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https://www.readbyqxmd.com/read/29156751/identification-of-potential-tissue-specific-cancer-biomarkers-and-development-of-cancer-versus-normal-genomic-classifiers
#1
Akram Mohammed, Greyson Biegert, Jiri Adamec, Tomáš Helikar
Machine learning techniques for cancer prediction and biomarker discovery can hasten cancer detection and significantly improve prognosis. Recent "OMICS" studies which include a variety of cancer and normal tissue samples along with machine learning approaches have the potential to further accelerate such discovery. To demonstrate this potential, 2,175 gene expression samples from nine tissue types were obtained to identify gene sets whose expression is characteristic of each cancer class. Using random forests classification and ten-fold cross-validation, we developed nine single-tissue classifiers, two multi-tissue cancer-versus-normal classifiers, and one multi-tissue normal classifier...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156494/comparative-analysis-of-vestibular-ecomorphology-in-birds
#2
Roger B J Benson, Ethan Starmer-Jones, Roger A Close, Stig A Walsh
The bony labyrinth of vertebrates houses the semicircular canals. These sense rotational accelerations of the head and play an essential role in gaze stabilisation during locomotion. The sizes and shapes of the semicircular canals have hypothesised relationships to agility and locomotory modes in many groups, including birds, and a burgeoning palaeontological literature seeks to make ecological interpretations from the morphology of the labyrinth in extinct species. Rigorous tests of form-function relationships for the vestibular system are required to support these interpretations...
December 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/29156475/transient-severe-respiratory-motion-artifacts-after-application-of-gadoxetate-disodium-what-we-currently-know
#3
Lennart Well, Julius Matthias Weinrich, Gerhard Adam, Peter Bannas
Background Gadoxetate disodium is an intracellular contrast agent for magnetic resonance imaging (MRI) of the liver. Recent publications revealed that injection of gadoxetate disodium can lead to imaging artifacts due to transient severe motion (TSM) in the arterial phase of contrast-enhanced liver MRI. In this review we present and discuss published frequencies of TSM, contrast injection and image acquisition protocols, potential risk factors, and proposed strategies to avoid or minimize the effects of TSM...
November 20, 2017: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
https://www.readbyqxmd.com/read/29156436/impact-of-changes-in-labor-resources-and-transfers-of-land-use-rights-on-agricultural-non-point-source-pollution-in-jiangsu-province-china
#4
Hua Lu, Hualin Xie
This study systematically explores the likely mechanisms driving the effect of the transfer of agricultural land use rights (ALURs) on agricultural non-point source pollution (ANSP) in the context of changing agricultural labor resources. It quantitatively estimates the direction and degree of this influence from a microeconomic perspective using data from rural households. The results reveal that economies of scale caused by ALURs transfers contribute to reducing both the ANSP and marginal costs of inputs...
November 17, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/29156423/under-pressure-evolutionary-engineering-of-yeast-strains-for-improved-performance-in-fuels-and-chemicals-production
#5
REVIEW
Robert Mans, Jean-Marc G Daran, Jack T Pronk
Evolutionary engineering, which uses laboratory evolution to select for industrially relevant traits, is a popular strategy in the development of high-performing yeast strains for industrial production of fuels and chemicals. By integrating whole-genome sequencing, bioinformatics, classical genetics and genome-editing techniques, evolutionary engineering has also become a powerful approach for identification and reverse engineering of molecular mechanisms that underlie industrially relevant traits. New techniques enable acceleration of in vivo mutation rates, both across yeast genomes and at specific loci...
November 17, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29156418/characterization-of-domestic-pig-spermatogenesis-using-spermatogonial-stem-cell-markers-in-the-early-months-of-life
#6
Julio Almunia, Kotono Nakamura, Mami Murakami, Shigeo Takashima, Masaki Takasu
In pigs, spermatogonial stem cells (SSCs), which include gonocytes and undifferentiated spermatogonia, are classically defined as being present till up to 2 months of life. However, knowledge about this transition from gonocytes to undifferentiated spermatogonia in pigs is limited. In this study, we characterized pig SSCs in neonatal (n = 6), one-month-old (1-mo-old, n = 6), two-month-old (2-mo-old, n = 6), and adult testes (n = 6) anatomically, histologically, and immunohistologically. Anatomically, testicular circumference (TC) was measured at each development stage...
