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https://www.readbyqxmd.com/read/27914278/fdstools-a-software-package-for-analysis-of-massively-parallel-sequencing-data-with-the-ability-to-recognise-and-correct-str-stutter-and-other-pcr-or-sequencing-noise
#1
Jerry Hoogenboom, Kristiaan J van der Gaag, Rick H de Leeuw, Titia Sijen, Peter de Knijff, Jeroen F J Laros
Massively parallel sequencing (MPS) is on the advent of a broad scale application in forensic research and casework. The improved capabilities to analyse evidentiary traces representing unbalanced mixtures is often mentioned as one of the major advantages of this technique. However, most of the available software packages that analyse forensic short tandem repeat (STR) sequencing data are not well suited for high throughput analysis of such mixed traces. The largest challenge is the presence of stutter artefacts in STR amplifications, which are not readily discerned from minor contributions...
November 27, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27914063/episweep-computationally-driven-reengineering-of-therapeutic-proteins-to-reduce-immunogenicity-while-maintaining-function
#2
Yoonjoo Choi, Deeptak Verma, Karl E Griswold, Chris Bailey-Kellogg
Therapeutic proteins are yielding ever more advanced and efficacious new drugs, but the biological origins of these highly effective therapeutics render them subject to immune surveillance within the patient's body. When recognized by the immune system as a foreign agent, protein drugs elicit a coordinated response that can manifest a range of clinical complications including rapid drug clearance, loss of functionality and efficacy, delayed infusion-like allergic reactions, more serious anaphylactic shock, and even induced auto-immunity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27912911/hesperidin-ameliorates-immunological-outcome-and-reduces-neuroinflammation-in-the-mouse-model-of-multiple-sclerosis
#3
Dariush Haghmorad, Mohammad Bagher Mahmoudi, Zohreh Salehipour, Zoleikha Jalayer, Amir Abbas Momtazi Brojeni, Maryam Rastin, Parviz Kokhaei, Mahmoud Mahmoudi
Multiple sclerosis (MS) is the most abundant central nervous system (CNS) inflammatory disease, which is due to the reaction of auto reactive T cells with own myelin proteins, leading to physical disorder and paralysis among people suffering the disease. Hesperidin, a flavanone glycoside found abundantly in citrus fruits possesses a wide range of pharmacological properties including potential anti-inflammatory and anti-cancer effects. This study was designed to reveal the molecular and cellular mechanisms underlying the effect of hesperidin on MS alleviation...
November 26, 2016: Journal of Neuroimmunology
https://www.readbyqxmd.com/read/27912169/non-harmonicity-in-high-frequency-components-of-the-intra-operative-corticogram-to-delineate-epileptogenic-tissue-during-surgery
#4
Evelien E Geertsema, Maryse A van 't Klooster, Nicole E C van Klink, Frans S S Leijten, Peter C van Rijen, Gerhard H Visser, Stiliyan N Kalitzin, Maeike Zijlmans
OBJECTIVE: We aimed to test the potential of auto-regressive model residual modulation (ARRm), an artefact-insensitive method based on non-harmonicity of the high-frequency signal, to identify epileptogenic tissue during surgery. METHODS: Intra-operative electrocorticography (ECoG) of 54 patients with refractory focal epilepsy were recorded pre- and post-resection at 2048Hz. The ARRm was calculated in one-minute epochs in which high-frequency oscillations (HFOs; fast ripples, 250-500Hz; ripples, 80-250Hz) and spikes were marked...
