Read by QxMD icon Read


Akira Shiraishi, Jun Murata, Erika Matsumoto, Shin Matsubara, Eiichiro Ono, Honoo Satake
Forsythia spp. are perennial woody plants which are one of the most extensively used medicinal sources of Chinese medicines and functional diets owing to their lignan contents. Lignans have received widespread attention as leading compounds in the development of antitumor drugs and healthy diets for reducing the risks of lifestyle-related diseases. However, the molecular basis of Forsythia has yet to be established. In this study, we have verified de novo deep transcriptome of Forsythia koreana leaf and callus using the Illumina HiSeq 1500 platform...
2016: PloS One
Pieter Uvin, Maarten Albersen, Ine Bollen, Maarten Falter, Emmanuel Weyne, Loes Linsen, Hanna Tinel, Peter Sandner, Trinity J Bivalacqua, Dirk Jmk De Ridder, Frank Van der Aa, Bert Brône, Koenraad Van Renterghem
OBJECTIVES: To evaluate the expression of the Rho/Rho associated protein kinase (ROCK) pathway in corpus cavernosum of patients with severe erectile dysfunction (ED) compared to healthy human corpus cavernosum, and to test the functional effects of two Rho Kinase Inhibitors (RKI) on erectile tissue of patients with severe ED, not responding to phosphodiesterase type 5 inhibitors (PDE5-i). PATIENTS AND METHODS: Human corpus cavernosum samples were obtained after consent from individuals undergoing penile prosthesis implantation (n = 7 for organ bath experiments, n = 17 for qPCR)...
October 20, 2016: BJU International
Brandi Wynne, Trinity Kronk, Otor Al-Khalili, Benjamin Ko, Franziska Theilig, Douglas Eaton, Robert Hoover
OBJECTIVE: Hypertension is characterized by increased sodium reabsorption along the aldosterone-sensitive distal nephron (ASDN) and systemic inflammation. Interleukin-6 (IL-6) is a possible mediator, signaling via the transmembrane IL-6 receptor alpha (IL-6Rα); however, whether IL-6Rα is present in the distal convoluted tubule (DCT) is unknown. Increased sodium reabsorption is not always correlated with increased aldosterone (Aldo). Thus, understanding how Aldo-independent sodium reabsorption occurs is critical...
September 2016: Journal of Hypertension
Rucha Harishbhai Mehta, Manivel Ponnuchamy, Jitendra Kumar, Nagaraja Reddy Rama Reddy
De novo assembly of reads produced by next-generation sequencing (NGS) technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Senna (Cassia angustifolia Vahl.) is a drought-tolerant annual undershrub of Caesalpiniaceae, a subfamily of Fabaceae. There are insufficient transcriptomic and genomic data in public databases for understanding the molecular mechanism underlying the drought tolerance of senna. Therefore, the main purpose of this study was to know the transcriptome profile of senna, with special reference to drought stress...
October 5, 2016: Functional & Integrative Genomics
Patrick Adu, David Larbi Simpong, Godfred Takyi, Richard K D Ephraim
Background. Blood transfusion is a therapeutic procedure usually undertaken in patients with severe anaemia. In Ghana, severe anaemia is mostly due to malaria caused by severe Plasmodium falciparum infection, road traffic accidents, and haemoglobinopathy-induced acute haemolysis. Method. This cross-sectional study evaluated coinheritance of sickle cell haemoglobin variant and G6PD enzymopathy among individuals that donated blood at the Holy Trinity Hospital, Berekum, in the Brong-Ahafo Region, Ghana. Demographic data and other pertinent information were captured using questionnaire...
2016: Advances in Hematology
Sufang Wang, Michael Gribskov
MOTIVATION: With the decreased cost of RNA-Seq, an increasing number of non-model organisms have been sequenced. Due to the lack of reference genomes, de novo transcriptome assembly is required. However, there is limited systematic research evaluating the quality of de novo transcriptome assemblies and how the assembly quality influences downstream analysis. RESULTS: We used two authentic RNA-Seq datasets from Arabidopsis thaliana, and produced transcriptome assemblies using eight programs with a series of k-mer sizes (from 25 to 71), including BinPacker, Bridger, IDBA-tran, Oases-Velvet, SOAPdenovo-Trans, SSP, Trans-ABySS and Trinity...
September 30, 2016: Bioinformatics
G H Wu, W W Tang, C Zhou
No abstract text is available yet for this article.
