cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4896836.v1
title: RNA-binging protein RBM14 regulates dissociation and association of non-homologous end joining proteins

description: Defects in DNA damage response (DDR) are associated with multiple diseases, including cancers and neurodegenerative disorders. Emerging evidence indicates involvement of RNA-binding proteins (RBPs) in DDR. However, functions of the RBPs in DDR pathways remain elusive. We have shown previously that the RNA-binding protein RBM14 is required for non-homologous end joining (NHEJ). Here we show that RBM14 is required for efficient recruitment of XRCC4 and XLF to chromatin and release of KU proteins from chromatin upon DNA damage. Failure of this process leads to accumulation of double-strand breaks (DSBs) in cells. Thus RBM14 plays crucial role in regulation of NHEJ upon DNA damage.
DOI: 10.6084/m9.figshare.4896665.v2
title: Temperature-induced three-phase equilibrium of medium-chain-length poly-3-hydroxyalkanoates-incorporated emulsion system for production of polymeric nanoparticle

description: The study investigated the effects of temperature on the phase behavior of medium-chain-length poly-3-hydroxyalkanoates (mcl-PHA)-incorporated emulsion system. It is suggested that the three-phase equilibrium consisting of lamellar liquid crystalline (L<sub>a</sub>), bi-continuous microemulsion (D), and oil-swollen micelle phases formed in the vicinity of optimal formulation when the combination of phase inversion composition (PIC) and phase inversion temperature (PIT) methods was applied. The interaction effects between two parameters, viz. temperature and mcl-PHA molecular weight, influenced the lamellar/bi-continuous microemulsion formation within the mcl-PHA-incorporated emulsion. It is suggested that the lamellar/bi-continuous microemulsion phase of mcl-PHA-incorporated emulsion can be thermally induced from multiple emulsion system proximately before EIP, and its hypothetical formation mechanism is elucidated in this study.
DOI: 10.6084/m9.figshare.4896533
title: Using Contingent Reinforcement to Augment Muscle Activation After Perinatal Brachial Plexus Injury: A Pilot Study

description: <i>Aim</i>: Examine the feasibility of increasing muscle activation with electromyographically (EMG)-triggered musical-video as reinforcement for children with perinatal brachial plexus injury (PBPI). <i>Methods</i>: Six children with PBPI (9.3 ± 6.3 months; 5 female, 1 male) and 13 typically developing (TD) controls (7.8 ± 3.5 months; 4 female, 9 males) participated. The left arm was affected in 5/6 children with PBPI. We recorded the integral (Vs) of biceps activation with surface EMG during two conditions per arm in one session: (1) 100 second (s) baseline without reinforcement and (2) 300 s reinforcement (musical-video triggered to play with biceps activation above threshold [V]). We examined the relation between the mean integral with reinforcement and hand preference. <i>Results</i>: Mean biceps activation significantly increased from baseline in the affected arm of the group with PBPI by the 2nd (<i>p</i> &lt; .008) and 3rd (<i>p</i> &lt; .0004) 100 s intervals of reinforcement. Six of 6 children with PBPI and 12/13 TD controls increased activation in at least one arm. A lower integral was linked with hand preference for the unaffected right side in the PBPI group. <i>Conclusion</i>: This study supports contingent reinforcement as a feasible method to increase muscle activation. Future work will examine training dose and intensity to increase arm function.
DOI: 10.6084/m9.figshare.4896665.v1
title: Temperature-Induced Three-Phase Equilibrium of Medium-Chain-length Poly-3-hydroxyalkanoates (mcl-PHA)-Incorporated Emulsion System for Production of Polymeric Nanoparticle

description: The study investigated the effects of temperature on the phase behavior of medium-chain-length poly-3-hydroxyalkanoates (mcl-PHA)-incorporated emulsion system. It is suggested that the three-phase equilibrium consisting of lamellar liquid crystalline (<i>L</i><sub><i>a</i></sub>), bi-continuous microemulsion (<i>D</i>) and oil-swollen micelle phases formed in the vicinity of optimal formulation when the combination of phase inversion composition (PIC) and phase inversion temperature (PIT) methods was applied. The interaction effects between two parameters <i>viz.</i> temperature and mcl-PHA molecular weight, influenced the lamellar/bi-continuous microemulsion formation within the mcl-PHA-incorporated emulsion. It is suggested that the lamellar/bi-continuous microemulsion phase of mcl-PHA-incorporated emulsion can be thermally induced from multiple emulsion system proximately before EIP and its hypothetical formation mechanism is elucidated in this study.
DOI: 10.6084/m9.figshare.4896533.v2
title: Using Contingent Reinforcement to Augment Muscle Activation After Perinatal Brachial Plexus Injury: A Pilot Study

