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https://www.readbyqxmd.com/read/29576952/squeezing-water-from-a-stone-high-throughput-sequencing-from-a-145-year-old-holotype-resolves-barely-a-cryptic-species-problem-in-flying-lizards
#1
Jimmy A McGuire, Darko D Cotoras, Brendan O'Connell, Shobi Z S Lawalata, Cynthia Y Wang-Claypool, Alexander Stubbs, Xiaoting Huang, Guinevere O U Wogan, Sarah M Hykin, Sean B Reilly, Ke Bi, Awal Riyanto, Evy Arida, Lydia L Smith, Heather Milne, Jeffrey W Streicher, Djoko T Iskandar
We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus . Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing...
2018: PeerJ
https://www.readbyqxmd.com/read/29575349/rapid-divergence-of-mussel-populations-despite-incomplete-barriers-to-dispersal
#2
Diede L Maas, Stefan Prost, Ke Bi, Lydia Smith, Ellie E Armstrong, Ludi P Aji, Abdul H A Toha, Rosemary G Gillespie, Leontine E Becking
Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment, and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and test relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp...
March 25, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29566978/the-relationship-of-travel-distance-with-cystectomy-access-and-outcomes
#3
Angela B Smith, Anne-Marie Meyer, Ke Meng, Matthew E Nielsen, Raj Pruthi, Eric Wallen, Michael Woods, Hung-Jui Tan
PURPOSE: Regionalization of care and travel distance may result in unintended consequences for complex surgery such as cystectomy. Our objective was to evaluate effect of differential distance on cystectomy receipt among patients with muscle-invasive bladder cancer (MIBC) and investigate the association between travel distance and cystectomy outcomes such as readmission. METHODS: Using a linked data resource combining the NC Central Cancer Registry with claims data from Medicare, Medicaid, and private insurance plans, we included 736 patients with MIBC and 1,082 who underwent cystectomy...
March 19, 2018: Urologic Oncology
https://www.readbyqxmd.com/read/29449035/usage-of-density-analysis-based-on-micro-ct-for-studying-lung-injury-associated-with-burn-blast-combined-injury
#4
Yang Chang, Dong-Hai Zhang, Quan Hu, Ling-Ying Liu, Yong-Hui Yu, Jia-Ke Chai
BACKGROUND: Burn-blast combined injury is a kind of injury caused by heat and blast at the same time. The lung injury after burn-blast combined injuries is of primary importance, and investigation of lung injury is needed in the clinical care of patients. Computed tomography (CT) is one of the standard tools used to observe the anatomical basis and pathophysiology of acute lung injury. METHODS: We applied a method of fast 3D (three-dimensional) reconstruction to calculate the density value of the lung injury by CT analysis...
February 12, 2018: Burns: Journal of the International Society for Burn Injuries
https://www.readbyqxmd.com/read/29282500/metabolism-of-a-sea-lamprey-pesticide-by-fish-liver-enzymes-part-a-identification-and-synthesis-of-tfm-metabolites
#5
Ugo Bussy, Yu-Wen Chung-Davidson, Tyler Buchinger, Ke Li, Scott A Smith, A Daniel Jones, Weiming Li
The sea lamprey (Petromyzon marinus) is a destructive invasive species in the Great Lakes that contributed to the collapse of native fish populations in the mid-1900s. 3-Trifluoromethyl-4-nitrophenol (TFM) is a selective pesticide that has been applied to sea lamprey infested tributaries of the Great Lakes to kill larvae since the 1960s and has reduced the populations by as much as 90%. However, the metabolism of TFM by sea lamprey and non-target species is not fully illuminated. Elucidation of TFM metabolism is critical for understanding its mode of action and possible environmental impact...
