keyword
MENU ▼
Read by QxMD icon Read
search

Alignment free

keyword
https://www.readbyqxmd.com/read/29229655/new-zealand-policy-experts-appraisal-of-interventions-to-reduce-smoking-in-young-adults-a-qualitative-investigation
#1
Jude Ball, Janet Hoek, El Shadan Tautolo, Heather Gifford
OBJECTIVES: Reducing smoking in young adults, particularly young Māori and Pacific, is vital for reducing tobacco harm and health inequalities in New Zealand (NZ). We investigated how NZ policy experts appraised the feasibility and likely effectiveness of interventions designed to reduce smoking prevalence among 18-24 year olds. DESIGN: We used a qualitative design, conducting semistructured interviews and applying thematic analysis. PARTICIPANTS: We interviewed 15 key informants, including politicians, senior policy analysts and leading tobacco control advocates...
December 10, 2017: BMJ Open
https://www.readbyqxmd.com/read/29228193/deepsf-deep-convolutional-neural-network-for-mapping-protein-sequences-to-folds
#2
Jie Hou, Badri Adhikari, Jianlin Cheng
Motivation: Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a target protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29227495/fluorescence-activated-droplet-sorting-of-lipolytic-microorganisms-using-a-compact-optical-system
#3
Yuxin Qiao, Xiaoyan Zhao, Jun Zhu, Ran Tu, Libing Dong, Li Wang, Zhiyang Dong, Qinhong Wang, Wenbin Du
Lipases are ubiquitous enzymes of great physiological significance that have been used extensively in multiple industries. Environmental microorganisms are a major source for the discovery of novel lipases with high catalytic efficiency and selectivity. However, current plate-based screening of lipase-producing strains is time consuming, labour intensive and inefficient. In this study, we developed an ultra-high throughput screening pipeline for lipase-producing strains based on fluorescence-activated droplet sorting (FADS) using a compact optical system that could be easily set up in an alignment-free manner...
December 11, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/29227372/osteofibrous-dysplasia-of-the-tibia-in-children-outcome-without-resection
#4
Daniel Westacott, Peter Kannu, Jennifer Stimec, Sevan Hopyan, Andrew Howard
BACKGROUND: The proposed association between osteofibrous dysplasia and adamantinoma has led some to advocate resection of the entire lesion, which can require major subsequent reconstruction. However, this link remains unproven and there is some support in more recent literature for a less aggressive approach. This study aims to describe our experience managing pediatric tibial osteofibrous dysplasia with such an approach and to report functional outcomes in children treated thus. METHODS: A total of 28 cases of osteofibrous dysplasia in 25 patients were managed at a referral center for pediatric bone tumors with observation in the first instance, then limited surgical intervention if required to address pain and deformity...
December 8, 2017: Journal of Pediatric Orthopedics
https://www.readbyqxmd.com/read/29222966/optimizing-functional-outcomes-in-mandibular-condyle-reconstruction-with-the-free-fibula-flap-using-computer-aided-design-and-manufacturing-technology
#5
Z-Hye Lee, Tomer Avraham, Casian Monaco, Ashish A Patel, David L Hirsch, Jamie P Levine
PURPOSE: Mandibular defects involving the condyle represent a complex reconstructive challenge for restoring proper function of the temporomandibular joint (TMJ) because it requires precise bone graft alignment for full restoration of joint function. The use of computer-aided design and manufacturing (CAD/CAM) technology can aid in accurate reconstruction of mandibular condyle defects with a vascularized free fibula flap without the need for additional adjuncts. The purpose of this study was to analyze clinical and functional outcomes after reconstruction of mandibular condyle defects using only a free fibula graft with the help of virtual surgery techniques...
November 15, 2017: Journal of Oral and Maxillofacial Surgery
https://www.readbyqxmd.com/read/29220512/a-survey-and-evaluations-of-histogram-based-statistics-in-alignment-free-sequence-comparison
#6
Brian B Luczak, Benjamin T James, Hani Z Girgis
Motivation: Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. Results: We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares...
December 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29219081/whole-genome-analysis-of-crispr-cas9-sgrna-off-target-homologies-via-an-efficient-computational-algorithm
#7
Hong Zhou, Michael Zhou, Daisy Li, Joseph Manthey, Ekaterina Lioutikova, Hong Wang, Xiao Zeng
BACKGROUND: The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA, single guide RNA (sgRNA), to cleave double stranded DNA, allowing the introduction of wanted mutations. Unfortunately, it has been reported repeatedly that the sgRNA can also guide Cas9 to off-target sites where the DNA sequence is homologous to sgRNA. RESULTS: Using human genome and Streptococcus pyogenes Cas9 (SpCas9) as an example, this article mathematically analyzed the probabilities of off-target homologies of sgRNAs and discovered that for large genome size such as human genome, potential off-target homologies are inevitable for sgRNA selection...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29211458/dopant-free-tetrakis-triphenylamine-hole-transporting-material-for-efficient-tin-based-perovskite-solar-cells
#8
Weijun Ke, Pragya Priyanka, Sureshraju Vegiraju, Constantinos C Stoumpos, Ioannis Spanopoulos, Chan Myae Myae Soe, Tobin J Marks, Ming-Chou Chen, M G Kanatzidis
Developing dopant-free hole transporting layers (HTLs) are critical in achieving high-performance and robust state-of-the-art perovskite photovoltaics, especially for the air-sensitive tin-based perovskite systems. The commonly used HTLs require hygroscopic dopants and additives for optimal performance that adds extra cost to manufacturing and limits long-term device stability. Here we demonstrate the use of a novel tetrakis-triphenylamine (TPE) small molecule prepared by a facile synthetic route as a superior dopant-free hole HTL for lead-free tin-based perovskite solar cells...
