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A path to success? A review ofevolution, development, and the predictable genomeby David L. Stern

Hope Hollocher, Charles H. Pence, Grant Ramsey, Michelle M. Wirth
2013 Evolution & Development  
Evolution, Development, and the Predictable Genome: Stern, David L. 2011. Roberts and Company Publishers, Greenwood Village, CO. xvi þ 264 pp. $40.50; ill.; index. ISBN: 978-1-936221-01-1.  ...  David Stern's book, Evolution, Development, and the Predictable Genome, is a bold attempt to synthesize population genetics and developmental biology.  ...  The synthesis that Stern hopes to accomplish is as difficult as it is necessary.  ... 
doi:10.1111/ede.12016 fatcat:lltuaymounhcpedycjvsgjkiuy


David H. Stern, Ralf Herbrich, Thore Graepel
2009 Proceedings of the 18th international conference on World wide web - WWW '09  
We present a probabilistic model for generating personalised recommendations of items to users of a web service. The Matchbox system makes use of content information in the form of user and item meta data in combination with collaborative filtering information from previous user behavior in order to predict the value of an item for a user. Users and items are represented by feature vectors which are mapped into a low-dimensional 'trait space' in which similarity is measured in terms of inner
more » ... ducts. The model can be trained from different types of feedback in order to learn user-item preferences. Here we present three alternatives: direct observation of an absolute rating each user gives to some items, observation of a binary preference (like/ don't like) and observation of a set of ordinal ratings on a userspecific scale. Efficient inference is achieved by approximate message passing involving a combination of Expectation Propagation (EP) and Variational Message Passing. We also include a dynamics model which allows an item's popularity, a user's taste or a user's personal rating scale to drift over time. By using Assumed-Density Filtering (ADF) for training, the model requires only a single pass through the training data. This is an on-line learning algorithm capable of incrementally taking account of new data so the system can immediately reflect the latest user preferences. We evaluate the performance of the algorithm on the MovieLens and Netflix data sets consisting of approximately 1,000,000 and 100,000,000 ratings respectively. This demonstrates that training the model using the on-line ADF approach yields state-of-the-art performance with the option of improving performance further if computational resources are available by performing multiple EP passes over the training data.
doi:10.1145/1526709.1526725 dblp:conf/www/SternHG09 fatcat:h3vaw3hnjbhtdkgflcf2dzfxka

Petrobactin protects against oxidative stress and enhances sporulation efficiency in Bacillus anthracis Sterne [article]

Ada K Hagan, Yael M. Plotnick, Ryan E Dingle, Zachary I Mendel, Stephen R Cendrowski, David H Sherman, Ashootosh Tripathi, Philip C Hanna
2018 bioRxiv   pre-print
Takamatsu H, Watabe K. 2002. Assembly and genetics of spore protective structures. Cell 508 Mol Life Sci 59:434-444. 509 15.  ...  This was 243 due to a four-log decrease in the CFU/mL of the asb mutant strain following treatment with 244 10mM H 2 O 2 ( Figure 4C ).  ... 
doi:10.1101/350611 fatcat:2igslyq7qzd75pmhpbn54feoem

Nuclear Microenvironments Modulate Transcription From Low-Affinity Enhancers [article]

Justin Crocker, Albert Tsai, Anand K Muthusamy, Luke D Lavis, Robert H Singer, David L Stern
2017 bioRxiv   pre-print
We thank all members of the Stern and Singer labs for 256 discussion. Albert Tsai is a Damon Runyon Fellow of the Damon Runyon Cancer 257 Research Foundation (DRG 2220-15). Robert H.  ...  R. & Stern, D. L. Quantitatively predictable control of 419 Drosophila transcriptional enhancers in vivo with engineered transcription 420 factors. Nat Genet 48, 292-298 (2016). 421 5.  ... 
doi:10.1101/128280 fatcat:n7x2ut2rtfey7br46ht4bkhs54

Microassembly based on hands free origami with bidirectional curvature

Noy Bassik, George M. Stern, David H. Gracias
2009 Applied Physics Letters  
Stewart, Nature ͑London͒ 448, 419 ͑2007͒. 3 H. J. In, S. Kumar, Y. Shao-Horn, and G. Barbastathis, Appl. Phys. Lett. 88, 083104 ͑2006͒.  ...  to create hollow regions in the sheet, all hinges are protected with photoresist ͑not shown͒. ͑g͒ The sacrificial layer is dissolved causing the sheet to assemble while lifting off of the substrate. ͑  ... 
doi:10.1063/1.3212896 pmid:19787072 pmcid:PMC2752473 fatcat:i3rnttkipfbbpjrzx4nrmbokve

Error enhancement in geomagnetic models derived from scalar data

David P. Stern, Joseph H. Bredekamp
1975 Journal of Geophysical Research  
gpterm recovery i n 3 iterations, for cases i n which data points are spread out aver a spherical s'mll bounded by ro 2 b Table 4 Ratios <+2k /e derived from the recursion relation A-1-1 No. of David  ...  s p h e r i c a l harmonic expansion of y , a i s t h e e a r t h ' s radius).  ... 
doi:10.1029/ja080i013p01776 fatcat:75i6l2ozpreqng4snkcbp6vo44

Accelerating calculations of RNA secondary structure partition functions using GPUs

Harry A Stern, David H Mathews
2013 Algorithms for Molecular Biology  
rules [11] , while a, b, and c are from the following estimate of the standard free energy change for multibranch loop initiation: G 0 = a + bn + ch (22) Here n is the number of unpaired nucleotides and h  ... 
doi:10.1186/1748-7188-8-29 pmid:24180434 pmcid:PMC4175106 fatcat:cc5aggzwzffc3plbzeqfotxvni

