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https://www.readbyqxmd.com/read/28334822/posigene-automated-and-easy-to-use-pipeline-for-genome-wide-detection-of-positively-selected-genes
#1
Arne Sahm, Martin Bens, Matthias Platzer, Karol Szafranski
Many comparative genomics studies aim to find the genetic basis of species-specific phenotypic traits. A prevailing strategy is to search genome-wide for genes that evolved under positive selection based on the non-synonymous to synonymous substitution ratio. However, incongruent results largely due to high false positive rates indicate the need for standardization of quality criteria and software tools. Main challenges are the ortholog and isoform assignment, the high sensitivity of the statistical models to alignment errors and the imperative to parallelize large parts of the software...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334608/parvalbumin-interneurons-modulate-striatal-output-and-enhance-performance-during-associative-learning
#2
Kwang Lee, Sandra M Holley, Justin L Shobe, Natalie C Chong, Carlos Cepeda, Michael S Levine, Sotiris C Masmanidis
The prevailing view is that striatal parvalbumin (PV)-positive interneurons primarily function to downregulate medium spiny projection neuron (MSN) activity via monosynaptic inhibitory signaling. Here, by combining in vivo neural recordings and optogenetics, we unexpectedly find that both suppressing and over-activating PV cells attenuates spontaneous MSN activity. To account for this, we find that, in addition to monosynaptic coupling, PV-MSN interactions are mediated by a competing disynaptic inhibitory circuit involving a variety of neuropeptide Y-expressing interneurons...
March 22, 2017: Neuron
https://www.readbyqxmd.com/read/28334304/livestock-grazing-shapes-the-vegetation-structure-and-subsequent-habitat-use-by-the-endangered-skipper-pyrgus-ruralis-lagunae-lepidoptera-hesperiidae
#3
Daniel A Marschalek, David K Faulkner, Douglas H Deutschman
Many species adapted to alpine and montane meadow ecosystems are at risk of extinction. The skipper Pyrgus ruralis lagunae Scott is a mountaintop butterfly restricted to San Diego County, CA, a federally listed endangered species, and is in imminent risk of extinction. Historically, P. r. lagunae was found in the Laguna and Palomar mountains. We did not detect the skipper in the Laguna Mountains, and the species has likely been extirpated from this area, which represents half of its historical range and is the type locality...
March 18, 2017: Environmental Entomology
https://www.readbyqxmd.com/read/28334161/elevated-co2-and-warming-effects-on-grassland-plant-mortality-are-determined-by-the-timing-of-rainfall
#4
Mark J Hovenden, Paul C D Newton, Meagan Porter
Background and aims: Global warming is expected to increase the mortality rate of established plants in water-limited systems because of its effect on evapotranspiration. The rising CO 2 concentration ([CO 2 ]), however, should have the opposite effect because it reduces plant transpiration, delaying the onset of drought. This potential for elevated [CO 2 ] (eCO 2 ) to modify the warming effect on mortality should be related to prevailing moisture conditions. This study aimed to determine the impacts of warming by 2 °C and eCO 2 (550 μmol mol -1 ) on plant mortality in an Australian temperate grassland over a 6-year period and to test how interannual variation in rainfall influenced treatment effects...
February 28, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334142/layer-specific-organization-of-local-excitatory-and-inhibitory-synaptic-connectivity-in-the-rat-presubiculum
#5
Yangfan Peng, Federico J Barreda Tomás, Constantin Klisch, Imre Vida, Jörg R P Geiger
The presubiculum is part of the parahippocampal spatial navigation system and contains head direction and grid cells upstream of the medial entorhinal cortex. This position within the parahippocampal cortex renders the presubiculum uniquely suited for analyzing the circuit requirements underlying the emergence of spatially tuned neuronal activity. To identify the local circuit properties, we analyzed the topology of synaptic connections between pyramidal cells and interneurons in all layers of the presubiculum by testing 4250 potential synaptic connections using multiple whole-cell recordings of up to 8 cells simultaneously...
February 25, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28334079/how-do-cold-adapted-plants-respond-to-climatic-cycles-interglacial-expansion-explains-current-distribution-and-genomic-diversity-in-primula-farinosa-l
#6
Spyros Theodoridis, Christophe Randin, Peter Szövényi, Florian C Boucher, Theofania S Patsiou, Elena Conti
Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model...
December 21, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28332202/calcium-signalling-silencing-in-atrial-fibrillation
#7
Maura Greiser
Sub-cellular calcium signalling silencing is a novel and distinct cellular and molecular adaptive response to rapid cardiac activation. Calcium signalling silencing develops during short-term sustained rapid atrial activation as seen clinically during paroxysmal atrial fibrillation (AF). It is the first 'anti-arrhythmic' adaptive response in the setting of AF and appears to counteract the maladaptive changes that lead to intracellular Ca(2+) signalling instability and Ca(2+) based arrhythmogenicity. Calcium signalling silencing results in a failed propagation of the [Ca(2+) ]i signal to the myocyte centre in both patients with AF and in a rabbit model...
