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Stanford Research Data
This data set is a compilation of the historical CMOS technology scaling data presented in the ITRS, journals, and conferences including IEDM and VLSI Technology from 1988 and onward. Chi-Shuen Lee, Jieying Luo, and H.-S. Philip Wong at Stanford University compiled the data; Thomas N. Theis at Columbia University provided the data originally compiled by Robert W. Keyes at IBM T.J. Watson Research Center and published in Figure 1 of Rolf Landauer's 1988 paper. The historical scaling trend of logic switching energy and integration density were published in Figure 1 and 2, respectively in the paper, "The End of Moore’s Law: A New Beginning for Information Technology" by Theis and Wong (see Related Published Work below for the full citation.
Collection
Stanford Research Data
In matrix recovery from random linear measurements, one is interested in recovering an unknown $M$-by-$N$ matrix $X_0$ from $n
Collection
Reproducible Research Support for Statistics of the Microbiome
Complete ribosomal sequence variant abundance data and analysis files for paper entitled: Multidomain Analyses of a Longitudinal Human Microbiome Intestinal Cleanout Perturbation Experiment. This work focuses on the stability, resilience, and response to perturbation of the bacterial communities in the human gut. Informative flash flood-like disturbances that eliminate most gastrointestinal biomass can be induced using a clinically-relevant iso-osmotic agent. We designed and executed such a disturbance in human volunteers using a dense longitudinal sampling scheme extending before and after induced diarrhea. This experiment has enabled a careful multidomain analysis of a controlled perturbation of the human gut microbiota with a new level of resolution. These new longitudinal multidomain data were analyzed using recently developed statistical methods that demonstrate improvements over current practices. By imposing sparsity constraints we have enhanced the interpretability of the analyses and by employing a new adaptive generalized principal components analysis, incorporated modulated phylogenetic information and enhanced interpretation through scoring of the portions of the tree most influenced by the perturbation. Our analyses leverage the taxa-sample duality in the data to show how the gut microbiota recovers this perturbation. Through a holistic approach that integrates phylogenetic, metagenomic and abundance information, we elucidate patterns of taxonomic and functional change that characterize the community recovery process across individuals. We provide complete code and illustrations of new statistical methods for high-dimensional, longitudinal multidomain data that provide greater interpretability than existing methods. Funded by NIH TR01 grant AI112401.
Collection
Stanford Research Data
# Data for Waskom and Wagner (2017) PNAS This repository contains data related to the following paper: Waskom M.L., Wagner A.D. (2017). Distributed representation of context by intrinsic subnetworks in prefrontal cortex. Proceedings of the National Academy of the Sciences, USA. The paper is available on the PNAS website: http://www.pnas.org/cgi/doi/10.1073/pnas.1615269114 Code implementing the results in the paper is included here and is also available on github: https://github.com/WagnerLabPapers/Waskom_PNAS_2017 The datasets in this repository are organized in subdirectories as follows: ## Preprocessed data - roi_cache: Preprocessed/denoised time series data from the ROIs in the paper ## Analysis results - decoding_analysis: Decoding analyses and estimated context preferences - spatial_analysis: Spatial organization analyses - correlation_analysis: Spontaneous correlation analyses ## Supporting data - mesh: Computationally reconstructed cortex models - reg: Functional template and registration relating it to anatomical space ## Analysis code - code: A copy of the analysis code repository available on github ## License Copyright (c) 2017, Michael Waskom and Anthony Wagner Released under a CC-BY 4.0 License
Collection
Stanford Research Data
This a snapshot of the NeuroVault.org database. It include all public collections of statistical maps deposited in NeuroVault as long as they were linked to an external publication. This snapshot is an attempt to improve chances of long term persistance of data deposited in NeuroVault.org.
Collection
Mapping the Republic of Letters
The json file(s) were created within the visualization application Palladio (hdlab.stanford.edu/palladio).