November 17, 2016: Clinical Neurophysiology: Official Journal of the International Federation of Clinical Neurophysiology
https://www.readbyqxmd.com/read/27910671/a-high-speed-compact-microwave-interferometer-for-density-fluctuation-measurements-in-sino-united-spherical-tokamak
#5
H Zhong, Y Tan, Y Q Liu, H Q Xie, Z Gao
A single-channel 3 mm interferometer has been developed for plasma density diagnostics in the Sino-UNIted Spherical Tokamak (SUNIST). The extremely compact microwave interferometer utilizes one corrugated feed horn antenna for both emitting and receiving the microwave. The beam path lies on the equatorial plane so the system would not suffer from beam path deflection problems due to the symmetry of the cross section. A focusing lens group and an oblique vacuum window are carefully designed to boost the signal to noise ratio, which allows this system to show good performance even with the small-diameter central column itself as a reflector, without a concave mirror...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910545/commercial-counterboard-for-10-ns-software-correlator-for-photon-and-fluorescence-correlation-spectroscopy
#6
Matteo Molteni, Fabio Ferri
A 10 ns time resolution, multi-tau software correlator, capable of computing simultaneous autocorrelation (A-A, B-B) and cross (A-B) correlation functions at count rates up to ∼10 MHz, with no data loss, has been developed in LabVIEW and C++ by using the National Instrument timer/counterboard (NI PCIe-6612) and a fast Personal Computer (PC) (Intel Core i7-4790 Processor 3.60 GHz ). The correlator works by using two algorithms: for large lag times (τ ≳ 1 μs), a classical time-mode scheme, based on the measure of the number of pulses per time interval, is used; differently, for τ ≲ 1 μs a photon-mode (PM) scheme is adopted and the correlation function is retrieved from the sequence of the photon arrival times...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910541/research-on-the-best-measurement-situation-between-optical-probe-and-tissue-surfaces-in-non-invasive-detection
#7
Xuyao Yu, Rong Liu, Hui Yu, Jiao Wang, Jun Wang, Kexin Xu
Near-infrared spectroscopy is often used for the non-invasive detection of composition in the human body, such as that of blood glucose and haemoglobin, due to its high penetration depth into tissues. Although it is feasible to position the optical probe precisely, contact situation between probe and human tissues is a difficult problem to determine because of physiological tremor and mechanical performance of bio-soft tissue. Here, we proposed a novel estimation method for the situation between the optical probe and tissue surfaces based on the dynamic auto-correlation matrix of two-dimensional correlation spectroscopy (2DCOS) and radar chart...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910205/neurosurgical-robotic-arm-drilling-navigation-system
#8
Chung-Chih Lin, Hsin-Cheng Lin, Wen-Yo Lee, Shih-Tseng Lee, Chieh-Tsai Wu
BACKGROUND: The aim of this work was to develop a neurosurgical robotic arm drilling navigation system that provides assistance throughout the complete bone drilling process. METHODS: The system comprised neurosurgical robotic arm navigation combining robotic and surgical navigation, 3D medical imaging based surgical planning that could identify lesion location and plan the surgical path on 3D images, and automatic bone drilling control that would stop drilling when the bone was to be drilled-through...
December 2, 2016: International Journal of Medical Robotics + Computer Assisted Surgery: MRCAS
https://www.readbyqxmd.com/read/27909842/the-relationship-between-nernst-equilibrium-variability-and-the-multifractality-of-interspike-intervals-in-the-hippocampus
#9
Stephen R Meier, Jarrett L Lancaster, Dustin Fetterhoff, Robert A Kraft, Robert E Hampson, Joseph M Starobin
Spatiotemporal patterns of action potentials are considered to be closely related to information processing in the brain. Auto-generating neurons contributing to these processing tasks are known to cause multifractal behavior in the inter-spike intervals of the output action potentials. In this paper we define a novel relationship between this multifractality and the adaptive Nernst equilibrium in hippocampal neurons. Using this relationship we are able to differentiate between various drugs at varying dosages...
December 1, 2016: Journal of Computational Neuroscience
https://www.readbyqxmd.com/read/27909154/towards-a-novel-modular-architecture-for-cern-radiation-monitoring
#10
Hamza Boukabache, Michel Pangallo, Gael Ducos, Nicola Cardines, Antonio Bellotta, Ciarán Toner, Daniel Perrin, Doris Forkel-Wirth
The European Organization for Nuclear Research (CERN) has the legal obligation to protect the public and the people working on its premises from any unjustified exposure to ionising radiation. In this context, radiation monitoring is one of the main concerns of the Radiation Protection Group. After 30 y of reliable service, the ARea CONtroller (ARCON) system is approaching the end of its lifecycle, which raises the need for new, more efficient radiation monitors with a high level of modularity to ensure better maintainability...
