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https://www.readbyqxmd.com/read/28449405/the-impact-of-lesion-location-on-dysphagia-incidence-pattern-and-complications-in-acute-stroke-part-2-oropharyngeal-residue-swallow-and-cough-response-and-pneumonia
#1
S Suntrup-Krueger, A Kemmling, T Warnecke, C Hamacher, S Oelenberg, T Niederstadt, W Heindel, H Wiendl, R Dziewas
BACKGROUND AND PURPOSE: Dysphagia is a well-known complication of acute stroke. Given the complexity of cerebral swallowing control it is still difficult to predict which patients are likely to develop swallowing dysfunction based on their neuroimaging. In Part 2 of a comprehensive voxel-based imaging study, whether the location of a stroke lesion can be correlated with further dysfunctional swallowing patterns, pulmonary protective reflexes and pneumonia was evaluated. METHODS: In all, 200 acute stroke cases were investigated applying flexible endoscopic evaluation of swallowing within 96 h from admission...
April 27, 2017: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/28449031/rnablueprint-flexible-multiple-target-nucleic-acid-sequence-design
#2
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L Hofacker, Sven Findeiß
Motivation: Realizing the value of synthetic biology in biotechnology and medicine requires the design of molecules with specialized functions. Due to its close structure to function relationship, and the availability of good structure prediction methods and energy models, RNA is perfectly suited to be synthetically engineered with predefined properties. However, currently available RNA design tools cannot be easily adapted to accommodate new design specifications. Furthermore, complicated sampling and optimization methods are often developed to suit a specific RNA design goal, adding to their inflexibility...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28448975/validation-of-a-case-finding-algorithm-for-hidradenitis-suppurativa-using-administrative-coding-from-a-clinical-database
#3
Andrew Strunk, Margaretta Midura, Vassiliki Papagermanos, Allireza Alloo, Amit Garg
BACKGROUND: Requisite to the application of clinical databases for observational research in hidradenitis suppurativa (HS) is the identification of an accurate case cohort. OBJECTIVE: To assess the validity of utilizing administrative codes to establish the HS cohort from a large clinical database. METHODS: In this retrospective study using chart review as the reference standard, we calculated several estimates of the diagnostic accuracy of at least 1 ICD-9 code for HS...
April 28, 2017: Dermatology: International Journal for Clinical and Investigative Dermatology
https://www.readbyqxmd.com/read/28448499/when-do-correlations-increase-with-firing-rates-in-recurrent-networks
#4
Andrea K Barreiro, Cheng Ly
A central question in neuroscience is to understand how noisy firing patterns are used to transmit information. Because neural spiking is noisy, spiking patterns are often quantified via pairwise correlations, or the probability that two cells will spike coincidentally, above and beyond their baseline firing rate. One observation frequently made in experiments, is that correlations can increase systematically with firing rate. Theoretical studies have determined that stimulus-dependent correlations that increase with firing rate can have beneficial effects on information coding; however, we still have an incomplete understanding of what circuit mechanisms do, or do not, produce this correlation-firing rate relationship...
April 27, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28448269/circulating-cell-free-micrornas-as-clinical-cancer-biomarkers
#5
REVIEW
Virginie Armand-Labit, Anne Pradines
MicroRNAs (miRNAs) are non-coding small RNAs that are master regulators of genic expression and consequently of many cellular processes. But their expression is often deregulated in human tumors leading to cancer development. Recently miRNAs were discovered in body fluids (serum, plasma and others) and their levels have often been reported to be altered in patients. Circulating miRNAs became one of the most promising biomarkers in oncology for early diagnosis, prognosis and therapeutic response prediction. Here we describe the origins and roles of miRNAs, and summarize the most recent studies focusing on their usefulness as cancer biomarkers in lung, breast, colon, prostate, ovary cancers and melanoma...
April 27, 2017: Biomolecular Concepts
https://www.readbyqxmd.com/read/28447708/protein-collapse-is-encoded-in-the-folded-state-architecture
#6
Himadri S Samanta, Pavel I Zhuravlev, Michael Hinczewski, Naoto Hori, Shaon Chakrabarti, D Thirumalai
Folded states of single domain globular proteins are compact with high packing density. The radius of gyration, Rg, of both the folded and unfolded states increase as N(ν) where N is the number of amino acids in the protein. The values of the Flory exponent ν are, respectively, ≈⅓ and ≈0.6 in the folded and unfolded states, coinciding with those for homopolymers. However, the extent of compaction of the unfolded state of a protein under low denaturant concentration (collapsibility), conditions favoring the formation of the folded state, is unknown...