March 22, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28330646/is-it-time-for-a-change-in-the-approach-to-chemical-burns-the-role-of-diphoterine-%C3%A2-in-the-management-of-cutaneous-and-ocular-chemical-injuries
#8
REVIEW
C J Lewis, A Al-Mousawi, A Jha, K P Allison
A multitude of household and occupational compounds have the potential to induce chemical burns to the eye and skin. Without prompt intervention, irreversible visual loss and disfigurement may prevail. Diphoterine(®) and Hexafluorine(®) are amphoteric and hypertonic chelating solutions used in the management of general chemical and hydrofluoric acid burns, respectively. They rapidly neutralise both acid and alkali agents without heat release and limit diffusion, making them superior to water irrigation alone...
February 27, 2017: Journal of Plastic, Reconstructive & Aesthetic Surgery: JPRAS
https://www.readbyqxmd.com/read/28330458/the-effects-of-an-extensive-exercise-programme-on-the-progression-of-mild-cognitive-impairment-mci-study-protocol-for-a-randomised-controlled-trial
#9
Kate E Devenney, Brian Lawlor, Marcel G M Olde Rikkert, Stefan Schneider
BACKGROUND: Exercise interventions to prevent dementia and delay cognitive decline have gained considerable attention in recent years. Human and animal studies have demonstrated that regular physical activity targets brain function by increasing cognitive reserve. There is also evidence of structural changes caused by exercise in preventing or delaying the genesis of neurodegeneration. Although initial studies indicate enhanced cognitive performance in patients with mild cognitive impairment (MCI) following an exercise intervention, little is known about the effect of an extensive, controlled and regular exercise regimen on the neuropathology of patients with MCI...
March 22, 2017: BMC Geriatrics
https://www.readbyqxmd.com/read/28329676/lineage-biased-stem-cells-maintain-estrogen-receptor-positive-and-negative-mouse-mammary-luminal-lineages
#10
Chunhui Wang, John R Christin, Maja H Oktay, Wenjun Guo
Delineating the mammary differentiation hierarchy is important for the study of mammary gland development and tumorigenesis. Mammary luminal cells are considered a major origin of human breast cancers. However, how estrogen-receptor-positive (ER(+)) and ER(-) luminal cells are developed and maintained remains poorly understood. The prevailing model suggests that a common stem/progenitor cell generates both cell types. Through genetic lineage tracing in mice, we find that SOX9-expressing cells specifically contribute to the development and maintenance of ER(-) luminal cells and, to a lesser degree, basal cells...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28328806/craniosynostosis-scheuermann-s-disease-and-intellectual-disability-resembling-shprintzen-goldberg-syndrome-a-report-on-a-family-over-4-generations-case-report
#11
Ali Al Kaissi, Zahra Marrakchi, Nabil M Nassib, Jochen Hofstaetter, Franz Grill, Rudolf Ganger, Susanne Gerit Kircher
RATIONALE: Craniosynostosis is a disorder characterized by premature fusion of cranial sutures with subsequent development of abnormal craniofacial contour associated with variable skeletal and extra-skeletal abnormalities. In this family syndromic type of craniosynostosis was recognized and the etiology behind diverse forms of deformities have been diagnosed. PATIENT CONCERNS: The negative impact of the disorder on the child and his family is enormous. Particularly when the diagnosis is late and little can be done...
March 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28328012/free-fatty-acid-receptor-1-ffar1-as-an-emerging-therapeutic-target-for-type-2-diabetes-mellitus-recent-progress-and-prevailing-challenges
#12
REVIEW
Zheng Li, Xue Xu, Wenlong Huang, Hai Qian
The free fatty acid receptor 1 (FFAR1/GPR40) amplifies glucose-dependent insulin secretion; therefore, it has attracted widespread attention as a promising antidiabetic target. Current clinical proof of concept also indicates that FFAR1 agonists achieve the initially therapeutic endpoint for the treatment of type 2 diabetes mellitus (T2DM) without the hypoglycemic risk. Thus, many pharmaceutical companies and academic institutes are competing to develop FFAR1 agonists. However, several candidates have been discontinued in clinical trials, often without reporting the underlying reasons...
March 22, 2017: Medicinal Research Reviews
https://www.readbyqxmd.com/read/28327964/imaging-approaches-to-stroke-and-neurovascular-disease
#13
Seena Dehkharghani, Jalal Andre
Imaging is paramount to the diagnosis and management of ischemic stroke, offering a battery of structural and functional probes of cerebrovascular physiology. The technical underpinnings of stroke imaging continue to evolve, bringing the neuroscience community increasingly closer to high-resolution, tissue-level biomarkers of brain perfusion, metabolism, and viability. The rapid expansion of neuroimaging in this domain has met with controversies, and in many respects, a lack of generalizable conclusions regarding optimized use in cerebrovascular disease...