November 3, 2017: Theriogenology
https://www.readbyqxmd.com/read/29156392/biofilms-as-a-sink-for-antibiotic-resistance-genes-args-in-the-yangtze-estuary
#7
Xing-Pan Guo, Yi Yang, Da-Pei Lu, Zuo-Shun Niu, Jing-Nan Feng, Yu-Ru Chen, Fei-Yun Tou, Emily Garner, Jiang Xu, Min Liu, Michael F Hochella
Biofilms are ubiquitous throughout aquatic environments and they are thought to promote the acquisition and dissemination of antibiotic resistant genes (ARGs). This study focused on the occurrence and distribution of five types of ARG in naturally-occurring biofilms, in comparison to associated sediment and water samples, from the Yangtze Estuary, which borders the meta-city of Shanghai, China. The detection frequency and abundances of most ARGs showed the following order: biofilm > sediment > water, which can be attributed to a high level of antibiotics and metals that can accelerate the generation and propagation of ARGs in biofilms...
November 13, 2017: Water Research
https://www.readbyqxmd.com/read/29156373/mitochondria-targeted-ubiquinone-mitoq-enhances-acetaldehyde-clearance-by-reversing-alcohol-induced-posttranslational-modification-of-aldehyde-dehydrogenase-2-a-molecular-mechanism-of-protection-against-alcoholic-liver-disease
#8
Liuyi Hao, Qian Sun, Wei Zhong, Wenliang Zhang, Xinguo Sun, Zhanxiang Zhou
Alcohol metabolism in the liver generates highly toxic acetaldehyde. Breakdown of acetaldehyde by aldehyde dehydrogenase 2 (ALDH2) in the mitochondria consumes NAD(+) and generates reactive oxygen/nitrogen species, which represents a fundamental mechanism in the pathogenesis of alcoholic liver disease (ALD). A mitochondria-targeted lipophilic ubiquinone (MitoQ) has been shown to confer greater protection against oxidative damage in the mitochondria compared to untargeted antioxidants. The present study aimed to investigate if MitoQ could preserve mitochondrial ALDH2 activity and speed up acetaldehyde clearance, thereby protects against ALD...
November 11, 2017: Redox Biology
https://www.readbyqxmd.com/read/29156357/generation-of-complement-molecular-complex-c5b-9-c5b-9-in-response-to-poly-traumatic-hemorrhagic-shock-and-evaluation-of-c5-cleavage-inhibitors-in-non-human-primates
#9
R Madelaine Paredes, Sarah Reyna, Philip Vernon, Douglas K Tadaki, Jurandir J Dallelucca, Forest Sheppard
Severe trauma initiates a systemic inflammatory cascade and that involves early activation of complement and cleavage of C5 into C5a (anaphylatoxin) and C5b (C5b-9 membrane attack complex). We examined activation of C5 in non-human primate (NHP) models of hemorrhagic shock. Blood plasma concentrations of C5b-9 were significantly increased in NHPs in response to hemorrhage alone and were further increased with the addition of tissue trauma. The onset of increased C5 cleavage was accelerated in NHPs that experienced decompensated poly-traumatic hemorrhagic shock...
November 17, 2017: International Immunopharmacology
https://www.readbyqxmd.com/read/29156260/towards-more-ecological-relevance-in-sediment-toxicity-testing-with-fish-evaluation-of-multiple-bioassays-with-embryos-of-the-benthic-weatherfish-misgurnus-fossilis
#10
Benjamin Schreiber, Jonas Fischer, Sabrina Schiwy, Henner Hollert, Ralf Schulz
The effects of sediment contamination on fish are of high significance for the protection of ecosystems, human health and economy. However, standardized sediment bioassays with benthic fish species, that mimic bioavailability of potentially toxic compounds and comply with the requirements of alternative test methods, are still scarce. In order to address this issue, embryos of the benthic European weatherfish (Misgurnus fossilis) were exposed to freeze-dried sediment (via sediment contact assays (SCA)) and sediment extracts (via acute fish embryo toxicity tests) varying in contamination level...
