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https://www.readbyqxmd.com/read/28938622/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#1
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28937594/molecular-tools-for-the-detection-and-the-identification-of-hymenoptera-parasitoids-in-tortricid-fruit-pests
#2
Pierre Franck, Mariline Maalouly-Matar, Jérôme Olivares
Biological control requires specific tools for the accurate detection and identification of natural enemies in order to estimate variations in their abundance and their impact according to changes in environmental conditions or agricultural practices. Here, we developed two molecular methods of detection based on PCR-RFLP with universal primers and on PCR with specific primers to identify commonly occurring larval parasitoids of the tortricid fruit pests and to estimate parasitism in the codling moth. Both methods were designed based on DNA sequences of the COI mitochondrial gene for a range of parasitoids that emerged from Cydia pomonella and Grapholitamolesta caterpillars (102 parasitoids; nine species) and a range of potential tortricid hosts (40 moths; five species) damaging fruits...
September 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28936667/rna-seq-data-analysis-from-raw-data-quality-control-to-differential-expression-analysis
#3
Weihong Qi, Ralph Schlapbach, Hubert Rehrauer
As a revolutionary technology for life sciences, RNA-seq has many applications and the computation pipeline has also many variations. Here, we describe a protocol to perform RNA-seq data analysis where the aim is to identify differentially expressed genes in comparisons of two conditions. The protocol follows the recently published RNA-seq data analysis best practice and applies quality checkpoints throughout the analysis to ensure reliable data interpretation. It is written to help new RNA-seq users to understand the basic steps necessary to analyze an RNA-seq dataset properly...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28936578/nitrates-and-phosphates-in-cave-waters-of-krak%C3%A3-w-cz%C3%A4-stochowa-upland-southern-poland
#4
Jacek Różkowski, Kazimierz Różkowski, Oimahmad Rahmonov, Hanna Rubin
The paper presents the varied presence of nitrates and phosphates in water from caves located in Częstochowa and Kraków, in urban, strongly anthropogenic conditions, representing the vadose zone of the fissure-karstic-porous massif of Upper Jurassic limestones. Hydrochemical research was carried out by the authors in the Cave on the Stone in Częstochowa in 2012-2015, in caves of the Zakrzówek horst from 1996 to 2002, and in the Dragon's Cave by the research team of J. Motyka in 1995-1998. A number of NO3 and PO4 measurements were performed in waters sampled at these research sites: 20 measurements each of NO3 and PO4 at the Cave on the Stone, 228 of NO3 and 422 of PO4 at Zakrzówek, and 19 each of NO3 and PO4 at the Dragon's Cave...
September 22, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28936558/how-do-treatment-aims-in-the-last-phase-of-life-relate-to-hospitalizations-and-hospital-mortality-a-mortality-follow-back-study-of-dutch-patients-with-five-types-of-cancer
#5
Mariska Oosterveld-Vlug, Gé Donker, Femke Atsma, Linda Brom, Yvonne de Man, Stef Groenewoud, Bregje Onwuteaka-Philipsen
PURPOSE: The purpose of this study is to describe and compare the relation between treatment aims, hospitalizations, and hospital mortality for Dutch patients who died from lung, colorectal, breast, prostate, or pancreatic cancer. METHODS: A mortality follow-back study was conducted within a sentinel network of Dutch general practitioners (GPs), who recorded the end-of-life care of 691 patients who died from one of the abovementioned cancer types between 2009 and 2015...
September 22, 2017: Supportive Care in Cancer: Official Journal of the Multinational Association of Supportive Care in Cancer
https://www.readbyqxmd.com/read/28935626/wide-variability-in-prethrombectomy-workflow-practices-in-the-united-states-a-multicenter-survey
#6
A P Kansagra, G C Meyers, M S Kruzich, D T Cross, C J Moran
BACKGROUND AND PURPOSE: Clinical outcomes in patients with acute ischemic stroke caused by large vessel occlusion depend on the speed and quality of workflows leading to mechanical thrombectomy. In the absence of universally accepted best practices for workflow, developing stroke hospitals can benefit from improved awareness of real-world workflows in effect at experienced centers. To this end, we surveyed prethrombectomy workflow practices at stroke centers throughout the United States...
