cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7067108
title: Tables S1, S2 from Control of seminal fluid protein expression via regulatory hubs in <i>Drosophila melanogaster</i>

description: Highly precise, yet flexible and responsive coordination of expression across groups of genes underpins the integrity of many vital functions. However, our understanding of gene regulatory networks (GRNs) is often hampered by the lack of experimentally tractable systems, by significant computational challenges derived from the large number of genes involved or from difficulties in the accurate identification and characterization of gene interactions. Here we used a tractable experimental system in which to study GRNs: the genes encoding the seminal fluid proteins that are transferred along with sperm (the ‘transferome’) in <i>Drosophila melanogaster</i> fruit flies. The products of transferome genes are core determinants of reproductive success and, to date, only transcription factors have been implicated in the modulation of their expression. Hence, as yet, we know nothing about the post-transcriptional mechanisms underlying the tight, responsive and precise regulation of this important gene set. We investigated this omission in the current study. We first used bioinformatics to identify potential regulatory motifs that linked the transferome genes in a putative interaction network. This predicted the presence of putative microRNA ‘hubs’. We then tested this prediction, that post-transcriptional regulation is important for the control of transferome genes, by knocking down miRNA expression in adult males. This abolished the ability of males to respond adaptively to the threat of sexual competition, indicating a regulatory role for miRNAs in the regulation of transferome function. Further bioinformatics analysis then identified candidate miRNAs as putative regulatory hubs and evidence for variation in the strength of miRNA regulation across the transferome gene set. The results revealed regulatory mechanisms that can underpin robust, precise and flexible regulation of multiple fitness-related genes. They also help to explain how males can adaptively modulate ejaculate composition.
DOI: 10.6084/m9.figshare.7067108.v1
title: Tables S1, S2 from Control of seminal fluid protein expression via regulatory hubs in <i>Drosophila melanogaster</i>

description: Highly precise, yet flexible and responsive coordination of expression across groups of genes underpins the integrity of many vital functions. However, our understanding of gene regulatory networks (GRNs) is often hampered by the lack of experimentally tractable systems, by significant computational challenges derived from the large number of genes involved or from difficulties in the accurate identification and characterization of gene interactions. Here we used a tractable experimental system in which to study GRNs: the genes encoding the seminal fluid proteins that are transferred along with sperm (the ‘transferome’) in <i>Drosophila melanogaster</i> fruit flies. The products of transferome genes are core determinants of reproductive success and, to date, only transcription factors have been implicated in the modulation of their expression. Hence, as yet, we know nothing about the post-transcriptional mechanisms underlying the tight, responsive and precise regulation of this important gene set. We investigated this omission in the current study. We first used bioinformatics to identify potential regulatory motifs that linked the transferome genes in a putative interaction network. This predicted the presence of putative microRNA ‘hubs’. We then tested this prediction, that post-transcriptional regulation is important for the control of transferome genes, by knocking down miRNA expression in adult males. This abolished the ability of males to respond adaptively to the threat of sexual competition, indicating a regulatory role for miRNAs in the regulation of transferome function. Further bioinformatics analysis then identified candidate miRNAs as putative regulatory hubs and evidence for variation in the strength of miRNA regulation across the transferome gene set. The results revealed regulatory mechanisms that can underpin robust, precise and flexible regulation of multiple fitness-related genes. They also help to explain how males can adaptively modulate ejaculate composition.
DOI: 10.6084/m9.figshare.7067096
title: Supporting data from Influence of early-life nutritional stress on songbird memory formation

description: In birds, vocal learning enables the production of sexually selected complex songs, dialects and song copy matching. But stressful conditions during development have been shown to affect song production and complexity, mediated by changes in neural development. However, to date, no studies have tested whether early-life stress affects the neural processes underlying vocal learning, in contrast to song production. Here, we hypothesized that developmental stress alters auditory memory formation and neural processing of song stimuli. We experimentally stressed male nestling zebra finches and, in two separate experiments, tested their neural responses to song playbacks as adults, using either Immediate Early Gene expression or electrophysiological response. Once adult, nutritionally stressed males exhibited a reduced response to tutor song playback, as demonstrated by reduced expressions of two IEGs (<i>Arc</i> and <i>ZENK</i>) and reduced neuronal response, in both the caudomedial nidopallium (NCM) and mesopallium (CMM). Furthermore, nutritionally stressed males also showed impaired neuronal memory for novel songs heard in adulthood. These findings demonstrate, for the first time, that developmental conditions affect auditory memories that subserve vocal learning. Although the fitness consequences of such memory impairments remain to be determined, this study highlights the lasting impact early-life experiences can have on cognitive abilities.
DOI: 10.6084/m9.figshare.7067096.v1
title: Supporting data from Influence of early-life nutritional stress on songbird memory formation