December 6, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29210404/silica-layered-double-hydroxide-core-shell-hybrid-materials
#9
Wing L J Kwok, Dana-Georgiana Crivoi, Chunping Chen, Jean-Charles Buffet, Dermot O'Hare
A series of silica@layered double hydroxides (SiO2@Mg2Al-CO3-AMO-LDHs) have been synthesised by in situ precipitation of Mg2Al-CO3-LDH at room temperature in the presence of amorphous spherical silica particles (∼500 nm). We have systematically investigated a number of synthetic parameters in order to evaluate their effects on the composition, morphological and physical properties of the isolated materials. Syntheses carried out at moderate stirring speeds (e.g. 500 rpm) were found to promote the formation of vertically aligned LDH platelets with respect to the silica surface...
December 6, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29209072/free-sepf-interferes-with-recruitment-of-late-cell-division-proteins
#10
Yongqiang Gao, Michaela Wenzel, Martijs J Jonker, Leendert W Hamoen
The conserved cell division protein SepF aligns polymers of FtsZ, the key cell division protein in bacteria, during synthesis of the (Fts)Z-ring at midcell, the first stage in cytokinesis. In addition, SepF acts as a membrane anchor for the Z-ring. Recently, it was shown that SepF overexpression in Mycobacterium smegmatis blocks cell division. Why this is the case is not known. Surprisingly, we found in Bacillus subtilis that SepF overproduction does not interfere with Z-ring assembly, but instead blocks assembly of late division proteins responsible for septum synthesis...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208552/controlling-human-corneal-stromal-stem-cell-contraction-to-mediate-rapid-cell-and-matrix-organization-of-real-architecture-for-3-dimensional-tissue-equivalents
#11
Dev Mukhey, James Phillips, Julie T Daniels, Alvena K Kureshi
The architecture of the human corneal stroma consists of a highly organized extracellular matrix (ECM) interspersed with keratocytes. Their progenitor cells; corneal stromal stem cells (CSSC) are located at the periphery, in the limbal stroma. A highly organized corneal ECM is critical for effective transmission of light but this structure may be compromised during injury or disease, resulting in loss of vision. Re-creating normal organization in engineered tissue equivalents for transplantation often involves lengthy culture times that are inappropriate for clinical use or utilisation of synthetic substrates that bring complications such as corneal melting...
December 2, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/29208371/integrated-semi-targeted-metabolomics-analysis-reveals-distinct-metabolic-dysregulation-in-pleural-effusion-caused-by-tuberculosis-and-malignancy
#12
Nanying Che, Yan Ma, Huabin Ruan, Lina Xu, Xueying Wang, Xinting Yang, Xiaohui Liu
BACKGROUND: Tuberculous pleural effusion (TPE) and malignant pleural effusion (MPE) are the 2 most frequent causes of exudative pleural effusions (PEs). However, the clinical differentiation is challenging. METHODS: Metabolic signatures in pleural effusion from 156 patients were profiled. An integrated semi-targeted metabolomics platform was incorporated for high throughput metabolite identification and quantitation. In this platform, orbitrap based mass spectrometry with data dependent MS/MS acquisition was applied in the analysis...
December 2, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29207566/the-osteogenic-and-tenogenic-differentiation-potential-of-c3h10t1-2-mesenchymal-stem-cell-model-cultured-on-pcl-pla-electrospun-scaffolds-in-the-absence-of-specific-differentiation-medium
#13
Timothée Baudequin, Ludovic Gaut, Marc Mueller, Angela Huepkes, Birgit Glasmacher, Delphine Duprez, Fahmi Bedoui, Cécile Legallais
The differentiation potential of mesenchymal stem cells (MSC) has been extensively tested on electrospun scaffolds. However, this potential is often assessed with lineage-specific medium, making it difficult to interpret the real contribution of the properties of the scaffold in the cell response. In this study, we analyzed the ability of different polycaprolactone/polylactic acid PCL/PLA electrospun scaffolds (pure or blended compositions, random or aligned fibers, various fiber diameters) to drive MSC towards bone or tendon lineages in the absence of specific differentiation medium...
