cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11494626.v2
title: Metadata record for: Reference data on in vitro anatomy and indentation response of tissue layers of musculoskeletal extremities

description: This dataset contains key characteristics about the data described in the Data Descriptor Reference data on in vitro anatomy and indentation response of tissue layers of musculoskeletal extremities. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11494626.v1
title: Metadata record for: Reference data on in vitro anatomy and indentation response of tissue layers of musculoskeletal extremities

description: This dataset contains key characteristics about the data described in the Data Descriptor Reference data on in vitro anatomy and indentation response of tissue layers of musculoskeletal extremities. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.11494539
title: lyricalpreferences_moralfoundations_big5personality

description: This is data associated with a line of research that investigated personality traits and moral reasoning styles as precursors to media preferences.
DOI: 10.6084/m9.figshare.11494110
title: sample_data.tar.gz

description: RNASeq sample dataset to test bulkRNASeqPIPE<br>
DOI: 10.6084/m9.figshare.11494110.v1
title: sample_data.tar.gz

description: RNASeq sample dataset to test bulkRNASeqPIPE<br>
DOI: 10.6084/m9.figshare.11494065
title: Supplementary Material for: Genes Positively Selected in Domesticated Mammals Are Significantly Dysregulated in the Blood of Individuals with Autism Spectrum Disorders

description: Human self-domestication (i.e., the presence of traits in our species that are commonly found in domesticated animals) has been hypothesized to have contributed to the emergence of many human-specific features, including aspects of our cognition and behavior. Signs of self-domestication have been claimed to be attenuated in individuals with autism spectrum disorders (ASD), this conceivably accounting for facets of their distinctive cognitive and behavioral profile, although this possibility needs to be properly tested. In this study, we have found that candidate genes for mammal domestication, but not for neural crest development and function, are significantly dysregulated in the blood of subjects with ASD. The set of differentially expressed genes (DEGs) is enriched in biological and molecular processes, as well as in pathological phenotypes, of relevance for the etiology of ASD, like lipid metabolism, cell apoptosis, the activity of the insulin-like growth factor, gene expression regulation, skin/hair anomalies, musculoskeletal abnormalities, and hearing impairment. Moreover, among the DEGs, there are known candidates for ASD and/or genes involved in biological processes known to be affected in ASD. Our findings give support to the view that one important aspect of the etiopathogenesis of ASD is the abnormal manifestation of features of human self-domestication.
DOI: 10.6084/m9.figshare.11493843
title: Proteome database of Bacillus amyloliquefaciens UMAF6639

description: Known as the original source for the BamHI restriction enzyme, <i>Bacillus amyloliquefaciens</i> is an important biocontrol strain useful for fighting root pathogens. This work sought to illuminate the proteome repertoire of <i>B. amyloliquefaciens</i> UMAF6639 by parsing the UniProt proteome file of the bacterium. Specifically, an in-house MATLAB proteome analysis software helps construct a proteome database comprising protein name, amino acid sequence, number of residues, molecular weight of protein and nucleotide sequence of protein. Available as an Excel file for ease of access and storage, the reported proteome database of <i>B. amyloliquefaciens</i> UMAF6639 should find use in guiding experimental molecular research seeking to understand the beneficial roles of this bacterium in agriculture and the environment. <br><br>
DOI: 10.6084/m9.figshare.11493843.v1
title: Proteome database of Bacillus amyloliquefaciens UMAF6639

description: Known as the original source for the BamHI restriction enzyme, <i>Bacillus amyloliquefaciens</i> is an important biocontrol strain useful for fighting root pathogens. This work sought to illuminate the proteome repertoire of <i>B. amyloliquefaciens</i> UMAF6639 by parsing the UniProt proteome file of the bacterium. Specifically, an in-house MATLAB proteome analysis software helps construct a proteome database comprising protein name, amino acid sequence, number of residues, molecular weight of protein and nucleotide sequence of protein. Available as an Excel file for ease of access and storage, the reported proteome database of <i>B. amyloliquefaciens</i> UMAF6639 should find use in guiding experimental molecular research seeking to understand the beneficial roles of this bacterium in agriculture and the environment. <br><br>
DOI: 10.6084/m9.figshare.11493840
title: Supplementary Material for: Ventilation with 18, 21, or 100% Oxygen during Cardiopulmonary Resuscitation of Asphyxiated Piglets: A Randomized Controlled Animal Trial