October 6, 2016: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
Weizhong Li, R Alexander Richter, Yunsup Jung, Qiyun Zhu, Robert W Li
BACKGROUND: Remarkable advances in Next Generation Sequencing (NGS) technologies, bioinformatics algorithms and computational technologies have significantly accelerated genomic research. However, complicated NGS data analysis still remains as a major bottleneck. RNA-seq, as one of the major area in the NGS field, also confronts great challenges in data analysis. RESULTS: To address the challenges in RNA-seq data analysis, we developed a web portal that offers three integrated workflows that can perform end-to-end compute and analysis, including sequence quality control, read-mapping, transcriptome assembly, reconstruction and quantification, and differential analysis...
September 27, 2016: BMC Genomics
Shan-Ce Niu, Qing Xu, Guo-Qiang Zhang, Yong-Qiang Zhang, Wen-Chieh Tsai, Jui-Ling Hsu, Chieh-Kai Liang, Yi-Bo Luo, Zhong-Jian Liu
Orchids are renowned for their spectacular flowers and ecological adaptations. After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris, we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds. Our aims were to contribute to a better understanding of the molecular mechanisms driving the analysed tissue characteristics and to enrich the available data for P...
September 27, 2016: Scientific Data
Thomas T Schulze, Jonathan M Ali, Maggie L Bartlett, Madalyn M McFarland, Emalie J Clement, Harim I Won, Austin G Sanford, Elyssa B Monzingo, Matthew C Martens, Ryan M Hemsley, Sidharta Kumar, Nicolas Gouin, Alan S Kolok, Paul H Davis
Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment...
2016: Journal of Genomics
Michelle E Roh, Caesar Oyet, Patrick Orikiriza, Martina Wade, Juliet Mwanga-Amumpaire, Yap Boum, Gertrude N Kiwanuka, Sunil Parikh
Despite the potential benefit of primaquine in reducing Plasmodium falciparum transmission and radical cure of Plasmodium vivax and Plasmodium ovale infections, concerns over risk of hemolytic toxicity in individuals with glucose-6-phosphate dehydrogenase deficiency (G6PDd) have hampered its deployment. A cross-sectional survey was conducted in 2014 to assess the G6PDd prevalence among 631 children between 6 and 59 months of age in southwestern Uganda, an area where primaquine may be a promising control measure...
September 26, 2016: American Journal of Tropical Medicine and Hygiene
Marina Mora-Ortiz, Martin T Swain, Martin J Vickers, Matthew J Hegarty, Rhys Kelly, Lydia M J Smith, Leif Skøt
BACKGROUND: Sainfoin (Onobrychis viciifolia) is a highly nutritious tannin-containing forage legume. In the diet of ruminants sainfoin can have anti-parasitic effects and reduce methane emissions under in vitro conditions. Many of these benefits have been attributed to condensed tannins or proanthocyanidins in sainfoin. A combination of increased use of industrially produced nitrogen fertilizer, issues with establishment and productivity in the first year and more reliable alternatives, such as red clover led to a decline in the use of sainfoin since the middle of the last century...
September 26, 2016: BMC Genomics
Margaret Cocks, Diana Taheri, Mark W Ball, Stephania M Bezerra, Maria Del Carmen Rodriguez, Bernardo F P Ricardo, Trinity J Bivalacqua, Rajni B Sharma, Alan Meeker, Alcides Chaux, Arthur L Burnett, George J Netto
Penile squamous cell carcinoma (SCC) is primarily treated by surgical resection. Locally advanced and metastatic disease require a multidisciplinary treatment approach. However, mortality and morbidity remain high and novel molecular and immunotherapeutic targets are actively being sought. We investigated the expression of immune checkpoint markers in penile cancers. Fifty-three invasive penile SCCs diagnosed between 1985 and 2013 were retrieved from our surgical pathology archives. Representative formalin-fixed, paraffin-embedded archival blocks were used for the construction of 2 high-density tissue microarrays (TMAs)...
September 20, 2016: Human Pathology
Robert F Coen, Kevin McCarroll, Miriam Casey, Helene McNulty, Eamon Laird, Anne M Molloy, M Ward, J J Strain, Leane Hoey, Catherine Hughes, Conal J Cunningham
BACKGROUND: The Frontal Assessment Battery (FAB) is a short battery designed to assess frontal executive functioning, but data for interpretation of performance are limited. OBJECTIVES: The Trinity, Ulster, Department of Agriculture (TUDA) study provided the opportunity to derive performance data from a large sample of community-dwelling hospital outpatient or general practitioner (GP) attenders. METHODS: Normative analysis based on 2508 TUDA participants meeting these criteria: Mini-Mental State Examination (MMSE) >26/30, not depressed (Center for Epidemiologic Studies Depression <16) or anxious (Hospital Anxiety and Depression Scale <8), no history of stroke, or transient ischemic attack...
