cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7891607
title: Targeted interplay between bacterial pathogens and host autophagy

description: Due to the critical role played by autophagy in pathogen clearance, pathogens have developed diverse strategies to subvert it. Despite previous key findings of bacteria-autophagy interplay, asystems-level insight into selective targeting by the host and autophagy modulation by the pathogens is lacking. We predicted potential interactions between human autophagy proteins and effector proteins from 56 pathogenic bacterial species by identifying bacterial proteins predicted to have recognition motifs for selective autophagy receptors SQSTM1/p62, CALCOCO2/NDP52 and MAP1LC3/LC3. Using structure-based interaction prediction, we identified bacterial proteins capable to modify core autophagy components. Our analysis revealed that autophagy receptors in general potentially target mostly genus-specific proteins, and not those present in multiple genera. The complementarity between the predicted SQSTM1/p62 and CALCOCO2/NDP52 targets, which has been shown for <i>Salmonella</i>, <i>Listeria</i> and <i>Shigella</i>, could be observed across other pathogens. This complementarity potentially leaves the host more susceptible to chronic infections upon the mutation of autophagy receptors. Proteins derived from enterotoxigenic and non-toxigenic <i>Bacillus</i> outer membrane vesicles indicated that autophagy targets pathogenic proteins rather than non-pathogenic ones. We also observed apathogen-specific pattern as to which autophagy phase could be modulated by specific genera. We found intriguing examples of bacterial proteins that could modulate autophagy, and in turn being targeted by autophagy as ahost defense mechanism. We confirmed experimentally an interplay between a <i>Salmonella</i> protease, YhjJ and autophagy. Our comparative meta-analysis points out key commonalities and differences in how pathogens could affect autophagy and how autophagy potentially recognizes these pathogenic effectors. <b>Abbreviations:</b> ATG5: autophagy related 5; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; GST: glutathione S-transferase; LIR: MAP1LC3/LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3 alpha; OMV: outer membrane vesicles; SQSTM1/p62: sequestosome 1; SCV: <i>Salmonella</i> containing vesicle; TECPR1: tectonin beta-propeller repeat containing 1; YhjJ: hypothetical zinc-protease.
DOI: 10.6084/m9.figshare.7891622.v1
title: gVCF_HG01506

description: 1000 Genomes gVCF mapped to hs37d5 for HG01506. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891523
title: gVCF_NA18924

description: 1000 Genomes gVCF mapped to hs37d5 for NA18924. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891595
title: gVCF_HG03114

description: 1000 Genomes gVCF mapped to hs37d5 for HG03114. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891607.v1
title: Targeted interplay between bacterial pathogens and host autophagy

description: Due to the critical role played by autophagy in pathogen clearance, pathogens have developed diverse strategies to subvert it. Despite previous key findings of bacteria-autophagy interplay, asystems-level insight into selective targeting by the host and autophagy modulation by the pathogens is lacking. We predicted potential interactions between human autophagy proteins and effector proteins from 56 pathogenic bacterial species by identifying bacterial proteins predicted to have recognition motifs for selective autophagy receptors SQSTM1/p62, CALCOCO2/NDP52 and MAP1LC3/LC3. Using structure-based interaction prediction, we identified bacterial proteins capable to modify core autophagy components. Our analysis revealed that autophagy receptors in general potentially target mostly genus-specific proteins, and not those present in multiple genera. The complementarity between the predicted SQSTM1/p62 and CALCOCO2/NDP52 targets, which has been shown for <i>Salmonella</i>, <i>Listeria</i> and <i>Shigella</i>, could be observed across other pathogens. This complementarity potentially leaves the host more susceptible to chronic infections upon the mutation of autophagy receptors. Proteins derived from enterotoxigenic and non-toxigenic <i>Bacillus</i> outer membrane vesicles indicated that autophagy targets pathogenic proteins rather than non-pathogenic ones. We also observed apathogen-specific pattern as to which autophagy phase could be modulated by specific genera. We found intriguing examples of bacterial proteins that could modulate autophagy, and in turn being targeted by autophagy as ahost defense mechanism. We confirmed experimentally an interplay between a <i>Salmonella</i> protease, YhjJ and autophagy. Our comparative meta-analysis points out key commonalities and differences in how pathogens could affect autophagy and how autophagy potentially recognizes these pathogenic effectors. <b>Abbreviations:</b> ATG5: autophagy related 5; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; GST: glutathione S-transferase; LIR: MAP1LC3/LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3 alpha; OMV: outer membrane vesicles; SQSTM1/p62: sequestosome 1; SCV: <i>Salmonella</i> containing vesicle; TECPR1: tectonin beta-propeller repeat containing 1; YhjJ: hypothetical zinc-protease.
DOI: 10.6084/m9.figshare.7891613.v1
title: Functional Annotation