description: <i>Aim</i>: Examine the feasibility of increasing muscle activation with electromyographically (EMG)-triggered musical-video as reinforcement for children with perinatal brachial plexus injury (PBPI). <i>Methods</i>: Six children with PBPI (9.3 ± 6.3 months; 5 female, 1 male) and 13 typically developing (TD) controls (7.8 ± 3.5 months; 4 female, 9 males) participated. The left arm was affected in 5/6 children with PBPI. We recorded the integral (Vs) of biceps activation with surface EMG during two conditions per arm in one session: (1) 100 second (s) baseline without reinforcement and (2) 300 s reinforcement (musical-video triggered to play with biceps activation above threshold [V]). We examined the relation between the mean integral with reinforcement and hand preference. <i>Results</i>: Mean biceps activation significantly increased from baseline in the affected arm of the group with PBPI by the 2nd (<i>p</i> &lt; .008) and 3rd (<i>p</i> &lt; .0004) 100 s intervals of reinforcement. Six of 6 children with PBPI and 12/13 TD controls increased activation in at least one arm. A lower integral was linked with hand preference for the unaffected right side in the PBPI group. <i>Conclusion</i>: This study supports contingent reinforcement as a feasible method to increase muscle activation. Future work will examine training dose and intensity to increase arm function.
DOI: 10.6084/m9.figshare.4896533.v1
title: Using Contingent Reinforcement to Augment Muscle Activation After Perinatal Brachial Plexus Injury: A Pilot Study

description: <i>Aim</i>: Examine the feasibility of increasing muscle activation with electromyographically (EMG)-triggered musical-video as reinforcement for children with perinatal brachial plexus injury (PBPI). <i>Methods</i>: Six children with PBPI (9.3 ± 6.3 months; 5 female, 1 male) and 13 typically developing (TD) controls (7.8 ± 3.5 months; 4 female, 9 males) participated. The left arm was affected in 5/6 children with PBPI. We recorded the integral (Vs) of biceps activation with surface EMG during two conditions per arm in one session: (1) 100 second (s) baseline without reinforcement and (2) 300 s reinforcement (musical-video triggered to play with biceps activation above threshold [V]). We examined the relation between the mean integral with reinforcement and hand preference. <i>Results</i>: Mean biceps activation significantly increased from baseline in the affected arm of the group with PBPI by the 2nd (<i>p</i> &lt; .008) and 3rd (<i>p</i> &lt; .0004) 100 s intervals of reinforcement. Six of 6 children with PBPI and 12/13 TD controls increased activation in at least one arm. A lower integral was linked with hand preference for the unaffected right side in the PBPI group. <i>Conclusion</i>: This study supports contingent reinforcement as a feasible method to increase muscle activation. Future work will examine training dose and intensity to increase arm function.
DOI: 10.6084/m9.figshare.4896080
title: Identification of the proteome complement of humanTLK1 reveals it binds and phosphorylates NEK1 regulating its activity

description: The Tousled Like kinases (TLKs) are involved in numerous cellular functions, including the DNA Damage Response (DDR), but only a handful of substrates have been identified thus far. Through a novel proteomic screen, we have now identified 165 human proteins interacting with TLK1, and we have focused this work on NEK1 because of its known role in the DDR, upstream of ATR and Chk1. TLK1 and NEK1 were found to interact by coIP, and their binding is strengthened following exposure of cells to H2O2. Following incubation with doxorubicin, TLK1 and NEK1 relocalize with nuclear repair foci along with γH2AX. TLK1 phosphorylated NEK1 at T141, which lies in the kinase domain, and caused an increase in its activity. Following DNA damage, addition of the TLK1 inhibitor, THD, or overexpression of NEK1-T141A mutant impaired ATR and Chk1 activation, indicating the existence of a TLK1&gt;NEK1&gt;ATR&gt;Chk1 pathway. Indeed, overexpression of the NEK1-T141A mutant resulted in an altered cell cycle response after exposure of cells to oxidative stress, including bypass of G1 arrest and implementation of an intra S-phase checkpoint.
DOI: 10.6084/m9.figshare.4895897
title: Transient exposure to androgens induces a remarkable self-sustained quiescent state in dispersed prostate cancer cells

