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https://www.readbyqxmd.com/read/28728152/use-of-the-putamen-as-a-surrogate-anatomical-marker-for-the-internal-segment-of-the-globus-pallidus-in-deep-brain-stimulation-surgery
#1
John A Thompson, Dali Yin, Steven G Ojemann, Aviva Abosch
OBJECTIVE: The success of deep brain stimulation (DBS) of the internal segment of the globus pallidus (GPi) depends on accurately placing the electrode into the GPi motor territory. Direct targeting can be difficult as GPi laminar borders are not always clearly identifiable on MRI. Here, we report a method for using the putamen (PUT) as a surrogate anatomical marker to target the GPi. METHODS: We developed a PUT-based GPi targeting using the FGATIR (fast gray matter acquisition T1-weighted inversion recovery) MRI sequence and compared it with consensus coordinate-based indirect targeting...
July 21, 2017: Stereotactic and Functional Neurosurgery
https://www.readbyqxmd.com/read/28727769/small-subunit-ribosomal-metabarcoding-reveals-extraordinary-trypanosomatid-diversity-in-brazilian-bats
#2
Maria Augusta Dario, Ricardo Moratelli Mendonça da Rocha, Philipp Schwabl, Ana Maria Jansen, Martin S Llewellyn
BACKGROUND: Bats are a highly successful, globally dispersed order of mammals that occupy a wide array of ecological niches. They are also intensely parasitized and implicated in multiple viral, bacterial and parasitic zoonosis. Trypanosomes are thought to be especially abundant and diverse in bats. In this study, we used 18S ribosomal RNA metabarcoding to probe bat trypanosome diversity in unprecedented detail. METHODOLOGY/PRINCIPAL FINDINGS: Total DNA was extracted from the blood of 90 bat individuals (17 species) captured along Atlantic Forest fragments of Espírito Santo state, southeast Brazil...
July 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28725923/assessing-3d-t2-fse-sequence-for-identification-of-the-normal-appendix-working-toward-a-single-sequence-mr-appendicitis-protocol
#3
Nattinee Leelakanok, Andrew S Phelps, Matthew A Zapala, Kambrie Kato, Michael Ohliger, Yi Li, Jesse Courtier
PURPOSES: To assess the ability of a single isotropic 3D T2 FSE sequence to identify the normal appendix in children with potential implication as alternative second-line modality in pediatric appendicitis. MATERIALS AND METHODS: Retrospective review of MR abdomino-pelvis or pelvis in children from Oct 2014-Dec 2016 was done. Only exams with 3D T2 FSE sequence performed on a single scanner type were selected. Patients with history of post appendectomy, studies in which field of view did not include ileocecal valve, with technical and protocol errors, or with fat-saturated acquisition were excluded...
July 19, 2017: Emergency Radiology
https://www.readbyqxmd.com/read/28724921/saliva-and-tooth-biofilm-bacterial-microbiota-in-adolescents-in-a-low-caries-community
#4
Linda Eriksson, Pernilla Lif Holgerson, Ingegerd Johansson
The oral cavity harbours a complex microbiome that is linked to dental diseases and serves as a route to other parts of the body. Here, the aims were to characterize the oral microbiota by deep sequencing in a low-caries population with regular dental care since childhood and search for association with caries prevalence and incidence. Saliva and tooth biofilm from 17-year-olds and mock bacteria communities were analysed using 16S rDNA Illumina MiSeq (v3-v4) and PacBio SMRT (v1-v8) sequencing including validity and reliability estimates...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724410/identification-and-characterization-of-long-non-coding-rnas-in-subcutaneous-adipose-tissue-from-castrated-and-intact-full-sib-pair-huainan-male-pigs
#5
Jing Wang, Liushuai Hua, Junfeng Chen, Jiaqing Zhang, Xianxiao Bai, Binwen Gao, Congjun Li, Zhihai Shi, Weidong Sheng, Yuan Gao, Baosong Xing
BACKGROUND: Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular systems and metabolic features. RESULTS: We identified lncRNAs in subcutaneous adipose tissue by deep RNA-sequencing using the intact and castrated Huainan male pigs...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28722703/deep-intronic-hotspot-variant-unraveling-rhabdoid-tumor-predisposition-syndrome-in-two-patients-with-atypical-teratoid-and-rhabdoid-tumor