description: Resulted dataset of functional annotation of final version of draft genome.
DOI: 10.6084/m9.figshare.7891523.v1
title: gVCF_NA18924

description: 1000 Genomes gVCF mapped to hs37d5 for NA18924. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891595.v1
title: gVCF_HG03114

description: 1000 Genomes gVCF mapped to hs37d5 for HG03114. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891391
title: gVCF_HG01503

description: 1000 Genomes gVCF mapped to hs37d5 for HG01503. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891400
title: Annotation Result

description: The resulted data matrices of basic annotation of the final version of draft genome.
DOI: 10.6084/m9.figshare.7891403
title: gVCF_NA18923

description: 1000 Genomes gVCF mapped to hs37d5 for NA18923. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891436
title: gVCF_HG03112

description: 1000 Genomes gVCF mapped to hs37d5 for HG03112. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891460
title: gVCF_HG01504

description: 1000 Genomes gVCF mapped to hs37d5 for HG01504. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891400.v1
title: Annotation Result

description: The resulted data matrices of basic annotation of the final version of draft genome.
DOI: 10.6084/m9.figshare.7891403.v1
title: gVCF_NA18923

description: 1000 Genomes gVCF mapped to hs37d5 for NA18923. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891460.v1
title: gVCF_HG01504

description: 1000 Genomes gVCF mapped to hs37d5 for HG01504. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891247
title: gVCF_NA18917

description: 1000 Genomes gVCF mapped to hs37d5 for NA18917. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891340
title: gVCF_HG03111

description: 1000 Genomes gVCF mapped to hs37d5 for HG03111. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891391.v1
title: gVCF_HG01503

description: 1000 Genomes gVCF mapped to hs37d5 for HG01503. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891436.v1
title: gVCF_HG03112

description: 1000 Genomes gVCF mapped to hs37d5 for HG03112. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891229
title: gVCF_NA18916

description: 1000 Genomes gVCF mapped to hs37d5 for NA18916. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891244
title: gVCF_HG01501

description: 1000 Genomes gVCF mapped to hs37d5 for HG01501. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891340.v1
title: gVCF_HG03111

description: 1000 Genomes gVCF mapped to hs37d5 for HG03111. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891220
title: gVCF_HG03109

description: 1000 Genomes gVCF mapped to hs37d5 for HG03109. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891223
title: Change of the tumor size.xlsx

description: Supporting file 1: Summary of the surgically treated cases.<br>Supporting file 2: Chenge of the tumor size from initial presentation
DOI: 10.6084/m9.figshare.7891229.v1
title: gVCF_NA18916

description: 1000 Genomes gVCF mapped to hs37d5 for NA18916. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891220.v1
title: gVCF_HG03109

description: 1000 Genomes gVCF mapped to hs37d5 for HG03109. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891244.v1
title: gVCF_HG01501

description: 1000 Genomes gVCF mapped to hs37d5 for HG01501. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891214
title: gVCF_HG01498

description: 1000 Genomes gVCF mapped to hs37d5 for HG01498. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891217
title: gVCF_HG01500

description: 1000 Genomes gVCF mapped to hs37d5 for HG01500. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891247.v1
title: gVCF_NA18917

description: 1000 Genomes gVCF mapped to hs37d5 for NA18917. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891211
title: gVCF_HG01497

description: 1000 Genomes gVCF mapped to hs37d5 for HG01497. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891214.v1
title: gVCF_HG01498

description: 1000 Genomes gVCF mapped to hs37d5 for HG01498. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891124
title: gVCF_HG01495

description: 1000 Genomes gVCF mapped to hs37d5 for HG01495. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891208
title: gVCF_NA18915

description: 1000 Genomes gVCF mapped to hs37d5 for NA18915. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891211.v1
title: gVCF_HG01497

description: 1000 Genomes gVCF mapped to hs37d5 for HG01497. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891217.v1
title: gVCF_HG01500

description: 1000 Genomes gVCF mapped to hs37d5 for HG01500. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891106
title: gVCF_HG01494

description: 1000 Genomes gVCF mapped to hs37d5 for HG01494. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891115
title: gVCF_HG03105