April 27, 2017: Soft Matter
https://www.readbyqxmd.com/read/28447381/land-use-influences-phosphatase-gene-microdiversity-in-soils
#7
Andrew L Neal, Maike Rossmann, Charles Brearley, Elsy Akkari, Cervin Guyomar, Ian M Clark, Elisa Allen, Penny R Hirsch
Phosphorus cycling exerts significant influence upon soil fertility and productivity - processes largely controlled by microbial activity. We adopted phenotypic and metagenomic approaches to investigate phosphatase genes within soils. Microbial communities in bare fallowed soil showed a marked capacity to utilise phytate for growth compared to arable or grassland soil communities. Bare fallowed soil contained lowest concentrations of orthophosphate. Analysis of metagenomes indicated phoA, phoD and phoX, and histidine acid and cysteine phytase genes were most abundant in grassland soil which contained the greatest amount of NaOH-EDTA extractable orthophosphate...
April 26, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28446914/constructing-integrated-networks-for-identifying-new-secondary-metabolic-pathway-regulators-in-grapevine-recent-applications-and-future-opportunities
#8
Darren C J Wong, José Tomás Matus
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28446748/discovering-charge-density-functionals-and-structure-property-relationships-with-prophet-a-general-framework-for-coupling-machine-learning-and-first-principles-methods
#9
Brian Kolb, Levi C Lentz, Alexie M Kolpak
Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446723/up-regulation-of-long-non-coding-rna-spry4-it1-promotes-tumor-cell-migration-and-invasion-in-lung-adenocarcinoma
#10
Xia Zhang, Qingyan Chi, Zhenhua Zhao
Long non-coding RNAs (lncRNAs) play important role in a variety of biological processes, and are tightly associated with tumorigenesis and cancer prognosis. However, the potential power of lncRNA signatures in predicting survival of patients with lung adenocarcinoma (LUAD) has not been investigated. Here, we identified a four-lncRNA signature (SPRY4-IT1, LINC00941,GPR158-AS1 and KCNK15-AS1) displaying prognostic values for LUAD using The Cancer Genome Atlas (TCGA) dataset. Based on the four-lncRNA signature, the LUAD patients can be classified into high-risk and low-risk groups with significantly different survival...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445614/two-common-human-cldn5-alleles-encode-different-open-reading-frames-but-produce-one-protein-isoform
#11
Ronald M Cornely, Barbara Schlingmann, Whitney S Shepherd, Joshua D Chandler, David C Neujahr, Michael Koval
Claudins provide tight junction barrier selectivity. The human CLDN5 gene contains a high-frequency single-nucleotide polymorphism (rs885985), where the G allele codes for glutamine (Q) and the A allele codes for an amber stop codon. Thus, these different CLDN5 alleles define nested open reading frames (ORFs) encoding claudin-5 proteins that are 303 or 218 amino acids in length. Interestingly, human claudin-16 and claudin-23 also have long ORFs. The long form of claudin-5 contrasts with the majority of claudin-5 proteins in the National Center for Biotechnology Information protein database, which are less than 220 amino acids in length...
April 26, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28445578/utility-of-a-noninvasive-2-gene-molecular-assay-for-cutaneous-melanoma-and-effect-on-the-decision-to-biopsy
#12
Laura K Ferris, Burkhard Jansen, Jonhan Ho, Klaus J Busam, Kenneth Gross, Doyle D Hansen, John P Alsobrook, Zuxu Yao, Gary L Peck, Pedram Gerami
Importance: Expression of long intergenic non-protein coding RNA 518 (LINC00518) and preferentially expressed antigen in melanoma (PRAME) genes, obtained via noninvasive adhesive patch biopsy, is a sensitive and specific method for detection of cutaneous melanoma. However, the utility of this test in biopsy decisions made by dermatologists has not been evaluated. Objective: To determine the utility of the pigmented lesion assay (PLA) for LINC00518/PRAME expression in decisions to biopsy a series of pigmented skin lesions...
April 26, 2017: JAMA Dermatology
https://www.readbyqxmd.com/read/28445069/targeted-dereplication-of-microbial-natural-products-by-high-resolution-ms-and-predicted-lc-retention-time
#13
Justine Chervin, Marc Stierhof, Ming Him Tong, Doe Peace, Kine Østnes Hansen, Dagmar Solveig Urgast, Jeanette Hammer Andersen, Yi Yu, Rainer Ebel, Kwaku Kyeremeh, Veronica Paget, Gabriela Cimpan, Albert Van Wyk, Hai Deng, Marcel Jaspars, Jioji N Tabudravu
A new strategy for the identification of known compounds in Streptomyces extracts that can be applied in the discovery of natural products is presented. The strategy incorporates screening a database of 5555 natural products including 5098 structures from Streptomyces sp., using a high-throughput LCMS data processing algorithm that utilizes HRMS data and predicted LC retention times (tR) as filters for rapid identification of known compounds in the natural product extract. The database, named StrepDB, contains for each compound the structure, molecular formula, molecular mass, and predicted LC retention time...
