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De Novo

Marta Sobas, Pau Montesinos, Blanca Boluda, Teresa Bernal, Edo Vellenga, Josep Nomdedeu, Jose González-Campos, Maria Chillón, Aleksandra Holowiecka, Jordi Esteve, Juan Bergua, José David González-Sanmiguel, Cristina Gil-Cortes, Mar Tormo, Olga Salamero, Felix Manso, Isolda Fernández, Javier de la Serna, María-José Moreno, Manuel Pérez-Encinas, Isabel Krsnik, Josep-Maria Ribera, Lourdes Escoda, Bob Lowenberg, Miguel Angel Sanz
Out of 956, there were 95 (10%) CD56+ APL patients treated with PETHEMA ATRA and chemotherapy. CD56+ expression was associated with high WBC, BCR3 isoform, and co-expression of CD2, CD34, CD7, HLA-DR, CD15, and CD117 antigens. CD56+ vs CD56- APL presented higher induction death rate (16% vs 8%, p = .02) and 5-years cumulative incidence of relapse (33% versus 10%, p = .006), irrespectively of the Sanz score (low-risk 47% versus 5%, p < .001; intermediate 23% versus 7%, p < .001; and high-risk 42% versus 21%, p = ...
October 15, 2018: Leukemia & Lymphoma
Alina I Esterhuizen, Heather C Mefford, Rajkumar S Ramesar, Shuyu Wang, Gemma L Carvill, Jo M Wilmshurst
PURPOSE: Dravet syndrome (DS) is a well-described, severe genetic epileptic encephalopathy with an increased risk of SUDEP. The incidence and genetic architecture of DS in African patients is virtually unknown, largely due to lack of awareness and unavailability of genetic testing. The clinical benefits of the available precision medicine approaches to treatment emphasise the importance of an early, correct diagnosis. We investigated the genetic causes and clinical features of DS in South African children to develop protocols for early, cost-effective diagnosis in the local setting...
September 14, 2018: Seizure: the Journal of the British Epilepsy Association
Eleni Vourla, Andreas Filis, Jan F Cornelius, Richard Bostelmann, Bernd Turowski, Piyush Kalakoti, Christian Rubbert, Marian Preetham Suresh, Angelo Tortora, Hans Jakob Steiger, Athanasios K Petridis
INTRODUCTION: De novo aneurysm formation after completely occluded aneurysms via clipping or coiling is generally not well studied. Although known to occur several years following initial aneurysm management, the natural history of de novo aneurysms is obscure. The current study investigated the formation of new aneurysms in patients who were previously treated for intracranial aneurysms. METHODS: In a retrospective, single-institutional series, eligible patients that underwent management for ruptured cerebral aneurysms between 2000-2011 were included...
October 12, 2018: World Neurosurgery
Duncan C Walton, Linda Cantwell, Steven Hiho, Joseph Ta, Stephen Wright, Lucy C Sullivan, Greg I Snell, Glen P Westall
The use of algorithms such as HLAMatchmaker to redefine donor-recipient HLA matching is gaining increasing attention. Our research has previously demonstrated that higher HLA class II eplet mismatches correlated with the development of chronic lung allograft dysfunction (CLAD). In this study of lung transplant recipients we prospectively examined the association between donor-recipient HLA eplet mismatches as defined by HLAMatchmaker (version 2.1) and de-novo anti-HLA donor-specific antibody (DSA) formation, as assessed by single antigen-bead solid phase assay...
October 12, 2018: Transplant Immunology
Xue-Ying He, Carl Dobkin, Song-Yu Yang
17β-Hydroxysteroid dehydrogenases are indispensable for downstream enzyme steps of the neurosteroidogenesis. Neurosteroids are synthesized de novo in neurons and glia from cholesterol transported into mitochondria, or by conversion from proneurosteroids, e. g. dehydroepiandrosterone (DHEA) and pregnenolone, through the same metabolic pathway as revealed in the de novo neurosteroidogenesis. Hormonal steroids generated from endocrine glands are transported into brain from the circulation to exert neuronal activity via genomic pathway, whereas neurosteroids produced in brain cells without genomic targets identified could bind to cell surface targets, e...
October 12, 2018: Molecular and Cellular Endocrinology
Thomas Duigou, Melchior du Lac, Pablo Carbonell, Jean-Loup Faulon
RetroRules is a database of reaction rules for metabolic engineering ( Reaction rules are generic descriptions of chemical reactions that can be used in retrosynthesis workflows in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors. The use of such rules is becoming increasingly important in the context of synthetic biology applied to de novo pathway discovery and in systems biology to discover underground metabolism due to enzyme promiscuity...