November 16, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29156171/the-use-of-decellularized-human-placenta-in-full-thickness-wound-repair-and%C3%A2-periarticular-soft-tissue-reconstruction-an-update-on-regenerative-healing
#11
REVIEW
Stephen A Brigido, Scott C Carrington, Nicole M Protzman
Prolonged or incomplete healing of the foot and ankle can pose significant challenges. Therefore, investigators have begun searching for alternative treatment strategies. With advances in tissue engineering, decellularized human placental connective tissue matrix has been suggested as a means to achieve more rapid and complete healing for various soft tissue and bone procedures. Basic science and clinical studies have shown that decellularized human placental connective tissue matrix can support regenerative healing through cellular migration, accelerated tissue remodeling, and the establishment of functional tissue...
January 2018: Clinics in Podiatric Medicine and Surgery
https://www.readbyqxmd.com/read/29156056/high-doses-of-cholecalciferol-alleviate-the-progression-of-hyperparathyroidism-in-patients-with-ckd-stages-3-4-results-of-a-12-week-double-blind-randomized-controlled-study
#12
Per-Anton Westerberg, Gunnar Sterner, Östen Ljunggren, Elin Isaksson, Fjölnir Elvarson, Hamid Dezfoolian, Torbjörn Linde
Background: Calcidiol insufficiency may accelerate the development of secondary hyperparathyroidism (SHPT). We tested the effect of a substantial increase in calcidiol on mineral metabolism in patients with chronic kidney disease (CKD). Methods: Ninety-five patients with CKD Stages 3-4, parathyroid hormone (PTH) above 6.8 pmol/L and calcidiol below 75 nmol/L were randomized to receive either cholecalciferol 8000 IU/day or placebo for 12 weeks. The primary endpoint was difference in the mean change in iPTH after 12 weeks...
May 30, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29155983/meox1-accelerates-myocardial-hypertrophic-decompensation-through-gata4
#13
Dan Lu, Jizheng Wang, Jing Li, Feifei Guan, Xu Zhang, Wei Dong, Ning Liu, Shan Gao, Lianfeng Zhang
Aims: Pathological hypertrophy is the result of gene network regulation, which ultimately leads to adverse cardiac remodelling and heart failure (HF), and is accompanied by the reactivation of a 'foetal gene programme'. The Mesenchyme homeobox 1 (Meox1) gene is one of the foetal programme genes. Meox1 may play a role in embryonic development, but its regulation of pathological hypertrophy is not known. Therefore, this study investigated the effect of Meox1 on pathological hypertrophy, including familial and pressure overload-induced hypertrophy, and its potential mechanism of action...
November 16, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/29155950/ensembl-2018
#14
Daniel R Zerbino, Premanand Achuthan, Wasiu Akanni, M Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Girón, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G Izuogu, Sophie H Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R Laird, Ilias Lavidas, Zhicheng Liu, Jane E Loveland, Thomas Maurel, William McLaren, Benjamin Moore, Jonathan Mudge, Daniel N Murphy, Victoria Newman, Michael Nuhn, Denye Ogeh, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Helen Schuilenburg, Dan Sheppard, Helen Sparrow, Kieron Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Amonida Zadissa, Adam Frankish, Sarah E Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Dan M Staines, Stephen J Trevanion, Bronwen L Aken, Fiona Cunningham, Andrew Yates, Paul Flicek
The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded in multiple directions. First, our resources describe multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155943/logical-engineering-of-d-arm-and-t-stem-of-trna-that-enhances-d-amino-acid-incorporation
#15
Takayuki Katoh, Yoshihiko Iwane, Hiroaki Suga
A bacterial translation factor EF-P alleviates ribosomal stalling caused by polyproline sequence by accelerating Pro-Pro formation. EF-P recognizes a specific D-arm motif found in tRNAPro isoacceptors, 9-nt D-loop closed by a stable D-stem sequence, for Pro-selective peptidyl-transfer acceleration. It is also known that the T-stem sequence on aminoacyl-tRNAs modulates strength of the interaction with EF-Tu, giving enhanced incorporation of non-proteinogenic amino acids such as some N-methyl amino acids. Based on the above knowledge, we logically engineered tRNA's D-arm and T-stem sequences to investigate a series of tRNAs for the improvement of consecutive incorporation of d-amino acids and an α, α-disubstituted amino acid...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155924/accounting-for-time-varying-confounding-in-the-relation-between-obesity-and-coronary-heart-disease-analysis-with-g-estimation-the-atherosclerosis-risk-in-communities-aric-study
#16
Maryam Shakiba, Mohammad Ali Mansournia, Arsalan Salari, Hamid Soori, Nasrin Mansournia, Jay S Kaufman
In longitudinal studies, standard analysis may yield biased estimates of exposure effect in the presence of time-varying confounders that are also intermediate variables. We aimed to quantify the relationship between obesity and coronary heart disease (CHD) by appropriately adjusting for time-varying confounders. This study performed on a subset of the Atherosclerosis Risk in Communities Study (1987-2010). General obesity defined as body mass index ≥30 kg/m2, abdominal obesity (AOB) defined as waist circumference ≥102 cm in men and ≥88 cm in women, and waist to hip ratio categorized at ≥0...