description: 1000 Genomes gVCF mapped to hs37d5 for HG03105. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891121
title: gVCF_HG03108

description: 1000 Genomes gVCF mapped to hs37d5 for HG03108. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891124.v1
title: gVCF_HG01495

description: 1000 Genomes gVCF mapped to hs37d5 for HG01495. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891208.v1
title: gVCF_NA18915

description: 1000 Genomes gVCF mapped to hs37d5 for NA18915. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.6084/m9.figshare.7891103
title: System identification dataset

description: The dataset contains two sub-folders:<br>1. Load sharing 2. function approximation<br>1. Load sharing ("data.zip"):<br>Each folder corresponds with a subject.<br>the monopolar, single differential and double differential data issaved in the corresponding sub-folders 'mono', 'sd' and 'dd' respectively.<br>In each subfolder, the data is saved as '30.mat','50mat',or '70.mat' corresponding with 30%,50% or 70% MVC isometric flexion-extension.<br>The recording protocol can be found the word file 'report.doc' in this folder inThe subsection: experimental recording.<br>Structure of the '.mat' files :<br>They all have the same structure:<br>Raw_Torque : The measured Torque in ADC numbersstructure 'TAB_ARV' , the EMG envelopes for 'BB', 'BR', 'TM', 'TL' (Read report for the methods and acronyms).<br>2. function approximation ("fun_approx.zip")<br><br>Multiple benchmark examples including a piecewise single variable function, five nonlinear dynamic plants with various nonlinear structures, the chaotic Mackey Glass time series (with different signal to noise ratio (SNR) and various chaotic degree) and the real-world Box-Jenkins gas furnace system are considered to verify the effectiveness of the proposed FJWNN model. <br>The description ("info.pdf") and the entire simulated data as well as the results of our method on the training and test sets (in excel files) were provided.
DOI: 10.6084/m9.figshare.7891121.v1
title: gVCF_HG03108

description: 1000 Genomes gVCF mapped to hs37d5 for HG03108. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.15468/dl.ngusrj
title: Occurrence Download

description: A dataset containing 640 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Yangtze finless porpoise in Yangtze River, China 2006"
 ]
}

 The dataset includes 640 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021264-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e113979
title: Replication data for: Immigrants, Productivity, and Labor Markets

description: Immigration has been a steady force acting on population and employment within countries throughout human history. Focusing on the last four decades, we show that the mix of immigrants to rich countries has been, overall, rather balanced between college and non-college educated. The growth of immigration has been driven by immigrants from nonrich countries. The economic impact of immigration on receiving economies needs to be understood by analyzing the specific skills brought by immigrants. The complementarity and substitutability between immigrants and natives in employment, and the response of receiving economies in terms of specialization and technological choices, are important when considering the general equilibrium effects of immigration. In the United States, a balanced composition of immigrants between college and noncollege educated, together with the adjustment of demand and technology, imply that general equilibrium effects on relative and absolute wages have been small.
DOI: 10.3886/e113979v1
title: Replication data for: Immigrants, Productivity, and Labor Markets

description: Immigration has been a steady force acting on population and employment within countries throughout human history. Focusing on the last four decades, we show that the mix of immigrants to rich countries has been, overall, rather balanced between college and non-college educated. The growth of immigration has been driven by immigrants from nonrich countries. The economic impact of immigration on receiving economies needs to be understood by analyzing the specific skills brought by immigrants. The complementarity and substitutability between immigrants and natives in employment, and the response of receiving economies in terms of specialization and technological choices, are important when considering the general equilibrium effects of immigration. In the United States, a balanced composition of immigrants between college and noncollege educated, together with the adjustment of demand and technology, imply that general equilibrium effects on relative and absolute wages have been small.
DOI: 10.3886/e113980v1
title: Replication data for: Is the Mediterranean the New Rio Grande? US and EU Immigration Pressures in the Long Run

description: How will worldwide changes in population affect pressures for international migration in the future? We examine the past three decades, during which population pressures contributed to substantial labor flows from neighboring countries into the United States and Europe, and contrast them with the coming three decades, which will see sharp reductions in labor-supply growth in Latin America but not in Africa or much of the Middle East. Using a gravity-style empirical model, we examine the contribution of changes in relative labor-supply to bilateral migration in the 2000s and then apply this model to project future bilateral flows based on long-run UN forecasts of working-age populations in sending and receiving countries. Because the Americas are entering an era of uniformly low population growth, labor flows across the Rio Grande are projected to slow markedly. Europe, in contrast, will face substantial demographically driven migration pressures from across the Mediterranean for decades to come. Although these projected inflows would triple the first-generation immigrant stocks of larger European countries between 2010 and 2040, they would still absorb only a small fraction of the 800-million-person increase in the working-age population of Sub-Saharan Africa that is projected to occur over this period.
DOI: 10.3886/e113981v1
title: Replication data for: Why Does China Allow Freer Social Media? Protests versus Surveillance and Propaganda