October 13, 2018: Nucleic Acids Research
Nicolas Veland, Yue Lu, Swanand Hardikar, Sally Gaddis, Yang Zeng, Bigang Liu, Marcos R Estecio, Yoko Takata, Kevin Lin, Mary W Tomida, Jianjun Shen, Debapriya Saha, Humaira Gowher, Hongbo Zhao, Taiping Chen
DNMT3L (DNMT3-like), a member of the DNMT3 family, has no DNA methyltransferase activity but regulates de novo DNA methylation. While biochemical studies show that DNMT3L is capable of interacting with both DNMT3A and DNMT3B and stimulating their enzymatic activities, genetic evidence suggests that DNMT3L is essential for DNMT3A-mediated de novo methylation in germ cells but is dispensable for de novo methylation during embryogenesis, which is mainly mediated by DNMT3B. How DNMT3L regulates DNA methylation and what determines its functional specificity are not well understood...
October 13, 2018: Nucleic Acids Research
M Rouard, G Droc, G Martin, J Sardos, Y Hueber, V Guignon, A Cenci, B Geigle, M S Hibbins, N Yahiaoui, F-C Baurens, V Berry, M W Hahn, A D'Hont, N Roux
Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M...
October 13, 2018: Genome Biology and Evolution
Saisai Sun, Qi Wu, Zhenling Peng, Jianyi Yang
Motivation: The de novo prediction of RNA tertiary structure remains a grand challenge. Predicted RNA solvent accessibility provides an opportunity to address this challenge. To the best of our knowledge, there is only one method (RNAsnap) available for RNA solvent accessibility prediction. However, its performance is unsatisfactory for protein-free RNAs. Results: We developed RNAsol, a new algorithm to predict RNA solvent accessibility. RNAsol was built based on improved sequence profiles from the covariance models and trained with the long short-term memory (LSTM) neural networks...
October 15, 2018: Bioinformatics
Arthur T O Melo, Iago Hale
Summary: GBS-SNP-CROP is a bioinformatics pipeline originally developed to support the cost-effective genome-wide characterization of plant genetic resources through paired-end genotyping-by-sequencing (GBS), particularly in the absence of a reference genome. Since its 2016 release, the pipeline's functionality has greatly expanded, its computational efficiency has improved, and its applicability to a broad set of genomic studies for both plants and animals has been demonstrated. This note details the suite of improvements to date, as realized in GBS-SNP-CROP v...
October 15, 2018: Bioinformatics
Ting-Yun Lin, Jia-Sin Liu, Szu-Chun Hung
Background: Obesity is a risk factor for de novo chronic kidney disease (CKD) in the general population. Obesity has been increasingly prevalent in patients with CKD and may lead to further progression of pre-existing CKD. However, whether obesity is associated with the development of end-stage renal disease (ESRD) in patients with CKD is not well understood. Objective: We investigated the impact of obesity on ESRD (needing chronic dialysis treatment or pre-emptive renal transplantation) or all-cause mortality in patients with moderate to advanced CKD...
October 13, 2018: American Journal of Clinical Nutrition
A Heald, M Lunt, M K Rutter, S G Anderson, G Cortes, M Edmonds, E Jude, A Boulton, G Dunn
AIM: To determine how routinely collected data can inform a risk model to predict de novo foot ulcer presentation in the primary care setting. METHODS: Data were available on 15 727 individuals without foot ulcers and 1125 individuals with new foot ulcers over a 12-year follow-up in UK primary care. We examined known risk factors and added putative risk factors in our logistic model. RESULTS: People with foot ulcers were 4.2 years older (95% CI 3...
October 15, 2018: Diabetic Medicine: a Journal of the British Diabetic Association
Song-Bai Liu, Qiao-Cheng Qiu, Xie-Bing Bao, Xiao Ma, Hong-Zhi Li, Yue-Jun Liu, Su-Ning Chen, Yao-Hua Song, De-Pei Wu, Sheng-Li Xue
FMS like tyrosine kinase 3 (FLT3) is one of the most frequently mutated genes in hematological malignancies. FLT3 internal tandem duplications (FLT3-ITDs) mutations located in juxtamembrane domain (JMD) and tyrosine kinase domain 1 (TKD1) regions account for two thirds of all FLT3 mutations, and the outcome of patients is still unsatisfactory with low survival rates. It is not yet known whether the different mutations within the FLT3 gene are all associated with outcome. Also, the cause of FLT3-ITD inframe duplication events remains unknown...