description: Cellular quiescence is a reversible cell growth arrest that is often assumed to require a persistence of non-permissive external growth conditions for its maintenance. In this work, we showed that androgen could induce a quiescent state that is self-sustained in a cell-autonomous manner through a “hit and run” mechanism in androgen receptor-expressing prostate cancer cells. This phenomenon required the set-up of a sustained redox imbalance and TGFβ/BMP signaling that were dependent on culturing cells at low density. At medium cell density, androgens failed to induce such a self-sustained quiescent state, which correlated with a lesser induction of cell redox imbalance and oxidative stress markers like CDKN1A. These effects of androgens could be mimicked by transient overexpression of CDKN1A that triggered its own expression and a sustained SMAD phosphorylation in cells cultured at low cell density. Overall, our data suggest that self-sustained but fully reversible quiescent states might constitute a general response of dispersed cancer cells to stress conditions.
DOI: 10.6084/m9.figshare.4896038
title: On the Complexity of Item Response Theory Models

description: Complexity in item response theory (IRT) has traditionally been quantified by simply counting the number of freely estimated parameters in the model. However, complexity is also contingent upon the functional form of the model. We examined four popular IRT models—exploratory factor analytic, bifactor, DINA, and DINO—with different functional forms but the same number of free parameters. In comparison, a simpler (unidimensional 3PL) model was specified such that it had 1 more parameter than the previous models. All models were then evaluated according to the minimum description length principle. Specifically, each model was fit to 1,000 data sets that were randomly and uniformly sampled from the complete data space and then assessed using global and item-level fit and diagnostic measures. The findings revealed that the factor analytic and bifactor models possess a strong tendency to fit any possible data. The unidimensional 3PL model displayed minimal fitting propensity, despite the fact that it included an additional free parameter. The DINA and DINO models did not demonstrate a proclivity to fit any possible data, but they did fit well to distinct data patterns. Applied researchers and psychometricians should therefore consider functional form—and not goodness-of-fit alone—when selecting an IRT model.
DOI: 10.6084/m9.figshare.4896038.v1
title: On the Complexity of Item Response Theory Models

description: Complexity in item response theory (IRT) has traditionally been quantified by simply counting the number of freely estimated parameters in the model. However, complexity is also contingent upon the functional form of the model. We examined four popular IRT models—exploratory factor analytic, bifactor, DINA, and DINO—with different functional forms but the same number of free parameters. In comparison, a simpler (unidimensional 3PL) model was specified such that it had 1 more parameter than the previous models. All models were then evaluated according to the minimum description length principle. Specifically, each model was fit to 1,000 data sets that were randomly and uniformly sampled from the complete data space and then assessed using global and item-level fit and diagnostic measures. The findings revealed that the factor analytic and bifactor models possess a strong tendency to fit any possible data. The unidimensional 3PL model displayed minimal fitting propensity, despite the fact that it included an additional free parameter. The DINA and DINO models did not demonstrate a proclivity to fit any possible data, but they did fit well to distinct data patterns. Applied researchers and psychometricians should therefore consider functional form—and not goodness-of-fit alone—when selecting an IRT model.
DOI: 10.6084/m9.figshare.4896080.v1
title: Identification of the proteome complement of humanTLK1 reveals it binds and phosphorylates NEK1 regulating its activity

