keyword
MENU ▼
Read by QxMD icon Read
search

functional prediction

keyword
https://www.readbyqxmd.com/read/28438015/genome-characteristics-of-lactobacillus-fermentum-strain-jdfm216-for-application-as-probiotic-bacteria
#1
Sung Yong Jang, Jaeyoung Heo, Mi Ri Park, Min-Ho Song, Jong Nam Kim, Sung Ho Jo, Do-Youn Jeong, Hak Kyo Lee, Younghoon Kim, Sangnam Oh
Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces, possesses an enhancement of longevity and immune response on Caenorhabditis elegans host. To explore the molecular characteristics of strain JDFM216, we performed a whole-genome sequencing using PacBio system. The single circular DNA chromosome of 2,076,427 bp was completely assembled and 2,623 encoding sequences were predicted. Phylogenetically featured five genes possibly related to longevity and immune response of host were identified in L...
April 25, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28437757/abnormal-loading-and-functional-deficits-are-present-in-both-limbs-before-and-after-unilateral-knee-arthroplasty
#2
A J Metcalfe, C J Stewart, N J Postans, P R Biggs, G M Whatling, C A Holt, A P Roberts
Unilateral knee replacement is often followed by a contralateral replacement in time and the biomechanics of the other knee before and after knee replacement remains poorly understood. The aim of this paper is to distinguish the features of arthritic gait in the affected and unaffected legs relative to a normal population and to assess the objective recovery of gait function post-operatively, with the aim of defining patients at risk of poor post-operative function. Twenty patients with severe knee OA but no pain or deformity in any other lower limb joint were compared to twenty healthy subjects of the same age...
April 4, 2017: Gait & Posture
https://www.readbyqxmd.com/read/28437677/localization-of-enhancer-of-try-and-cpc1-protein-in-arabidopsis-root-epidermis
#3
Rumi Tominaga-Wada, Tetsuya Kurata, Takuji Wada
CAPRICE (CPC) is a R3-type MYB transcription factor, which induces root-hair cell differentiation in Arabidopsis thaliana. The CPC homologous gene ENHANCER TRY AND CPC1 (ETC1) has a similar function to CPC, and acts in concert with CPC. The CPC protein moves between root epidermal cells, from hairless cells to the neighboring cells, and promotes root-hair differentiation. Therefore, ETC1 is predicted to have movement ability similar to that of CPC. In this study, we generated ETC1:ETC1:GFP and CPC:ETC1:GFP transgenic plants to clarify whether ETC1 exhibits cell-to-cell movement...
April 4, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28437675/whole-blood-sequencing-reveals-circulating-microrna-associations-with-high-risk-traits-in-non-st-segment-elevation-acute-coronary-syndrome
#4
Alice Wang, Lydia Coulter Kwee, Elizabeth Grass, Megan L Neely, Simon G Gregory, Keith A A Fox, Paul W Armstrong, Harvey D White, E Magnus Ohman, Matthew T Roe, Svati H Shah, Mark Y Chan
BACKGROUND AND AIMS: Although circulating microRNA (miRNAs) have emerged as biomarkers predicting mortality in acute coronary syndrome (ACS), more data are needed to understand these mechanisms. Mapping miRNAs to high-risk traits may identify miRNAs involved in pathways conferring risk for poor outcome in ACS. We aim to investigate the relationship between circulating miRNAs and high-risk traits in non-ST-segment elevation acute coronary syndrome (NSTE-ACS). METHODS: Whole-genome miRNA sequencing was performed on RNA extracted from whole blood of 199 patients with NSTE-ACS...
March 30, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28437613/evaluating-the-role-of-multidrug-resistance-protein-3-mdr3-inhibition-in-predicting-drug-induced-liver-injury-using-125-pharmaceuticals
#5
Michael D Aleo, Falgun Shah, Kan He, Paul D Bonin, A David Rodrigues
The role of bile salt export protein (BSEP) inhibition in drug-induced liver injury (DILI) has been investigated widely, while inhibition of the canalicular multidrug resistant protein 3 (MDR3) has received less attention. This transporter plays a pivotal role in secretion of phospholipids into bile and functions coordinately with BSEP to mediate the formation of bile acid-containing biliary micelles. Therefore, inhibition of MDR3 in human hepatocytes was examined across 125 drugs (70 of Most- and 55 of No-DILI-concern)...
