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Biomedical Science

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on Tue, 01/30/2018 - 04:11

Biology, Medicine, Health and Nutrition Science

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Congress has just greenlit horse slaughterhouses.  Horse meat will be on shelves across American within two weeks.

http://weeklyworldnews.com/headlines/40929/horse-meat-goes-on-sale-acros...

 

November 30, 2011

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Long-term use of both mobile and cordless phones is associated with an increased risk for glioma, the most common type of brain tumor, the latest research on the subject concludes.

https://www.medscape.com/viewarticle/834888

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Mobile phone and cordless phone use and the risk for glioma – Analysis of pooled case-control studies in Sweden, 1997–2003 and 2007–2009

https://www.sciencedirect.com/science/article/pii/S0928468014000649

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If you have a child or have been a child, you likely know about strep throat. Strep throat is a contagious bacterial infection of the throat that can be quite painful. It is most common in school-age children between the ages of 5 and 15 but can affect anyone. Because it is caused by a bacteria, it nearly always needs to be treated with antibiotics.

https://www.verywell.com/incubation-period-for-strep-throat-770659

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The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831151/

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In recent years, high-throughput protein interaction identification methods have generated a large amount of data. When combined with the results from other in vivo and in vitro experiments, a complex set of relationships between biological molecules emerges. The growing popularity of network analysis and data mining has allowed researchers to recognize indirect connections between these molecules. Due to the interdependent nature of network entities, evaluating proteins in this context can reveal relationships that may not otherwise be evident.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460923/

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Fetal cells can enter maternal blood during pregnancy but whether they can also cross the blood-brain barrier to enter the maternal brain remains poorly understood. Previous results suggest that fetal cells are summoned to repair damage to the mother's brain.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145981/

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Prognostic significance of IDH-1 and MGMT in patients with glioblastoma: One step forward, and one step back?

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199258/

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https://en.wikipedia.org/wiki/Allele

 

Short for Allelomorph

Derives From ParAllel... probably

 

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Whole tumor RNA-sequencing and deconvolution Reveal Glioma Transcriptional Signature

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581044/

 

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New computer algorithm deciphers DNA’s most well-kept secrets; may help find the links between genes and disease

 

https://zuckermaninstitute.columbia.edu/columbia-scientists-build-better...

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Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes.

http://www.pnas.org/content/early/2018/03/28/1714376115

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Whole tumor RNA-sequencing and deconvolution reveal a clinically-prognostic PTEN/PI3K-regulated glioma transcriptional signature

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581044/pdf/oncotarget-08-5...

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581044/

 

 

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Recent developments have enabled rapid, inexpensive RNA sequencing of thousands of individual cells from a single specimen, raising the possibility of unbiased and comprehensive expression profiling from complex tissues. Microwell arrays are a particularly attractive microfluidic platform for single cell analysis due to their scalability, cell capture efficiency, and compatibility with imaging. We report an automated microwell array platform for single cell RNA-Seq with significantly improved performance over previous implementations. We demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. We evaluate the level of cross-contamination in our platform by both tracking fluorescent cell lysate in sealed microwells and with a human-mouse mixed species RNA-Seq experiment. Finally, we apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue.

 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5037380/pdf/srep33883.pdf

 
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http://www.qwantz.com/index.php?comic=2588

 

Horses love you and eat carrots... unlike Cars 

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Nivolumab, marketed as Opdivo, is a medication used to treat cancer.[1][2] It is used as a first line treatment for inoperable or metastatic melanoma in combination with ipilimumab if the cancer does not have a mutation in BRAF,[2]as a second-line treatment following treatment with ipilimumab and if the cancer has a mutation in BRAF, with a BRAF inhibitor,[3] as a second-line treatment for squamous non-small cell lung cancer,[4] and as a second-line treatment for renal cell carcinoma.[2]

https://en.wikipedia.org/wiki/Nivolumab

 

 

Ipilimumab
Ipilimumab is a monoclonal antibody that works to activate the immune system by targeting CTLA-4, a protein receptor that downregulates the immune system. Cytotoxic T lymphocytes can recognize and destroy cancer cells. Wikipedia
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Fastq Dump Error number 95

 

https://github.com/ncbi/sra-tools/issues/95

 

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Neuropsychological research on the neural basis of behaviour generally posits that brain mechanisms will ultimately suffice to explain all psychologically described phenomena. This assumption stems from the idea that the brain is made up entirely of material particles and fields, and that all causal mechanisms relevant to neuroscience can therefore be formulated solely in terms of properties of these elements. Thus, terms having intrinsic mentalistic and/or experiential content (e.g. ‘feeling’, ‘knowing’ and ‘effort’) are not included as primary causal factors. This theoretical restriction is motivated primarily by ideas about the natural world that have been known to be fundamentally incorrect for more than three-quarters of a century.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569494/

 

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: a novel centrality algorithm applied to biological networks

https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017...

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Selecting biologically informative genes in co-expression networks with a centrality score

https://link.springer.com/article/10.1186%2F1745-6150-9-12

 

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Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC)

https://www.sciencedirect.com/science/article/pii/S2213596017301368

 

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Loading required package: data.table

Warning message:

In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called data.table

https://stackoverflow.com/questions/35490887/installing-data-table-resul...

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The sma package is deprecated since many years...

...however, by request from collaborators last year, I recompiled it
to fix that error you are mention (see below).  I just added a
namespace (required in R 2.14.0).  You can download it from:

  http://braju.com/R/repos/sma_0.5.17.tar.gz
  http://braju.com/R/repos/sma_0.5.17.zip
 

https://stat.ethz.ch/pipermail/r-devel/2011-November/062724.html

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Package: Hmisc
Version: 3.6-1
Date: 2009-04-27
Title: Harrell Miscellaneous

 

https://github.com/harrelfe/Hmisc/blob/release_3.6/DESCRIPTION

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Matt Dowle

@MattDowle

Main author of R's data.table 

https://twitter.com/MattDowle

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Rdatatable/data.table

adaptive moving average done with na.rm, exact support

https://ci.appveyor.com/project/Rdatatable/data-table/build/job/bq89q2ar...

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cytoHubba

Predicts and explores important nodes and subnetworks in a given network by several topological algorithms.

http://apps.cytoscape.org/apps/cytohubba

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Step 3.1 : View The Result   next page

Hubba provides the analyzed results computed by 12 methods, including Degreeclustering coefficient

http://hub.iis.sinica.edu.tw/cytoHubba/tutorial.php?step=3_1

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RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216918/pdf/1765.pdf

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Quality Control in Neuroradiology: Discrepancies in Image Interpretation among Academic Neuroradiologists

http://www.ajnr.org/content/33/1/37

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ingle-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4123637/

 

supp: 

http://dmm.biologists.org/content/dmm/suppl/2014/12/22/8.1.45.DC1/DMM018...

 

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A mouse carrying a cancer patient's tumor graft under its skin is displayed in a Champions Oncology lab in Baltimore.

https://www.statnews.com/2016/12/06/immunotherapy-cancer-treatment-mice/

 

 

 

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