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https://www.readbyqxmd.com/read/28343098/developmental-validation-of-qiagen-investigator-%C3%A2-24plex-qs-kit-and-investigator-%C3%A2-24plex-go-kit-two-6-dye-multiplex-assays-for-the-extended-codis-core-loci
#1
Melanie Kraemer, Anke Prochnow, Michael Bussmann, Mario Scherer, Ralf Peist, Carolyn Steffen
The original CODIS database based on 13 core STR loci has been overwhelmingly successful for matching suspects with evidence. In order to increase the power of discrimination, reduce the possibility of adventitious matches, and expand global data sharing, the CODIS Core Loci Working Group determined the expansion of the CODIS core loci to 20 STR plus three additional "highly recommended" loci (SE33, DY391, Amelogenin) Hares, 2015, 2012 [1,2]. The QIAGEN Investigator 24plex QS and Investigator 24plex GO! Kits are 6-dye multiplex assays that contain all markers of the expanded 23 CODIS core loci along with a unique internal performance control that is co-amplified with the STR markers...
March 12, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28343097/strait-razor-v2s-advancing-sequence-based-str-allele-reporting-and-beyond-to-other-marker-systems
#2
Jonathan L King, Frank R Wendt, Jie Sun, Bruce Budowle
STRait Razor has provided the forensic community a free-to-use, open-source tool for short tandem repeat (STR) analysis of massively parallel sequencing (MPS) data. STRait Razor v2s (SRv2s) allows users to capture physically phased haplotypes within the full amplicon of both commercial (ForenSeq) and "early access" panels (PowerSeq, Mixture ID). STRait Razor v2s may be run in batch mode to facilitate population-level analysis and is supported by all Unix distributions (including MAC OS). Data are reported in tables in string (haplotype), length-based (e...
March 12, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28343068/the-role-of-trail-in-fatigue-induced-by-repeated-stress-from-radiotherapy
#3
Li Rebekah Feng, Simeng Suy, Sean P Collins, Leorey N Saligan
Fatigue is one of the most common and debilitating side effects of cancer and cancer treatment, and yet its etiology remains elusive. The goal of this study is to understand the role of chronic inflammation in fatigue following repeated stress from radiotherapy. Fatigue and non-fatigue categories were assessed using ≥ 3-point change in Functional Assessment of Cancer Therapy-Fatigue questionnaire (FACT-F) administered to participants at baseline/before radiotherapy and one year post-radiotherapy. Whole genome microarray and cytokine multiplex panel were used to examine fatigue-related transcriptome and serum cytokine changes, respectively...
March 20, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28340310/viruses-in-cystic-fibrosis-patients-airways
#4
Lisa Billard, Rozenn Le Berre, Léa Pilorgé, Christopher Payan, Geneviève Héry-Arnaud, Sophie Vallet
Although bacteria have historically been considered to play a major role in cystic fibrosis (CF) airway damage, a strong impact of respiratory viral infections (RVI) is also now recognized. Emerging evidence confirms that respiratory viruses are associated with deterioration of pulmonary function and exacerbation and facilitation of bacterial colonization in CF patients. The aim of this review is to provide an overview of the current knowledge on respiratory viruses in CF airways, to discuss the resulting inflammation and RVI response, to determine how to detect the viruses, and to assess their clinical consequences, prevalence, and interactions with bacteria...
March 24, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28337594/diagnostic-accuracy-of-high-risk-hpv-dna-genotyping-for-primary-cervical-cancer-screening-and-triage-of-hpv-positive-women-compared-to-cytology-preliminary-results-of-the-pipavir-study
#5
Kimon Chatzistamatiou, Theodoros Moysiadis, Eleftherios Angelis, Andreas Kaufmann, Alkmini Skenderi, Pidder Jansen-Duerr, Irini Lekka, Vasilis Kilintzis, Stamatia Angelidou, Evangelia Katsiki, Ingke Hagemann, Athena Tsertanidou, Isabel Koch, Oliver Boecher, Erwin Soutschek, Nikolaos Maglaveras, Theodoros Agorastos
PURPOSE: The purpose of the presented PIPAVIR (persistent infections with human papillomaviruses; http://www.pipavir.com ) subanalysis is to assess the performance of high-risk (hr) HPV-DNA genotyping as a method of primary cervical cancer screening and triage of HPV positive women to colposcopy compared to liquid-based cytology (LBC) in an urban female population. METHODS: Women, aged 30-60, provided cervicovaginal samples at the Family-Planning Centre, Hippokratio Hospital of Thessaloniki, Greece, and the Department of Gynecology and Obstetrics in Mare Klinikum, Kiel, Germany...