September 19, 2016: Journal of Geriatric Psychiatry and Neurology
Sonia A Duffy, David L Ronis, Carrie A Karvonen-Gutierrez, Lee A Ewing, Stephanie V Hall, James J Yang, Patricia L Thomas, Christine M Olree, Kimberly A Maguire, Lisa Friedman, Donna Gray, Neil Jordan
INTRODUCTION: This study determined the effectiveness of the Tobacco Tactics intervention. DESIGN/SETTING/PARTICIPANTS: This was a pragmatic, quasi-experimental study conducted from 2010 to 2013 and analyzed from 2014 to 2015 in five Michigan community hospitals; three received the Tobacco Tactics intervention, and two received usual care. Smokers (N=1,528) were identified during hospitalization, and sent surveys and cotinine tests after 6 months. Changes in pre- to post-intervention quit rates in the intervention sites were compared with usual care control sites...
October 2016: American Journal of Preventive Medicine
L J Wang, X W Sun, F Y Guo, Y J Zhao, Z H Zhang, Z Q Zhao
Transcriptome analysis of Inner Mongolia Cashmere goat and Dazu black goat generated 38,772,947 and 38,771,668 clean pair end reads, respectively, which were assembled into 72,422 and 80,069 unigenes by Trinity, respectively. For Inner Mongolia Cashmere goat, 26,051 and 10,100 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups, respectively. A total of 32,772 unigenes can comment to SWISS-Prot database, and the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 24,420 unigenes...
September 20, 2016: Reproduction in Domestic Animals, Zuchthygiene
Brandi Wynne, Trinity Kronk, Otor Al-Khalili, Benjamin Ko, Franziska Theilig, Douglas Eaton, Robert Hoover
OBJECTIVE: Hypertension is characterized by increased sodium reabsorption along the aldosterone-sensitive distal nephron (ASDN) and systemic inflammation. Interleukin-6 (IL-6) is a possible mediator, signaling via the transmembrane IL-6 receptor alpha (IL-6Rα); however, whether IL-6Rα is present in the distal convoluted tubule (DCT) is unknown. Increased sodium reabsorption is not always correlated with increased aldosterone (Aldo). Thus, understanding how Aldo-independent sodium reabsorption occurs is critical...
September 2016: Journal of Hypertension
Hotaka Matsui, Biljana Musicki, Nikolai A Sopko, Xiaopu Liu, Paula J Hurley, Arthur L Burnett, Trinity J Bivalacqua, Johanna L Hannan
OBJECTIVE: To assess neurite sprouting and gene expression of neurotrophic factors, nerve markers and apoptosis in the major pelvic ganglia (MPG) of T2DM rats as it relates to erectile function. MATERIALS AND METHODS: Male rats were fed high-fat diet (HFD) for 2 weeks followed by 2 low-dose injections of streptozotocin (20mg/kg). In three groups (controls, 3 week or 5 week T2DM) erectile function was measured by ratios of intracavernosal pressure to mean arterial pressure after cavernous nerve stimulation...
September 14, 2016: Urology
Aaron Brant, Max Kates, Meera R Chappidi, Hiten D Patel, Nikolai A Sopko, George J Netto, Alex S Baras, Noah M Hahn, Phillip M Pierorazio, Trinity J Bivalacqua
PURPOSE: We estimated the proportion of patients who received neoadjuvant chemotherapy for muscle-invasive bladder cancer whose tumors were downstaged by transurethral resection. MATERIALS AND METHODS: We identified patients with cT2 N0 urothelial carcinoma who underwent cystectomy at our institution from 2005 to 2014-overall, 139 underwent transurethral resection without chemotherapy, and 146 underwent transurethral resection with chemotherapy. Pathologic response was defined as<pT2 N0...
September 14, 2016: Urologic Oncology
Melissa Kane, Trinity M Zang, Suzannah J Rihn, Fengwen Zhang, Tonya Kueck, Mudathir Alim, John Schoggins, Charles M Rice, Sam J Wilson, Paul D Bieniasz
Interferons (IFNs) exert their anti-viral effects by inducing the expression of hundreds of IFN-stimulated genes (ISGs). The activity of known ISGs is insufficient to account for the antiretroviral effects of IFN, suggesting that ISGs with antiretroviral activity are yet to be described. We constructed an arrayed library of ISGs from rhesus macaques and tested the ability of hundreds of individual macaque and human ISGs to inhibit early and late replication steps for 11 members of the retroviridae from various host species...
September 14, 2016: Cell Host & Microbe
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"