description: The Tousled Like kinases (TLKs) are involved in numerous cellular functions, including the DNA Damage Response (DDR), but only a handful of substrates have been identified thus far. Through a novel proteomic screen, we have now identified 165 human proteins interacting with TLK1, and we have focused this work on NEK1 because of its known role in the DDR, upstream of ATR and Chk1. TLK1 and NEK1 were found to interact by coIP, and their binding is strengthened following exposure of cells to H2O2. Following incubation with doxorubicin, TLK1 and NEK1 relocalize with nuclear repair foci along with γH2AX. TLK1 phosphorylated NEK1 at T141, which lies in the kinase domain, and caused an increase in its activity. Following DNA damage, addition of the TLK1 inhibitor, THD, or overexpression of NEK1-T141A mutant impaired ATR and Chk1 activation, indicating the existence of a TLK1&gt;NEK1&gt;ATR&gt;Chk1 pathway. Indeed, overexpression of the NEK1-T141A mutant resulted in an altered cell cycle response after exposure of cells to oxidative stress, including bypass of G1 arrest and implementation of an intra S-phase checkpoint.
DOI: 10.6084/m9.figshare.4895897.v1
title: Transient exposure to androgens induces a remarkable self-sustained quiescent state in dispersed prostate cancer cells

description: Cellular quiescence is a reversible cell growth arrest that is often assumed to require a persistence of non-permissive external growth conditions for its maintenance. In this work, we showed that androgen could induce a quiescent state that is self-sustained in a cell-autonomous manner through a “hit and run” mechanism in androgen receptor-expressing prostate cancer cells. This phenomenon required the set-up of a sustained redox imbalance and TGFβ/BMP signaling that were dependent on culturing cells at low density. At medium cell density, androgens failed to induce such a self-sustained quiescent state, which correlated with a lesser induction of cell redox imbalance and oxidative stress markers like CDKN1A. These effects of androgens could be mimicked by transient overexpression of CDKN1A that triggered its own expression and a sustained SMAD phosphorylation in cells cultured at low cell density. Overall, our data suggest that self-sustained but fully reversible quiescent states might constitute a general response of dispersed cancer cells to stress conditions.
DOI: 10.6084/m9.figshare.4893320
title: DrugSig

description: We collected drug response microarray data and annotated related drug and targets information from public databases and scientific literature. By selecting top 500 up-regulated and down-regulated genes as drug signatures, we manually established the DrugSig database. Currently DrugSig contains more than 1300 drugs, 7000 microarray and 800 targets. Database URL: http://biotechlab.fudan.edu.cn/database/drugsig/.<br> <br>
DOI: 10.6084/m9.figshare.4893323
title: Picidae Dataset.zip

description: The proposed dataset contains 1669 labeled audio files from the following Picidae species doing 3 types of birdsongs: call, drumming and song. Audio data are organized in thirteen folders: twelve containing the labeled audios of each birdsong type from every Picidae specie listed in what follows and one folder containing the background sound samples. <br>1- DendrocoposLeucotos - call.2- DendrocoposLeucotos - drumming.3- DendrocoposMajor - call.4- DendrocoposMajor - drumming.5- DendrocoposMedius - call.6- DendrocoposMedius - song.7- DendrocoposMinor - call.8- DendrocoposMinor - drumming.9- DryocopusMartius - call.10- DryocopusMartius - drumming.11- JynxTorquilla - song.12- PicusViridis - song.13- Silence (or background noise).Licence type: CC-BY-SA
DOI: 10.6084/m9.figshare.4893353
title: Neurosynth LDA topics (v4)

description: Topic keys and study loadings for all Neurosynth LDA topic sets found on the Neurosynth website as of July 2015.
DOI: 10.6084/m9.figshare.4893260
title: Sources of variance in immunological traits: evidence of congruent latitudinal trends across species

description: We studied among-population differences of two parameters reflecting constitutive immunity – phenoloxidase (PO) and lytic activity – using common garden design on three distantly related moth species represented by populations ranging from northern Finland to Georgia (Caucasus).
DOI: 10.6084/m9.figshare.4893320.v1
title: DrugSig

description: We collected drug response microarray data and annotated related drug and targets information from public databases and scientific literature. By selecting top 500 up-regulated and down-regulated genes as drug signatures, we manually established the DrugSig database. Currently DrugSig contains more than 1300 drugs, 7000 microarray and 800 targets. Database URL: http://biotechlab.fudan.edu.cn/database/drugsig/.<br> <br>
DOI: 10.6084/m9.figshare.4893215
title: GDP data-Lixiong Yang.xlsx