April 24, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28437362/sonotubometric-assessment-for-severity-of-patulous-eustachian-tube
#6
Iori Takata, Ryoukichi Ikeda, Tetsuaki Kawase, Yoko Suzuki, Takeshi Sato, Yukio Katori, Toshimitsu Kobayashi
OBJECTIVE: To investigate the relationship between the morphological patency of the eustachian tube (ET) and sound transmission via the ET. STUDY DESIGN: Retrospective chart review and model experiment. SETTING: Tertiary referral center. SUBJECTS: A total of 56 ears of 28 patients (9 men and 19 women, aged from 12 to 82 yr, mean 40.4 ± 21.5 yr) who underwent sonotubometric measurement using postural change as well as computed tomography (CT) of the ET in the sitting position, including 26 ears with definite patulous ET, 9 ears with possible patulous ET, and 21 ears without patulous ET...
April 21, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28437094/rational-design-of-an-ultrasensitive-quorum-sensing-switch
#7
Weiqian Zeng, Pei Du, Qiuli Lou, Lili Wu, Haoqian M Zhang, Chunbo Lou, Hongli Wang, Qi Ouyang
One of the purposes of synthetic biology is to develop rational methods that accelerate the design of genetic circuits, saving time and effort spent on experiments and providing reliably predictable circuit performance. We applied a reverse engineering approach to design an ultrasensitive transcriptional quorum-sensing switch. We want to explore how systems biology can guide synthetic biology in the choice of specific DNA sequences and their regulatory relations to achieve a targeted function. The workflow comprises network enumeration that achieves the target function robustly, experimental restriction of the obtained candidate networks, global parameter optimization via mathematical analysis, selection and engineering of parts based on these calculations, and finally, circuit construction based on the principles of standardization and modularization...
April 24, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28436948/mitochondrial-elongation-mediated-glucose-metabolism-reprogramming-is-essential-for-tumour-cell-survival-during-energy-stress
#8
J Li, Q Huang, X Long, X Guo, X Sun, X Jin, Z Li, T Ren, P Yuan, X Huang, H Zhang, J Xing
To date, mechanisms of tumour cell survival under energy stress are not well understood. Cumulative evidence is beginning to reveal that specific mitochondrial morphologies are often associated with energetic states and survival of cells. However, the functional roles of mitochondria in the metabolic adaptation of tumour cells to energy stress remain to be elucidated. In this study, we first investigated the changes in mitochondrial morphology induced by nutrition deprivation in tumour cells, and the underlying molecular mechanism...
April 24, 2017: Oncogene
https://www.readbyqxmd.com/read/28436895/online-learning-algorithm-based-on-adaptive-control-theory
#9
Jian-Wei Liu, Jia-Jia Zhou, Mohamed S Kamel, Xiong-Lin Luo
This paper proposes a new online learning algorithm which is based on adaptive control (AC) theory, thus, we call this proposed algorithm as AC algorithm. Comparing to the gradient descent (GD) and exponential gradient (EG) algorithm which have been applied to online prediction problems, we find a new form of AC theory for online prediction problems and investigate two key questions: how to get a new update law which has a tighter upper bound on the error than the square loss? How to compare the upper bound for accumulated losses for the three algorithms? We obtain a new update law which fully utilizes model reference AC theory...
April 18, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28436885/investigating-correlation-between-protein-sequence-similarity-and-semantic-similarity-using-gene-ontology-annotations
#10
Najmul Ikram, Muhammad Qadir, Muhammad Afzal
Sequence similarity is a commonly used measure to compare proteins. With the increasing use of ontologies, semantic (function) similarity is getting importance. The correlation between these measures has been applied in the evaluation of new semantic similarity methods, and in protein function prediction. In this research, we investigate the relationship between the two similarity methods. The results suggest absence of a strong correlation between sequence and semantic similarities. There is a large number of proteins with low sequence similarity and high semantic similarity...
April 18, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28436884/novelty-indicator-for-enhanced-prioritization-of-predicted-gene-ontology-annotations
#11
Davide Chicco, Fernando Palluzzi, Marco Masseroli
Biomolecular controlled annotations have become pivotal in computational biology, because they allow scientists to analyze large amounts of biological data to better understand test results, and to infer new knowledge. Yet, biomolecular annotation databases are incomplete by definition, like our knowledge of biology, and might contain errors and inconsistent information. In this context, machine-learning algorithms able to predict and prioritize new annotations are both effective and efficient, especially if compared with time-consuming trials of biological validation...