March 23, 2017: Archives of Gynecology and Obstetrics
https://www.readbyqxmd.com/read/28336715/monitoring-cell-surface-n-glycoproteome-dynamics-by-quantitative-proteomics-reveals-mechanistic-insights-into-macrophage-differentiation
#6
Mathias Kalxdorf, Stephan Gade, H Christian Eberl, Marcus Bantscheff
The plasma membrane proteome plays a crucial role in inter- and intracellular signaling, cell survival and cell identity. As such it is a prominent target for pharmacological intervention. The relatively low abundance of this subproteome in conjunction with challenging extractability and solubility still hampers their comprehensive analysis. Here, we combined a chemical glycoprotein tagging strategy with mass spectrometry to enable comprehensive analysis of the cell surface glycoprotome. To benchmark this workflow and provide guidance for cell line selection for functional experiments, we generated an inventory of the N-linked cell surface glycoproteome of 15 standard laboratory human cell lines and three primary lymphocytic cell types...
March 23, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28336361/a-novel-multiplex-pcr-assay-for-simultaneous-detection-of-nine-clinically-significant-bacterial-pathogens-associated-with-bovine-mastitis
#7
Aqeela Ashraf, Muhammad Imran, Tahir Yaqub, Muhammad Tayyab, Wasim Shehzad, Peter C Thomson
For rapid and simultaneous detection of nine bovine mastitic pathogens, a sensitive and specific multiplex PCR assay was developed. The assay was standardized using reference strains and validated on mastitic milk cultures which were identified to species level based on 16S rRNA sequencing. Multiplex PCR assay also efficiently detected the target bacterial strains directly from milk. Detection limit of the assay was up to 50 pg for DNA isolated from pure cultures and 10(4) CFU/ml for spiked milk samples. As estimated by latent class analysis, the assay was sensitive up to 88% and specific up to 98% for targeted mastitic pathogens, compared with the bacterial culture method and the 16S rRNA sequence analysis...
March 20, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28336264/genomic-imbalances-in-syndromic-congenital-heart-disease
#8
Miriam C Molck, Milena Simioni, Társis P Vieira, Ilária C Sgardioli, Fabíola P Monteiro, Josiane Souza, Agnes C Fett-Conte, Têmis M Félix, Isabella L Monlléo, Vera Lúcia Gil-da-Silva-Lopes
OBJECTIVE: To identify pathogenic genomic imbalances in patients presenting congenital heart disease (CHD) with extra cardiac anomalies and exclusion of 22q11.2 deletion syndrome (22q11.2 DS). METHODS: 78 patients negative for the 22q11.2 deletion, previously screened by fluorescence in situ hybridization (FISH) and/or multiplex ligation probe amplification (MLPA) were tested by chromosomal microarray analysis (CMA). RESULTS: Clinically significant copy number variations (CNVs ≥300kb) were identified in 10% (8/78) of cases...
March 20, 2017: Jornal de Pediatria
https://www.readbyqxmd.com/read/28335102/efficacy-of-a-multiplex-paclitaxel-emission-stent-using-a-pluronic-%C3%A2-mixture-membrane-versus-a-covered-metal-stent-in-malignant-biliary-obstruction-a-prospective-randomized-comparative-study
#9
Sung Ill Jang, Se Joon Lee, Seok Jeong, Don Haeng Lee, Myung-Hwan Kim, Hong Jin Yoon, Dong Ki Lee
Background/Aims: A drug-eluting stent for unresectable malignant biliary obstruction was developed to increase stent patency by preventing tumor ingrowth. The safety and efficacy of a new generation of metallic stents covered with a paclitaxel-incorporated membrane using a Pluronic(®) mixture (MSCPM-II) were compared prospectively with those of covered metal stents (CMSs) in patients with malignant biliary obstructions. Methods: This study was initially designed as a prospective randomized trial but was closed early because of a high incidence of early occlusion...