description: <b><i>Background:</i></b> In previous piglet experiments of profound asphyxia and cardiac arrest, recovery was similar when 21 and 100% oxygen were used for positive pressure ventilation (PPV). There was no consistent reduction in inflammation and oxidative stress in piglets ventilated with 21 or 100% oxygen. <b><i>Objectives:</i></b> We aimed to investigate hypoxic resuscitation, i.e., PPV with 18% oxygen, in profoundly asphyxiated piglets with cardiac arrest. We hypothesized that resuscitation with 18% oxygen would result in less inflammation and oxidative stress compared to 21 or 100% oxygen. <b><i>Method:</i></b> Twenty-four piglets were exposed to 30 min of normocapnic hypoxia followed by asphyxia until asystole. The piglets were randomized to PPV with 18% oxygen (<i>n</i> = 8), 21% oxygen (<i>n</i> = 8), or 100% oxygen (<i>n</i> = 8), and resuscitated with chest compressions and intravenous epinephrine. Return of spontaneous circulation (ROSC) was defined as an unassisted heart rate ≥100 bpm for 15 s. Lactate, GSH (total glutathione), GSSG (oxidized glutathione), and GSSG/GSH ratio were measured in myocardial and frontoparietal cortex homogenates. Interleukin (IL)-8, IL-6, IL-1β and tumor necrosis factor α were measured in frontoparietal cortex homogenates. <b><i>Results:</i></b> There was no difference in time to ROSC or inflammation and oxidative stress in the 3 oxygen groups. <b><i>Conclusions:</i></b> Resuscitation with 18% oxygen did not result in differences in inflammation and oxidative stress when compared to 21 or 100% oxygen.
DOI: 10.6084/m9.figshare.11493834
title: Supplementary Material for: Growth Differentiation Factor 15 Promotes Progression of Esophageal Squamous Cell Carcinoma via TGF-β Type II Receptor Activation

description: <b><i>Objectives:</i></b> Growth differentiation factor 15 (GDF15), which is derived from tumor-associated macrophages (TAM) and cancer cells, promotes progression of esophageal squamous cell carcinomas (ESCC). However, its role in the ESCC microenvironment remains unclear. Here, we examined the effects of GDF15 on ESCC cell lines and tissues. <b><i>Methods:</i></b> Western blotting, MTS, and Transwell migration/invasion assays were used to evaluate cell signaling, proliferation, and migration/invasion, respectively, in ESCC cell lines treated with recombinant human GDF15 (rhGDF15). ESCC cell lines were administered a TGF-βRI/II inhibitor (LY2109761), small interfering RNA against TGF-β type II receptor (TGF-βRII), or neutralizing antibody against TGF-βRII to study the role of TGF-βRII in mediating the effects of rhGDF15. The localization of GDF15 and TGF-βRII in ESCC cell lines was observed by immunofluorescence. TGF-βRII expression in ESCC tissues was analyzed by immunohistochemistry, and the relationship between clinicopathological factors and prognosis in ESCC patients was evaluated. <b><i>Results:</i></b> rhGDF15 increased levels of phosphorylated Akt, Erk1/2, and TGF-βRII in ESCC cell lines. Inhibition/knockdown of TGF-βRII suppressed rhGDF15-induced activation of Akt and Erk1/2 and enhancement of cellular proliferation, migration, and invasion. Immunofluorescence revealed that TGF-βRII and GDF15 were colocalized in ESCC cell lines. High TGF-βRII expression in ESCC tissues, as determined by immunohistochemistry, correlated with depth of invasion and increased number of infiltrating TAMs. ESCC patients with high TGF-βRII expression showed a tendency toward poor prognosis. <b><i>Conclusions:</i></b> GDF15 promotes ESCC progression by increasing cellular proliferation, migration, and invasion via TGF-βRII signaling.
DOI: 10.6084/m9.figshare.11493840.v1
title: Supplementary Material for: Ventilation with 18, 21, or 100% Oxygen during Cardiopulmonary Resuscitation of Asphyxiated Piglets: A Randomized Controlled Animal Trial