description: In birds, vocal learning enables the production of sexually selected complex songs, dialects and song copy matching. But stressful conditions during development have been shown to affect song production and complexity, mediated by changes in neural development. However, to date, no studies have tested whether early-life stress affects the neural processes underlying vocal learning, in contrast to song production. Here, we hypothesized that developmental stress alters auditory memory formation and neural processing of song stimuli. We experimentally stressed male nestling zebra finches and, in two separate experiments, tested their neural responses to song playbacks as adults, using either Immediate Early Gene expression or electrophysiological response. Once adult, nutritionally stressed males exhibited a reduced response to tutor song playback, as demonstrated by reduced expressions of two IEGs (<i>Arc</i> and <i>ZENK</i>) and reduced neuronal response, in both the caudomedial nidopallium (NCM) and mesopallium (CMM). Furthermore, nutritionally stressed males also showed impaired neuronal memory for novel songs heard in adulthood. These findings demonstrate, for the first time, that developmental conditions affect auditory memories that subserve vocal learning. Although the fitness consequences of such memory impairments remain to be determined, this study highlights the lasting impact early-life experiences can have on cognitive abilities.
DOI: 10.6084/m9.figshare.7067075
title: Kale: A System for Enabling Human-in-the-loop Interactivity in HPC Workflows

description: Scientific problem-solving frequently requires interactive, iterative exploration and analysis. Web-based interactive electronic notebook interfaces such as Jupyter offer an important mechanism for scientists to capture analyses in a reproducible narrative context. An increasing number of science gateway environments are providing support for Jupyter Notebooks as a means to enable custom, ad-hoc analyses on scientific data. However, Jupyter Notebooks alone are not enough to fulfill the needs of scientific researchers today. Scientists are producing and consuming large amounts of data, and require significant computational resources to process and analyze that data, causing scientific workflows to become increasingly asynchronous in nature as processing is off-loaded to remote resources. Many scientific researchers turn to HPC systems for processing, but the traditional asynchronous batch-queue environment used in HPC for such computationally intensive tasks is largely separate from interactive Notebook-based workflows, producing a fragmented workflow for scientists that does not facilitate rapid scientific inquiry. We introduce our system “Kale” that enables Jupyter Notebooks to seamlessly interface with HPC workflows, leveraging distributed computational resources for iterative human-in-the-loop scientific exploration.
DOI: 10.6084/m9.figshare.7067075.v3
title: Kale: A System for Enabling Human-in-the-loop Interactivity in HPC Workflows

description: Scientific problem-solving frequently requires interactive, iterative exploration and analysis. Web-based interactive electronic notebook interfaces such as Jupyter offer an important mechanism for scientists to capture analyses in a reproducible narrative context. An increasing number of science gateway environments are providing support for Jupyter Notebooks as a means to enable custom, ad-hoc analyses on scientific data. However, Jupyter Notebooks alone are not enough to fulfill the needs of scientific researchers today. Scientists are producing and consuming large amounts of data, and require significant computational resources to process and analyze that data, causing scientific workflows to become increasingly asynchronous in nature as processing is off-loaded to remote resources. Many scientific researchers turn to HPC systems for processing, but the traditional asynchronous batch-queue environment used in HPC for such computationally intensive tasks is largely separate from interactive Notebook-based workflows, producing a fragmented workflow for scientists that does not facilitate rapid scientific inquiry. We introduce our system “Kale” that enables Jupyter Notebooks to seamlessly interface with HPC workflows, leveraging distributed computational resources for iterative human-in-the-loop scientific exploration.
DOI: 10.6084/m9.figshare.7067075.v2
title: Kale: A System for Enabling Human-in-the-loop Interactivity in HPC Workflows

