keyword
MENU ▼
Read by QxMD icon Read
search

Trinity

keyword
https://www.readbyqxmd.com/read/28104421/assessing-cancer-progression-and-stable-disease-after-neoadjuvant-chemotherapy-for-organ-confined-muscle-invasive-bladder-cancer
#1
Meera R Chappidi, Max Kates, Aaron Brant, Alexander S Baras, George J Netto, Phillip M Pierorazio, Noah M Hahn, Trinity J Bivalacqua
OBJECTIVE: To propose and validate a new approach to stratify clinically staged organ-confined muscle-invasive bladder cancer patients (cT2N0M0) that are pathologic non-responders to neoadjuvant chemotherapy (NAC) to better characterize NAC non-response. METHODS: We retrospectively identified radical cystectomy patients with cT2N0M0 disease at our institution (2005-2014) and in the National Cancer Database (NCDB, 2004-2012) for external validation. Patients were stratified as stable (pT2N0M0) or progressors (>pT2 and/or pN+)...
January 16, 2017: Urology
https://www.readbyqxmd.com/read/28097264/lymph-node-density-predicts-recurrence-and-death-after-inguinal-lymph-node-dissection-for-penile-cancer
#2
Mark W Ball, Zeyad R Schwen, Joan S Ko, Alexa Meyer, George J Netto, Arthur L Burnett, Trinity J Bivalacqua
PURPOSE: To determine the impact of lymph node density (LND) on survival after inguinal lymph node dissection (ILND) for penile cancer. MATERIALS AND METHODS: Our institutional penile cancer database was queried for patients who underwent ILND. Clinicopathologic characteristics including LND and total number of positive lymph nodes (LNs) were analyzed to determine impact on recurrence-free survival (RFS) and overall survival (OS). LND, or the percent of positive LN out of total LN, was calculated as a categorical variable at varying thresholds...
January 2017: Investigative and Clinical Urology
https://www.readbyqxmd.com/read/28095660/draft-genome-of-toxocara-canis-a-pathogen-responsible-for-visceral-larva-migrans
#3
Jinhwa Kong, Jungim Won, Jeehee Yoon, UnJoo Lee, Jong-Il Kim, Sun Huh
This study aimed at constructing a draft genome of the adult female worm Toxocara canis using next-generation sequencing (NGS) and de novo assembly, as well as to find new genes after annotation using functional genomics tools. Using an NGS machine, we produced DNA read data of T. canis. The de novo assembly of the read data was performed using SOAPdenovo. RNA read data were assembled using Trinity. Structural annotation, homology search, functional annotation, classification of protein domains, and KEGG pathway analysis were carried out...
December 2016: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/28086804/comparative-analysis-of-the-root-transcriptomes-of-cultivated-sweetpotato-ipomoea-batatas-l-lam-and-its-wild-ancestor-ipomoea-trifida-kunth-g-don
#4
Sathish K Ponniah, Jyothi Thimmapuram, Ketaki Bhide, Venu Kal Kalavacharla, Muthusamy Manoharan
BACKGROUND: The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (Ib), and its immediate ancestral species, Ipomoea trifida (It), which does not form SRs, may provide insights into the molecular mechanisms underlying SR formation in sweetpotato. RESULTS: Illumina paired-end sequencing generated ~208 and ~200 million reads for Ib and It, respectively...
January 13, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28073196/mri-us-fusion-prostate-biopsy-our-initial-experience
#5
Vito Lacetera, Bernardo Cervelli, Antonio Cicetti, Giuliana Gabrielloni, Michele Montesi, Roberto Morcellini, Gianni Parri, Emilio Recanatini, Gianluca Giglioni, Andrea Benedetto Galosi, Valerio Beatrici
AIM: The objective of this study is to present our initial experience with magnetic resonance imaging/ultrasound (MRI/US) fusion biopsy using the Koelis Trinity device after the first consecutive 59 patients. MATERIALS AND METHODS: 59 consecutive patients with suspected prostate cancer (PCA) underwent prostate biopsy using Trinity Koelis® (Koelis, Grenoble, France). We divided the patients into 2 groups: patients with a previous negative mapping underwent to a MRI/US fusion re-biopsy (Group A); and biopsy-naïve patients who underwent to a first stereotactic 3-D mapping of the prostate (Group B)...