description: <b><i>Background:</i></b> In previous piglet experiments of profound asphyxia and cardiac arrest, recovery was similar when 21 and 100% oxygen were used for positive pressure ventilation (PPV). There was no consistent reduction in inflammation and oxidative stress in piglets ventilated with 21 or 100% oxygen. <b><i>Objectives:</i></b> We aimed to investigate hypoxic resuscitation, i.e., PPV with 18% oxygen, in profoundly asphyxiated piglets with cardiac arrest. We hypothesized that resuscitation with 18% oxygen would result in less inflammation and oxidative stress compared to 21 or 100% oxygen. <b><i>Method:</i></b> Twenty-four piglets were exposed to 30 min of normocapnic hypoxia followed by asphyxia until asystole. The piglets were randomized to PPV with 18% oxygen (<i>n</i> = 8), 21% oxygen (<i>n</i> = 8), or 100% oxygen (<i>n</i> = 8), and resuscitated with chest compressions and intravenous epinephrine. Return of spontaneous circulation (ROSC) was defined as an unassisted heart rate ≥100 bpm for 15 s. Lactate, GSH (total glutathione), GSSG (oxidized glutathione), and GSSG/GSH ratio were measured in myocardial and frontoparietal cortex homogenates. Interleukin (IL)-8, IL-6, IL-1β and tumor necrosis factor α were measured in frontoparietal cortex homogenates. <b><i>Results:</i></b> There was no difference in time to ROSC or inflammation and oxidative stress in the 3 oxygen groups. <b><i>Conclusions:</i></b> Resuscitation with 18% oxygen did not result in differences in inflammation and oxidative stress when compared to 21 or 100% oxygen.
DOI: 10.6084/m9.figshare.11493810
title: Calculations needed for the proof of Theorem 1 (Mathematica file Computation Th1.nb and its description Computation Th1.pdf) from Second-order PDEs in four dimensions with half-flat conformal structure

description: We study second-order PDEs in four dimensions for which the conformal structure defined by the characteristic variety of the equation is half-flat (self-dual or anti-self-dual) on every solution. We prove that this requirement implies the Monge–Ampère property. Since half-flatness of the conformal structure is equivalent to the existence of a nontrivial dispersionless Lax pair, our result explains the observation that all known scalar second-order integrable dispersionless PDEs in dimensions four and higher are of Monge–Ampère type. Some partial classification results of Monge–Ampère equations in four dimensions with half-flat conformal structure are also obtained.
DOI: 10.6084/m9.figshare.11493777
title: Data from manuscript "Effects of DOC and temperature on the performance of droplet digital PCR quantification of fish populations from water samples"

description: This data include the .glp files generated by the QX200 droplet digital PCR reader (and associated software) and a description of the samples analyses in each ddPCR run (Data_information.xlsx file). This data corresponds to the ddPCR amplification nine-spined sticklebacks (COI mitochondrial gene)<br>
DOI: 10.6084/m9.figshare.11493810.v1
title: Calculations needed for the proof of Theorem 1 (Mathematica file Computation Th1.nb and its description Computation Th1.pdf) from Second-order PDEs in four dimensions with half-flat conformal structure

description: We study second-order PDEs in four dimensions for which the conformal structure defined by the characteristic variety of the equation is half-flat (self-dual or anti-self-dual) on every solution. We prove that this requirement implies the Monge–Ampère property. Since half-flatness of the conformal structure is equivalent to the existence of a nontrivial dispersionless Lax pair, our result explains the observation that all known scalar second-order integrable dispersionless PDEs in dimensions four and higher are of Monge–Ampère type. Some partial classification results of Monge–Ampère equations in four dimensions with half-flat conformal structure are also obtained.
DOI: 10.6084/m9.figshare.11493756
title: Identification of a four immune-related genes signature based on an immunogenomic landscape analysis of clear cell renal cell carcinoma

description: Rawdata and codes
DOI: 10.6084/m9.figshare.11493777.v1
title: Data from manuscript "Effects of DOC and temperature on the performance of droplet digital PCR quantification of fish populations from water samples"

description: This data include the .glp files generated by the QX200 droplet digital PCR reader (and associated software) and a description of the samples analyses in each ddPCR run (Data_information.xlsx file). This data corresponds to the ddPCR amplification nine-spined sticklebacks (COI mitochondrial gene)<br>
DOI: 10.6084/m9.figshare.11493681
title: Proteome database of Bacillus cereus Rock3-44

description: A facultative anaerobic bacterium, <i>Bacillus cereus</i> is one member of a larger family of microorganisms that are closely-related and which are characterized as <i>Bacillus cereus</i> group. Rod shaped and Gram-positive, <i>B. cereus</i> forms colonies with waxy appearance on blood agar. This work sought to provide fundamental information of this bacterium by parsing the UniProt proteome file of <i>B. cereus</i> Rock3-44 with an in-house MATLAB proteome analysis software. The ensuing proteome database comprise protein name, amino acid sequence, number of residues, molecular weight, and nucleotide sequence of all proteins of the bacterium, and should help in a variety of fundamental and applied research involving <i>B. cereus</i>. <br><br>
DOI: 10.6084/m9.figshare.11493609
title: Supplementary Material for: Immunohistochemical Analysis of mTOR Pathway-Related Proteins in Kaposiform Hemangioendothelioma