#6
Arnault Tauziède-Espariat, Julien Masliah-Planchon, Laurence Brugières, Stéphanie Puget, Christelle Dufour, Pascale Schneider, Annie Laquerrière, Thierry Frebourg, Damien Bodet, Emmanuèle Lechapt-Zalcman, Gaëlle Pierron, Olivier Delattre, Pascale Varlet, Franck Bourdeaut
About one third of patients with rhabdoid tumors (RT) harbor a heterozygous germline variant in SMARCB1. Molecular diagnosis therefore keeps a crucial place in the diagnosis of RT, and genetic counseling should be systematically recommended. However, immunohistochemistry has progressively replaced molecular tools to assess the status of SMARCB1 in tumors; the necessity of analyzing SMARCB1 status in the tumor may thus be less considered by neuropathologists and pediatric neuro-oncologists. In the present manuscript as aforementioned, we report on two patients with bifocal RT in the first month of life and in whom no germline variant was initially found in the SMARCB1 coding sequence...
July 19, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28720895/rapid-response-of-eastern-mediterranean-deep-sea-microbial-communities-to-oil
#7
Jiang Liu, Stephen M Techtmann, Hannah L Woo, Daliang Ning, Julian L Fortney, Terry C Hazen
Deep marine oil spills like the Deepwater Horizon (DWH) in the Gulf of Mexico have the potential to drastically impact marine systems. Crude oil contamination in marine systems remains a concern, especially for countries around the Mediterranean Sea with off shore oil production. The goal of this study was to investigate the response of indigenous microbial communities to crude oil in the deep Eastern Mediterranean Sea (E. Med.) water column and to minimize potential bias associated with storage and shifts in microbial community structure from sample storage...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720701/de-novo-peptide-sequencing-by-deep-learning
#8
Ngoc Hieu Tran, Xianglilan Zhang, Lei Xin, Baozhen Shan, Ming Li
De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720072/tissue-and-cell-specific-transcriptomes-in-cotton-reveal-the-subtleties-of-gene-regulation-underlying-the-diversity-of-plant-secondary-cell-walls
#9
Colleen P MacMillan, Hannah Birke, Aaron Chuah, Elizabeth Brill, Yukiko Tsuji, John Ralph, Elizabeth S Dennis, Danny Llewellyn, Filomena A Pettolino
BACKGROUND: Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a 'typical' lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre...
July 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28719667/assessing-intragenomic-variation-of-the-internal-transcribed-spacer-two-adapting-the-illumina-metagenomics-protocol
#10
Lo'ai Alanagreh, Caitlin Pegg, Amritha Harikumar, Mark Buchheim
Primary and secondary structural data from the internal transcribed spacer two (ITS2) have been used extensively for diversity studies of many different eukaryotic organisms, including the green algae. Ease of amplification is due, at least in part, to the fact that ITS2 is part of the tandemly-repeated rRNA array. The potential confounding influence of intragenomic variability has yet to be addressed except in a few organisms. Moreover, few of the assessments of intragenomic variation have taken advantage of the deep sequencing capacity of sequence-by-synthesis protocols...
2017: PloS One
https://www.readbyqxmd.com/read/28719561/arterial-topographic-anatomy-near-the-femoral-head-neck-perforation-with-surgical-relevance
#11
Paulo Rego, Vasco Mascarenhas, Diego Collado, Ana Coelho, Luis Barbosa, Reinhold Ganz
BACKGROUND: Knowledge of the vascular supply of the femoral head is crucial for hip-preserving surgical procedures. The critical area for reshaping cam deformity is at the retinacular vessel penetration, an area with ill-defined topographic anatomy. We performed a cadaver study of the extension of the lateral retinaculum near the head-neck junction, distribution of the arterial vascular foramina, and initial intracapital course of these vessels. METHODS: In 16 fresh proximal parts of the femur without head-neck deformities, the deep branch of the medial femoral circumflex artery was injected with gadolinium for magnetic resonance imaging (MRI) sequences to identify arterial structures...
