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https://www.readbyqxmd.com/read/29353236/deep-brain-stimulation-for-parkinson-s-disease-defining-the-optimal-location-within-the-subthalamic-nucleus
#1
Maarten Bot, P Richard Schuurman, Vincent J J Odekerken, Rens Verhagen, Fiorella Maria Contarino, Rob M A De Bie, Pepijn van den Munckhof
BACKGROUND: Individual motor improvement after deep brain stimulation (DBS) of the subthalamic nucleus (STN) for Parkinson's disease (PD) varies considerably. Stereotactic targeting of the dorsolateral sensorimotor part of the STN is considered paramount for maximising effectiveness, but studies employing the midcommissural point (MCP) as anatomical reference failed to show correlation between DBS location and motor improvement. The medial border of the STN as reference may provide better insight in the relationship between DBS location and clinical outcome...
January 20, 2018: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/29353061/next-generation-sequencing-to-detect-deletion-of-rb1-and-erbb4-genes-in-chromophobe-renal-cell-carcinoma-a-potential-role-in-distinguishing-chromophobe-renal-cell-carcinoma-from-renal-oncocytoma
#2
Qingqing Liu, Kristine M Cornejo, Liang Cheng, Lloyd Hutchinson, Mingsheng Wang, Shaobo Zhang, Keith Tomaszewicz, Ediz F Cosar, Bruce A Woda, Zhong Jiang
Overlapping morphological, immunohistochemical, and ultrastructural features make it difficult to diagnose chromophobe renal cell carcinoma (ChRCC) and renal oncocytoma (RO). Since ChRCC is a malignant tumor, whereas RO is a tumor with benign behavior, it is important to distinguish these two entities. We aimed to identify genetic markers that distinguish ChRCC from RO by using next-generation sequencing (NGS). NGS for hotspot mutations or gene copy number changes was performed on 12 renal neoplasms including seven ChRCC and five RO cases...
January 15, 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/29351612/a-mutational-signature-associated-with-alcohol-consumption-and-prognostically-significantly-mutated-driver-genes-in-esophageal-squamous-cell-carcinoma
#3
X C Li, M Y Wang, M Yang, H J Dai, B F Zhang, W Wang, X L Chu, X Wang, H Zheng, R F Niu, W Zhang, K X Chen
Background: Esophageal squamous cell carcinoma (ESCC) is often diagnosed at an advanced and incurable stage. Information on driver genes and prognosticators in ESCC remains incomplete. The objective was to elucidate significantly mutated genes (SMGs), mutational signatures, and prognosticators in ESCC. Patients and Methods: Three MutSig algorithms (i.e. MutSigCV, MutSigCL and MutSigFN) and "20/20+" ratio-metric were employed to identify SMGs. Nonnegative matrix factorization was used to decipher mutational signatures...
January 16, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29351588/sorghum-root-system-classification-in-contrasting-p-environments-reveals-three-main-rooting-types-and-root-architecture-related-marker-trait-associations
#4
Sebastian Parra-Londono, Mareike Kavka, Birgit Samans, Rod Snowdon, Silke Wieckhorst, Ralf Uptmoor
Background and Aims: Roots facilitate acquisition of macro- and micronutrients, which are crucial for plant productivity and anchorage in the soil. Phosphorus (P) is rapidly immobilized in the soil and hardly available for plants. Adaptation to P scarcity relies on changes in root morphology towards rooting systems well suited for topsoil foraging. Root-system architecture (RSA) defines the spatial organization of the network comprising primary, lateral and stem-derived roots and is important for adaptation to stress conditions...
January 17, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29351315/large-scale-mapping-of-bioactive-peptides-in-structural-and-sequence-space
#5
Agustina E Nardo, M Cristina Añón, Gustavo Parisi
Health-enhancing potential bioactive peptide (BP) has driven an interest in food proteins as well as in the development of predictive methods. Research in this area has been especially active to use them as components in functional foods. Apparently, BPs do not have a given biological function in the containing proteins and they do not evolve under independent evolutionary constraints. In this work we performed a large-scale mapping of BPs in sequence and structural space. Using well curated BP deposited in BIOPEP database, we searched for exact matches in non-redundant sequences databases...