description: <b><i>Background:</i></b> Mammalian target of rapamycin (mTOR) inhibitors have been shown to have excellent effects in the management of kaposiform hemangioendothelioma (KHE); however, the mechanism of action is unclear. This study identified the expressions of mTOR pathway-related proteins in different vascular tumors to provide insight into the pathogenesis of KHE. <b><i>Methods:</i></b> We retrospectively reviewed the pathologic specimens of 30 patients (KHE, 15; tufted angioma [TA], 5; infantile hemangioma [IH], 5; and lymphatic malformation [LM], 5). The immunohistochemical expression of mTOR-related proteins tuberous sclerosis complex 2 (TSC2), phosphatase and tensin homologue (PTEN), phosphorylated eukaryotic translation initiation factor 4E binding protein 1 (p-4EBP1), phosphorylated mTOR (p-mTOR), and phosphorylated ribosomal protein S6 kinase B1 (p-P70S6K) were analyzed using Image-Pro Plus software. KHE had the following pattern of expression in the spindle vascular endothelial cells: TSC2 (–); PTEN (–); p-4EBP1 (+); p-mTOR (+); and p-P70S6K (+). <b><i>Results:</i></b> All 3 patients treated with sirolimus had good responses. The TA results were similar to KHE with no significant differences (p-4EBP1: <i>p</i> = 0.0687; p-mTOR: <i>p</i> = 0.0832). The expressions of TSC2, PTEN, p-4EBP1, p-mTOR, and p-P70S6K were negative or weakly positive in IH with a statistically significant difference compared to KHE (p-4EBP1: <i>p</i> &lt; 0.001; p-mTOR: <i>p</i> &lt; 0.001; p-P70S6K: <i>p</i> &lt; 0.001). LM had no significant differences when compared to KHE. <b><i>Conclusions:</i></b> The absence of TSC2 and PTEN caused abnormal activation of the mTOR signaling pathway and may be involved in the pathogenesis of KHE. The expression of mTOR-related proteins in TA and LM was similar to KHE, unlike IH. The KHE pattern of expression [PTEN (–), TSC2 (–), p-mTOR (+), p-P70S6K (+), and p-4EBP1 (+)] suggested that sirolimus may be a good therapeutic choice.
DOI: 10.6084/m9.figshare.11493609.v1
title: Supplementary Material for: Immunohistochemical Analysis of mTOR Pathway-Related Proteins in Kaposiform Hemangioendothelioma

description: <b><i>Background:</i></b> Mammalian target of rapamycin (mTOR) inhibitors have been shown to have excellent effects in the management of kaposiform hemangioendothelioma (KHE); however, the mechanism of action is unclear. This study identified the expressions of mTOR pathway-related proteins in different vascular tumors to provide insight into the pathogenesis of KHE. <b><i>Methods:</i></b> We retrospectively reviewed the pathologic specimens of 30 patients (KHE, 15; tufted angioma [TA], 5; infantile hemangioma [IH], 5; and lymphatic malformation [LM], 5). The immunohistochemical expression of mTOR-related proteins tuberous sclerosis complex 2 (TSC2), phosphatase and tensin homologue (PTEN), phosphorylated eukaryotic translation initiation factor 4E binding protein 1 (p-4EBP1), phosphorylated mTOR (p-mTOR), and phosphorylated ribosomal protein S6 kinase B1 (p-P70S6K) were analyzed using Image-Pro Plus software. KHE had the following pattern of expression in the spindle vascular endothelial cells: TSC2 (–); PTEN (–); p-4EBP1 (+); p-mTOR (+); and p-P70S6K (+). <b><i>Results:</i></b> All 3 patients treated with sirolimus had good responses. The TA results were similar to KHE with no significant differences (p-4EBP1: <i>p</i> = 0.0687; p-mTOR: <i>p</i> = 0.0832). The expressions of TSC2, PTEN, p-4EBP1, p-mTOR, and p-P70S6K were negative or weakly positive in IH with a statistically significant difference compared to KHE (p-4EBP1: <i>p</i> &lt; 0.001; p-mTOR: <i>p</i> &lt; 0.001; p-P70S6K: <i>p</i> &lt; 0.001). LM had no significant differences when compared to KHE. <b><i>Conclusions:</i></b> The absence of TSC2 and PTEN caused abnormal activation of the mTOR signaling pathway and may be involved in the pathogenesis of KHE. The expression of mTOR-related proteins in TA and LM was similar to KHE, unlike IH. The KHE pattern of expression [PTEN (–), TSC2 (–), p-mTOR (+), p-P70S6K (+), and p-4EBP1 (+)] suggested that sirolimus may be a good therapeutic choice.
DOI: 10.6084/m9.figshare.11493570
title: Male and female stingray behaviours at four sound levels and five frequencies from Field assessment of behavioural responses of southern stingrays (<i>Hypanus americanus</i>) to acoustic stimuli