November 30, 2016: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/27908207/anti-sulfatide-reactivity-in-patients-with-celiac-disease
#11
Domenica Saccomanno, Carolina Tomba, Francesca Magri, Philippe Backelandt, Leda Roncoroni, Luisa Doneda, Maria Teresa Bardella, Giacomo Pietro Comi, Nereo Bresolin, Dario Conte, Luca Elli
OBJECTIVE: To explore a possible significance of the presence of anti-ganglioside and anti-sulfatide antibodies in sera of adult patients with celiac disease (CD) in different clinical scenario. METHODS: We selected 22 adult patients with newly diagnosed CD and 20 age-sex matched non-CD controls. Patients' serum was tested - before and after at least 6 months on a gluten-free diet (GFD) - for anti-GM1, GM2, GM3, GD1a, GD1b, GD3, GT1a, GT1b, GQ1b and sulfatide IgM, IgG and IgA auto-antibodies, by means of a dot blot technique and enzyme-linked immunosorbent assay (ELISA)...
December 1, 2016: Scandinavian Journal of Gastroenterology
https://www.readbyqxmd.com/read/27908011/principal-dynamic-mode-analysis-of-neural-mass-model-for-the-identification-of-epileptic-states
#12
Yuzhen Cao, Liu Jin, Fei Su, Jiang Wang, Bin Deng
The detection of epileptic seizures in Electroencephalography (EEG) signals is significant for the diagnosis and treatment of epilepsy. In this paper, in order to obtain characteristics of various epileptiform EEGs that may differentiate different states of epilepsy, the concept of Principal Dynamic Modes (PDMs) was incorporated to an autoregressive model framework. First, the neural mass model was used to simulate the required intracerebral EEG signals of various epileptiform activities. Then, the PDMs estimated from the nonlinear autoregressive Volterra models, as well as the corresponding Associated Nonlinear Functions (ANFs), were used for the modeling of epileptic EEGs...
November 2016: Chaos
https://www.readbyqxmd.com/read/27907810/prediction-of-autosomal-str-typing-success-in-ancient-and-second-world-war-bone-samples
#13
Irena Zupanič Pajnič, Tomaž Zupanc, Jože Balažic, Živa Miriam Geršak, Oliver Stojković, Ivan Skadrić, Matija Črešnar
Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded...
November 19, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27907165/pre-and-postcycloplegic-refractions-in-children-and-adolescents
#14
Dan Zhu, Yan Wang, Xianrong Yang, Dayong Yang, Kai Guo, Yuanyuan Guo, Xinxia Jing, Chen-Wei Pan
PURPOSE: To determine the difference between cycloplegic and non-cycloplegic refractive error and its associated factors in Chinese children and adolescents with a high prevalence of myopia. METHODS: A school-based study including 1565 students aged 6 to 21 years was conducted in 2013 in Ejina, Inner Mongolia, China. Comprehensive eye examinations were performed. Pre-and postcycloplegic refractive error were measured using an auto-refractor. For cycloplegic refraction, one drop of topical 1...
2016: PloS One
https://www.readbyqxmd.com/read/27905903/immediate-effect-of-cpap-titration-on-perceived-health-related-quality-of-life-a-prospective-observational-study
#15
Serena Iacono Isidoro, Adriana Salvaggio, Anna Lo Bue, Salvatore Romano, Oreste Marrone, Giuseppe Insalaco
BACKGROUND: Perceived Health Related Quality of Life (HRQoL) is impaired in obstructive sleep apnea (OSA). This study examines changes in HRQoL aspects occurring immediately after CPAP titration. Furthermore, we analyzed variations in each gender and in patients undergoing home or laboratory-based CPAP titration pathways. METHODS: Twohundredfive outpatients (151 M) (56.7 ± 10.3 years) were evaluated, before first visit and nocturnal diagnostic examination (T0), and the morning after CPAP titration (T1)...
