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https://www.readbyqxmd.com/read/27926995/frozen-but-no-accident-why-the-20-standard-amino-acids-were-selected
#1
REVIEW
Andrew J Doig
The 20 standard amino acids encoded by the Genetic Code were adopted during the RNA World, around 4 billion years ago. This amino acid set could be regarded as a frozen accident, implying that other possible structures could equally well have been chosen to use in proteins. Amino acids were not primarily selected for their ability to support catalysis, since the RNA World already had highly effective cofactors to perform reactions, such as oxidation, reduction and transfer of small molecules. Rather, they were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets...
December 7, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27926991/human-mitochondrial-nucleases
#2
REVIEW
Francesco Bruni, Robert N Lightowlers, Zofia M Chrzanowska-Lightowlers
Mitochondria are cytosolic organelles that have many essential roles including ATP production via oxidative phosphorylation, apoptosis, iron-sulphur cluster biogenesis, heme and steroid synthesis, calcium homeostasis and regulation of cellular redox state. One of the unique features of these organelles is the presence of an extra-chromosomal mitochondrial genome (mtDNA), together with all the machinery required to replicate and transcribe mtDNA. The accurate maintenance of mitochondrial gene expression is essential for correct organellar metabolism, and is in part dependent on the levels of mtDNA and mt-RNA, which are regulated by balancing synthesis against degradation...
December 7, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27926819/a-plea-for-linguistic-accuracy-also-for-candidatus-taxa
#3
Aharon Oren
While all names of new taxa submitted to the International Journal of Systematic and Evolutionary Microbiology), either in direct submissions or in validation requests for names effectively published elsewhere, are subject to nomenclatural review to ensure that they are acceptable based on the rules of the International Code of Nomenclature of Prokaryotes, the names of Candidatus taxa have not been subjected to such a review. Formally, this was not necessary because the rank of Candidatus is not covered by the Code, and the names lack the priority afforded validly published names...
December 7, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926678/cost-minimization-analysis-of-open-and-endoscopic-carpal-tunnel-release
#4
Steven Zhang, Molly Vora, Alex H S Harris, Laurence Baker, Catherine Curtin, Robin N Kamal
BACKGROUND: Carpal tunnel release is the most common upper-limb surgical procedure performed annually in the U.S. There are 2 surgical methods of carpal tunnel release: open or endoscopic. Currently, there is no clear clinical or economic evidence supporting the use of one procedure over the other. We completed a cost-minimization analysis of open and endoscopic carpal tunnel release, testing the null hypothesis that there is no difference between the procedures in terms of cost. METHODS: We conducted a retrospective review using a private-payer and Medicare Advantage database composed of 16 million patient records from 2007 to 2014...
December 7, 2016: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/27926651/factors-underlying-the-temporal-increase-in-maternal-mortality-in-the-united-states
#5
K S Joseph, Sarka Lisonkova, Giulia M Muraca, Neda Razaz, Yasser Sabr, Azar Mehrabadi, Enrique F Schisterman
OBJECTIVE: To identify the factors underlying the recent increase in maternal mortality ratios (maternal deaths per 100,000 live births) in the United States. METHODS: We carried out a retrospective study with data on maternal deaths and live births in the United States from 1993 to 2014 obtained from the birth and death files of the Centers for Disease Control and Prevention. Underlying causes of death were examined between 1999 and 2014 using International Classification of Diseases, 10th Revision (ICD-10) codes...
December 2, 2016: Obstetrics and Gynecology
https://www.readbyqxmd.com/read/27926523/long-non-coding-rna-neat1-overexpression-is-associated-with-poor-prognosis-in-cancer-patients-a-systematic-review-and-meta-analysis
#6
Chao Yang, Zhuo Li, Yajun Li, Rui Xu, Yongfeng Wang, Yu Tian, Wei Chen
OBJECTIVES: Long non-coding RNAs (lncRNAs) are playing important roles in cancer progression and metastasis. Recent studies have demonstrated that the lncRNA, nuclear paraspeckle assembly transcript 1 (NEAT1), was aberrantly up-regulated in various types of cancers and was reported to be associated with unfavorable prognosis in cancer patients. This study examined the relationship between NEAT1 and relevant clinical outcomes. RESULTS: A total of 1354 patients from 11 eligible studies were included in the meta-analysis...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27926382/prediction-of-anti-cancer-drug-response-by-kernelized-multi-task-learning
#7
Mehmet Tan
MOTIVATION: Chemotherapy or targeted therapy are two of the main treatment options for many types of cancer. Due to the heterogeneous nature of cancer, the success of the therapeutic agents differs among patients. In this sense, determination of chemotherapeutic response of the malign cells is essential for establishing a personalized treatment protocol and designing new drugs. With the recent technological advances in producing large amounts of pharmacogenomic data, in silico methods have become important tools to achieve this aim...