March 24, 2017: Gut and Liver
https://www.readbyqxmd.com/read/28334883/selective-impairment-of-hippocampus-and-posterior-hub-areas-in-alzheimer-s-disease-an-meg-based-multiplex-network-study
#10
Meichen Yu, Marjolein M A Engels, Arjan Hillebrand, Elisabeth C W van Straaten, Alida A Gouw, Charlotte Teunissen, Wiesje M van der Flier, Philip Scheltens, Cornelis J Stam
Although frequency-specific network analyses have shown that functional brain networks are altered in patients with Alzheimer's disease, the relationships between these frequency-specific network alterations remain largely unknown. Multiplex network analysis is a novel network approach to study complex systems consisting of subsystems with different types of connectivity patterns. In this study, we used magnetoencephalography to integrate five frequency-band specific brain networks in a multiplex framework...
March 16, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334691/dna-functionalized-photonic-crystal-microspheres-for-multiplex-detection-of-toxic-metal-ions
#11
Zhengyu Yan, Chunqing Tian, Xincheng Qu, Weiyang Shen, Baofen Ye
A novel type of suspension array for multiplex detection of heavy metal ions with photonic crystal hydrogel microspheres was reported. The photonic crystal hydrogel microspheres have close-packed photonic crystal particles as their encoding units and ssDNA-functionalized hydrogel as the sensing units. The developed microspheres were successfully applied in multiplex detection of heavy metal ions.
March 8, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28334208/morphologically-constrained-spectral-unmixing-by-dictionary-learning-for-multiplex-fluorescence-microscopy
#12
Murad Megjhani, Pedro Correa de Sampaio, Julienne Leigh Carstens, Raghu Kalluri, Badrinath Roysam
Motivation: Current spectral unmixing methods for multiplex fluorescence microscopy have a limited ability to cope with high spectral overlap as they only analyze spectral information over individual pixels. Here, we present adaptive Morphologically Constrained Spectral Unmixing (MCSU) algorithms that overcome this limitation by exploiting morphological differences between sub-cellular structures, and their local spatial context. Results: The proposed method was effective at improving spectral unmixing performance by exploiting: (i) a set of dictionary-based models for object morphologies learned from the image data; and (ii) models of spatial context learned from the image data using a total variation algorithm...
March 2, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333409/missed-opportunities-for-antimicrobial-stewardship-in-pre-school-children-admitted-to-hospital-with-lower-respiratory-tract-infection
#13
Tony Walls, Erika Stark, Philip Pattemore, Lance Jennings
AIM: To describe the usage of multiplex polymerase chain reaction on nasopharyngeal swab (NPS) samples in pre-school children presenting with lower respiratory tract infection (LRTI) at Christchurch Hospital, and its impact on the use of antibiotics empirically and at discharge. METHODS: This retrospective cohort study included 237 children, ages 3 months to 5 years, admitted to hospital during the winter months of 2012-2015 with a diagnosis of community-acquired LRTI...
March 23, 2017: Journal of Paediatrics and Child Health
https://www.readbyqxmd.com/read/28332898/herpes-simplex-virus-1-and-cytomegalovirus-dnas-detection-in-the-inner-ear-of-implanted-patients-with-non-congenital-infection
#14
Walter Di Nardo, Roberta Anzivino, Paola Cattani, Rosaria Santangelo, Eugenio De Corso, Gaetano Paludetti
CONCLUSIONS: The detection of cytomegalovirus (CMV) and herpes simplex virus-1 (HSV-1) genome in perilymph of patients with negative serology or clinical history for congenital infections supports the hypothesis that Herpesviridae, even after acquired postnatal infections, could remain in latent phase in the spiral ganglion and damage the cochlea by a possible subsequent reactivation. Further studies are needed to identify the markers of such reactivation. OBJECTIVE: To identify the presence of certain viral species in the endolabyrinthic fluid of deaf patients with non-congenital infection...
March 23, 2017: Acta Oto-laryngologica
https://www.readbyqxmd.com/read/28332823/from-dual-mode-triboelectric-nanogenerator-to-smart-tactile-sensor-a-multiplexing-design
#15
Tao Li, Jingdian Zou, Fei Xing, Meng Zhang, Xia Cao, Ning Wang, Zhong Lin Wang
Triboelectric nanogenerators (TENGs) can be applied for the next generation of artificial intelligent products, where skin-like tactile sensing advances the ability of robotics to feel and interpret environment. In this paper, a flexible and thin tactile sensor was developed on the basis of dual-mode TENGs. The effective transduction of touch and pressure stimulus into independent and interpretable electrical signals permits the instantaneous sensing of location and pressure with a plane resolution of 2 mm, a high-pressure-sensing sensitivity up to 28 mV·N(-1), and a linear pressure detection ranging from 40 to 140 N...