description: The quarterly GDP data for the period 2001Q1–2013Q4, including both the headline GDP estimates and the three components. To assess the quality of China’s preliminary data of the quarterly GDP, we examine the unbiasedness and efficiency of the preliminary data of the headline GDP and the three components. We modify the tests for unbiasedness and efficiency by incorporating the Fourier approximation to capture the effect of the state of the economy.
DOI: 10.6084/m9.figshare.4893323.v1
title: Picidae Dataset.zip

description: The proposed dataset contains 1669 labeled audio files from the following Picidae species doing 3 types of birdsongs: call, drumming and song. Audio data are organized in thirteen folders: twelve containing the labeled audios of each birdsong type from every Picidae specie listed in what follows and one folder containing the background sound samples. <br>1- DendrocoposLeucotos - call.2- DendrocoposLeucotos - drumming.3- DendrocoposMajor - call.4- DendrocoposMajor - drumming.5- DendrocoposMedius - call.6- DendrocoposMedius - song.7- DendrocoposMinor - call.8- DendrocoposMinor - drumming.9- DryocopusMartius - call.10- DryocopusMartius - drumming.11- JynxTorquilla - song.12- PicusViridis - song.13- Silence (or background noise).
DOI: 10.6084/m9.figshare.4893260.v2
title: Sources of variance in immunological traits: evidence of congruent latitudinal trends across species

description: We studied among-population differences of two parameters reflecting constitutive immunity – phenoloxidase (PO) and lytic activity – using common garden design on three distantly related moth species represented by populations ranging from northern Finland to Georgia (Caucasus).
DOI: 10.6084/m9.figshare.4893170
title: Figure 45-corner plot.png

description: Parameter space for a model refined from x-ray pair distribution function data.
DOI: 10.6084/m9.figshare.4893170.v1
title: Figure 45-corner plot.png

description: Parameter space for a model refined from x-ray pair distribution function data.
DOI: 10.6084/m9.figshare.4893260.v1
title: Sources of variance in immunological traits: evidence of congruent latitudinal trends across species

description: We studied among-population differences of two parameters reflecting constitutive immunity – phenoloxidase (PO) and lytic activity – using common garden design on three distantly related moth species represented by populations ranging from northern Finland to Georgia (Caucasus).
DOI: 10.6084/m9.figshare.4892897
title: binfalse.de

description: My blog at http://binfalse.de
DOI: 10.6084/m9.figshare.4892897.v1
title: binfalse.de

description: My blog at http://binfalse.de
DOI: 10.6084/m9.figshare.4893167.v1
title: DEG

description: DEGs
DOI: 10.6084/m9.figshare.4892864
title: RNA-seq raw data of biological replicate 3 of PS-C

description: RNA-seq raw data of biological replicate 3 of cytoplasmic male sterility line C48-2 spikelets at pollen mother cell stage
DOI: 10.6084/m9.figshare.4892768
title: ACTwatch Outlet Survey Files: Thailand 2016

description: ACTwatch Thailand 2016 files This fileset contains the questionnaire, codebook, reference document and dataset (in Stata .dta format) for the Thailand 2016 ACTwatch outlet survey. Started in 2008, ACTwatch was intended to fill evidence gaps related to malaria diagnostics, antimalarial medicines and fever case management in the private and public sectors. ACTwatch collected data to inform evidence-based malaria control policies and programmes. ACTwatch was a PSI research project in partnership with LSHTM. ACTwatch measured nationally representative surveys to all public and private health outlets within selected regions, across a total of 12 countries in sub-Saharan Africa and the Greater Mekong Sub-region and multiple years. Outlet Surveys monitored trends in the availability, volumes, and prices of antimalarials in the public and private sectors, which included the informal sector. All outlet types with the potential to sell antimalarials were included, from hospitals to private pharmacies to street hawkers. The collection and processing of these data provided sound evidence for country-specific policy recommendations. The use of standardized indicators allowed for broad trends to be identified and global policy recommendations to be implemented into policy and action.A guidance document containing comprehensive information on the ACTwatch project, design, questionnaires and data can be found by clicking on the reference link below.All potential data users are encouraged to review this document before analyzing any ACTwatch data.Note: version 2 of this record replaces the original files containing indirect identifying information in the outlet survey<br>