Collection
Stanford Research Data
Group II chaperonins are ring-shaped chaperones. Their ATP-dependent allosteric regulation remains ill-defined. Given their complex oligomeric topology, structural techniques have had limited success in suggesting allosteric determinants. High sequence conservation among chaperonins has also hindered the prediction of allosteric networks, as many mathematical covariation approaches cannot be applied to conserved proteins. Here, we develop an information theoretic strategy robust to residue conservation and apply it to group II chaperonins. We identify a contiguous network of covarying residues that connects all nucleotide binding pockets within each chaperonin ring. An interfacial residue between the networks of neighboring subunits controls positive cooperativity by communicating nucleotide occupancy. Strikingly, chaperonin allostery is tunable through mutations at this position. Naturally occurring variants that double the extent of positive cooperativity are less prevalent in nature. We propose that being less cooperative that attainable allows the chaperonins to support robust folding over a wider range of metabolic conditions.
Collection
Stanford Research Data
Electrophysiological data from implanted electrodes in humans are rare. Most recordings that have been performed are with epilepsy patients who have electrocorticographic (ECoG) electrodes implanted in the course of diagnostic localization of seizure focus prior to surgical resection. Only a small group of scientists have had the opportunity to work with these patients, and access to ECoG data has remained somewhat exclusive. It is recorded at only a few institutions around the country, often with different amplification setups, sampling rates, and behavioral variations (even within the same institution). Therefore, we have compiled a set of 16 benchmark experiments, with over 200 individual datasets made with the same amplifiers, at the same settings, with the same person interacting with the subject and performing the experiment. Depending on where the electrodes were placed for clinical indication, we performed experiments known to be associated with covered brain areas. In every case, electrode positions have been registered to brain anatomy. All data, anatomic, and analysis files (MATLAB code) are in a common, intuitive file structure. Every study/task has at least 4 subjects with confirmed task‐modulated signal change in at least 1 electrode. Our sampling rate and data format were kept uniform, and the anatomic localization was determined rigorously in each case. In the course of analyzing these data, a large number of novel analysis techniques were developed. We will release our code base with the data, in such a way that all figures from published manuscripts describing these data could be directly reproduced. Four of the experiments have not been published. These data, along with behavioral parameterizations, anatomic localizations, and brain‐surface renderings are now available for download worldwide, without restriction on use (other than proper citation). The experiments/analyses contained in the library are: • Baseline fixation (low freq), Folder name 'base_pwrlaw', Number of Subjects 16; The basic baseline fixation task was performed by the subjects fixating with their eyes open on an “X”, on the wall 3 m away, for 2 to 3 minutes. Original Manuscript Miller et al., 2009a • Simple cue-based movement of hand&tongue, Folder name 'mot_t_h', Number of Subjects 19; Subjects performed simple, repetitive, motor tasks of hand (synchronous flexion and extension of all fingers, i.e., clenching and releasing a fist at a self-paced rate of ~1-2 Hz) or tongue (opening of mouth with protrusion and retraction of the tongue, i.e., sticking the tongue in and out, also at ~1-2 Hz). Original Manuscript Miller et al., 2007 • Individual finger movements , Folder name 'dg', Number of Subjects 9; During the finger movement task, subjects were cued with a word displayed on a bedside monitor indicating which finger (contralateral to grid placement) to move during 2- second movement trials. The subject performed self-paced movements in response to each of these cues while a dataglove recorded finger position.Original Manuscript Miller et al., 2009b, Miller et al., 2012 • Joystick tracking , Folder name 'JoystickTracking', Number of Subjects 4; The patient used a joystick to track a counter-clockwise moving target (hand contralateral to grid).Original Manuscript Schalk et al., 2007 • Gestures , Folder name 