February 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29279987/metabolism-of-a-sea-lamprey-pesticide-by-fish-liver-enzymes-part-b-method-development-and-application-in-quantification-of-tfm-metabolites-formed-in-vivo
#6
Ugo Bussy, Yu-Wen Chung-Davidson, Tyler Buchinger, Ke Li, Scott A Smith, A Daniel Jones, Weiming Li
The sea lamprey (Petromyzon marinus) is a destructive invasive species in the Great Lakes. Since the 1960s, tons of the lampricide 3-trifluoromethyl-4-nitrophenol (TFM) has been applied to selected tributaries each year to eliminate or reduce sea lamprey larval populations. Therefore, the environmental impact of TFM needs to be evaluated. However, the metabolism of TFM and its mechanism of selective toxicity in sea lamprey is not yet fully understood. Based upon our previous report on the identification, synthesis, and characterization of TFM metabolites observed in liver incubates from sea lamprey and non-target fishes, we now provide a robust assay for quantifying TFM and its metabolites in fish liver tissue...
February 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29250217/atrial-fibrillation-is-associated-with-increased-pacemaker-implantation-rates-in-the-placement-of-aortic-transcatheter-valve-partner-trial
#7
Angelo B Biviano, Tamim Nazif, Jose Dizon, Hasan Garan, Mark Abrams, Jessica Fleitman, Dua Hassan, Samir Kapadia, Vasilis Babaliaros, Ke Xu, Josep Rodes-Cabau, Wilson Y Szeto, William F Fearon, Danny Dvir, Todd Dewey, Mathew Williams, Steven Kindsvater, Michael J Mack, John G Webb, D Craig Miller, Craig R Smith, Martin B Leon, Susheel Kodali
Atrial fibrillation (AF) is associated with worse outcomes in many cardiovascular diseases. There are few data examining pacemaker implantation rates and indications in patients with AF who undergo transcatheter aortic valve replacement (TAVR). To examine the impact of AF on the incidence of and indications for pacemakers in patients undergoing TAVR, we evaluated data of 1723 patients without pre-existing pacemakers who underwent TAVR in the Placement of AoRTic TraNscathetER Valve (PARTNER) trial. Permanent pacemaker implantation rates and indications were compared in groups based on baseline and discharge heart rhythm: sinus rhythm (SR) vs...
June 2017: Journal of Atrial Fibrillation
https://www.readbyqxmd.com/read/29083151/a-red-algal-bourbonane-sesquiterpene-synthase-defined-by-microgram-scale-nmr-coupled-crystalline-sponge-x-ray-diffraction-analysis
#8
Roland D Kersten, Shoukou Lee, Daishi Fujita, Tomáš Pluskal, Susan Kram, Jennifer E Smith, Takahiro Iwai, Joseph P Noel, Makoto Fujita, Jing-Ke Weng
Sesquiterpene scaffolds are the core backbones of many medicinally and industrially important natural products. A plethora of sesquiterpene synthases, widely present in bacteria, fungi, and plants, catalyze the formation of these intricate structures often with multiple stereocenters starting from linear farnesyl diphosphate substrates. Recent advances in next-generation sequencing and metabolomics technologies have greatly facilitated gene discovery for sesquiterpene synthases. However, a major bottleneck limits biochemical characterization of recombinant sesquiterpene synthases: the absolute structural elucidation of the derived sesquiterpene products...
November 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28985687/evaluating-the-swelling-erosion-and-compaction-properties-of-cellulose-ethers
#9
Muhammad U Ghori, Liam M Grover, Kofi Asare-Addo, Alan M Smith, Barbara R Conway
Swelling, erosion, deformation, and consolidation properties can affect the performance of cellulose ethers, the most commonly used matrix former in hydrophilic sustained tablet formulations. The present study was designed to comparatively evaluate the swelling, erosion, compression, compaction, and relaxation properties of the cellulose ethers in a comprehensive study using standardised conditions. The interrelationship between various compressional models and the inherent deformation and consolidation properties of the polymers on the derived swelling and erosion parameters are consolidated...
