open data sets

datasets for deep learning

https://www.analyticsvidhya.com/blog/2018/03/comprehensive-collection-deep-learning-datasets/

NIH uncolicited applications

Did you know that the majority of funded NIH proposals are unsolicited?  That is, they are not in response to a specific funding opportunity announcement!

https://www.niaid.nih.gov/grants-contracts/unsolicited-investigator-initiated-research  although this guidance is specific to NIAID (allergy and infectious disease), the same applies to almost all of NIH – especially NCI – the wealthiest of all at NIH.

Please see the attached presentation from Program Officer, Dr. David Berrigan at NCI.  Last week at meetings at UTK, he took us through the top 10 list of research gems from the Division of Cancer Control and Population Sciences.  These are applicable to anywhere at NIH, not just NCI.

Zoom course instruction with iPad

1) Zoom on MacBook, sharescreen with iPad through airplay or cable. (Sometimes, airplay or cable does not work).

2) Zoom on Mackbook, iPad screen shared with Zoom App.  Make sure microphone is muted. Record on both Mackbook.  Make sure personal app, emails are closed.

journal of computational biology

Journal of Computational Biology Special Issue: The 13th International Symposium on Bioinformatics Research and Applications (ISBRA2017) This Special Issue includes a selection of papers presented at the 13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017) which was held in Honolulu, Hawaii on May 30–June 2, 2017. ISBRA provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. Enjoy FREE ACCESS through April 9, 2018. Read Now: Preface: 13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017) Zhipeng Cai, Pavel Skums, Alexander Zelikovsky  Read Now Reconstructing One-Articulated Networks with Distance Matrices Kuang-Yu Chang, Yun Ciu, Siu-Ming Yiu, Wing-Kai Hon  Read Now ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer Zihao Wang, Yu Chen, Jingrong Zhang, Lun Li, Xiaohua Wan, Zhiyong Liu, Fei Sun, Fa Zhang  Read Now Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry Michał Aleksander Ciach, Mateusz Krzysztof Łącki, Błażej Miasojedow, Frederik Lermyte, Dirk Valkenborg, Frank Sobott, Anna Gambin  Read Now A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting Ruofan Xia, Yu Lin, Jun Zhou, Bing Feng, Jijun Tang  Read Now Convolutional Neural Network for Histopathological Analysis of Osteosarcoma Rashika Mishra, Ovidiu Daescu, Patrick Leavey, Dinesh Rakheja, Anita Sengupta  Read Now Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing Albert Ng, Dong Si  Read Now An Optimized Method for Bayesian Connectivity Change Point Model Xiuchun Xiao, Bing Liu, Jing Zhang, Xueli Xiao, Yi Pan  Read Now Unbiased Taxonomic Annotation of Metagenomic Samples Bruno Fosso, Graziano Pesole, Francesc Rosselló, Gabriel Valiente  Read Now

BioID2 protein interaction detection

BioID2
http://www.molbiolcell.org/content/early/2016/02/11/mbc.E15-12-0844.full.pdf 

Finding your inner modler

UIC .NSF wortkshop, Finding your inner modler

microbiology plate imaging systems

https://800ezmicro.com/equipment/anaerobic-hypoxic-systems/32-petrifoto-plate-imaging-system.html

vendors and purchasing infor

https://www.biocompare.com/Lab-Equipment/6487-General-Equipment/

particle tracking algrithm

https://www.ncbi.nlm.nih.gov/pubmed/23396281

A Lee, K Tsekouras, C Calderon, C Bustamante, and S Press.. Unraveling the thousand word picture: An introduction to super-resolution data analysis. Chem. Rev., 117:7276, 2017.

KWelsher and H Yang. Multi-resolution 3D visualization of the early stages of cellular uptake of peptide-coated nanoparticles. Nat. Nanotechnol., 9:198, 2014.

MK Cheezum, WF Walker, and WH Guilford. Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys. J., 81:2378, 2001.

active shape model

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

outfti suite

microscopy image tracker

http://www.oufti.org/

UAB, march aging newsletter

• 
  The companion dog as model for human morbidity and mortality.
• Sex specific regulation of aging in Caenorhabditis elegans.

Headline vs Study

• Headline: Easing the brakes on the “immortality” enzyme could slow aging.
• Study: A single nucleotide incorporation step limits human telomerase repeat addition activity.
• Headline: “Axis of aging” mechanism uncovered in worms.
• Study: Brain-gut communications via distinct neuroendocrine signals bidirectionally regulate longevity in C. elegans.

Contrary or Null Findings

• Genetic ablation of p16 does not protect against cellular senescence in a mouse model of COPD.
• Higher peripheral IGF-1 better for aging brain in women.
• Carnitine supplementation does not improve muscle strength nor blood parameters in older women.

Energetics/Nutrition

• 40% dietary restriction improves glucose tolerance for a least 2 months after being returned to ad libitum diet.
• Calorie restriction reduces mTOR signaling in gut stem cells causing improved intestinal epithelium regenerative capacity.
• Water based aquatic exercise improves functional capacity and quality of life in elderly women.

Basic Biology

• Does a declining immune system cause the age-related increases in cancer incidence?
• Geropathology grading platform: a new way to assess aging rate.
• Yeast replicative lifespan limited by increased ribosomal DNA instability and reduced double stranded break repair.
• Metformin supplementation changes adipose and muscle transcriptomic profiles in older adults.
• Insulin signaling regulates oocyte quality maintenance with age via cathepsin B activity.
• Satellite cell mutations drive age-related skeletal muscle function.
• Circadian rhythms in cytosine modifications involved in epigenetic diversity and aging.
• Specific alleles of FOXO3 are associated with self-rated health in older adults.
• A novel mouse model of Alzheimer’s disease has alleviated symptoms with NAD+ supplementation.
• Review: The genetics of longevity in humans and mice.
• Review: Protein turnover in aging and longevity.
• y Only 15% of lifespan extending genetic interventions in mice actually slow the rate of aging.
• In mice, older fathers, faster aging.

Ecology & Evolution

• Stronger social bonds do not always predict greater longevity in a gregarious primate.
• Life history traits of a long-lived Australian fish, the leatherjacket.
• Environmental conditions and body mass senescence in the yellow-bellied marmot.
• Life-history traits of the alpine fly Drosophila nigrosparsa.
• Women who have reproduced have shorter telomeres than nulliparous women.

Novel Organisms/Comparative

• Aging and longevity in the flatworm Macrostomum lignano.
• Cellular senescence in naked mole rats.
• Telomere lengths in long-lived bats.
• The green vervet as model for neurodegenerative disease.
• Increased depth, increased longevity: Sessile marine taxa are longer lived at lower ocean depths.
• Review: FOXO3 and exceptional longevity: Insights from hydra to humans.

Epidemiology/Demography

• Cardiometabolic health is worse in older blacks compared to whites and Hispanics.
• Jail inmates develop geriatric conditions at younger ages than non-incarcerated adults.
• Heavy alcohol use is associated with increased risk of early onset dementia. (pdf)
• Socioeconomic depravation is associated with decreased survival in older adults.

Policy/Ethics

• Age differences in age perceptions.

Clinical

• The power of a positive attitude? Older adults with the APOE4 allele are 50% less likely to develop dementia if they view aging positively.
• Obese older adults are more likely to fall, but less likely to be injured by a fall, than normal weight individuals.

Odds & Ends

• Reproducibility of preclinical animal research improves with heterogeneity of study samples.