November 16, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29155910/probing-plasma-fluorinated-graphene-via-spectromicroscopy
#17
C Struzzi, M Scardamaglia, N Reckinger, H Sezen, M Amati, L Gregoratti, J-F Colomer, C Ewels, R Snyders, C Bittencourt
Plasma fluorination of graphene is studied using a combination of spectroscopy and microscopy techniques, giving insight into the yield and fluorination mechanism for functionalization of supported graphene with both CF4 and SF6 gas precursors. Ion acceleration during fluorination is used to probe the effect on grafting functionalities. Adatom clustering, which occurs with CF4 plasma treatment, is suppressed when higher kinetic energy is supplied to the ions. During SF6 plasma functionalization, the sulfur atoms tend to bond to bare copper areas instead of affecting the graphene chemistry, except when the kinetic energy of the ions is restricted...
November 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29155856/treatment-with-solubilized-silk-derived-protein-sdp-enhances-rabbit-corneal-epithelial-wound-healing
#18
Waleed Abdel-Naby, Brigette Cole, Aihong Liu, Jingbo Liu, Pengxia Wan, Ryan Schreiner, David W Infanger, Nicholas B Paulson, Brian D Lawrence, Mark I Rosenblatt
There is a significant clinical need to improve current therapeutic approaches to treat ocular surface injuries and disease, which affect hundreds of millions of people annually worldwide. The work presented here demonstrates that the presence of Silk-Derived Protein (SDP) on the healing rabbit corneal surface, administered in an eye drop formulation, corresponds with an enhanced epithelial wound healing profile. Rabbit corneas were denuded of their epithelial surface, and then treated for 72-hours with either PBS or PBS containing 5 or 20 mg/mL SDP in solution four times per day...
2017: PloS One
https://www.readbyqxmd.com/read/29155850/pre-pubertal-exposure-with-phthalates-and-bisphenol-a-and-pubertal-development
#19
Monika Kasper-Sonnenberg, Jürgen Wittsiepe, Katharina Wald, Holger M Koch, Michael Wilhelm
OBJECTIVE: Epidemiological studies indicate associations between childhood exposure with phthalates and bisphenol A (BPA) and the pubertal development. We examined associations between the pre-pubertal phthalate and BPA body burden and the longitudinally assessed sexual maturation of eight- to thirteen-year-old children. METHODS: We started with eight- to ten-year-old children in the baseline study and quantified phthalate metabolites and BPA in 472 urine samples (250 boys; 222 girls; mean age: 8...
2017: PloS One
https://www.readbyqxmd.com/read/29155821/progress-towards-a-leprosy-free-country-the-experience-of-oman
#20
Salah T Al Awaidy
INTRODUCTION: The World Health Organization (WHO) released the Global Leprosy Strategy 2016-2020 towards a leprosy-free world. The author described the progress made towards the elimination of leprosy and suggested recommendations for the acceleration towards a Leprosy-free country according to WHO laid out criterion. METHODOLOGY: Case record review of Leprosy patients managed between the years 1992 to 2015 were registered and analyzed. Data were collected from annual reports of the Ministry of Health including demographics, classification of leprosy new cases, relapse, childhood, grades of disability (GD) and multidrug therapy (MDT) completion rates...
November 20, 2017: PLoS Neglected Tropical Diseases
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