journal
MENU ▼
Read by QxMD icon Read
search

Methods: a Companion to Methods in Enzymology

journal
https://www.readbyqxmd.com/read/28919042/new-tools-for-the-visualization-of-biological-pathways
#1
Tomojit Ghosh, Xiaofeng Ma, Michael Kirby
This paper presents several geometrically motivated techniques for the visualization of high-dimensional biological data sets. The Grassmann manifold provides a robust framework for measuring data similarity in a subspace context. Sparse radial basis function classification as a visualization technique leverages recent advances in radial basis function learning via convex optimization. In the spirit of deep belief networks, supervised centroid-encoding is proposed as a way to exploit class label information...
September 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28917725/a-computational-approach-for-phenotypic-comparisons-of-cell-populations-in-high-dimensional-cytometry-data
#2
Ludovic Platon, David Pejoski, Guillaume Gautreau, Brice Targat, Roger Le Grand, Anne-Sophie Beignon, Nicolas Tchitchek
BACKGROUND: Cytometry is an experimental technique used to measure molecules expressed by cells at a single cell resolution. Recently, several technological improvements have made possible to increase greatly the number of cell markers that can be simultaneously measured. Many computational methods have been proposed to identify clusters of cells having similar phenotypes. Nevertheless, only a limited number of computational methods exist to compare the phenotypes of the cell clusters identified by different clustering approaches...
September 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28917724/backward-genotype-transcript-phenotype-association-mapping
#3
Seunghak Lee, Haohan Wang, Eric P Xing
Genome-wide association studies have discovered a large number of genetic variants associated with complex diseases such as Alzheimer's disease. However, the genetic background of such diseases is largely unknown due to the complex mechanisms underlying genetic effects on traits, as well as a small sample size (e.g., 1000) and a large number of genetic variants (e.g., 1 million). Fortunately, datasets that contain genotypes, transcripts, and phenotypes are becoming more readily available, creating new opportunities for detecting disease-associated genetic variants...
September 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28916149/wavelet-based-tracking-of-bacteria-in-unreconstructed-off-axis-holograms
#4
Zach Marin, J Kent Wallace, Jay Nadeau, Andre Khalil
We propose an automated wavelet-based method of tracking particles in unreconstructed off-axis holograms to provide rough estimates of the presence of motion and particle trajectories in digital holographic microscopy (DHM) time series. The wavelet transform modulus maxima segmentation method is adapted and tailored to extract Airy-like diffraction disks, which represent bacteria, from DHM time series. In this exploratory analysis, the method shows potential for estimating bacterial tracks in low-particle-density time series, based on a preliminary analysis of both living and dead Serratia marcescens, and for rapidly providing a single-bit answer to whether a sample chamber contains living or dead microbes or is empty...
September 12, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28916148/chemokine-receptor-directed-imaging-and-therapy
#5
REVIEW
Andreas K Buck, Antje Stolzenburg, Heribert Hänscheid, Andreas Schirbel, Katharina Lückerath, Margret Schottelius, Hans-Jürgen Wester, Constantin Lapa
The C - X - C chemokine receptor 4 (CXCR4) and its natural ligand CXCL12 are key factors in the process of cell migration, homing of hematopoietic stem cells to the bone marrow, and represent important mediators of angiogenesis and cell proliferation. The CXCR4/CXCL12 interplay can be disrupted by CXCR4 antagonists such as Plerixafor which are already in daily clinical use, i.e. for mobilization and subsequent harvesting of hematopoietic progenitor cells and stem cell transplantation. In a pathological condition, involvement in the process of metastasis and homing of cancer cells to a protective niche has been described, making CXCR4 an attractive target for imaging and treatment of malignant diseases...
September 12, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28890129/bioinformatics-approaches-to-predict-target-genes-from-transcription-factor-binding-data
#6
REVIEW
Alexandra Essebier, Marnie Lamprecht, Michael Piper, Mikael Boden
Transcription factors regulate gene expression and play an essential role in development by maintaining proliferative states, driving cellular differentiation and determining cell fate. Transcription factors are capable of regulating multiple genes over potentially long distances making target gene identification challenging. Currently available experimental approaches to detect distal interactions have multiple weaknesses that have motivated the development of computational approaches. Although an improvement over experimental approaches, existing computational approaches are still limited in their application, with different weaknesses depending on the approach...
September 7, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28887085/visualizing-omics-and-clinical-data-which-challenges-for-dealing-with-their-variety
#7
REVIEW
Fleur Mougin, David Auber, Romain Bourqui, Gayo Diallo, Isabelle Dutour, Vianney Jouhet, Frantz Thiessard, Rodolphe Thiébaut, Patricia Thébault
Life sciences are currently going through a great number of transformations raised by the in-going revolution in high-throughput technologies for the acquisition of data. The integration of their high dimensionality, ranging from omics to clinical data, is becoming one of the most challenging stages. It involves inter-disciplinary developments with the aim to move towards an enhanced understanding of human physiology for caring purposes. Biologists, bioinformaticians, physicians and other experts related to the healthcare domain have to accompany each step of the analysis process in order to investigate and expertise these various data...