October 15, 2018: Cancer Science
Alex Bishara, Eli L Moss, Mikhail Kolmogorov, Alma E Parada, Ziming Weng, Arend Sidow, Anne E Dekas, Serafim Batzoglou, Ami S Bhatt
Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques...
October 15, 2018: Nature Biotechnology
Muzammil Kuddushi, Nehal K Patel, Sargam Rajput, Ankit Shah, Omar A El Seoud, Naved I Malek
An ionic liquid-based surfactant with ester functionality self-aggregates in an aqueous medium and forms ionogels at 8.80% (w/v) concentration at physiological pH. The ionogel exhibited a remarkable change in its appearance with temperature from fibrillar opaque to transparent because of the dynamic changes within its supramolecular structure. This gel-to-gel phase transition occurs below the melting point of the solid ionic liquid. The ionogels were investigated using turbidity, differential scanning calorimetry, scanning electron microscopy (SEM), field emission SEM (FE-SEM), inverted microscopy, transmission electron microscopy imaging, Fourier transform infrared spectroscopy, and rheological measurements...
September 30, 2018: ACS Omega
Stefan Reuscher, Tomoyuki Furuta, Kanako Bessho-Uehara, Michele Cosi, Kshirod K Jena, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Motoyuki Ashikari
The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content...
2018: Communications biology
Plácido L Vidal, Joaquim de Moura, Jorge Novo, Manuel G Penedo, Marcos Ortega
Nowadays, among the main causes of blindness in developed countries are age-related macular degeneration (AMD) and the diabetic macular edema (DME). Both diseases present, as a common symptom, the appearance of cystoid fluid regions inside the retinal layers. Optical coherence tomography (OCT) image modality was one of the main medical imaging techniques for the early diagnosis and monitoring of AMD and DME via this intraretinal fluid detection and characterization. We present a novel methodology to identify these fluid accumulations by means of generating binary maps (offering a direct representation of these areas) and heat maps (containing the region confidence)...
October 1, 2018: Biomedical Optics Express
Zsófia Lengyel, Caroline M Rufo, Yurii S Moroz, Olga V Makhlynets, Ivan V Korendovych
Self-assembly of short de novo designed peptides gives rise to catalytic amyloids capable of facilitating multiple chemical transformations. We show that catalytic amyloids can efficiently hydrolyze paraoxon, a widely used, highly toxic organophosphate pesticide. Moreover, these robust and inexpensive metal-containing materials can be easily deposited on various surfaces producing catalytic flow devices. Finally, functional promiscuity of catalytic amyloids promotes tandem hydrolysis/oxidation reactions. High efficiency discovered in a very small library of peptides suggests an enormous potential for further improvement of catalytic properties both in terms of catalytic efficiency and substrate scope...
January 5, 2018: ACS Catalysis
Kristoffer Krogerus, Richard Preiss, Brian Gibson
An unknown interspecies Saccharomyces hybrid, "Muri," was recently isolated from a "kveik" culture, a traditional Norwegian farmhouse brewing yeast culture (Preiss et al., 2018). Here we used whole genome sequencing to reveal the strain as an allodiploid Saccharomyces cerevisiae × Saccharomyces uvarum hybrid. Phylogenetic analysis of its sub-genomes revealed that the S. cerevisiae and S. uvarum parent strains of Muri appear to be most closely related to English ale and Central European cider and wine strains, respectively...
2018: Frontiers in Microbiology
Hanna Wimberg, Dorit Lev, Keren Yosovich, Prasanthi Namburi, Eyal Banin, Dror Sharon, Karl-Wilhelm Koch
Over 100 mutations in GUCY2D that encodes the photoreceptor guanylate cyclase GC-E are known to cause two major diseases: autosomal recessive Leber congenital amaurosis (arLCA) or autosomal dominant cone-rod dystrophy (adCRD) with a poorly understood mechanism at the molecular level in most cases. Only few mutations were further characterized for their enzymatic and molecular properties. GC-E activity is under control of neuronal Ca2+ -sensor proteins, which is often a possible route to dysfunction. We investigated five recently-identified GC-E mutants that have been reported in patients suffering from arLCA (one large family) and adCRD/maculopathy (four families)...
2018: Frontiers in Molecular Neuroscience
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