April 18, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28436723/asymptomatic-peripheral-artery-disease-can-limit-maximal-exercise-capacity-in-chronic-obstructive-pulmonary-disease-patients-regardless-of-airflow-obstruction-and-lung-hyperinflation
#12
Ernesto Crisafulli, Chiara Scelfo, Panagiota Tzani, Marina Aiello, Giuseppina Bertorelli, Alfredo Chetta
Background Silent/asymptomatic peripheral artery disease may occur in patients with chronic obstructive pulmonary disease, but it is poorly investigated. The primary aim of this study was to evaluate in chronic obstructive pulmonary disease patients the impact of asymptomatic/silent peripheral artery disease on maximal exercise capacity; the secondary aim was to search for predictors of peripheral artery disease. Methods We prospectively enrolled chronic obstructive pulmonary disease outpatients. Data on anthropometric characteristics, lung function, cardiopulmonary exercise test and ankle-brachial index were recorded...
January 1, 2017: European Journal of Preventive Cardiology
https://www.readbyqxmd.com/read/28436673/unique-rhizosphere-micro-characteristics-facilitate-phytoextraction-of-multiple-metals-in-soil-by-the-hyperaccumulating-plant-sedum-alfredii
#13
Dandi Hou, Kai Wang, Ting Liu, Haixin Wang, Zhi Lin, Jie Qian, Lingli Lu, Shengke Tian
Understanding the strategies that the roots of hyperaccumulating plants use to extract heavy metals from soils is important for optimizing phytoremediation. The rhizosphere characteristics of Sedum alfredii, a hyperaccumulator, were investigated 6 months after planting in weathered field soils contaminated with 5.8 μg·g-1 Cd, 1985.1 μg·g-1 Zn, 667.5 μg·g-1 Pb, and 698.8 μg·g-1 Cu. In contrast with the non-hyperaccumulating ecotype (NHE), the hyperaccumulating ecotype (HE) of S. alfredii was more tolerant to the metals and accumulated higher levels of Cd and Zn...
April 24, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28436662/multiconfiguration-pair-density-functional-theory-predicts-spin-state-ordering-in-iron-complexes-with-the-same-accuracy-as-complete-active-space-second-order-perturbation-theory-at-a-significantly-reduced-computational-cost
#14
Liam Wilbraham, Pragya Verma, Donald G Truhlar, Laura Gagliardi, Ilaria Ciofini
The spin-state orderings in nine Fe(II) and Fe(III) complexes with ligands of diverse ligand-field strength were investigated with multiconfiguration pair-density functional theory (MC-PDFT). The performance of this method was compared to that of complete active space second-order perturbation theory (CASPT2) and Kohn-Sham density functional theory. We also investigated the dependence of CASPT2 and MC-PDFT results on the size of the active-space. MC-PDFT reproduces the CASPT2 spin-state ordering, the dependence on the ligand field strength, and the dependence on active space at a computational cost that is significantly reduced as compared to CASPT2...
April 24, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28436661/performance-of-van-der-waals-corrected-functionals-for-guest-adsorption-in-the-m2-dobdc-metal-organic-frameworks
#15
Bess Vlaisavljevich, Johanna M Huck, Zeric Hulvey, Kyuho Lee, Jarad A Mason, Jeffrey B Neaton, Jeffrey R Long, Craig M Brown, Dario Alfè, Angelos Michaelides, Berend Smit
Small molecule binding in metal-organic frameworks (MOFs) can be accurately studied both experimentally and computationally, provided the proper tools are employed. Herein, we compare and contrast properties associated with guest binding by means of density functional theory (DFT) calculations using nine different functionals for the M2(dobdc) (dobdc4- = 2,5-dioxido,1,4-benzenedicarboxylate) series where M = Mg, Mn, Fe, Co, Ni, Cu, and Zn. Additionally, we perform Quantum Monte Carlo (QMC) calculations for one system to determine if this method can be used to assess the performance of DFT...