July 19, 2017: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/28718617/initial-reduction-of-co2-on-pd-ru-and-cu-doped-ceo2-111-surfaces-effects-of-surface-modification-on-catalytic-activity-and-selectivity
#12
Chen Guo, Shuxian Wei, Sainan Zhou, Tian Zhang, Zhaojie Wang, Siu Pang Ng, Xiaoqing Lu, Chi-Man Lawrence Wu, Wenyue Guo
Surface modification by metal doping is an effective treatment technique for improving surface properties for CO2 reduction. Herein, the effects of doped Pd, Ru, and Cu on the adsorption, activation, and reduction selectivity of CO2 on CeO2(111) were investigated by periodic density functional theory. The doped metals distorted the configuration of a perfect CeO2(111) by weakening the adjacent Ce-O bond strength, and Pd doping was beneficial for generating a highly active O vacancy. The analyses of adsorption energy, charge density difference, and density of states confirmed that the doped metals were conducive for enhancing CO2 adsorption, especially for Cu/CeO2(111)...
July 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28717665/identification-of-an-alu-element-mediated-deletion-in-the-promoter-region-of-gne-in-siblings-with-gne-myopathy
#13
Jennifer Garland, Joshi Stephen, Bradley Class, Angela Gruber, Carla Ciccone, Aaron Poliak, Christina P Hayes, Vandana Singhal, Christina Slota, John Perreault, Ralitza Gavrilova, Joseph A Shrader, Prashant Chittiboina, Galen Joe, John Heiss, William A Gahl, Marjan Huizing, Nuria Carrillo, May Christine V Malicdan
BACKGROUND: GNE myopathy is a rare genetic disease characterized by progressive muscle atrophy and weakness. It is caused by biallelic mutations in the GNE gene that encodes for the bifunctional enzyme, uridine diphosphate (UDP)-N-acetylglucosamine (GlcNAc) 2-epimerase/N-acetylmannosamine (ManNAc) kinase. Typical characteristics of GNE myopathy include progressive myopathy, first involving anterior tibialis muscle and sparing the quadriceps, and rimmed vacuoles on muscle biopsy. Identifying biallelic mutations by sequencing of the GNE gene confirms the diagnosis of GNE myopathy...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28717203/genome-wide-identification-and-characterization-of-circular-rnas-by-high-throughput-sequencing-in-soybean
#14
Wei Zhao, Yihui Cheng, Chi Zhang, Qingbo You, Xinjie Shen, Wei Guo, Yongqing Jiao
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716668/incomplete-penetrance-in-mitochondrial-optic-neuropathies
#15
Leonardo Caporali, Alessandra Maresca, Mariantonietta Capristo, Valentina Del Dotto, Francesca Tagliavini, Maria Lucia Valentino, Chiara La Morgia, Valerio Carelli
Incomplete penetrance characterizes the two most frequent inherited optic neuropathies, Leber's Hereditary Optic Neuropathy (LHON) and dominant optic atrophy (DOA), due to genetic errors in the mitochondrial DNA (mtDNA) and the nuclear DNA (nDNA), respectively. For LHON, compelling evidence has accumulated on the complex interplay of mtDNA haplogroups and environmental interacting factors, whereas the nDNA remains essentially non informative. However, a compensatory mechanism of activated mitochondrial biogenesis and increased mtDNA copy number, possibly driven by a permissive nDNA background, is documented in LHON; when successful it maintains unaffected the mutation carriers, but in some individuals it might be hampered by tobacco smoking or other environmental factors, resulting in disease onset...