The yellow gene influences Drosophila male mating success through sex comb melanization [article]

Jonathan H Massey, Daayun Chung, Igor Siwanowicz, David L Stern, Patricia J Wittkopp
2019 bioRxiv   pre-print
(H) Inter pulse interval. (D-774 H) Show individual points that represent single fly replicates. Circles represent means and lines 775 SD.  ...  J., Sunayama-Morita, T., Coen, P., Murthy, M. & Stern, D. L. (2013). Multi-channel 513 acoustic recording and automated analysis of Drosophila courtship songs. BMC Biol.  ... 
doi:10.1101/673756 fatcat:qad6pwhotvfjvnegrx7fc2xntm

The Chlamydomonas reinhardtii Plastid Chromosome

Jude E. Maul, Jason W. Lilly, Liying Cui, Claude W. dePamphilis, Webb Miller, Elizabeth H. Harris, David B. Stern
2002 The Plant Cell  
The genes or braced areas labeled D to H denote features discussed in the text.  ...  Stern, unpublished results). One hypothesis for the function of at least one SDR is transcriptional regulation.  ... 
doi:10.1105/tpc.006155 pmid:12417694 pmcid:PMC153795 fatcat:ygc72cjzsngenbung7ru4ipe5e

Nuclear microenvironments modulate transcription from low-affinity enhancers

Albert Tsai, Anand K Muthusamy, Mariana RP Alves, Luke D Lavis, Robert H Singer, David L Stern, Justin Crocker
2017 eLife  
We thank all members of the Stern and Singer labs for discussion.  ...  Singer, David L Stern, Justin Crocker, Decision letter and Author response Decision letter  ...  Singer, Resources, Supervision, Funding acquisition, Writing-review and editing, Conceived of and designed the experiments; David L Stern, Conceptualization, Supervision, Funding acquisition, Investigation  ... 
doi:10.7554/elife.28975 pmid:29095143 pmcid:PMC5695909 fatcat:ohdygbdhyvb7td5bcquu4t52gq

Ischemic stroke and depression

2003 Journal of the International Neuropsychological Society  
A comprehensive battery of neuropsychological tests developed for use in epidemiologic studies of dementia (Stern et al., 1992) was also given at that time.  ... 
doi:10.1017/s1355617703930086 pmid:12666767 fatcat:ur5hqabdpbdzfjuok5w5mhx32y

Increased anterior cingulate and caudate activity in bipolar mania

Hilary P Blumberg, Emily Stern, Diana Martinez, Sally Ricketts, Jose de Asis, Thomas White, Jane Epstein, P.Anne McBride, David Eidelberg, James H Kocsis, David A Silbersweig
2000 Biological Psychiatry  
Methods: We utilized a high-sensitivity H 2 15 0 positron emission tomography technique to investigate regions of increased brain activity in mania, compared to euthymia, in bipolar disorder.  ...  H 2 15 0 delivery and data acquisition were performed according to a previously published technique (Silbersweig et al 1993) .  ...  SPECT 7 (7) Increased dorsal AC Subjects manic after lithium discontinuation Gyulai et al 1997 IMP SPECT 3 Increased right Ͼ left anterior temporal (in 2/3) Blumberg et al 1999 H  ... 
doi:10.1016/s0006-3223(00)00962-8 pmid:11094137 fatcat:gvuwuftccbg4xnygfnjxxxcyqq

A mobile web for enhancing statistics and mathematics education [article]

Jamie Lentin, Anna H. Jonsdottir, David Stern, Victoria Mokua and Gunnar Stefansson
2014 arXiv   pre-print
Results with similar solutions at school and diploma level (Manyala, Mbasu, Stern & Stern, 2014) have shown the potential to impact performance and motivation across a broad range of the academic spectrum  ... 
arXiv:1406.5004v2 fatcat:wfc2p3cw4bgndgmnauyosexhga

Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola [article]

Jonathan H Massey, Jun Li, David Stern, Patricia Wittkopp
2020 bioRxiv   pre-print
Acknowledgements 432 We thank members of the Wittkopp, Stern, and Rebeiz labs for helpful discussions. For fly 433 strains, we thank J. True (Stony Brook University).  ...  In brief, stocks were maintained at 23ºC on a 12 h light-dark cycle.  ...  Trends in Genetics, 30(12), 547-554. 532 533 Stern, D. L., & Orgogozo, V. (2008). The loci of evolution: how predictable is genetic 534 evolution?.  ... 
doi:10.1101/2020.06.28.176735 fatcat:4h7wcbsp2raoriied7cd4d5crm

Neuromuscular embodiment of feedback control elements in Drosophila flight [article]

Samuel C Whitehead, Sofia Leone, Theodore Lindsay, Matthew R Meiselman, Noah Cowan, Michael H Dickinson, Nilay Yapici, David Stern, Troy Shirangi, Itai Cohen
2022 bioRxiv   pre-print
Figure 1G ,H show photomontages of responses to b1 motoneuron excitation (G) and inhibition (H) viewed from the side.  ...  G,H Photomontages of example flies undergoing optogenetic excitation (G; Mov. S1,S2) and silencing (H; Mov. S3,S4) of the b1 motoneuron using CsChrimson and GtACR1, respectively.  ... 
doi:10.1101/2022.02.22.481344 fatcat:st3p2dqmt5hllkpfj6mnrpfaiu
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