description: Scientific problem-solving frequently requires interactive, iterative exploration and analysis. Web-based interactive electronic notebook interfaces such as Jupyter offer an important mechanism for scientists to capture analyses in a reproducible narrative context. An increasing number of science gateway environments are providing support for Jupyter Notebooks as a means to enable custom, ad-hoc analyses on scientific data. However, Jupyter Notebooks alone are not enough to fulfill the needs of scientific researchers today. Scientists are producing and consuming large amounts of data, and require significant computational resources to process and analyze that data, causing scientific workflows to become increasingly asynchronous in nature as processing is off-loaded to remote resources. Many scientific researchers turn to HPC systems for processing, but the traditional asynchronous batch-queue environment used in HPC for such computationally intensive tasks is largely separate from interactive Notebook-based workflows, producing a fragmented workflow for scientists that does not facilitate rapid scientific inquiry. We introduce our system “Kale” that enables Jupyter Notebooks to seamlessly interface with HPC workflows, leveraging distributed computational resources for iterative human-in-the-loop scientific exploration.
DOI: 10.6084/m9.figshare.7066853
title: Additional file 1: of Three-dimensional analysis of dental arch forms in Italian population

description: Data analysed during this study. (XLSX 35 kb).
DOI: 10.6084/m9.figshare.7066853.v1
title: Additional file 1: of Three-dimensional analysis of dental arch forms in Italian population

description: Data analysed during this study. (XLSX 35 kb).
DOI: 10.6084/m9.figshare.7066787
title: Supplemental data 2.xlsx

description: The central part of the medial preoptic nucleus (MPNc) is associated with sexual arousal induction in male rats. However, it is largely unclear how males are sexually aroused and achieve their first copulation. In this study, we performed DNA microarray analysis of the MPNc in sexually naïve males and males after they copulated for their first and second times to explore the molecules responsible for sexual arousal induction.
DOI: 10.6084/m9.figshare.7066772
title: Supplemental_Table_1.xlsx

description: Supplemental_Table_1.xlsx
DOI: 10.6084/m9.figshare.7066787.v1
title: Supplemental data 2.xlsx

description: The central part of the medial preoptic nucleus (MPNc) is associated with sexual arousal induction in male rats. However, it is largely unclear how males are sexually aroused and achieve their first copulation. In this study, we performed DNA microarray analysis of the MPNc in sexually naïve males and males after they copulated for their first and second times to explore the molecules responsible for sexual arousal induction.
DOI: 10.6084/m9.figshare.7066769
title: plant nutrients

description: plant nutrient concentrations
DOI: 10.6084/m9.figshare.7066772.v1
title: Supplemental_Table_1.xlsx

description: Supplemental_Table_1.xlsx
DOI: 10.6084/m9.figshare.7066760

description: <b>Effects of WER on plant growth</b>
DOI: 10.6084/m9.figshare.7066766
title: Specific root length

description: Specific root length was defined as total root length divided by fresh root
mass.
DOI: 10.6084/m9.figshare.7066760.v1
title: plant morphologies

description: <b>Effects of WER on plant growth</b>
DOI: 10.6084/m9.figshare.7066754
title: Supplemental data 1.xlsx

description: The central part of the medial preoptic nucleus (MPNc) is associated with sexual arousal induction in male rats. However, it is largely unclear how males are sexually aroused and achieve their first copulation. In this study, we performed DNA microarray analysis of the MPNc in sexually naïve males and males after they copulated for their first and second times to explore the molecules responsible for sexual arousal induction.
DOI: 10.6084/m9.figshare.7066754.v2
title: Supplemental data 1.xlsx

description: The central part of the medial preoptic nucleus (MPNc) is associated with sexual arousal induction in male rats. However, it is largely unclear how males are sexually aroused and achieve their first copulation. In this study, we performed DNA microarray analysis of the MPNc in sexually naïve males and males after they copulated for their first and second times to explore the molecules responsible for sexual arousal induction.
DOI: 10.6084/m9.figshare.7066754.v1
title: Supplemental data 1.xlsx

