT2 [PIAS2], F-Box and Leucine rich repeat protein 21 [FBXL21], Mouse Double Minute 2 homolog [MDM2], Ubiquitin Carboxyl-Terminal Hydrolase-L1 [UCHL1] and Ubiquitin Conjugating Enzyme E2D1 [UBE2D1]) involved in these neuronal processes, within the dorsolateral prefrontal cortex of post-mortem schizophrenia subjects and matched controls (n = 30/group), in addition to across neurodevelopmental time-points (juvenile, adolescent and adult stages of life), utilizing a well-established neurodevelopmental phencyclidine (PCP) animal model of schizophrenia...
January 18, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28225990/visceral-adiposity-index-and-triglyceride-high-density-lipoprotein-cholesterol-ratio-in-hypogonadism
#13
Cem Haymana, Alper Sonmez, Aydogan Aydogdu, Serkan Tapan, Yalcin Basaran, Coskun Meric, Kamil Baskoy, Mustafa Dinc, Mahmut Yazici, Abdullah Taslipinar, Cem Barcin, Mahmut Ilker Yilmaz, Erol Bolu, Omer Azal
Background: Cardiometabolic risk is high in patients with hypogonadism. Visceral adiposity index (VAI) and triglyceride/high-density lipoprotein cholesterol (TG/HDL-C) ratio are the practical markers of atherosclerosis and insulin resistance and independent predictors of cardiaovascular risk. To date, no study has evaluated VAI levels and TG/HDL-C ratio in hypogonadism. Subjects and methods: A total of 112 patients with congenital hypogonadotrophic hypogonadism (CHH) (mean age, 21...
February 13, 2017: Archives of Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28225907/characterisation-of-iunh-gene-knockout-strain-from-mycobacterium-tuberculosis
#14
Anne Drumond Villela, Valnês da Silva Rodrigues, Antônio Frederico Michel Pinto, Priscila Lamb Wink, Zilpa Adriana Sánchez-Quitian, Guilherme Oliveira Petersen, Maria Martha Campos, Luiz Augusto Basso, Diógenes Santiago Santos
BACKGROUND: Tuberculosis (TB) is an infectious disease caused mainly by the bacillus Mycobacterium tuberculosis. The better understanding of important metabolic pathways from M. tuberculosis can contribute to the development of novel therapeutic and prophylactic strategies to combat TB. Nucleoside hydrolase (MtIAGU-NH), encoded by iunH gene (Rv3393), is an enzyme from purine salvage pathway in M. tuberculosis. MtIAGU-NH accepts inosine, adenosine, guanosine, and uridine as substrates, which may point to a pivotal metabolic role...
March 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28225889/roles-of-monocyte-chemotactic-protein-1-and-nuclear-factor-%C3%AE%C2%BAb-in-immune-response-to-spinal-tuberculosis-in-a-new-zealand-white-rabbit-model
#15
X H Guo, Z Bai, B Qiang, F H Bu, N Zhao
This study aimed to explore the roles of monocyte chemotactic protein 1 (MCP-1) and nuclear factor kappa B (NF-κB) in immune response to spinal tuberculosis in a New Zealand white rabbit model. Forty-eight New Zealand white rabbits were collected and divided into four groups: experimental group (n=30, spinal tuberculosis model was established), the sham group (n=15, sham operation was performed) and the blank group (n=3). The qRT-PCR assay and western blotting were applied to detect the mRNA and protein expressions of MCP-1 and NF-κB in peripheral blood...
February 20, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28225865/continuous-blood-purification-treatment-for-endotoxin-induced-acute-respiratory-distress-syndrome
#16
Y Jiang, R Lin, Y Xu, S Zhang, K Cui, M Zhu, A Li, C Chen, J Yang, W Yang
This study aimed to explore the effects of continuous blood purification (CBP) treatment in pigs affected with acute respiratory distress syndrome (ARDS). A total of 12 healthy male pigs, weighing 12±1.8 kg, were randomly and equally assigned to the control and experimental groups. The ARDS pig model was prepared by intravenous injections of endotoxin (20 µg/kg). The control group was given conventional supportive therapy, while the experimental group was given continuous veno-venous hemofiltration therapy...
February 16, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28225829/inhibition-of-arabidopsis-chloroplast-%C3%AE-amylase-bam3-by-maltotriose-suggests-a-mechanism-for-the-control-of-transitory-leaf-starch-mobilisation
#17
Jing Li, Wenxu Zhou, Perigio Francisco, Russell Wong, Dongke Zhang, Steven M Smith
Starch breakdown in leaves at night is tightly matched to the duration of the dark period, but the mechanism by which this regulation is achieved is unknown. In Arabidopsis chloroplasts, β-amylase BAM3 hydrolyses transitory starch, producing maltose and residual maltotriose. The aim of the current research was to investigate the regulatory and kinetic properties of BAM3. The BAM3 protein was expressed in Escherichia coli and first assayed using a model substrate. Enzyme activity was stimulated by treatment with dithiothreitol and was increased 40% by 2-10 μM Ca2+ but did not require Mg2+...
2017: PloS One
https://www.readbyqxmd.com/read/28225828/systematic-analysis-of-non-structural-protein-features-for-the-prediction-of-ptm-function-potential-by-artificial-neural-networks
#18
Henry M Dewhurst, Matthew P Torres
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality encompasses less than 5% of this data. We previously developed SAPH-ire (Structural Analysis of PTM Hotspots) for the prioritization of eukaryotic PTMs based on function potential of discrete modified alignment positions (MAPs) in a set of 8 protein families...
2017: PloS One
https://www.readbyqxmd.com/read/28225803/bacterial-expression-correct-membrane-targeting-and-functional-folding-of-the-hiv-1-membrane-protein-vpu-using-a-periplasmic-signal-peptide
#19
Arpan Deb, William A Johnson, Alexander P Kline, Boston J Scott, Lydia R Meador, Dustin Srinivas, Jose M Martin-Garcia, Katerina Dörner, Chad R Borges, Rajeev Misra, Brenda G Hogue, Petra Fromme, Tsafrir S Mor
Viral protein U (Vpu) is a type-III integral membrane protein encoded by Human Immunodeficiency Virus-1 (HIV- 1). It is expressed in infected host cells and plays several roles in viral progeny escape from infected cells, including down-regulation of CD4 receptors. But key structure/function questions remain regarding the mechanisms by which the Vpu protein contributes to HIV-1 pathogenesis. Here we describe expression of Vpu in bacteria, its purification and characterization. We report the successful expression of PelB-Vpu in Escherichia coli using the leader peptide pectate lyase B (PelB) from Erwinia carotovora...
2017: PloS One
https://www.readbyqxmd.com/read/28225631/conformational-changes-in-c-reactive-protein-affect-binding-to-curved-membranes-in-a-lipid-bilayer-model-of-the-apoptotic-cell-surface
#20
Aml Abd Alnaas, Carrie L Moon, Mitchell Alton, Scott M Reed, Michelle K Knowles
C-reactive protein (CRP) is a serum protein that binds to damaged membranes through a phosphatidylcholine binding site. The membrane binding process can initiate the complement immune response and facilitates the clearance of apoptotic cells, likely aiding in the protection of autoimmunity. The initiation of an immune response relies on a conformation change from a native, pentameric form to a modified form, where the modified form binds complement proteins (i.e. C1q) and regulatory proteins substantially better than the native form...
February 22, 2017: Journal of Physical Chemistry. B
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