April 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28436608/a-fukui-function-guided-genetic-algorithm-assessment-on-structural-prediction-of-sin-n%C3%A2-%C3%A2-12-20-clusters
#16
Osvaldo Yañez, Alejandro Vásquez-Espinal, Diego Inostroza, Lina Ruiz, Ricardo Pino-Rios, William Tiznado
Theoretical studies are essential for the structural characterization of clusters, when it comes to rationalize their unique size-dependent properties and composition. However, the rapid growth of local minima on the potential energy surface (PES), with respect to cluster size, makes the candidate identification a challenging undertaking. In this article, we introduce a hybrid strategy to explore the PES of clusters. This proposal involves the use of a biased initial population of a genetic algorithm procedure...
April 24, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28436535/the-role-of-the-long-range-exchange-corrections-in-the-description-of-electron-delocalization-in-aromatic-species
#17
Dariusz W Szczepanik, Miquel Solà, Marcin Andrzejak, Barbara Pawełek, Justyna Dominikowska, Mercedes Kukułka, Karol Dyduch, Tadeusz M Krygowski, Halina Szatylowicz
In this article, we address the role of the long-range exchange corrections in description of the cyclic delocalization of electrons in aromatic systems at the density functional theory level. A test set of diversified monocyclic and polycyclic aromatics is used in benchmark calculations involving various exchange-correlation functionals. A special emphasis is given to the problem of local aromaticity in acenes, which has been a subject of long-standing debate in the literature. The presented results indicate that the noncorrected exchange-correlation functionals significantly overestimate cyclic delocalization of electrons in heteroaromatics and aromatic systems with fused rings, which in the case of acenes leads to conflicting local aromaticity predictions from different criteria...
April 24, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28436483/itraq-based-proteomic-analysis-reveals-key-proteins-affecting-muscle-growth-and-lipid-deposition-in-pigs
#18
Zhixiu Wang, Peng Shang, Qinggang Li, Liyuan Wang, Yangzom Chamba, Bo Zhang, Hao Zhang, Changxin Wu
Growth rate and meat quality, two economically important traits in pigs, are controlled by multiple genes and biological pathways. In the present study, we performed a proteomic analysis of longissimus dorsi muscle from six-month-old pigs from two Chinese native mini-type breeds (TP and DSP) and two introduced western breeds (YY and LL) using isobaric tag for relative and absolute quantification (iTRAQ). In total, 4,815 peptides corresponding to 969 proteins were detected. Comparison of expression patterns between TP-DSP and YY-LL revealed 288 differentially expressed proteins (DEPs), of which 169 were up-regulated and 119 were down-regulated...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28436462/mir-146b-is-down-regulated-during-the-chondrogenic-differentiation-of-human-bone-marrow-derived-skeletal-stem-cells-and-up-regulated-in-osteoarthritis
#19
Emma Budd, María C de Andrés, Tilman Sanchez-Elsner, Richard O C Oreffo
Articular cartilage injury can result in chondrocyte loss and diminishment of specialised extracellular matrix, which can progress to an osteoarthritic (OA) phenotype. Stem cells have emerged as a favourable approach for articular cartilage regeneration. Identification of miRNAs which influence stem cell fate offers new approaches for application of miRNAs to regenerate articular cartilage. Skeletal stem cells (SSCs) isolated from human bone marrow were cultured as high density micromass' using TGF-β3 to induce chondrogenesis...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28436435/structure-and-function-of-the-divalent-anion-na-symporter-from-vibrio-cholerae-and-a-humanized-variant
#20
Rongxin Nie, Steven Stark, Jindrich Symersky, Ronald S Kaplan, Min Lu
Integral membrane proteins of the divalent anion/Na(+) symporter (DASS) family translocate dicarboxylate, tricarboxylate or sulphate across cell membranes, typically by utilizing the preexisting Na(+) gradient. The molecular determinants for substrate recognition by DASS remain obscure, largely owing to the absence of any substrate-bound DASS structure. Here we present 2.8-Å resolution X-ray structures of VcINDY, a DASS from Vibrio cholerae that catalyses the co-transport of Na(+) and succinate. These structures portray the Na(+)-bound VcINDY in complexes with succinate and citrate, elucidating the binding sites for substrate and two Na(+) ions...
April 24, 2017: Nature Communications
keyword
keyword
21321
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"