description: The central part of the medial preoptic nucleus (MPNc) is associated with sexual arousal induction in male rats. However, it is largely unclear how males are sexually aroused and achieve their first copulation. In this study, we performed DNA microarray analysis of the MPNc in sexually naïve males and males after they copulated for their first and second times to explore the molecules responsible for sexual arousal induction.
DOI: 10.6084/m9.figshare.7066727

description: soil ORP during the day (12:00) and at night (24:00)<br>
DOI: 10.6084/m9.figshare.7066727.v1
title: Soil ORP

description: soil ORP during the day (12:00) and at night (24:00)<br>
DOI: 10.26180/5b9614661e54e
title: SILVA library w FOO and RRA calculation

description: Data for "Molecular analysis of predator scats reveals role of salps in temperate inshore foodwebs" under review in Frontiers in Marine Science (Manuscript ID: 407577). Full methods will be in the published manuscript.<br>The first spreadsheet in this workbook contains the library of identified mOTUs and the samples they appear in. Further spreadsheets in the workbook include the calculations for frequency of occurrence and relative read abundance and the final FOO and RRA sheets.<br>These samples were collected from Phillip Island in southeastern Australia under ethics permit No. 2.2014 approved by Phillip Island Nature Parks Animal Ethics Committee number and Research Permit No. 10006148 from the Department of Environment, Land, Water and Planning.<br>
DOI: 10.26180/5b95c4ea50ec0
title: Investigating PFI using SSVEPs

description: Working repository for ongoing PFI-SSVEP project.
DOI: 10.6084/m9.figshare.7066703
title: Ichnofabric oscillatory curves reveal the tide-dominated depositional system in Samarinda, Kutai Basin (Indonesia)

description: Since the interaction of fluvial, wave and tidal processes was proven in Samarinda, Kutai Basin (Indonesia), then the interpretation of the depositional system lead to a deltaic system. However, interpretation of depositional system remained a challenge, because other systems (e.g., estuary, strandplain and lagoon) could be formed within a deltaic system. Here, we demonstrate the testing by ichnofabric methods to reveal the paleoenvironmental processes in a deltaic system. The bioturbation index (BI), ichnodiversity (ID), number of behavior (NB), penetration depth (PD), ichnofossil diameter (Dm), in ichnofabric units were scrutinized. The data were processed by principal component analysis (PCA). The main findings were (1) the PC-1 and PC-2 oscillatory curves, and (2) the phase between PC-1 and PC-2 curves (i.e., out of phase and in phase). The PC-1 curve was loaded by BI, ID, and NB and the PC-2 was loaded by PD and Dm. The generated curves were interpreted as the indicators of colonization window, organism mobility, and space using by the organism. The oscillatory curve suggested how the organism interact with the substrate are repeated. In conclusion, the generated curves associated with the change of the intensity of fluvial, tidal, and wave processes that occurred in tide-dominated depositional systems.
DOI: 10.6084/m9.figshare.7066685.v1
title: Week-Mobility-Network

description: Movement between locations
DOI: 10.6084/m9.figshare.7066685.v3
title: Week-Mobility-Network

description: Movement between locations
DOI: 10.6084/m9.figshare.7066685.v2
title: Week-Mobility-Network

description: Movement between locations
DOI: 10.25374/mcri.7066661
title: Data Request 3688243 - Research Data Views provided

description: Research data views (datasets) provided after approval of data request by HealthNuts study.
DOI: 10.6084/m9.figshare.7066673.v1
title: GPS-Location

description: Mobility
DOI: 10.25374/mcri.7066661.v1
title: Data Request 3688243 - Research Data Views provided

description: Research data views (datasets) provided after approval of data request by HealthNuts study.
DOI: 10.6084/m9.figshare.7066658
title: quiho: Automated Performance Regression Testing Using Inferred Resource Utilization Profiles.