December 4, 2017: Materials
https://www.readbyqxmd.com/read/29206863/blood-collection-in-cell-stabilizing-tubes-does-not-impact-germline-dna-quality-for-pediatric-patients
#14
Bruce M Wollison, Edwin Thai, Aimee Mckinney, Abigail Ward, Andrea Clapp, Catherine Clinton, Anwesha Nag, Aaron R Thorner, Julie M Gastier-Foster, Brian D Crompton
OBJECTIVES: Liquid biopsy technologies allow non-invasive tumor profiling for patients with solid tumor malignancies by sequencing circulating tumor DNA. These studies may be useful in risk-stratification, monitoring for relapse, and understanding tumor evolution. The quality of DNA obtained for these studies is improved when blood samples are collected in tubes that stabilizing white blood cells (WBC). However, ongoing germline research in pediatric oncology generally requires obtaining blood samples in EDTA tubes, which do not contain a WBC-stabilizing preservative...
2017: PloS One
https://www.readbyqxmd.com/read/29206456/real-time-conformational-changes-and-controlled-orientation-of-native-proteins-inside-a-protein-nanoreactor
#15
Veerle Van Meervelt, Misha Soskine, Shubham Singh, Gea Schuurman-Wolters, Hein J Wijma, Bert Poolman, Giovanni Maglia
Protein conformations play crucial roles in most, if not all, biological processes. Here we show that the current carried through a nanopore by ions allows monitoring conformational changes of native substrate-binding domains (SBD) of an ATP-Binding Cassette importer in real-time. Comparison with single-molecule Förster Resonance Energy Transfer (smFRET) and ensemble measurements revealed that proteins trapped inside the nanopore have bulk-like properties. Two ligand-free and two ligand-bound conformations of SBD proteins were inferred and their kinetic constants were determined...
December 5, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29204218/interpreting-the-mechanism-of-apoe-p-leu167del-mutation-in-the-incidence-of-familial-hypercholesterolemia-an-in-silico-approach
#16
REVIEW
Omran Mohammed Rashidi, Fatima Amanullah H Nazar, Mohamed Nabil Alama, Zuhier Ahmed Awan
Background: Apolipoprotein E (APOE) gene is a ligand protein in humans which mediates the metabolism of cholesterol by binding to the low-density lipoprotein receptor (LDLR). P.Leu167del mutation in APOE gene was recently connected with Familial Hypercholesterolemia, a condition associated with premature cardiovascular disease. The consequences of this mutation on the protein structure and its receptor binding capacity remain largely unknown. Objective: The current study aims to further decipher the underlying mechanism of this mutation using advanced software-based algorithms...
2017: Open Cardiovascular Medicine Journal
https://www.readbyqxmd.com/read/29197323/alignment-free-comparative-genomic-screen-for-structured-rnas-using-coarse-grained-secondary-structure-dot-plots
#17
Yuki Kato, Jan Gorodkin, Jakob Hull Havgaard
BACKGROUND: Structured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computationally heavy for use in full genomic screens or rely on pre-aligned sequences. METHODS: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level...
December 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29188788/mechanistic-insights-of-the-min-oscillator-via-cell-free-reconstitution-and-imaging
#18
Kiyoshi Mizuuchi, Anthony G Vecchiarelli
The MinD and MinE proteins of Escherichia coli self-organize into a standing-wave oscillator on the membrane to help align division at mid-cell. When unleashed from cellular confines, MinD and MinE form a spectrum of patterns on artificial bilayers - static amoebas, traveling waves, traveling mushrooms, and bursts with standing-wave dynamics. We recently focused our cell-free studies on bursts because their dynamics recapitulate many features of Min oscillation observed in vivo. The data unveiled a patterning mechanism largely governed by MinE regulation of MinD interaction with membrane...
November 30, 2017: Physical Biology
https://www.readbyqxmd.com/read/29187143/dmrfinder-efficiently-identifying-differentially-methylated-regions-from-methylc-seq-data
#19
John M Gaspar, Ronald P Hart
BACKGROUND: DNA methylation is an epigenetic modification that is studied at a single-base resolution with bisulfite treatment followed by high-throughput sequencing. After alignment of the sequence reads to a reference genome, methylation counts are analyzed to determine genomic regions that are differentially methylated between two or more biological conditions. Even though a variety of software packages is available for different aspects of the bioinformatics analysis, they often produce results that are biased or require excessive computational requirements...
November 29, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29180773/chiral-liquid-crystal-colloids
#20
Ye Yuan, Angel Martinez, Bohdan Senyuk, Mykola Tasinkevych, Ivan I Smalyukh
Colloidal particles disturb the alignment of rod-like molecules of liquid crystals, giving rise to long-range interactions that minimize the free energy of distorted regions. Particle shape and topology are known to guide this self-assembly process. However, how chirality of colloidal inclusions affects these long-range interactions is unclear. Here we study the effects of distortions caused by chiral springs and helices on the colloidal self-organization in a nematic liquid crystal using laser tweezers, particle tracking and optical imaging...
November 27, 2017: Nature Materials
keyword
keyword
57908
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"