2018: PloS One
https://www.readbyqxmd.com/read/29350150/role-of-environmental-factors-in-shaping-spatial-distribution-of-salmonella-enterica-serovar-typhi-fiji
#6
Ruklanthi de Alwis, Conall Watson, Birgit Nikolay, John H Lowry, Nga Tran Vu Thieu, Tan Trinh Van, Dung Tran Thi Ngoc, Kitione Rawalai, Mere Taufa, Jerimaia Coriakula, Colleen L Lau, Eric J Nilles, W John Edmunds, Mike Kama, Stephen Baker, Jorge Cano
Fiji recently experienced a sharp increase in reported typhoid fever cases. To investigate geographic distribution and environmental risk factors associated with Salmonella enterica serovar Typhi infection, we conducted a cross-sectional cluster survey with associated serologic testing for Vi capsular antigen-specific antibodies (a marker for exposure to Salmonella Typhi in Fiji in 2013. Hotspots with high seroprevalence of Vi-specific antibodies were identified in northeastern mainland Fiji. Risk for Vi seropositivity increased with increased annual rainfall (odds ratio [OR] 1...
February 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29348066/multi-scale-measurements-show-limited-soil-greenhouse-gas-emissions-in-kenyan-smallholder-coffee-dairy-systems
#7
Daniel Ortiz-Gonzalo, Andreas de Neergaard, Philippe Vaast, Víctor Suárez-Villanueva, Myles Oelofse, Todd S Rosenstock
Efforts have been made in recent years to improve knowledge about soil greenhouse gas (GHG) fluxes from sub-Saharan Africa. However, data on soil GHG emissions from smallholder coffee-dairy systems have not hitherto been measured experimentally. This study aimed to quantify soil GHG emissions at different spatial and temporal scales in smallholder coffee-dairy farms in Murang'a County, Central Kenya. GHG measurements were carried out for one year, comprising two cropping seasons, using vented static chambers and gas chromatography...
January 16, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29343757/the-early-conversion-of-deep-sea-wood-falls-into-chemosynthetic-hotspots-revealed-by-in-situ-monitoring
#8
D Kalenitchenko, E Péru, L Contreira Pereira, C Petetin, P E Galand, N Le Bris
Wood debris on the ocean floor harbor flourishing communities, which include invertebrate taxa thriving in sulfide-rich habitats belonging to hydrothermal vent and methane seep deep-sea lineages. The formation of sulfidic niches from digested wood material produced by woodborers has been known for a long time, but the temporal dynamics and sulfide ranges encountered on wood falls remains unknown. Here, we show that wood falls are converted into sulfidic hotpots, before the colonization by xylophagaid bivalves...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343185/exploring-protein-protein-intermolecular-recognition-between-meprin-%C3%AE-and-endogenous-protease-regulator-cystatinc-coupled-with-pharmacophore-elucidation
#9
Ankur Chaudhuri, Sampa Biswas, Sibani Chakraborty
Meprins are a group of zinc metalloproteases of the astacin family which play pivotal role in several physiological and pathologocal diseases. The inhibition of the meprins by various inhibitors; macromolecular and small molecules are crucial in the control of several diseases. Human cystatinC, an amyloidogenic protein is reported to be an endogenous inhibitor of meprin-α. In this computational study, we elucidate a rational model for meprinα-cystatinC complex by using protein-protein docking. The complex model as well as the unbound form was evaluated by molecular dynamics simulation...
January 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29342275/hot-spot-kif5a-mutations-cause-familial-als
#10
David Brenner, Rüstem Yilmaz, Kathrin Müller, Torsten Grehl, Susanne Petri, Thomas Meyer, Julian Grosskreutz, Patrick Weydt, Wolfgang Ruf, Christoph Neuwirth, Markus Weber, Susana Pinto, Kristl G Claeys, Berthold Schrank, Berit Jordan, Antje Knehr, Kornelia Günther, Annemarie Hübers, Daniel Zeller, Christian Kubisch, Sibylle Jablonka, Michael Sendtner, Thomas Klopstock, Mamede de Carvalho, Anne Sperfeld, Guntram Borck, Alexander E Volk, Johannes Dorst, Joachim Weis, Markus Otto, Joachim Schuster, Kelly Del Tredici, Heiko Braak, Karin M Danzer, Axel Freischmidt, Thomas Meitinger, Tim M Strom, Albert C Ludolph, Peter M Andersen, Jochen H Weishaupt
Heterozygous missense mutations in the N-terminal motor or coiled-coil domains of the kinesin family member 5A (KIF5A) gene cause monogenic spastic paraplegia (HSP10) and Charcot-Marie-Tooth disease type 2 (CMT2). Moreover, heterozygous de novo frame-shift mutations in the C-terminal domain of KIF5A are associated with neonatal intractable myoclonus, a neurodevelopmental syndrome. These findings, together with the observation that many of the disease genes associated with amyotrophic lateral sclerosis disrupt cytoskeletal function and intracellular transport, led us to hypothesize that mutations in KIF5A are also a cause of amyotrophic lateral sclerosis...