description: We introduce _quiho_, a framework for profiling application performance that can be used in automated performance regression tests. _quiho_ profiles an application by applying sensitivity analysis, in particular statistical regression analysis (SRA), using application-independent performance feature vectors that characterize the performance of machines. The result of the SRA, feature importance specifically, is used as a proxy to identify hardware and low-level system software behavior. The relative importance of these features serve as a performance profile of an application (termed inferred resource utilization profile or IRUP), which is used to automatically validate performance behavior across multiple revisions of an application's code base without having to instrument code or obtain performance counters. We demonstrate that _quiho_ can successfully discover performance regressions by showing its effectiveness in profiling application performance for synthetically introduced regressions as well as those found in real-world applications.
DOI: 10.6084/m9.figshare.7066679.v6
title: Rab10 as a novel downstream regulator of TrkB retrograde axonal transport

description: Poster presented on the NGF meetings 2018. Salamanca, Spain. Shows work on the role of Rab10 in axonal retrograde sorting of TrkB receptors internalised from the axon terminal.
DOI: 10.25374/mcri.7066640
title: Data Request 3688243 - Metadata provided

description: Data dictionary and other metadata files.
DOI: 10.6084/m9.figshare.7066658.v1
title: quiho: Automated Performance Regression Testing Using Inferred Resource Utilization Profiles.

description: We introduce _quiho_, a framework for profiling application performance that can be used in automated performance regression tests. _quiho_ profiles an application by applying sensitivity analysis, in particular statistical regression analysis (SRA), using application-independent performance feature vectors that characterize the performance of machines. The result of the SRA, feature importance specifically, is used as a proxy to identify hardware and low-level system software behavior. The relative importance of these features serve as a performance profile of an application (termed inferred resource utilization profile or IRUP), which is used to automatically validate performance behavior across multiple revisions of an application's code base without having to instrument code or obtain performance counters. We demonstrate that _quiho_ can successfully discover performance regressions by showing its effectiveness in profiling application performance for synthetically introduced regressions as well as those found in real-world applications.
DOI: 10.25374/mcri.7066640.v2
title: Data Request 3688243 - Metadata provided

description: Data dictionary and other metadata files.
DOI: 10.25374/mcri.7066640.v1
title: Data Request 3688243 - Metadata provided

description: Data dictionary and other metadata files.
DOI: 10.6084/m9.figshare.7066619
title: Brusch_etal_Water_python

description: Data for Brusch et al 20XX
DOI: 10.6084/m9.figshare.7066619.v1
title: Brusch_etal_Water_python

description: Data for Brusch et al 20XX
DOI: 10.6084/m9.figshare.7066592
title: tave.0000788832.glob.nc.tar.gz

description: 3D model output from MITgcm-Michigan-phosphorus. This contains temperature and current velocities for simulation year 2010.
DOI: 10.6084/m9.figshare.7066592.v1
title: tave.0000788832.glob.nc.tar.gz

description: 3D model output from MITgcm-Michigan-phosphorus. This contains temperature and current velocities for simulation year 2010.
DOI: 10.6084/m9.figshare.7066598
title: Saliva and tooth biofilm bacterial microbiota in adolescents in a low caries community- part two

description: sequences
DOI: 10.6084/m9.figshare.7066598.v1
title: Saliva and tooth biofilm bacterial microbiota in adolescents in a low caries community- part two

description: sequences
DOI: 10.6084/m9.figshare.7066586
title: tave.0000473040.glob.nc.tar.gz

description: 3D model output from MITgcm-Michigan-phosphorus. This contains temperature and current velocities for simulation year 2008.
DOI: 10.6084/m9.figshare.7066589
title: tave.0000631152.glob.nc.tar.gz

description: 3D model output from MITgcm-Michigan-phosphorus. This contains temperature and current velocities for simulation year 2009.
DOI: 10.6084/m9.figshare.7066586.v1
title: tave.0000473040.glob.nc.tar.gz

description: 3D model output from MITgcm-Michigan-phosphorus. This contains temperature and current velocities for simulation year 2008.
DOI: 10.6084/m9.figshare.7066589.v1
title: tave.0000631152.glob.nc.tar.gz

description: 3D model output from MITgcm-Michigan-phosphorus. This contains temperature and current velocities for simulation year 2009.
DOI: 10.6084/m9.figshare.7066571
title: ptr_tave.0000788832.glob.nc.tar.gz

description: 3D model output from MITgcm-Michigan-phosphorus for simulation year 2010. This contains phosphorus concentration in the lake associated with 11 rivers.