September 21, 2017: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/28935348/outcomes-after-sleeve-lung-resections-versus-pneumonectomy-in-the-united-states
#7
Zaid M Abdelsattar, K Robert Shen, Sai Yendamuri, Stephen Cassivi, Francis C Nichols, Dennis A Wigle, Mark S Allen, Shanda H Blackmon
BACKGROUND: The current national trends, practice patterns, and outcomes after sleeve resection compared with pneumonectomy in the United States are not known. In addition, whether hospital sleeve-to-pneumonectomy (S:P) ratios are a valid marker of hospital quality is unclear. We describe practice patterns and evaluate the utility of the S:P ratio. METHODS: We identified all patients (N = 23,964) undergoing sleeve resection (n = 1,713) or pneumonectomy (n = 22,251) in the National Cancer Data Base between 1998 and 2012 at 644 hospitals...
September 18, 2017: Annals of Thoracic Surgery
https://www.readbyqxmd.com/read/28935110/strategies-in-the-design-and-use-of-synthetic-internal-glycan-vaccines
#8
Abirami Lakshminarayanan, Balakumar Vijayakrishnan, Hagan Bayley, Benjamin G Davis
The relative structural conservation of "internal glycans" in the cell walls of pathogens suggests that they might as target epitopes less prone to variation and hence with greater potential universality as vaccine targets. Examples of such glycans include the inner core sugars of lipopolysaccharides in Gram-negative bacteria. However, due to the buried nature of such internal epitopes, this approach has been rarely adopted. Here we briefly review and compare strategic approaches and outline practical methods associated with evaluating one synergistic strategy that combines (i) blocking of the display of "external glycans" with (ii) vaccination targeted at "internal glycans...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28934962/age-and-sex-corrected-normal-reference-values-of-t1-t2%C3%A2-t2-and-ecv-in-healthy-subjects-at-3t-cmr
#9
Clotilde Roy, Alisson Slimani, Christophe de Meester, Mihaela Amzulescu, Agnès Pasquet, David Vancraeynest, Jean-Louis Vanoverschelde, Anne-Catherine Pouleur, Bernhard L Gerber
BACKGROUND: Myocardial T1, T2 and T2* imaging techniques become increasingly used in clinical practice. While normal values for T1, T2 and T2* times are well established for 1.5 Tesla (T) cardiovascular magnetic resonance (CMR), data for 3T remain scarce. Therefore we sought to determine normal reference values relative to gender and age and day to day reproducibility for native T1, T2, T2* mapping and extracellular volume (ECV) at 3T in healthy subjects. METHODS: After careful exclusion of cardiovascular abnormality, 75 healthy subjects aged 20 to 90 years old (mean 56 ± 19 years, 47% women) underwent left-ventricular T1 (3-(3)-3-(3)-5 MOLLI)), T2 (8 echo- spin echo-imaging) and T2 * (8 echo gradient echo imaging) mapping at 3T CMR (Philips Ingenia 3T and computation of extracellular volume after administration of 0...
September 21, 2017: Journal of Cardiovascular Magnetic Resonance
https://www.readbyqxmd.com/read/28933634/development-of-a-multiplexed-opsonophagocytic-killing-assay-mopa-for-group-b-streptococcus
#10
Min Joo Choi, Ji Yun Noh, Hee Jin Cheong, Woo Joo Kim, Shun-Mei Lin, Yong Zhi, Jae Hyang Lim, Sangyong Lim, Ho Seong Seo, Joon Young Song
Group B Streptococcus (GBS) is a leading cause of sepsis in infants as well as chorioamnionitis in pregnant women. Opsonophagocytic killing assays (OPAs) are an essential technique in vaccine studies of encapsulated bacteria for estimating serotype-specific functional antibody levels in vitro. Here, we developed a three-fold multiplexed OPA (MOPA) to enable practical, large-scale assessment of GBS vaccine immunogenicity, including against serotypes Ia, III, and V. First, three target bacteria strains resistant to streptomycin, spectinomycin, or kanamycin were generated by natural selection through exposure to increasing antibiotic concentrations...