February 2018: Pharmaceutical Development and Technology
https://www.readbyqxmd.com/read/28677678/srsf1-dependent-nuclear-export-inhibition-of-c9orf72-repeat-transcripts-prevents-neurodegeneration-and-associated-motor-deficits
#10
Guillaume M Hautbergue, Lydia M Castelli, Laura Ferraiuolo, Alvaro Sanchez-Martinez, Johnathan Cooper-Knock, Adrian Higginbottom, Ya-Hui Lin, Claudia S Bauer, Jennifer E Dodd, Monika A Myszczynska, Sarah M Alam, Pierre Garneret, Jayanth S Chandran, Evangelia Karyka, Matthew J Stopford, Emma F Smith, Janine Kirby, Kathrin Meyer, Brian K Kaspar, Adrian M Isaacs, Sherif F El-Khamisy, Kurt J De Vos, Ke Ning, Mimoun Azzouz, Alexander J Whitworth, Pamela J Shaw
Hexanucleotide repeat expansions in the C9ORF72 gene are the commonest known genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. Expression of repeat transcripts and dipeptide repeat proteins trigger multiple mechanisms of neurotoxicity. How repeat transcripts get exported from the nucleus is unknown. Here, we show that depletion of the nuclear export adaptor SRSF1 prevents neurodegeneration and locomotor deficits in a Drosophila model of C9ORF72-related disease. This intervention suppresses cell death of patient-derived motor neuron and astrocytic-mediated neurotoxicity in co-culture assays...
July 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28628103/a-common-haplotype-lowers-pu-1-expression-in-myeloid-cells-and-delays-onset-of-alzheimer-s-disease
#11
Kuan-Lin Huang, Edoardo Marcora, Anna A Pimenova, Antonio F Di Narzo, Manav Kapoor, Sheng Chih Jin, Oscar Harari, Sarah Bertelsen, Benjamin P Fairfax, Jake Czajkowski, Vincent Chouraki, Benjamin Grenier-Boley, Céline Bellenguez, Yuetiva Deming, Andrew McKenzie, Towfique Raj, Alan E Renton, John Budde, Albert Smith, Annette Fitzpatrick, Joshua C Bis, Anita DeStefano, Hieab H H Adams, M Arfan Ikram, Sven van der Lee, Jorge L Del-Aguila, Maria Victoria Fernandez, Laura Ibañez, Rebecca Sims, Valentina Escott-Price, Richard Mayeux, Jonathan L Haines, Lindsay A Farrer, Margaret A Pericak-Vance, Jean Charles Lambert, Cornelia van Duijn, Lenore Launer, Sudha Seshadri, Julie Williams, Philippe Amouyel, Gerard D Schellenberg, Bin Zhang, Ingrid Borecki, John S K Kauwe, Carlos Cruchaga, Ke Hao, Alison M Goate
A genome-wide survival analysis of 14,406 Alzheimer's disease (AD) cases and 25,849 controls identified eight previously reported AD risk loci and 14 novel loci associated with age at onset. Linkage disequilibrium score regression of 220 cell types implicated the regulation of myeloid gene expression in AD risk. The minor allele of rs1057233 (G), within the previously reported CELF1 AD risk locus, showed association with delayed AD onset and lower expression of SPI1 in monocytes and macrophages. SPI1 encodes PU...
August 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28212664/the-impact-of-high-total-cholesterol-and-high-low-density-lipoprotein-on-avascular-necrosis-of-the-femoral-head-in-low-energy-femoral-neck-fractures
#12
Xianshang Zeng, Ke Zhan, Lili Zhang, Dan Zeng, Weiguang Yu, Xinchao Zhang, Mingdong Zhao, Zhicheng Lai, Runzhen Chen
BACKGROUND: Avascular necrosis of the femoral head (AVNFH) typically constitutes 5 to 15% of all complications of low-energy femoral neck fractures, and due to an increasingly ageing population and a rising prevalence of femoral neck fractures, the number of patients who develop AVNFH is increasing. However, there is no consensus regarding the relationship between blood lipid abnormalities and postoperative AVNFH. The purpose of this retrospective study was to investigate the relationship between blood lipid abnormalities and AVNFH following the femoral neck fracture operation among an elderly population...