December 1, 2016: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/27905889/influence-of-posterior-corneal-astigmatism-on-postoperative-refractive-astigmatism-in-pseudophakic-eyes-after-cataract-surgery
#16
Maki Sano, Takahiro Hiraoka, Yuta Ueno, Hideo Itagaki, Tomohiro Ogami, Tetsuro Oshika
BACKGROUND: To examine the influence of posterior corneal astigmatism on postoperative refractive astigmatism in pseudophakic eyes after cataract surgery. METHODS: The study enrolled 64 pseudophakic eyes of 50 patients (71.8 ± 9.9 years old, mean ± standard deviation) who had undergone phacoemulsification with non-toric IOL implantation. Refractive astigmatism was measured using an auto ref-keratometer with a 0.01- diopter (D) scale. Two types of corneal astigmatism were calculated using anterior segment optical coherence tomography; keratometric and total corneal astigmatism...
December 1, 2016: BMC Ophthalmology
https://www.readbyqxmd.com/read/27903991/role-of-oxidative-stress-and-inflammatory-factors-in-diabetic-kidney-disease
#17
Esmat Aghadavod, Samaneh Khodadadi, Azar Baradaran, Parto Nasri, Mahmood Bahmani, Mahmoud Rafieian-Kopaei
Diabetic nephropathy (DN) is a serious complication of diabetes mellitus, and its prevalence has been increasing in developed countries. Diabetic nephropathy has become the most common single cause of end-stage renal disease worldwide. Oxidative stress and inflammation factors are hypothesized to play a role in the development of late diabetes complications. Chronic hyperglycemia increases oxidative stress, significantly modifies the structure and function of proteins and lipids, and induces glycoxidation and peroxidation...
November 2016: Iranian Journal of Kidney Diseases
https://www.readbyqxmd.com/read/27903052/assessing-spatial-inequalities-in-accessing-community-pharmacies-a-mixed-geographically-weighted-approach
#18
Alexander Domnich, Lucia Arata, Daniela Amicizia, Alessio Signori, Roberto Gasparini, Donatella Panatto
Geographical accessibility is an important determinant for the utilisation of community pharmacies. The present study explored patterns of spatial accessibility with respect to pharmacies in Liguria, Italy, a region with particular geographical and demographic features. Municipal density of pharmacies was proxied as the number of pharmacies per capita and per km2, and spatial autocorrelation analysis was performed to identify spatial clusters. Both non-spatial and spatial models were constructed to predict the study outcome...
November 16, 2016: Geospatial Health
https://www.readbyqxmd.com/read/27902924/simple-mechanisms-of-early-life-simulation-model-on-the-origin-of-semi-cells
#19
Adrian Klein, Martin Bock, Wolfgang Alt
The development of first cellular structures played an important role in the early evolution of life. Early evolution of life probably took place on a molecular level in a reactive environment. The iron-sulfur theory postulates the formation of cell-like structures on catalytic surfaces. Experiments show that H2S together with FeS and other metallic centers drive auto-catalytic surface reactions, in which organic molecules such as pyruvic and amino acids occur. It is questionable which mechanisms are needed to form cell-like structures under these conditions...
November 27, 2016: Bio Systems
https://www.readbyqxmd.com/read/27900999/evaluating-anti-smd1-amino-acid-83-119-peptide-reactivity-in-children-with-systemic-lupus-erythematosus-and-other-immunological-diseases
#20
Hai-Ou Yang, Xiao-Qing Zhang, Qi-Hua Fu
BACKGROUND: SmD1-amino-acid 83-119 peptide (SmD183-119) is the major epitope of Smith (Sm) antigen, which is specific for adult systemic lupus erythematosus (SLE). The anti-SmD183-119 antibody has exhibited higher sensitivity and specificity than anti-Sm antibody in diagnosing adult SLE. However, the utility of anti-SmD183-119antibodies remains unclear in children with SLE (cSLE). This study aimed to assess the characteristics of anti-SmD183-119antibody in the diagnosis of cSLE. METHODS: Samples from 242 children with different rheumatological and immunological disorders, including autoimmune diseases (SLE [n = 46] and ankylosing spondylitis [AS, n = 11]), nonautoimmune diseases (Henoch-Schonlein purpura [HSP, n = 60], idiopathic thrombocytopenia purpura [n = 27], hematuria [n = 59], and arthralgia [n = 39]) were collected from Shanghai Children's Medical Center from March 6, 2012 to February 27, 2014...
2016: Chinese Medical Journal
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