September 21, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28933291/pharmacotranscriptomic-biomarkers-in-glucocorticoid-treatment-of-pediatric-inflammatory-bowel-disease
#11
Marianna Lucafò, Biljana Stankovic, Nikola Kotur, Alessia Di Silvestre, Stefano Martelossi, Alessandro Ventura, Branka Zukic, Sonya Pavlovic, Giuliana Decorti
Pharmacotranscriptomics aims to reach more accurate drug dosing based on interindividual transcriptome variations. Here, we provide an overview of RNA biomarkers that could predict the response to glucocorticoids (GCs), considered the standard for treatment of inflammatory bowel diseases (IBD), both in adult and pediatric patients. Although new biological agents are very effective in the IBD treatment, GCs are still widely used for induction of remission in IBD patients with moderate to severe disease. It is important to identify patients that are poor responders to GCs therapy, because suboptimal response is frequent and associated with various side effects...
September 20, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28932153/oral-squamous-cell-carcinoma-masquerading-as-gingival-overgrowth
#12
Roshni Ramesh, Arun Sadasivan
Gingival enlargements are frequently encountered in dental practice. There are different types of gingival enlargements and they vary according to the etiologic factors and pathologic processes that produce them. The exact diagnosis of the enlargement is important as some gingival enlargements can cause extensive morbidity or even mortality. Oral cancers especially squamous cell carcinomas present with variations in clinical presentation and the sites affected. A detailed medical history, clinical examination and radiographic evaluation will help identify the lesion...
July 2017: European Journal of Dentistry
https://www.readbyqxmd.com/read/28931509/development-and-validation-of-qmortality-risk-prediction-algorithm-to-estimate-short-term-risk-of-death-and-assess-frailty-cohort-study
#13
Julia Hippisley-Cox, Carol Coupland
Objectives To derive and validate a risk prediction equation to estimate the short term risk of death, and to develop a classification method for frailty based on risk of death and risk of unplanned hospital admission.Design Prospective open cohort study.Participants Routinely collected data from 1436 general practices contributing data to QResearch in England between 2012 and 2016. 1079 practices were used to develop the scores and a separate set of 357 practices to validate the scores. 1.47 million patients aged 65-100 years were in the derivation cohort and 0...
September 20, 2017: BMJ: British Medical Journal
https://www.readbyqxmd.com/read/28931399/principles-practices-and-knowledge-of-clinicians-when-assessing-febrile-children-a-qualitative-study-in-kenya
#14
Anneka M Hooft, Kelsey Ripp, Bryson Ndenga, Francis Mutuku, David Vu, Kimberly Baltzell, Linnet N Masese, John Vulule, Dunstan Mukoko, A Desiree LaBeaud
BACKGROUND: Clinicians in low resource settings in malaria endemic regions face many challenges in diagnosing and treating febrile illnesses in children. Given the change in WHO guidelines in 2010 that recommend malaria testing prior to treatment, clinicians are now required to expand the differential when malaria testing is negative. Prior studies have indicated that resource availability, need for additional training in differentiating non-malarial illnesses, and lack of understanding within the community of when to seek care play a role in effective diagnosis and treatment...
September 20, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28931382/using-peer-review-to-distribute-group-work-marks-equitably-between-medical-students
#15
Alex R Cook, Mikael Hartman, Nan Luo, Judy Sng, Ngan Phoon Fong, Wei Yen Lim, Mark I-Cheng Chen, Mee Lian Wong, Natarajan Rajaraman, Jeannette Jen-Mai Lee, Gerald Choon-Huat Koh
BACKGROUND: Although peer assessment has been used for evaluating performance of medical students and practicing doctors, it has not been studied as a method to distribute a common group work mark equitably to medical students working in large groups where tutors cannot observe all students constantly. METHODS: The authors developed and evaluated a mathematical formulation whereby a common group mark could be distributed among group members using peer assessment of individual contributions to group work, maintaining inter-group variation in group work scores...