January 12, 2018: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29342139/structure-and-mutagenesis-reveal-essential-capsid-protein-interactions-for-kshv-replication
#11
Xinghong Dai, Danyang Gong, Hanyoung Lim, Jonathan Jih, Ting-Ting Wu, Ren Sun, Z Hong Zhou
Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer that commonly affects patients with AIDS and which is endemic in sub-Saharan Africa. The KSHV capsid is highly pressurized by its double-stranded DNA genome, as are the capsids of the eight other human herpesviruses. Capsid assembly and genome packaging of herpesviruses are prone to interruption and can therefore be targeted for the structure-guided development of antiviral agents. However, herpesvirus capsids-comprising nearly 3,000 proteins and over 1,300 Å in diameter-present a formidable challenge to atomic structure determination and functional mapping of molecular interactions...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29341449/digging-deeper-a-holistic-perspective-of-factors-affecting-soil-organic-carbon-sequestration-in-agroecosystems
#12
Rattan Lal
The global magnitude (Pg) of soil organic carbon (SOC) is 677 to 0.3-m, 993 to 0.5-m, and 1505 to 1-m depth. Thus, ~55% of SOC to 1-m lies below 0.3-m depth. Soils of agroecosystems are depleted of their SOC stock and have a low use efficiency of inputs of agronomic yield. This review is a collation and synthesis of articles published in peer-reviewed journals. The rates of SOC sequestration are scaled up to the global level by linear extrapolation. Soil C sink capacity depends on depth, clay content and mineralogy, plant available water holding capacity, nutrient reserves, landscape position, and the antecedent SOC stock...
January 17, 2018: Global Change Biology
https://www.readbyqxmd.com/read/29341374/validation-of-the-digital-pcr-system-in-tyrosine-kinase-inhibitor-resistant-egfr-mutant-non-small-cell-lung-cancer
#13
Katsuhiro Masago, Shiro Fujita, Akito Hata, Chiyuki Okuda, Yuko Yoshizumi, Reiko Kaji, Nobuyuki Katakami, Yukio Hirata, Yasushi Yatabe
The aim of this study was to compare the accuracy of the QuantStudio 3D Digital polymerase chain reaction (dPCR) system and a PCR-based next generation sequencing (NGS) system for detecting a secondary mutation in the epidermal growth factor receptor (EGFR) gene T790M in non-small cell lung cancer (NSCLC) patients previously diagnosed with EGFR-activating mutations. Twenty-five patients with NSCLC previously treated with EGFR-TKIs were examined. The patients were treated daily with either erlotinib or gefitinib...
January 17, 2018: Pathology International
https://www.readbyqxmd.com/read/29340796/the-complete-plastome-of-macaw-palm-acrocomia-aculeata-jacq-lodd-ex-mart-and-extensive-molecular-analyses-of-the-evolution-of-plastid-genes-in-arecaceae
#14
Amanda de Santana Lopes, Túlio Gomes Pacheco, Tabea Nimz, Leila do Nascimento Vieira, Miguel P Guerra, Rubens O Nodari, Emanuel Maltempi de Souza, Fábio de Oliveira Pedrosa, Marcelo Rogalski
The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections...