March 23, 2017: ACS Nano
https://www.readbyqxmd.com/read/28332631/integrated-dna-and-rna-extraction-using-magnetic-beads-from-viral-pathogens-causing-acute-respiratory-infections
#16
Hui He, Rongqun Li, Yi Chen, Ping Pan, Wenjuan Tong, Xueyan Dong, Yueming Chen, Daojun Yu
Current extraction methods often extract DNA and RNA separately, and few methods are capable of co-extracting DNA and RNA from sputum. We established a nucleic acid co-extraction method from sputum based on magnetic beads and optimized the method by evaluating influencing factors, such as the guanidinium thiocyanate (GTC) and dithiothreitol (DTT) concentrations, magnetic bead amount, incubation temperature, lysis buffer pH and RNA carrier type. The feasibility of the simultaneous nucleic acid co-extraction method was evaluated by amplifying DNA and RNA viruses from a single clinical specimen with a multiplex RT-qPCR method...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28332571/profiling-protein-expression-in-circulating-tumour-cells-using-microfluidic-western-blotting
#17
Elly Sinkala, Elodie Sollier-Christen, Corinne Renier, Elisabet Rosàs-Canyelles, James Che, Kyra Heirich, Todd A Duncombe, Julea Vlassakis, Kevin A Yamauchi, Haiyan Huang, Stefanie S Jeffrey, Amy E Herr
Circulating tumour cells (CTCs) are rare tumour cells found in the circulatory system of certain cancer patients. The clinical and functional significance of CTCs is still under investigation. Protein profiling of CTCs would complement the recent advances in enumeration, transcriptomic and genomic characterization of these rare cells and help define their characteristics. Here we describe a microfluidic western blot for an eight-plex protein panel for individual CTCs derived from estrogen receptor-positive (ER+) breast cancer patients...
March 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28332368/multiplex-ligation-dependent-probe-amplification-in-x-linked-recessive-muscular-dystrophy-in-korean-subjects
#18
Mi Ri Suh, Kyung A Lee, Eun Young Kim, Jiho Jung, Won Ah Choi, Seong Woong Kang
PURPOSE: Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are similar genetic disorders whose patterns of mutation and disease phenotypes might be expected to show differences among different countries. We analyzed multiplex ligation-dependent probe amplification (MLPA) data in a large number of Korean patients with DMD/BMD. MATERIALS AND METHODS: We obtained 130 positive MLPA results (86 DMD, 27 BMD, and 17 female carriers) from 272 candidates (237 clinically suspected patients and 35 possible female carriers) who took part in this study...
May 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/28332161/real-time-pcr-identification-of-six-malassezia-species
#19
Amin Ilahi, Inès Hadrich, Sourour Neji, Houaida Trabelsi, Fattouma Makni, Ali Ayadi
Lipophilic yeast Malassezia species is widely found on the skin surface of humans and other animals. This fungus can cause pityriasis versicolor, Malassezia folliculitis, and seborrheic dermatitis. Still now, there is a problem with species identification of Malassezia with conventional methods. We developed a real-time polymerase chain reaction (PCR) assay with multiple hybridization probes for detecting M. globosa, M. furfur, M. restricta, M. sympodialis, M. slooffiae, and M. pachydermatis. The amplification curves and specific melting peaks of the probes hybridized with real-time PCR product were used for species identifications...
March 22, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28331958/nucleic-acid-sensing-with-enzyme-dna-binding-protein-conjugates-cascade-and-simple-dna-nanostructures
#20
Gülsen Betül Aktas, Vasso Skouridou, Lluis Masip
A versatile and universal DNA sensing platform is presented based on enzyme-DNA binding protein tags conjugates and simple DNA nanostructures. Two enzyme conjugates were thus prepared, with horseradish peroxidase linked to the dimeric single-chain bacteriophage Cro repressor protein (HRP-scCro) and glucose oxidase linked to the dimeric headpiece domain of Escherichia coli LacI repressor protein (GOx-dHP), and used in conjunction with a hybrid ssDNA-dsDNA detection probe. This probe served as a simple DNA nanostructure allowing first for target recognition through its target-complementary single-stranded DNA (ssDNA) part and then for signal generation after conjugate binding on the double-stranded DNA (dsDNA) containing the specific binding sites for the dHP and scCro DNA binding proteins...
March 22, 2017: Analytical and Bioanalytical Chemistry
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