description: Our data is presented as contrast values, representing the time each stingray spent exhibiting behaviours (swimming, resting, side-swimming, surface breach) during sound presentation compared to the one minute prior to sound, at each frequency and decibel level played to the animals.
DOI: 10.6084/m9.figshare.11493570.v1
title: Male and female stingray behaviours at four sound levels and five frequencies from Field assessment of behavioural responses of southern stingrays (<i>Hypanus americanus</i>) to acoustic stimuli

description: Our data is presented as contrast values, representing the time each stingray spent exhibiting behaviours (swimming, resting, side-swimming, surface breach) during sound presentation compared to the one minute prior to sound, at each frequency and decibel level played to the animals.
DOI: 10.6084/m9.figshare.11493510
title: Demonstration of a portable intracortical brain-computer interface

description: While recent advances in intracortical brain-computer interfaces (iBCI) have demonstrated the ability to restore motor and communication functions, such demonstrations have generally been confined to controlled experimental settings and have required bulky laboratory hardware. Here, we developed and evaluated a self-contained portable iBCI that enabled the user to interact with various computer programs. The iBCI, which weighs 1.5 kg, consists of digital headstages, a small signal processing hub, and a tablet PC. A human participant tested the portable iBCI in laboratory and home settings under an FDA Investigational Device Exemption (NCT01894802). The participant successfully completed 96% of trials in a 2D cursor center-out task with the portable iBCI, a rate indistinguishable from that achieved with the standard laboratory iBCI. The participant also completed a variety of free-form tasks, including drawing, gaming, and typing.
DOI: 10.6084/m9.figshare.11493510.v2
title: Demonstration of a portable intracortical brain-computer interface

description: While recent advances in intracortical brain-computer interfaces (iBCI) have demonstrated the ability to restore motor and communication functions, such demonstrations have generally been confined to controlled experimental settings and have required bulky laboratory hardware. Here, we developed and evaluated a self-contained portable iBCI that enabled the user to interact with various computer programs. The iBCI, which weighs 1.5 kg, consists of digital headstages, a small signal processing hub, and a tablet PC. A human participant tested the portable iBCI in laboratory and home settings under an FDA Investigational Device Exemption (NCT01894802). The participant successfully completed 96% of trials in a 2D cursor center-out task with the portable iBCI, a rate indistinguishable from that achieved with the standard laboratory iBCI. The participant also completed a variety of free-form tasks, including drawing, gaming, and typing.
DOI: 10.21227/ynef-mt11
title: DESIGN AND ANALYSIS OF FILTENNA FOR Ku-BAND APPLICATION

description: Filtenna or filtering antenna is a term used to represent a structure which has filtering as well as radiating function on same substrate. Because of this, the component size can be reduced and noise performance can be increased. The filtenna is designed to operate at 15GHz for Ku-band application. The measured and simulated return loss of filtenna is less than -15dB and the measured and simulated bandwidth is 785MHz and 1.125GHz respectively.
DOI: 10.21227/sdsy-4097
title: DESIGN AND ANALYSIS OF FILTENNA FOR Ku-BAND APPLICATION

description: Filtenna or filtering antenna is a term used to represent a structure which has filtering as well as radiating function on same substrate. Because of this, the component size can be reduced and noise performance can be increased. The filtenna is designed to operate at 15GHz for Ku-band application. The measured and simulated return loss of filtenna is less than -15dB and the measured and simulated bandwidth is 785MHz and 1.125GHz respectively.
DOI: 10.6084/m9.figshare.11493420
title: data_and_code_for_Mobike_v4.zip

description: The dataset and sourcecode for shared bike paper.