'gestures', Number of Subjects 5; A series of hand motor tasks where patients performed cued simple figure movements, cued gestures, or self-generated gestures, while finger position was recorded with a dataglove (hand used was contralateral to grid).Data not yet published • Movement imagery (hand&tongue, with movement data as well), Folder name 'Imagery_t_h', Number of Subjects 8; Subjects first performed an overt hand and tongue cued movement task. Following the overt movement experiment, each subject performed an imagery task, imagining making identical movement rather than executing the movement.Original Manuscript Miller et al., 2010b • One Dimensional Cursor control by imagery-based feedback (With movement and imagery data), Folder name 'Mot_Im_FB', Number of Subjects 4; Subjects first performed a cue-based movement, then cue-based imagery, then one dimensional cursor control feedback task.Original Manuscript Miller et al., 2010b • Realtime Mapping, Speech Noun reading & Verb generation, Folder name 'rtlang', Number of Subjects 7; Patients participated in a simple verb-generation task, where nouns (approximately 2.5 cm high, and 8-12 cm wide) were presented on a screen approximately 1 m from the patient, at the bedside. The patient’s task was to speak a verb that was connected to the noun: for example, if the cue read “ball”, the patient might say “kick”. Original Manuscript Miller et al., 2011 • N-back working memory task with pictures of houses, Folder name 'nback', Number of Subjects 4; After a period of baseline fixation, patients performed an n-back working memory task using pictures of houses. First they identified a 'target' house picture which appeared during a sequence of presented house pictures (0 back). Second, they identified when a picture had been shown twice in a row (1 back). Finally, they identified when a picture had been repeated with a distracting image in between (2-back).Data not yet published • Visual search task, Folder name 'vissearch', Number of Subjects 5; The visual search task consisted of a 4-by-5 array of colored squares, and the subject would navigate between the boxes depending on a cue to state the color of the cued square. Original Manuscript Miller et al., 2010a • Basic Face-house picture presentation, Folder name 'fhpred', Number of Subjects 11; Simple face/house pictures were shown in random order for 400 ms each, with 400ms inter-stimulus blank screen. Original Manuscript Miller et al., 2015 • Noise-masked face-house picture presentation, Folder name 'fhnoisy', Number of Subjects 7; After performing a simple face and house picture viewing task, subjects also performed a face-detection task using phase-scrambled close-up pictures of faces and houses.Original Manuscript manuscript in submission • Baseline fixation Phase Amplitude Coupling, Folder name 'base_PAC', Number of Subjects 10; The basic baseline fixation task was performed by the subjects fixating with their eyes open on an ““X””, on the wall 3 m away, for 2 to 3 minutes. Original Manuscript Miller et al., 2012 • Baseline fixation (high frequency), Folder name 'base_HighFreq', Number of Subjects 4; The basic baseline fixation task was performed by the subjects fixating with their eyes open on an ““X””, on the wall 3 m away, for 2 to 3 minutes, while recording at 10kHz. Original Manuscript Miller et al., 2009a • Mouse tracking, Folder name 'MouseTracking', Number of Subjects 4; The patient used a mouse on a mousepad to track a counter-clockwise moving target (hand contralateral to grid).Data not yet published • Repeat runs: Noun reading & Verb generation, Folder name 'NounVerb_lists', Number of Subjects 4; These files form a set of speech data for lists of nouns that were first read directly, and then used to produce associated action verbs. There were 2 noun lists, and each list was presented 3 times for noun reading, then 3 times for verb production. Data not yet published References: Miller, K.J., Hermes, D., Pestilli, F., Wig, G.S., Ojemann, J.G., Face percept formation in human ventral temporal cortex, In Submission Miller, K.J., Schalk, G., Hermes, D., Ojemann, J.G., Rao, R.P.N., 2016, Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change, PLoS Computational Biology, 12(1): e1004660. doi:10.1371/journal. pcbi.1004660 Miller, K.J., Hermes, D., Witthoft, N., Rao, R.P.N., Ojemann, J.G., 2015, The physiology of perception in human temporal lobe is specialized for contextual novelty, Journal of Neurophysiology, 114(1): 256-63. Miller, K.J., Hermes, D., Honey, C.J., Hebb, A.O., Parvizi, J, Ramsey, N.F., Knight, R.T., Ojemann, J.G., Fetz, E.E., 2012, Human motor cortical activity is selectively phase-entrained on underlying rhythms, PLoS Computational Biology 8 (9), e1002655 Miller, K.J., Abel, T.J., Hebb, A.O., Ojemann, J.G., 2011, Rapid online language mapping with electrocorticography, J Neurosurg Pediatrics 7:482-490 Miller,K.J., Hermes, D., Honey, C.J., Sharma, M., Rao, R.P.N., den Nijs, M., Fetz, E.E., Sejnowski, T.J., Hebb, A.O., Ojemann, J.G., Makeig, S., Leuthardt, E.C., 2010a, Dynamic modulation of local population activity by rhythm phase in human occipital cortex during a visual search task, Front. Hum. Neurosci. 