September 6, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28887084/tethered-growth-factors-on-biocompatible-scaffolds-improve-stemness-of-cultured-rat-and-human-neural-stem-cells-and-growth-of-oligodendrocyte-progenitors
#8
Lisamarie Moore, Nolan B Skop, Deborah E Rothbard, Lucas R Corrubia, Steven W Levison
Currently, there is no widely accepted technique to efficiently and reproducibly grow stem and progenitor cells in vitro. Stem cells require contact with extracellular matrices as well as signals from growth factors to proliferate and to retain their stemness. We have developed a novel tissue culture platform (StemTrix cultureware) that transforms standard tissue culture plasticware into a multi-functional chitosan-based scaffold that supports the expansion of neural stem cells. The StemTrix scaffold is comprised of chitosan with immobilized heparin which in turn tethers heparin-binding growth factors...
September 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28867501/stem-cell-transplantation-for-huntington-s-diseases
#9
REVIEW
Kyung-Ah Choi, Yeonho Choi, Sunghoi Hong
Therapeutic approaches based on stem cells have received considerable attention as potential treatments for Huntington's disease (HD), which is a fatal, inherited neurodegenerative disorder, caused by progressive loss of GABAergic medium spiny neurons (MSNs) in the striatum of the forebrain. Transplantation of stem cells or their derivatives in animal models of HD, efficiently improved functions by replacing the damaged or lost neurons. In particular, neural stem cells (NSCs) for HD treatments have been developed from various sources, such as the brain itself, the pluripotent stem cells (PSCs), and the somatic cells of the HD patients...
September 1, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28867500/review-of-combinations-of-experimental-and-computational-techniques-to-identify-and-understand-genes-involved-in-innate-immunity-and-effector-triggered-defence
#10
REVIEW
Henrik U Stotz, Rodrigo de Oliveira Almeida, Neil Davey, Volker Steuber, Guilherme T Valente
The innate immune system includes a first layer of defence that recognises conserved pathogen-associated molecular patterns that are essential for microbial fitness. Resistance (R) gene-based recognition of pathogen effectors, which function in modulation or avoidance of host immunity, activates a second layer of plant defence. In this review, experimental and computational techniques are considered to improve understanding of the plant immune system. Biocomputation contributes to discovery of the molecular genetic basis of host resistance against pathogens...
September 1, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28864354/methods-of-reactivation-and-reprogramming-of-neural-stem-cells-for-neural-repair
#11
REVIEW
Zuojun Tian, Qiuge Zhao, Sangita Biswas, Wenbin Deng
Research on the biology of adult neural stem cells (NSCs) and induced NSCs (iNSCs), as well as NSC-based therapies for diseases in central nervous system (CNS) has started to generate the expectation that these cells may be used for treatments in CNS injuries or disorders. Recent technological progresses in both NSCs themselves and their derivatives have brought us closer to therapeutic applications. Adult neurogenesis presents in particular regions in mammal brain, known as neurogenic niches such as the dental gyrus (DG) in hippocampus and the subventricular zone (SVZ), within which adult NSCs usually stay for long periods out of the cell cycle, in G0...
August 31, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28864353/manipulation-of-neural-progenitor-fate-through-the-oxygen-sensing-pathway
#12
REVIEW
Yuan Xie, William E Lowry
Neural progenitor cells hold significant promise in a variety of clinical settings. While both the brain and spinal cord harbor endogenous neural progenitor or stem cells, they typically are not capable of repopulating neural populations in case of injury or degenerative disease. In vitro systems for the culture of neural progenitors has come a long ways due to advances in the method development. Recently, many groups have shown that manipulation of the oxygen-sensing pathway leading to activation of hypoxia inducible factors (HIFs) that can influence the proliferation, differentiation or maturation of neural progenitors...
August 31, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28864356/lensless-digital-holographic-microscopy-and-its-applications-in-biomedicine-and-environmental-monitoring
#13
REVIEW
Yichen Wu, Aydogan Ozcan
Optical compound microscope has been a major tool in biomedical imaging for centuries. Its performance relies on relatively complicated, bulky and expensive lenses and alignment mechanics. In contrast, the lensless microscope digitally reconstructs microscopic images of specimens without using any lenses, as a result of which it can be made much smaller, lighter and lower-cost. Furthermore, the limited space-bandwidth product of objective lenses in a conventional microscope can be significantly surpassed by a lensless microscope...