February 17, 2017: Journal of Orthopaedic Surgery and Research
https://www.readbyqxmd.com/read/28186784/uniform-additivity-in-classical-and-quantum-information
#13
Andrew Cross, Ke Li, Graeme Smith
Information theory quantifies the optimal rates of resource interconversions, usually in terms of entropies. However, nonadditivity often makes evaluating entropic formulas intractable. In a few auspicious cases, additivity allows a full characterization of optimal rates. We study uniform additivity of formulas, which is easily evaluated and captures all known additive quantum formulas. Our complete characterization of uniform additivity exposes an intriguing new additive quantity and identifies a remarkable coincidence-the classical and quantum uniformly additive functions with one auxiliary variable are identical...
January 27, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28150499/synthesis-and-spectroscopic-investigation-of-a-series-of-push-pull-boron-dipyrromethenes-bodipys
#14
Sunting Xuan, Ning Zhao, Xiangyi Ke, Zehua Zhou, Frank R Fronczek, Karl M Kadish, Kevin M Smith, M Graça H Vicente
A series of push-pull BODIPYs bearing multiple electron-donating and electron-acceptor groups were synthesized regioselectively from 2,3,5,6,8-pentachloro-BODIPY, and characterized by NMR spectroscopy, HRMS, and X-ray crystallography. The influence of the push-pull substituents on the spectroscopic and electrochemical properties of BODIPYs was investigated. Bathochromic shifts were observed for both absorbance (up to 37 nm) and emission (up to 60 nm) in different solvents upon introduction of the push-pull moieties...
March 3, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28032251/long-term-t-dna-insert-stability-and-transgene-expression-consistency-in-field-propagated-sugarcane
#15
Kerry Hosmer Caffall, Chengkun He, Michele Smith-Jones, Kristin Mayo, Pearl Mai, Shujie Dong, John Ke, Erik Dunder, Michele Yarnall, Rachel Whinna, Joe DeMaio, Weining Gu, Judith Sheldon, Martin Allen, Tricia Costello, Kristin Setliff, Rakesh Jain, Ada Snyder, Clark Lovelady, Eric Rawls, Eric Palmer, Yan Zhang, Nicholas Bate, Liang Shi, Ian Jepson
This study addresses T-DNA insert stability and transgene expression consistency in multiple cycles of field propagated sugarcane. T-DNA inserts are stable; no transgene rearrangements were observed. AmCYAN1 and PMI protein accumulation levels were maintained. There was no evidence that production of either protein declined across generations and no transgene silencing was observed in three commercial sugarcane varieties through commercially relevant ratooning, propagation-by-setts, and micro-propagation generation processes over 4 years of field testing...
March 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/27919785/a-comparative-assessment-of-preclinical-chemotherapeutic-response-of-tumors-using-quantitative-non-gaussian-diffusion-mri
#16
COMPARATIVE STUDY
Junzhong Xu, Ke Li, R Adam Smith, John C Waterton, Ping Zhao, Zhaohua Ding, Mark D Does, H Charles Manning, John C Gore
BACKGROUND: Diffusion-weighted MRI (DWI) signal attenuation is often not mono-exponential (i.e. non-Gaussian diffusion) with stronger diffusion weighting. Several non-Gaussian diffusion models have been developed and may provide new information or higher sensitivity compared with the conventional apparent diffusion coefficient (ADC) method. However the relative merits of these models to detect tumor therapeutic response is not fully clear. METHODS: Conventional ADC, and three widely-used non-Gaussian models, (bi-exponential, stretched exponential, and statistical model), were implemented and compared for assessing SW620 human colon cancer xenografts responding to barasertib, an agent known to induce apoptosis via polyploidy...