December 30, 2016: Archivio Italiano di Urologia, Andrologia
https://www.readbyqxmd.com/read/28066712/de-novo-transcriptome-assembly-of-shrimp-palaemon-serratus
#6
Alejandra Perina, Ana M González-Tizón, Iago F Meilán, Andrés Martínez-Lage
: The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000) to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28057343/effect-of-salinity-on-mercury-methylating-benthic-microbes-and-their-activities-in-great-salt-lake-utah
#7
Eric S Boyd, Ri-Qing Yu, Tamar Barkay, Trinity L Hamilton, Bonnie K Baxter, David L Naftz, Mark Marvin-DiPasquale
Surface water and biota from Great Salt Lake (GSL) contain some of the highest documented concentrations of total mercury (THg) and methylmercury (MeHg) in the United States. In order to identify potential biological sources of MeHg and controls on its production in this ecosystem, THg and MeHg concentrations, rates of Hg(II)-methylation and MeHg degradation, and abundances and compositions of archaeal and bacterial 16 rRNA gene transcripts were determined in sediment along a salinity gradient in GSL. Rates of Hg(II)-methylation were inversely correlated with salinity and were at or below the limits of detection in sediment sampled from areas with hypersaline surface water...
January 2, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28046012/transcriptome-analysis-of-taxillusi-chinensis-dc-danser-seeds-in-response-to-water-loss
#8
Shugen Wei, Xiaojun Ma, Limei Pan, Jianhua Miao, Jine Fu, Longhua Bai, Zhonglian Zhang, Yanhong Guan, Changming Mo, Hao Huang, Maoshan Chen
BACKGROUND: Taxillus chinensis (DC.) Danser, the official species of parasitic loranthus that grows by parasitizing other plants, is used in various traditional Chinese medicine prescriptions. ABA-dependent and ABA-independent pathways are two major pathways in response to drought stress for plants and some genes have been reported to play a key role during the dehydration including dehydration-responsive protein RD22, late embryogenesis abundant (LEA) proteins, and various transcription factors (TFs) like MYB and WRKY...
2017: PloS One
https://www.readbyqxmd.com/read/28035767/oxygenic-and-anoxygenic-photosynthesis-in-a-microbial-mat-from-an-anoxic-and-sulfidic-spring
#9
Dirk de Beer, Miriam Weber, Arjun Chennu, Trinity Hamilton, Christian Lott, Jennifer Macalady, Judith Klatt
Oxygenic and anoxygenic photosynthesis were studied with microsensors in microbial mats found at 9-10 m depth in anoxic and sulfidic water in Little Salt Spring (Florida, USA). The lake sediments were covered with a 1-2 mm thick red mat dominated by filamentous Cyanobacteria, below which Green Sulfur Bacteria (GSB, Chlorobiaceae) were highly abundant. Within 4 mm inside the mats, the incident radiation was attenuated to undetectable levels. In situ microsensor data showed both oxygenic photosynthesis in the red surface layer and light-induced sulfide dynamics up to 1 cm depth...
December 30, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27995074/de-novo-transcriptome-assembly-of-the-mycoheterotrophic-plant-monotropa-hypopitys
#10
Alexey V Beletsky, Mikhail A Filyushin, Eugeny V Gruzdev, Alexander M Mazur, Egor B Prokhortchouk, Elena Z Kochieva, Andrey V Mardanov, Nikolai V Ravin, Konstantin G Skryabin
Monotropa hypopitys (pinesap) is a non-photosynthetic obligately mycoheterotrophic plant of the family Ericaceae. It obtains the carbon and other nutrients from the roots of surrounding autotrophic trees through the associated mycorrhizal fungi. In order to understand the evolutionary changes in the plant genome associated with transition to a heterotrophic lifestyle, we performed de novo transcriptomic analysis of M. hypopitys using next-generation sequencing. We obtained the RNA-Seq data from flowers, flower bracts and roots with haustoria using Illumina HiSeq2500 platform...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27994980/next-generation-sequencing-of-mixed-genomic-dna-allows-efficient-assembly-of-rearranged-mitochondrial-genomes-in-amolops-chunganensis-and-quasipaa-boulengeri
#11
Siqi Yuan, Yun Xia, Yuchi Zheng, Xiaomao Zeng
Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS...