September 20, 2017: BMC Medical Education
https://www.readbyqxmd.com/read/28930845/pure-laparoscopic-donor-right-hepatectomy-in-a-living-donor-with-type-3a-biliary-variation-a-case-report
#16
Young Seok Han, Heontak Ha, Hyung Jun Kwon, Jae Min Chun
RATIONALE: With refinements in the operative technique, laparoscopic surgery has become the standard practice for liver resection. In the field of living donor liver transplantation, a few centers adopted laparoscopic surgery as an alternative to conventional open donor hepatectomy, and the application of pure laparoscopic donor right hepatectomy has been limited to the donors with simple, favorable biliary anatomy. PATIENT CONCERNS: The candidate donor was a 19-year-old woman with type 3a bile duct variation...
September 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28929184/metabolic-changes-in-primary-secondary-and-lipid-metabolism-in-tobacco-leaf-in-response-to-topping
#17
Jieyu Zhao, Lili Li, Yanni Zhao, Chunxia Zhao, Xia Chen, Pingping Liu, Huina Zhou, Junjie Zhang, Chunxiu Hu, Aiguo Chen, Guanshan Liu, Xiaojun Peng, Xin Lu, Guowang Xu
As an important cultivation practice used for flue-cured tobacco, topping affects diverse biological processes in the later stages of development and growth. Some studies have focused on using tobacco genes to reflect the physiological changes caused by topping. However, the complex metabolic shifts in the leaf resulting from topping have not yet been investigated in detail. In this study, a comprehensive metabolic profile of primary, secondary, and lipid metabolism in flue-cured tobacco leaf was generated with use of a multiple platform consisting of gas chromatography-mass spectrometry, capillary electrophoresis-mass spectrometry, and liquid chromatography-mass spectrometry/ultraviolet spectroscopy...
September 19, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28928756/prioritizing-crop-management-to-increase-nitrogen-use-efficiency-in-australian-sugarcane-crops
#18
Peter J Thorburn, Jody S Biggs, Jeda Palmer, Elizabeth A Meier, Kirsten Verburg, Danielle M Skocaj
Sugarcane production relies on the application of large amounts of nitrogen (N) fertilizer. However, application of N in excess of crop needs can lead to loss of N to the environment, which can negatively impact ecosystems. This is of particular concern in Australia where the majority of sugarcane is grown within catchments that drain directly into the World Heritage listed Great Barrier Reef Marine Park. Multiple factors that impact crop yield and N inputs of sugarcane production systems can affect N use efficiency (NUE), yet the efficacy many of these factors have not been examined in detail...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928727/composted-cattle-manure-increases-microbial-activity-and-soil-fertility-more-than-composted-swine-manure-in-a-submerged-rice-paddy
#19
Suvendu Das, Seung Tak Jeong, Subhasis Das, Pil Joo Kim
Livestock waste composts with minimum inorganic fertilizer as a soil amendment in low-input intensive farming are a feasible agricultural practice to improve soil fertility and productivity and to mitigate soil degradation. The key benefits of the practice rely on the activities of soil microorganisms. However, the role of different livestock composts [composted cattle manure (CCM) vs. composted swine manure (CSM)] on soil microbes, their activities and the overall impact on soil fertility and productivity in a flooded paddy remains elusive...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28928526/the-growing-season-impacts-the-accumulation-and-composition-of-flavonoids-in-grape-skins-in-two-crop-a-year-viticulture
#20
Lei Zhu, Yu Huang, Yali Zhang, Changmou Xu, Jiang Lu, Ying Wang
The influence of growing season (winter vs. summer) on the flavonoid accumulation and composition was studied in the skins of three grape cultivars for two consecutive years under a two-crop-a-year viticulture practice in Southwest China. The total anthocyanin, flavonol and flavan-3-ol contents in winter berry skins were significantly higher than those in summer berry skins for 'Kyoho' and 'Muscat Hamburg'. Reversely, the content of anthocyanin in 'NW196' winter berry was lower than summer berry. However, the percentage of diglycosylated, trihydroxylated, methylated, and acylated anthocyanins, trihydroxylated and methylated flavonols, and flavan-3-ol polymers were higher in the summer berry skins than the winter berry skins among all the three grape cultivars...
August 2017: Journal of Food Science and Technology
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