4:197. Miller, K.J., Schalk, G.S., Fetz,E.E., den Nijs, M., Ojemann, J.G., Rao, R.P.N. 2010b, Cortical Activity During Motor Movement, Motor Imagery, and Imagery-Based Online Feedback, PNAS 107(9 )4430-4435 Miller, K.J.; Sorensen, L.B.; Ojemann, J.G.; den Nijs, M, 2009a, Power-Law Scaling in the Brain Surface Electric Potential. PLOS Computational Biology, 5(12): e1000609. Miller, K.J., S. Zanos, E.E. Fetz, M. den Nijs, and J.G. Ojemann, 2009b, Decoupling the Cortical Power Spectrum Reveals Real-Time Representation of Individual Finger Movements in Humans. Journal of Neuroscience, 2009. 29(10): p. 3132. Schalk, G., K.J. Miller; N.R. Anderson; J.A. Wilson; M.D. Smyth, J.G. Ojemann; D.W. Moran; J.R. Wolpaw; E.C. Leuthardt, 2008, Two-Dimensional Movement Control Using Electrocorticographic Signals in Humans J Neural Eng. 5(1): p. 75-84. Miller, K.J., Leuthardt, E.C., Schalk, G., Anderson, N., Rao, R.P.N., Moran, D., Ojemann, J.G., 2007. Spectral Changes in Cortical Surface Potentials during Motor Movement, Journal of Neuroscience, 27(9):2424–2432
Collection
OpenfMRI Datasets
Dataset Information The Stockholm Sleepy Brain Study I is a functional brain imaging study where 48 younger (20-30 years) and 36 older (65-75 years) healthy participants underwent magnetic resonance imaging after normal sleep and partial sleep deprivation in a crossover design. We performed three experiments investigating emotional mimicry, empathy for pain, and cognitive reappraisal, as well as resting state functional magnetic resonance imaging (fMRI). We also acquired T1- and T2-weighted structural images and diffusion tensor images. On the night before imaging, participants were monitored with ambulatory polysomnography and were instructed to sleep either as usual or only three hours. Participants came to the scanner the following evening. Besides MRI scanning, participants underwent behavioral tests and contributed blood samples, which have been stored in a biobank and used for DNA analyses. Participants also completed a variety of self-report measures. The resulting multimodal dataset may be useful for hypothesis generation or independent validation of effects of sleep deprivation and aging, as well as investigation of cross-sectional associations between our different outcomes. Dataset Notes The faces, hands, and arrows task-based fMRI experiment data will be published at a later time. Update (2016/06/21): resting state fMRI will also be published at a later time. The currently published data set includes: Demographics, surveys, questionnaire data Eye tracking data High resolution T1-weighted and T2-weighted structural scans B0 field map data Diffusion-weighted imaging scans Polysomnography raw data DNA analysis results Data Descriptor Manuscript A preprint of the corresponding data descriptor manuscript (submitted) is available at the Karolinska Institutet open archive.
Collection
Mapping the Republic of Letters
This json file that can be read with Palladio, a visualization platform developed at Stanford University for the Mapping the Republic of Letters project. The interactive visualizations include two maps with accompanying facet filters, timeline histograms, timespan charts and tables. Together, these correspondence and correspondents visualizations allow you to investigate and probe the changing nature and make-up of Franklin’s network during the London Decades (1757-1775) in your own way.
Collection
Reproducible Research Support for Statistics of the Microbiome
High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or OTU composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97\% similarity and normalize the data by subsampling to eqalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, whether parametric or non-parametric. We provide examples of using the R packages dada2, phyloseq, DESeq2 and vegan to filter, visualize and test microbiome data and community networks.