2016: PeerJ
https://www.readbyqxmd.com/read/27987021/impaired-contraction-and-decreased-detrusor-innervation-in-a-female-rat-model-of-pelvic-neuropraxia
#12
Johanna L Hannan, Shelby A Powers, Vinson M Wang, Fabio Castiglione, Petter Hedlund, Trinity J Bivalacqua
INTRODUCTION AND HYPOTHESIS: Bilateral pelvic nerve injury (BPNI) is a model of post-radical hysterectomy neuropraxia, a common sequela. This study assessed the time course of changes to detrusor autonomic innervation, smooth muscle (SM) content and cholinergic-mediated contraction post-BPNI. METHODS: Female Sprague-Dawley rats underwent BPNI or sham surgery and were evaluated 3, 7, 14, and 30 days post-BPNI (n = 8/group). Electrical field-stimulated (EFS) and carbachol-induced contractions were measured...
December 16, 2016: International Urogynecology Journal
https://www.readbyqxmd.com/read/27938328/combining-independent-de-novo-assemblies-optimizes-the-coding-transcriptome-for-nonconventional-model-eukaryotic-organisms
#13
Nicolas Cerveau, Daniel J Jackson
BACKGROUND: Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonconventional model organisms one major problem with the currently dominant NGS platform (Illumina) stems from the obligatory fragmentation of nucleic acid material that occurs prior to sequencing during library preparation. This step creates a significant bioinformatic challenge for accurate de novo assembly of novel transcriptome data...
December 9, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27936609/direct-pb-isotopic-analysis-of-a-nuclear-fallout-debris-particle-from-the-trinity-nuclear-test
#14
Jeremy J Bellucci, Joshua F Snape, Martin W Whitehouse, Alexander A Nemchin
The Pb isotope composition of a nuclear fallout debris particle has been directly measured in post-detonation materials produced during the Trinity nuclear test by a secondary ion mass spectrometry (SIMS) scanning ion image technique (SII). This technique permits the visual assessment of the spatial distribution of Pb and can be used to obtain full Pb isotope compositions in user-defined regions in a 70 μm x 70 μm analytical window. In conjunction with BSE and EDS mapping of the same particle, the Pb measured in this fallout particle cannot be from a major phase in the precursor arkosic sand...
December 12, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27932416/a-phase-ii-trial-of-dovitinib-in-bcg-unresponsive-urothelial-carcinoma-with-fgfr3-mutations-or-over-expression-hoosier-cancer-research-network-trial-hcrn-12-157
#15
Noah M Hahn, Trinity J Bivalacqua, Ashley E Ross, George J Netto, Alexander S Baras, Jong Chul Park, Carolyn Chapman, Timothy A Masterson, Michael O Koch, Richard Bihrle, Richard S Foster, Thomas A Gardner, Liang Cheng, David R Jones, Kyle McElyea, George E Sandusky, Timothy Breen, Ziyue Liu, Costantine Albany, Marietta L Moore, Rhoda A Loman, Angela Reed, Scott A Turner, Francine B de Abreu, Torrey L Gallagher, Gregory J Tsongalis, Elizabeth R Plimack, Richard E Greenberg, Daniel M Geynisman
PURPOSE: To assess the clinical and pharmacodynamic activity of dovitinib in a treatment resistant, molecularly enriched NMIUC population. EXPERIMENTAL DESIGN: A multi-site pilot phase 2 trial was conducted. Key eligibility criteria included: BCG unresponsive NMIUC (> 2 prior intravesical regimens) with increased phosphorylated FGFR3 (pFGFR3) expression by centrally analyzed immunohistochemistry (IHC+) or FGFR3 mutations (Mut+) assessed in a CLIA-licensed laboratory...