October 2016: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/27926356/inhibitory-control-of-correlated-intrinsic-variability-in-cortical-networks
#8
Carsen Stringer, Marius Pachitariu, Nicholas A Steinmetz, Michael Okun, Peter Bartho, Kenneth D Harris, Maneesh Sahani, Nicholas A Lesica
Cortical networks exhibit intrinsic dynamics that drive coordinated, large-scale fluctuations across neuronal populations and create noise correlations that impact sensory coding. To investigate the network-level mechanisms that underlie these dynamics, we developed novel computational techniques to fit a deterministic spiking network model directly to multi-neuron recordings from different rodent species, sensory modalities, and behavioral states. The model generated correlated variability without external noise and accurately reproduced the diverse activity patterns in our recordings...
December 7, 2016: ELife
https://www.readbyqxmd.com/read/27925839/validation-of-the-v66-7-code-for-palliative-care-consultation-in-a-single-academic-medical-center
#9
May Hua, Guohua Li, Caitlin Clancy, R Sean Morrison, Hannah Wunsch
BACKGROUND: Use of administrative data to study the effectiveness of specialized palliative care is limited by the lack of a reliable method to identify patients receiving palliative care consultation. The International Classification of Diseases, Ninth Revision (ICD-9) code V66.7 has been used, but its validity for this purpose is unknown. OBJECTIVE: To examine the validity of the ICD-9 code V66.7 for identifying whether hospitalized patients received palliative care consultation...
December 7, 2016: Journal of Palliative Medicine
https://www.readbyqxmd.com/read/27925581/on-cross-frequency-phase-phase-coupling-between-theta-and-gamma-oscillations-in-the-hippocampus
#10
Robson Scheffer-Teixeira, Adriano Bl Tort
Phase-amplitude coupling between theta and multiple gamma sub-bands is a hallmark of hippocampal activity and believed to take part in information routing. More recently, theta and gamma oscillations were also reported to exhibit phase-phase coupling, or n:m phase-locking, suggesting an important mechanism of neuronal coding that has long received theoretical support. However, by analyzing simulated and actual LFPs, here we question the existence of theta-gamma phase-phase coupling in the rat hippocampus. We show that the quasi-linear phase shifts introduced by filtering lead to spurious coupling levels in both white noise and hippocampal LFPs, which highly depend on epoch length, and that significant coupling may be falsely detected when employing improper surrogate methods...
December 7, 2016: ELife
https://www.readbyqxmd.com/read/27925421/reducing-the-incidence-of-hospital-associated-venous-thromboembolism-within-a-network-of-academic-hospitals-findings-from-five-university-of-california-medical-centers
#11
REVIEW
Ian H Jenkins, Richard H White, Alpesh N Amin, Nasim Afsarmanesh, Andrew D Auerbach, Raman Khanna, Gregory A Maynard
BACKGROUND: Almost 700 patients suffered from hospital-associated venous thromboembolism (HA-VTE) across 5 University of California hospitals in calendar year 2011. OBJECTIVE: Optimize venous thromboembolism (VTE) prophylaxis (VTEP) in adult medical/surgical inpatients and reduce HA-VTE by at least 20% within 3 years. DESIGN: Prospective, unblinded, open-intervention study with historical controls. SETTING: Five independent but cooperating academic hospitals...
December 2016: Journal of Hospital Medicine: An Official Publication of the Society of Hospital Medicine
https://www.readbyqxmd.com/read/27925368/reflections-on-the-encouragement-of-altruism-in-dental-education
#12
A C L Holden
Dental ethics and professionalism are often relegated to being taught on the coat-tails of other disciplines, if they are taught at all. The assumption that students develop professionalism as a by-product of other learned competencies in dentistry is well documented to be false, and yet, little has been done in many institutions to deal with this. This article seeks to propose that altruism should be championed in dental education and that traditional learning through the preaching of professional codes is not the appropriate way to achieve this...
December 7, 2016: European Journal of Dental Education: Official Journal of the Association for Dental Education in Europe
https://www.readbyqxmd.com/read/27925252/the-gpu-enabled-divide-expand-consolidate-ri-mp2-method-dec-ri-mp2
#13
Dmytro Bykov, Thomas Kjaergaard
We report porting of the Divide-Expand-Consolidate Resolution of the Identity second-order Møller-Plesset perturbation (DEC-RI-MP2) method to the graphic processing units (GPUs) using OpenACC compiler directives. It is shown that the OpenACC compiler directives implementation efficiently accelerates the rate-determining step of the DEC-RI-MP2 method with minor implementation effort. Moreover, the GPU acceleration results in a better load balance and thus in an overall scaling improvement of the DEC algorithm...
December 7, 2016: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/27925173/potential-of-long-non-coding-rnas-in-cancer-patients-from-bio-markers-to-therapeutic-targets
#14
REVIEW
Subash Chandra Gupta, Yashoda Nandan Tripathi
Because of high specificity and easy detection in the tissues, serum, plasma, urine and saliva, interest in exploring the potential of long non-coding RNAs (lncRNAs) in cancer patients continues to increase. LncRNAs have shown potential as a bio-marker in the diagnosis and prognosis of bladder cancer, prostate cancer, gastric cancer, pancreatic cancer, breast cancer, and many other cancer types. Some lncRNAs have also been used as adjunct to improve the specificity and sensitivity of existing biomarkers. The molecular tools such as RNA-seq, RNA-FISH, ic-SHAPE and quantitative real-time PCR have been used for examining the lncRNAs' potential...