July 14, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28715249/durable-molecular-remissions-in-chronic-lymphocytic-leukemia-treated-with-cd19-specific-chimeric-antigen-receptor-modified-t-cells-after-failure-of-ibrutinib
#16
Cameron J Turtle, Kevin A Hay, Laïla-Aïcha Hanafi, Daniel Li, Sindhu Cherian, Xueyan Chen, Brent Wood, Arletta Lozanski, John C Byrd, Shelly Heimfeld, Stanley R Riddell, David G Maloney
Purpose We evaluated the safety and feasibility of anti-CD19 chimeric antigen receptor-modified T (CAR-T) cell therapy in patients with chronic lymphocytic leukemia (CLL) who had previously received ibrutinib. Methods Twenty-four patients with CLL received lymphodepleting chemotherapy and anti-CD19 CAR-T cells at one of three dose levels (2 × 10(5), 2 × 10(6), or 2 × 10(7) CAR-T cells/kg). Nineteen patients experienced disease progression while receiving ibrutinib, three were ibrutinib intolerant, and two did not experience progression while receiving ibrutinib...
July 17, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28713353/functional-characterization-of-novel-faecalibacterium-prausnitzii-strains-isolated-from-healthy-volunteers-a-step-forward-in-the-use-of-f-prausnitzii-as-a-next-generation-probiotic
#17
Rebeca Martín, Sylvie Miquel, Leandro Benevides, Chantal Bridonneau, Véronique Robert, Sylvie Hudault, Florian Chain, Olivier Berteau, Vasco Azevedo, Jean M Chatel, Harry Sokol, Luis G Bermúdez-Humarán, Muriel Thomas, Philippe Langella
Faecalibacterium prausnitzii is a major member of the Firmicutes phylum and one of the most abundant bacteria in the healthy human microbiota. F. prausnitzii depletion has been reported in several intestinal disorders, and more consistently in Crohn's disease (CD) patients. Despite its importance in human health, only few microbiological studies have been performed to isolate novel F. prausnitzii strains in order to better understand the biodiversity and physiological diversity of this beneficial commensal species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28713347/generic-amplicon-deep-sequencing-to-determine-ilarvirus-species-diversity-in-australian-prunus
#18
Wycliff M Kinoti, Fiona E Constable, Narelle Nancarrow, Kim M Plummer, Brendan Rodoni
The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS) of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp) gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28712841/long-term-impact-of-subthalamic-stimulation-on-cognitive-function-in-patients-with-advanced-parkinson-s-disease
#19
M Acera, A Molano, B Tijero, G Bilbao, I Lambarri, R Villoria, J Somme, E Ruiz de Gopegui, I Gabilondo, J C Gomez-Esteban
OBJECTIVE: The aim of this study was to evaluate the effects of deep brain stimulation of the subthalamic nucleus (DBS-SN) on cognitive function in patients with Parkinson's disease (PD) 5 years after surgery. MATERIAL AND METHODS: We conducted a prospective study including 50 patients with PD who underwent DBS-SN (62.5% were men; mean age of 62.2±8.2 years; mean progression time of 14.1±6.3 years). All patients were assessed before the procedure and at one year after surgery; 40 patients were further followed up until the 5-year mark...
July 13, 2017: Neurología: Publicación Oficial de la Sociedad Española de Neurología
https://www.readbyqxmd.com/read/28712340/deep-sequencing-reveals-the-mitochondrial-dna-variation-landscapes-of-breast-to-brain-metastasis-blood-samples
#20
Rhiannon E McGeehan, Lewis A Cockram, D Timothy J Littlewood, Kathleen Keatley, Diana M Eccles, Qian An
Breast-to-brain metastasis (BBM) often represents a terminal event, due to the inability of many systemic treatments to cross the blood-brain barrier (BBB), rendering the brain a sanctuary site for tumour cells. Identifying genetic variations that can predict the patients who will develop BBM would allow targeting of adjuvant treatments to reduce risk while disease bulk is minimal. Germ-line genetic variations may contribute to whether a BBM forms by influencing the primary tumour subtype that presents, or by influencing the host response to the tumour or treatment regimen, or by facilitating transition of tumour cells across the BBB and establish a viable brain metastasis...
July 15, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
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