January 16, 2018: Planta
https://www.readbyqxmd.com/read/29339490/structural-basis-of-sterol-recognition-and-nonvesicular-transport-by-lipid-transfer-proteins-anchored-at-membrane-contact-sites
#15
Junsen Tong, Mohammad Kawsar Manik, Young Jun Im
Membrane contact sites (MCSs) in eukaryotic cells are hotspots for lipid exchange, which is essential for many biological functions, including regulation of membrane properties and protein trafficking. Lipid transfer proteins anchored at membrane contact sites (LAMs) contain sterol-specific lipid transfer domains [StARkin domain (SD)] and multiple targeting modules to specific membrane organelles. Elucidating the structural mechanisms of targeting and ligand recognition by LAMs is important for understanding the interorganelle communication and exchange at MCSs...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339274/geochemical-sources-of-metal-contamination-in-a-coal-mining-area-in-chhattisgarh-india-using-lead-isotopic-ratios
#16
Avijit Das, Subhra Sarita Patel, Rajeev Kumar, K V S S Krishna, Saikat Dutta, Manik Chandra Saha, Siladitya Sengupta, Dipayan Guha
A geochemical study of the trace metals and lead isotopic ratios of soil and sediments in Korba, Chhattisgarh, India is presented here for the first time. Korba, the nation's 'power hub' is also the fifth among its eighty-eight most critically polluted industrial hotspots. A very high mean concentration (in mg kg-1) of V (308), Cr (567), Mn (3442), Co (92), Cu (218), Zn (426), Pb (311), Th (123) and U (32) characterized the sediments of the studied area with mean Igeo values of the trace metals ranging from -2...
January 8, 2018: Chemosphere
https://www.readbyqxmd.com/read/29336852/brazilian-species-of-calliandra-benth-tribe-ingeae-are-nodulated-by-diverse-strains-of-paraburkholderia
#17
Verônica Cordeiro Silva, Patricia Alves Casaes Alves, Mariana Ferreira Kruschewsky Rhem, José Miguel Ferreira Dos Santos, Euan K James, Eduardo Gross
The Chapada Diamantina in NE of Brazil is a biodiversity hotspot and a center of radiation for many Neotropical legume genera, such as Calliandra and Mimosa. The present study aimed to evaluate nodulation in Calliandra species endemic to various environments, and to characterize the diversity of their symbiotic rhizobia using housekeeping (16S rRNA, recA) and plasmid-borne, symbiosis-related (nifH and nodC) genes. The nodulation ability of selected isolates was assessed. All of the 126 bacterial isolates from 18 Calliandra species collected in six different vegetation types were identified as Paraburkholderia according to their housekeeping and symbiosis gene phylogenies...
January 5, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29335638/clearcutting-alters-decomposition-processes-and-initiates-complex-restructuring-of-fungal-communities-in-soil-and-tree-roots
#18
Petr Kohout, Markéta Charvátová, Martina Štursová, Tereza Mašínová, Michal Tomšovský, Petr Baldrian
Forest management practices often severely affect forest ecosystem functioning. Tree removal by clearcutting is one such practice, producing severe impacts due to the total reduction of primary productivity. Here, we assessed changes to fungal community structure and decomposition activity in the soil, roots and rhizosphere of a Picea abies stand for a 2-year period following clearcutting compared to data from before tree harvest. We found that the termination of photosynthate flow through tree roots into soil is associated with profound changes in soil, both in decomposition processes and fungal community composition...
January 15, 2018: ISME Journal
https://www.readbyqxmd.com/read/29335467/an-engineered-cars-substrate-with-giant-field-enhancement-in-crisscross-dimer-nanostructure
#19
Jia Zhang, Shu Chen, Junqiao Wang, Kaijun Mu, Chunzhen Fan, Erjun Liang, Pei Ding
We theoretically investigate the optical properties of a nanostructure consisting of the two identical and symmetrically arranged crisscrosses. A plasmonic Fano resonance is induced by a strong interplay between bright mode and dark modes, where the bright mode is due to electric dipole resonance while dark modes originate from the magnetic dipole induced by LC resonances. In this article, we find that the electric field "hotspots" corresponding to three different wavelengths can be positioned at the same spatial position, and its spectral tunability is achieved by changing geometric parameters...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29334956/identification-and-characterization-of-areas-of-high-and-low-risk-for-asymptomatic-malaria-infections-at-sub-village-level-in-ratanakiri-cambodia
#20
Lies Durnez, Myrthe Pareyn, Vanna Mean, Saorin Kim, Nimol Khim, Didier Menard, Marc Coosemans, Tho Sochantha, Vincent Sluydts
BACKGROUND: Malaria elimination needs a concentration of activities towards identification of residual transmission foci and intensification of efforts to eliminate the last few infections, located in so-called 'malaria hotspots'. Previous work on characterizing malaria transmission hotspots has mainly focused on falciparum malaria and especially on symptomatic cases, while the malaria reservoir is expected to be mainly concentrated in the asymptomatic human population when transmission is low...
January 15, 2018: Malaria Journal
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