January 28, 2017: Neurosurgery
https://www.readbyqxmd.com/read/28326066/beneficial-microorganisms-for-corals-bmc-proposed-mechanisms-for-coral-health-and-resilience
#14
REVIEW
Raquel S Peixoto, Phillipe M Rosado, Deborah Catharine de Assis Leite, Alexandre S Rosado, David G Bourne
The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28325890/environmental-filtering-triggers-community-assembly-of-forest-understorey-plants-in-central-european-pine-stands
#15
Werner Ulrich, Piotr Sewerniak, Radosław Puchałka, Marcin Piwczyński
Habitat filtering models predict ecologically similar plant species to jointly colonize sites due to comparable environmental characteristics leading to an aggregated pattern of species spatial occurrence. Models focused on interspecific competition expect species with similar ecological requirements to be spatially segregated. While both models are corroborated by field work, few empirical studies have tried to infer under which habitat conditions these patterns of co-occurrence prevail. Here we use an exceptional data set on central European pine forest understorey plant communities to assess the change in community structure along gradients of soil productivity and heterogeneity...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325876/comprehensive-and-quantitative-mapping-of-rna-protein-interactions-across-a-transcribed-eukaryotic-genome
#16
Richard She, Anupam K Chakravarty, Curtis J Layton, Lauren M Chircus, Johan O L Andreasson, Nandita Damaraju, Peter L McMahon, Jason D Buenrostro, Daniel F Jarosz, William J Greenleaf
RNA-binding proteins (RBPs) control the fate of nearly every transcript in a cell. However, no existing approach for studying these posttranscriptional gene regulators combines transcriptome-wide throughput and biophysical precision. Here, we describe an assay that accomplishes this. Using commonly available hardware, we built a customizable, open-source platform that leverages the inherent throughput of Illumina technology for direct biophysical measurements. We used the platform to quantitatively measure the binding affinity of the prototypical RBP Vts1 for every transcript in the Saccharomyces cerevisiae genome...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28323431/au38-sph-24-au38-protected-with-aromatic-thiolate-ligands
#17
Milan Rambukwella, Shayna Burrage, Marie Neubrander, Oscar Baseggio, Edoardo Aprà, Mauro Stener, Alessandro Fortunelli, Amala Dass
Au38(SR)24 is one of the most extensively investigated gold nanomolecules along with Au25(SR)18 and Au144(SR)60. However, so far it has only been prepared using aliphatic-like ligands, where R = -SC6H13, -SC12H25 and -SCH2CH2Ph. Au38(SCH2CH2Ph)24 when reacted with HSPh undergoes core-size conversion to Au36(SPh)24, and existing literature suggests that Au38(SPh)24 cannot be synthesized. Here, contrary to prevailing knowledge, we demonstrate that Au38(SPh)24 can be prepared if the ligand exchanged conditions are optimized, under delicate conditions, without any formation of Au36(SPh)24...
March 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28323405/oxygen-vacancy-enables-markedly-enhanced-magnetic-resonance-imaging-guided-photothermal-therapy-of-a-gd-3-doped-contrast-agent
#18
Dalong Ni, Jiawen Zhang, Jing Wang, Ping Hu, Yingying Jin, Zhongmin Tang, Zhenwei Yao, Wenbo Bu, Jianlin Shi
Gd(3+)-based contrast agents (CAs) are the most prevailing and widely used for enhanced magnetic resonance imaging (MRI). Numbers of approaches have been developed to regulate the key parameters in order to obtain high-relaxivity CAs, according to the classic Solomon-Bloembergen-Morgen theory. Herein, a method of controlling oxygen vacancies in inorganic nanosized CAs has been developed for largely accelerated proton relaxation to obtain a high r1 value. Such a strategy is verified on oxygen-deficient PEG-NaxGdWO3 nanorods, which exhibit a remarkable r1 value up to 80 mM(-1) s(-1) (at 0...
March 23, 2017: ACS Nano
https://www.readbyqxmd.com/read/28323391/metagenomic-analysis-reveals-changes-of-the-drosophila-suzukii-microbiota-in-the-newly-colonised-regions
#19
Isabel Martinez-Sañudo, Mauro Simonato, Andrea Squartini, Nicola Mori, Laura Marri, Luca Mazzon
The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North-America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D...
March 21, 2017: Insect Science
https://www.readbyqxmd.com/read/28321002/five-year-outcomes-of-the-first-pivotal-clinical-trial-of-balloon-expandable-transcatheter-aortic-valve-replacement-in-japan-prevail-japan
#20
Yoshiki Sawa, Morimasa Takayama, Tsuyoshi Goto, Shuichiro Takanashi, Tatsuhiko Komiya, Tetsuya Tobaru, Koichi Maeda, Toru Kuratani, Yasushi Sakata
BACKGROUND: Transcatheter aortic valve replacement (TAVR) has been an alternative less invasive therapy for high-surgical risk/inoperable patients with aortic valve stenosis (AS) in Japan. We report 5-year outcomes of the first pivotal clinical trial of TAVR in Japan (PREVAIL JAPAN).Methods and Results:A total of 64 patients with AS who were considered unsuitable candidates for surgery were enrolled at 3 centers in Japan (mean age: 84.3±6.1 years, female: 65.6%, STS score: 9.0±4...
March 17, 2017: Circulation Journal: Official Journal of the Japanese Circulation Society
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