December 8, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27917525/a-comparison-study-of-multivariate-fixed-models-and-gene-association-with-multiple-traits-gamut-for-next-generation-sequencing
#16
Chi-Yang Chiu, Jeesun Jung, Yifan Wang, Daniel E Weeks, Alexander F Wilson, Joan E Bailey-Wilson, Christopher I Amos, James L Mills, Michael Boehnke, Momiao Xiong, Ruzong Fan
In this paper, extensive simulations are performed to compare two statistical methods to analyze multiple correlated quantitative phenotypes: (1) approximate F-distributed tests of multivariate functional linear models (MFLM) and additive models of multivariate analysis of variance (MANOVA), and (2) Gene Association with Multiple Traits (GAMuT) for association testing of high-dimensional genotype data. It is shown that approximate F-distributed tests of MFLM and MANOVA have higher power and are more appropriate for major gene association analysis (i...
January 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/27914286/multi-centre-field-evaluation-of-the-performance-of-the-trinity-biotech-uni-gold-hiv-1-2-rapid-test-as-a-first-line-screening-assay-for-gay-and-bisexual-men-compared-with-4th-generation-laboratory-immunoassays
#17
P Keen, D P Conway, P Cunningham, A McNulty, D L Couldwell, S C Davies, D E Smith, J Gray, M Holt, C C O'Connor, P Read, D Callander, G Prestage, R Guy
BACKGROUND: The Trinity Biotech Uni-Gold HIV test (Uni-Gold) is often used as a supplementary rapid test in testing algorithms. OBJECTIVE: To evaluate the operational performance of the Uni-Gold as a first-line screening test among gay and bisexual men (GBM) in a setting where 4th generation HIV laboratory assays are routinely used. STUDY DESIGN: We compared the performance of Uni-Gold with conventional HIV serology conducted in parallel among GBM attending 22 testing sites...
January 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/27899505/an-interview-with-david-mcclay
#18
Aidan Maartens
David McClay is the Arthur S. Pearse Professor of Biology at Trinity College of Arts and Sciences, Duke University, North Carolina. His lab works on the transcriptional control of morphogenesis in the sea urchin embryo. We caught up with David at the 2016 Society for Developmental Biology - International Society of Differentiation joint meeting in Boston, where he received the Lifetime Achievement Award.
December 1, 2016: Development
https://www.readbyqxmd.com/read/27898765/transcriptome-assembly-and-comparison-of-an-allotetraploid-weed-species-annual-bluegrass-with-its-two-diploid-progenitor-species-schrad-and-kunth
#19
Shu Chen, J Scott McElroy, Fenny Dane, Leslie R Goertzen
Annual bluegrass ( L.) is one of the most widespread weed species in this world. As a young allotetraploid, has occupied diverse environments from Antarctic area to subtropical regions. To unveil the evolutionary mystery behind 's wide distribution, extensive adaptability and phenotypic plasticity needs collaboration from multiple research scopes from ecology and plant physiology to population genetics and molecular biology. However, the lack of omic data and reference has greatly hampered the study. This is the first comprehensive transcriptome study on species...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27872818/de-novo-transcriptome-assembly-of-schisandra-chinensis-turcz-baill
#20
Zhang Qing-Tian, Fan Shu-Tian, Yang Yi-Ming, Xu Pei-Lei, Ai Jun
The fruit of Schisandra chinensis Turcz. (Baill.), namely "Wuweizi" in China, is a well-known herbal medicine and health food. At present, research focused on the extraction of effective chemical component and function identification. Little known about the secondary metabolism gene pathway of chemical composition. Its fruit color usually red, however, the white fruit color variation has been found. It made us interested in exploring which gene change lead to this result. In order to understand the genetic background of S...
December 2016: Genomics Data
keyword
keyword
42365
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"