April 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/27241806/an-evaluation-of-transcriptome-based-exon-capture-for-frog-phylogenomics-across-multiple-scales-of-divergence-class-amphibia-order-anura
#17
Daniel M Portik, Lydia L Smith, Ke Bi
Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers in nonmodel organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, typically using a reference genome to identify intron-exon boundaries to exclude shorter exons (<200 bp). Here, we test directly using transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Using 1260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic scales for frogs, including outgroups ~100 Myr divergent from the ingroup...
September 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27194729/increased-gvhd-related-mortality-with-broad-spectrum-antibiotic-use-after-allogeneic-hematopoietic-stem-cell-transplantation-in-human-patients-and-mice
#18
Yusuke Shono, Melissa D Docampo, Jonathan U Peled, Suelen M Perobelli, Enrico Velardi, Jennifer J Tsai, Ann E Slingerland, Odette M Smith, Lauren F Young, Jyotsna Gupta, Sophia R Lieberman, Hillary V Jay, Katya F Ahr, Kori A Porosnicu Rodriguez, Ke Xu, Marco Calarfiore, Hendrik Poeck, Silvia Caballero, Sean M Devlin, Franck Rapaport, Jarrod A Dudakov, Alan M Hanash, Boglarka Gyurkocza, George F Murphy, Camilla Gomes, Chen Liu, Eli L Moss, Shannon B Falconer, Ami S Bhatt, Ying Taur, Eric G Pamer, Marcel R M van den Brink, Robert R Jenq
Intestinal bacteria may modulate the risk of infection and graft-versus-host disease (GVHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients often develop neutropenic fever, which is treated with antibiotics that may target anaerobic bacteria in the gut. We retrospectively examined 857 allo-HSCT recipients and found that treatment of neutropenic fever with imipenem-cilastatin and piperacillin-tazobactam antibiotics was associated with increased GVHD-related mortality at 5 years (21...
May 18, 2016: Science Translational Medicine
https://www.readbyqxmd.com/read/27096412/omnidirectionally-stretchable-high-performance-supercapacitor-based-on-isotropic-buckled-carbon-nanotube-films
#19
Jiali Yu, Weibang Lu, Shaopeng Pei, Ke Gong, Liyun Wang, Linghui Meng, Yudong Huang, Joseph P Smith, Karl S Booksh, Qingwen Li, Joon-Hyung Byun, Youngseok Oh, Yushan Yan, Tsu-Wei Chou
The emergence of stretchable electronic devices has attracted intensive attention. However, most of the existing stretchable electronic devices can generally be stretched only in one specific direction and show limited specific capacitance and energy density. Here, we report a stretchable isotropic buckled carbon nanotube (CNT) film, which is used as electrodes for supercapacitors with low sheet resistance, high omnidirectional stretchability, and electro-mechanical stability under repeated stretching. After acid treatment of the CNT film followed by electrochemical deposition of polyaniline (PANI), the resulting isotropic buckled acid treated CNT@PANI electrode exhibits high specific capacitance of 1147...
May 24, 2016: ACS Nano
https://www.readbyqxmd.com/read/27074457/performance-variations-among-clinically-available-deformable-image-registration-tools-in-adaptive-radiotherapy-how-should-we-evaluate-and-interpret-the-result
#20
Ke Nie, Jean Pouliot, Eric Smith, Cynthia Chuang
The purpose of this study is to evaluate the performance variations in commercial deformable image registration (DIR) tools for adaptive radiation therapy and further to interpret the differences using clinically available terms. Three clinical examples (prostate, head and neck (HN), and cranial spinal irradiation (CSI) with L-spine boost) were evaluated in this study. Firstly, computerized deformed CT images were generated using simulation QA software with virtual deformations of bladder filling (prostate), neck flexion/bite-block repositioning/tumor shrinkage (HN), and vertebral body rotation (CSI)...
March 8, 2016: Journal of Applied Clinical Medical Physics
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