description: In this paper, we document basic facts regarding public debates about controversial political issues on Chinese social media. Our documentation is based on a dataset of 13.2 billion blog posts published on Sina Weibo--the most prominent Chinese microblogging platform--during the 2009-2013 period. Our primary finding is that a shockingly large number of posts on highly sensitive topics were published and circulated on social media. For instance, we find millions of posts discussing protests, and these posts are informative in predicting the occurrence of specific events. We find an even larger number of posts with explicit corruption allegations, and that these posts predict future corruption charges of specific individuals. Our findings challenge a popular view that an authoritarian regime would relentlessly censor or even ban social media. Instead, the interaction of an authoritarian government with social media seems more complex.
DOI: 10.3886/e114113
title: Replication data for: Are Chinese Growth and Inflation Too Smooth? Evidence from Engel Curves

description: China has experienced remarkably stable growth and inflation in recent years according to official statistics. We use systematic discrepancies between cross-sectional and time-series Engel curves to construct alternative estimates of Chinese growth and inflation. Our estimates suggest that official statistics present a smoothed version of reality. Official inflation rose in the 2000s, but our estimates indicate that true inflation was still higher and consumption growth was overstated. In contrast, inflation was overstated and growth understated during the low-inflation 1990s. These patterns hold for the food Engel curve, and for numerous other categories, such as grain as a fraction of food.
DOI: 10.3886/e114113v1
title: Replication data for: Are Chinese Growth and Inflation Too Smooth? Evidence from Engel Curves

description: China has experienced remarkably stable growth and inflation in recent years according to official statistics. We use systematic discrepancies between cross-sectional and time-series Engel curves to construct alternative estimates of Chinese growth and inflation. Our estimates suggest that official statistics present a smoothed version of reality. Official inflation rose in the 2000s, but our estimates indicate that true inflation was still higher and consumption growth was overstated. In contrast, inflation was overstated and growth understated during the low-inflation 1990s. These patterns hold for the food Engel curve, and for numerous other categories, such as grain as a fraction of food.
DOI: 10.5281/zenodo.3483828
title: Supplementary Data 4

description: Supplementary Data 4
DOI: 10.5281/zenodo.3483829
title: Supplementary Data 4

description: Supplementary Data 4
DOI: 10.3886/e113445
title: Replication data for: Productivity Dispersion in Medicine and Manufacturing

description: The conventional wisdom in health economics is that large differences in average productivity across US hospitals are the result of idiosyncratic features of the healthcare sector which dull the role of market forces. Strikingly, however, we find that productivity dispersion in heart attack treatment across hospitals is, if anything, smaller than in narrowly defined manufacturing industries such as ready-mixed concrete. While this fact admits multiple interpretations, it suggests that healthcare may have more in common with "traditional" sectors than is often assumed, and relatedly, that insights from research on productivity and allocation in other sectors may enrich analysis of healthcare.
DOI: 10.3886/e113446
title: Replication data for: Market Regulations, Prices, and Productivity

description: This study is, to our knowledge, the first attempt to infer the consequences on productivity entailed by anticompetitive regulations in product and labor markets through their impacts on production prices and wages. Results show that changes in production prices and wages at country*industry levels are informative about the creation of rents impeding productivity in different ways and to different extents. A simulation based on OECD regulation indicators suggests that nearly all countries could expect sizeable gains in multifactor productivity from the implementation of large structural reform programs changing anticompetitive regulation practices on product and labor markets.
DOI: 10.3886/e113446v1
title: Replication data for: Market Regulations, Prices, and Productivity

description: This study is, to our knowledge, the first attempt to infer the consequences on productivity entailed by anticompetitive regulations in product and labor markets through their impacts on production prices and wages. Results show that changes in production prices and wages at country*industry levels are informative about the creation of rents impeding productivity in different ways and to different extents. A simulation based on OECD regulation indicators suggests that nearly all countries could expect sizeable gains in multifactor productivity from the implementation of large structural reform programs changing anticompetitive regulation practices on product and labor markets.