April 26, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28444302/draft-genome-of-the-lined-seahorse-hippocampus-erectus
#14
Qiang Lin, Ying Qiu, Ruobo Gu, Meng Xu, Jia Li, Chao Bian, Huixian Zhang, Geng Qin, Yanhong Zhang, Wei Luo, Jieming Chen, Xinxin You, Mingjun Fan, Min Sun, Pao Xu, Byrappa Venkatesh, Junming Xu, Hongtuo Fu, Qiong Shi
Background: The lined seahorse, Hippocampus erectus , is an Atlantic species and mainly inhabits shallow sea-beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding...
April 22, 2017: GigaScience
https://www.readbyqxmd.com/read/28444139/multi-label-classifier-based-on-histogram-of-gradients-for-predicting-the-anatomical-therapeutic-chemical-class-classes-of-a-given-compound
#15
Loris Nanni, Sheryl Brahnam
Motivation: Given an unknown compound, is it possible to predict its ATC (Anatomical Therapeutic Chemical) class/classes? This is a challenging yet important problem since such a prediction could be used to deduce not only a compound's possible active ingredients but also its therapeutic, pharmacological, and chemical properties, thereby substantially expediting the pace of drug development. The problem is challenging because some drugs and compounds belong to two or more ATC classes, making machine learning extremely difficult...
April 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28444127/hla-class-i-binding-prediction-via-convolutional-neural-networks
#16
Yeeleng S Vang, Xiaohui Xie
Motivation: Many biological processes are governed by protein-ligand interactions. One such example is the recognition of self and nonself cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases...
April 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28443494/expression-profiling-of-long-non-coding-rna-identifies-linc-ror-as-a-prognostic-biomarker-in-oral-cancer
#17
Ganesan Arunkumar, Arunagiri Kuha Deva Magendhra Rao, Mayakannan Manikandan, Kanagaraj Arun, Vilvanathan Vinothkumar, Sundaramoorthy Revathidevi, Kottayasamy Seenivasagam Rajkumar, Ramamurthy Rajaraman, Arasambattu Kannan Munirajan
Oral squamous cell carcinoma is the most aggressive cancer that is associated with high recurrence, metastasis, and poor treatment outcome. Dysregulation of long non-coding RNAs has been shown to promote tumor growth and metastasis in several cancers. In this study, we investigated the expression of 11 selected long non-coding RNAs that are associated with cell proliferation, metastasis, and tumor suppression in oral squamous cell carcinomas and normal tissues by quantitative real-time polymerase chain reaction...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28443117/seed-biology-updates-highlights-and-new-discoveries-in-seed-dormancy-and-germination-research
#18
REVIEW
Hiroyuki Nonogaki
An understanding of the biology of seeds has been greatly advanced in recent years. The progresses, particularly in the field of seed dormancy and germination research, have been made at a remarkable speed. Some of the possible epigenetic mechanisms, including an involvement of non-coding RNA, which were predicted for DELAY OF GERMINATION1 just a few years ago, have now been demonstrated with strong molecular and genetic evidence. Imprinting, or parent-of-origin-specific gene silencing/expression, which was characterized particularly for developing seeds, was also found in imbibed seeds and suggested for dormancy mechanisms...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28442185/modified-frailty-index-is-an-effective-risk-assessment-tool-in-primary-total-knee-arthroplasty
#19
Robert P Runner, Jaime L Bellamy, CatPhuong Cathy L Vu, Greg A Erens, Mara L Schenker, George N Guild
BACKGROUND: "Frailty" is a marker of physiological decline of multiple organ systems, and the frailty index identifies patients who are more susceptible to postoperative complications. The purpose of this study is to validate the modified frailty index (MFI) as a predictor of postoperative complications, reoperations, and readmissions in patients who underwent primary total knee arthroplasty (TKA). METHODS: The American College of Surgeons National Surgical Quality Improvement Program database from 2005 to 2014 was queried by the Current Procedural Terminology code for primary TKA (27447)...
March 29, 2017: Journal of Arthroplasty
https://www.readbyqxmd.com/read/28441901/patient-emergency-assessment-following-deliberate-self-poisoning-with-benzodiazepines-can-cognitive-markers-predict-recall-of-the-psychiatric-interview-a-pilot-study
#20
J Salles, J Pariente, C Dimeglio, P Gandia, B Lemesle, A Giron, N Franchitto, L Schmitt, E Very
STUDY HYPOTHESIS: In cases of deliberate self-poisoning (DSP), patients often ingest benzodiazepines (BZDs), known to alter memory. Experts recommend recovery of the patient's cognitive capacity before psychiatric assessment. Unfortunately, there is no validated tool in common practice to assess whether sufficient cognitive recovery has occurred after DSP with BZDs to ensure patient memory of the assessment. OBJECTIVE: The aim of the study was to identify cognitive functions and markers which predict preserved memory of the mental health care plan proposed at the emergency department after DSP...
April 1, 2017: Journal of Psychopharmacology
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