Collection
OpenfMRI Datasets
Thirty female subjects performed a passive viewing task with blocks of food and nonfood images. More procedures can be found in the publication" Allured or alarmed: counteractive control responses to food temptations in the brain.  "During scanning, subjects alternately viewed 24 s blocks of palatable food images (8 blocks) and non-food images (i.e., office utensils; 8 blocks), interspersed with 8–16 s rest blocks showing a crosshair (12 s on average). Halfway the task there was a 10 s break. In the image blocks, 8 images were presented for 2.5 s each with a 0.5 s inter-stimulus interval. All pictures were of equal size and displayed the (food) object on a white background. Food pictures were selected to represent foods that are both attractive and ‘forbidden’ (i.e., fattening), congruent with our definition of temptations." Dataset Contains: BOLD-contrast fMRI data and T1-weighted high resolution structural scans
Collection
OpenfMRI Datasets
Subjects performed two blocks of an event-related probabilistic classification learning task. They then performed two more blocks of the same task with the reward contingencies reversed.
Collection
Stanford Research Data
The data and code provided here are supplementary information for the paper “Incoherence of Partial Component Sampling in multidimensional NMR" by H. Monajemi, D.L. Donoho, J.C. Hoch, and A.D. Schuyler. Please read INSTRUCTION.TXT for reproducing the results of the article. Abstract of the article: In NMR spectroscopy, random undersampling in the indirect dimensions causes reconstruction artifacts whose size can be bounded using the so-called {\it coherence}. In experiments with multiple indirect dimensions, new undersampling approaches were recently proposed: random phase detection (RPD) \cite{Maciejewski11} and its generalization, partial component sampling (PCS) \cite{Schuyler13}. The new approaches are fully aware of the fact that high-dimensional experiments generate hypercomplex-valued free induction decays; they randomly acquire only certain low-dimensional components of each high-dimensional hypercomplex entry. We provide a classification of various hypercomplex-aware undersampling schemes, and define a hypercomplex-aware coherence appropriate for such undersampling schemes; we then use it to quantify undersampling artifacts of RPD and various PCS schemes.
Collection
Stanford Research Data
This data repository contains the code used to calculate mean values of d13C and of soil respiration and to perform sensitivity tests on the analysis. To calculate soil respiration requires the installation of two packages ("soilresp" and "CRGfunc"), both of which are included in this data repository. Additionally included is the .csv file which contains the compilation of d13C data. The output of these R scripts are Figure 2 (main text) and DR Figures 3-9 (Data Repository).
Dataset
1 online resource Digital: data file; text file.
Collection
Government Information United States Federal Collection
  • December 2016 state-by-state data
  • December 2016 state-by-state spreadsheet sources by column.
This excel table contains the most up to date state-level data available related to certain provisions of the Affordable Care Act. This table includes data on the uninsured, private market reforms, employer coverage, Medicaid, the individual market (including the Health Insurance Marketplace), and Medicare. These data are drawn from previously published sources and new analyses. Also includes a text document with sources and additional details.
Collection
VISTA Lab
Illumination plays an important role in the image capture process. Too little or too much energy in particular wavelengths can impact the scene appearance in a way that is difficult to manage by color constancy post processing methods. We use an adjustable multispectral flash to modify the spectral illumination of a scene. The flash is composed of a small number of narrowband lights, and the imaging system takes a sequence of images of the scene under each of those lights. Pixel data is used to estimate the spectral power distribution of the ambient light, and to adjust the flash spectrum either to match or to complement the ambient illuminant. The optimized flash spectrum can be used in subsequent captures, or a synthetic image can be computationally rendered from the available data. Under extreme illumination conditions images captured with the matching flash have no color cast, and the complementary flash produces more balanced colors. The proposed system also improves the quality of images captured in underwater environments. This repository contains sample data and results to be used with the released Matlab implementation of the algorithms.
Collection
Mapping the Republic of Letters
Three tables of data offered for the 3443 documents, 774 individuals or groups, and 339 places associated with the correspondence network of Benjamin Franklin during the London Years (1757-1775). For a rationale and explanation, please see the accompanying data schema.
Collection
Reproducible Research Support for Statistics of the Microbiome
This is the repository accompanying the Nature Methods paper on DADA2. The repository contains the Extreme, Balanced and HMP data sets as well as five complete R markdown workflows and their html output. DADA2 is a software package that models and corrects Illumina- sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.
Collection
Payne Paleobiology Lab Data Files
This file contains the data file analyzed for the paper published at Payne et al. (2016) in Biology Letters.