August 29, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28864355/separation-of-neural-stem-cells-by-whole-cell-membrane-capacitance-using-dielectrophoresis
#14
REVIEW
Tayloria N G Adams, Alan Y L Jiang, Prema D Vyas, Lisa A Flanagan
Whole cell membrane capacitance is an electrophysiological property of the plasma membrane that serves as a biomarker for stem cell fate potential. Neural stem and progenitor cells (NSPCs) that differ in ability to form neurons or astrocytes are distinguished by membrane capacitance measured by dielectrophoresis (DEP). Differences in membrane capacitance are sufficient to enable the enrichment of neuron- or astrocyte-forming cells by DEP, showing the separation of stem cells on the basis of fate potential by membrane capacitance...
August 29, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28843611/function-and-structure-based-screening-of-compounds-peptides-and-proteins-to-identify-drug-candidates
#15
Vidhi Malik, Jaspreet Kaur Dhanjal, Anjani Kumari, Navaneethan Radhakrishnan, Kamya Singh, Durai Sundar
Drug discovery in simple words is all about finding small molecular compounds that possess the potential to interact with specific bio-macromolecules, mainly proteins, thereby bringing a desired effect in the functioning of the target molecules. Virtual screening of large compound libraries using computational approaches has come up as a great alternative to cost and labor-intensive high-throughput screening carried out in laboratories. Virtual high-throughput screening enormously reduces the number of compounds for systematic analysis using biochemical assays before entering the clinical trials...
August 24, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28842259/a-cytometric-approach-to-follow-variation-and-dynamics-of-the-salivary-microbiota
#16
Susanna van Gelder, Nicola Röhrig, Florian Schattenberg, Nicolas Cichocki, Joachim Schumann, Gerhard Schmalz, Rainer Haak, Dirk Ziebolz, Susann Müller
Microbial flow cytometry is an established fast and economic technique for complex ecosystem studies and enables visualization of rapidly changing community structures by measuring characteristics of single microbial cells. Cytometric evaluation routines are available such as flowCyBar which are useful for automatic data processing. Here, a cytometric workflow was established which allows to routinely analyze salivary microbiomes on the example of ten oral healthy subjects. First, saliva was collected within a 3-month period, cytometrically analyzed and the evolution of the microbiomes followed as well as the calculation of their intra- and inter-subject similarity...
August 22, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28813689/large-scale-machine-learning-of-media-outlets-for-understanding-public-reactions-to-nation-wide-viral-infection-outbreaks
#17
Sungwoon Choi, Jangho Lee, Min-Gyu Kang, Hyeyoung Min, Yoon-Seok Chang, Sungroh Yoon
From May to July 2015, there was a nation-wide outbreak of Middle East respiratory syndrome (MERS) in Korea. MERS is caused by MERS-CoV, an enveloped, positive-sense, single stranded RNA virus belonging to the family Coronaviridae. Despite expert opinions that the danger of MERS might be exaggerated, there was an overreaction by the public according to the Korean mass media, which led to a noticeable reduction in social and economic activities during the outbreak. To explain this phenomenon, we presumed that machine learning-based analysis of media outlets would be helpful and collected a number of Korean mass media articles and short-text comments produced during the 10-week outbreak...
August 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28807723/identifying-consistent-disease-subnetworks-using-dnet
#18
Jiajie Peng, Junya Lu, Xuequn Shang, Jin Chen
It is critical to identify disease-specific subnetworks from the vastly available genome-wide gene expression data for elucidating how genes perform high-level biological functions together. Various algorithms have been developed for disease gene identification. However, the topological structure of the disease networks (or even the fraction of the networks) has been left largely unexplored. In this article, we present DNet, a method for the identification of significant disease subnetworks by integrating both the network structure and gene expression information...
August 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28802715/elucidating-virus-entry-using-a-tetracysteine-tagged-virus
#19
REVIEW
Bjorn-Patrick Mohl, Polly Roy
Fluorescent tags constitute an invaluable tool in facilitating a deeper understanding of the mechanistic processes governing virus-host interactions. However, when selecting a fluorescent tag for in vivo imaging of cells, a number of parameters and aspects must be considered. These include whether the tag may affect and interfere with protein conformation or localization, cell toxicity, spectral overlap, photo-stability and background. Cumulatively, these constitute challenges to be overcome. Bluetongue virus (BTV), a member of the Orbivirus genus in the Reoviridae family, is a non-enveloped virus that is comprised of two architecturally complex capsids...
August 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28802714/in-silico-structure-based-approaches-to-discover-protein-protein-interaction-targeting-drugs
#20
REVIEW
Woong-Hee Shin, Charles W Christoffer, Daisuke Kihara
A core concept behind modern drug discovery is finding a small molecule that modulates a function of a target protein. This concept has been successfully applied since the mid-1970s. However, the efficiency of drug discovery is decreasing because the druggable target space in the human proteome is limited. Recently, protein-protein interaction (PPI) has been identified asan emerging target space for drug discovery. PPI plays a pivotal role in biological pathways including diseases. Current human interactome research suggests that the number of PPIs is between 130,000 and 650,000, and only a small number of them have been targeted as drug targets...
August 9, 2017: Methods: a Companion to Methods in Enzymology
journal
journal
31806
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"