December 7, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27925121/review-of-deaths-correction-methods-and-quality-dimensions-of-the-underlying-cause-for-accidents-and-violence-in-brazil
#15
Adauto Martins Soares, Juan José Cortez-Escalante, Elisabeth França
This review article aims to perform analysis and critical discussion about the literature on methods correcting mortality from accidents and violence reported to the Brazilian Mortality Information System. We consulted Medline and SciELO databases, as well as the Global Burden of Disease site, using time filter for the 1996-2015 interval. Of the 77 studies identified, we selected 29, and 14 met the corrections production criteria for cases of underreporting: underreporting of deaths in the Mortality Information System, deaths declared as ill-defined causes or deaths from external causes declared with nonspecific codes...
December 2016: Ciência & Saúde Coletiva
https://www.readbyqxmd.com/read/27924936/genomic-duplication-and-translocation-of-reactivation-transactivator-and-bzip-homolog-genes-is-a-conserved-event-in-alcelaphine-herpesvirus-1
#16
Françoise Myster, Steven J van Beurden, Océane Sorel, Nicolás M Suárez, Alain Vanderplasschen, Andrew J Davison, Benjamin G Dewals
Alcelaphine herpesvirus 1 (AlHV-1) is a gammaherpesvirus carried asymptomatically by wildebeest. Upon cross-species transmission, AlHV-1 induces malignant catarrhal fever (MCF), a fatal lymphoproliferative disease of ruminants, including cattle. The strain C500 has been cloned as an infectious, pathogenic bacterial artificial chromosome (BAC) that is used to study MCF. Although AlHV-1 infection can be established in cell culture, multiple passages in vitro cause a loss of virulence associated with rearrangements of the viral genome...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924865/quantum-error-correction-protects-quantum-search-algorithms-against-decoherence
#17
Panagiotis Botsinis, Zunaira Babar, Dimitrios Alanis, Daryus Chandra, Hung Nguyen, Soon Xin Ng, Lajos Hanzo
When quantum computing becomes a wide-spread commercial reality, Quantum Search Algorithms (QSA) and especially Grover's QSA will inevitably be one of their main applications, constituting their cornerstone. Most of the literature assumes that the quantum circuits are free from decoherence. Practically, decoherence will remain unavoidable as is the Gaussian noise of classic circuits imposed by the Brownian motion of electrons, hence it may have to be mitigated. In this contribution, we investigate the effect of quantum noise on the performance of QSAs, in terms of their success probability as a function of the database size to be searched, when decoherence is modelled by depolarizing channels' deleterious effects imposed on the quantum gates...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924849/transcriptional-regulation-of-notch1-expression-by-nkx6-1-in-neural-stem-progenitor-cells-during-ventral-spinal-cord-development
#18
Ying Li, Evangeline Tzatzalos, Kelvin Y Kwan, Martin Grumet, Li Cai
Notch1 signaling plays a critical role in maintaining and determining neural stem/progenitor cell (NSPC) fate, yet the transcriptional mechanism controlling Notch1 specific expression in NSPCs remains incomplete. Here, we show transcription factor Nkx6.1 interacts with a cis-element (CR2, an evolutionarily conserved non-coding fragment in the second intron of Notch1 locus) and regulates the expression of Notch1 in ventral NSPCs of the developing spinal cord. We show that the Notch1 expression is modulated by the interaction of Nkx6...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924668/parenting-of-children-with-down-syndrome-compared-to-fragile-x-syndrome
#19
Audra Sterling, Steven F Warren
Children with Down syndrome (DS) and fragile X syndrome (FXS) struggle with language development. Parenting variables, such as responsiveness to children's communication attempts (Maternal Responsivity), and techniques used to support and teach appropriate behavior (Behavior Management) are known to have a significant impact on early child development. We examined these two aspects of parenting style via coded, videotaped parent-child interactions in two groups of participants matched on child age (2-5 years) and child expressive language level: mothers of children with DS and mothers of children with FXS...
December 7, 2016: Developmental Neurorehabilitation
https://www.readbyqxmd.com/read/27924586/rna-sequencing-analysis-of-salivary-extracellular-rna
#20
Blanca Majem, Feng Li, Jie Sun, David T W Wong
Salivary biomarkers for disease detection, diagnostic and prognostic assessments have become increasingly well established in recent years. In this chapter we explain the current leading technology that has been used to characterize salivary non-coding RNAs (ncRNAs) from the extracellular RNA (exRNA) fraction: HiSeq from Illumina® platform for RNA sequencing. Therefore, the chapter is divided into two main sections regarding the type of the library constructed (small and long ncRNA libraries), from saliva collection, RNA extraction and quantification to cDNA library generation and corresponding QCs...
2017: Methods in Molecular Biology
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