cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7831913.v1
title: Cross-strain Reused Growth Medium Experiments Datasets

description: This dataset includes data collected during an experiment designed to test the growth response of three marine microalgae strains to the growth medium derived conditioned by a single algae strain. Bacteria communities in the algae cultures were also sequenced and identified. Metadata includes descriptions of variables in each data table. More information about the experiments and data collection methods are available in the publication that will accompany this dataset.
DOI: 10.6084/m9.figshare.7831772.v1
title: Data from: Unravelling intra- and intersegmental neuronal connectivity between central pattern generating networks in a multi-legged locomotor system

description: This fileset contains extracellular recordings from four different experimental setups:<br>1) Meso-Meta recordings (Meso_Meta)<br>2) Meso-Meta recordings comparing intact and cut connectives (Cut connectives)<br>3) Pro-Meso recordings (Pro_Meso)4) Pro-Meso-Meta recordings (Pro_Meso_Meta)<br><br>The order of the electrodes is either defined in the header of the file or in a separate channel.txt file.<b> </b>Additionally, the Spike2 recordings (Experiments: 1 and 3) can be found in a subfolder labeled "Spike Files".
DOI: 10.6084/m9.figshare.7831778
title: Supplementary Material for: Novel Face-Name Paired Associate Learning and Famous Face Recognition in Mild Cognitive Impairment: A Neuropsychological and Brain Volumetric Study

description: <b><i>Purpose:</i></b> To assess visual associative learning and famous face recognition ability among subjects with stable amnestic mild cognitive impairment (MCI) relative to early stage dementia due to Alzheimer’s disease (AD) and cognitively normal healthy controls (NC) and to correlate these differences with volumetric changes on MRI. <b><i>Methods:</i></b> A hospital-based cross-sectional observational study was conducted on 61 participants. The subjects underwent neuropsychological evaluation, including validated newly designed tests for novel face-name paired association learning recall and famous face recognition. MRI volumetry was done on a subset of patients to ascertain the topographical patterns of volume loss. <b><i>Results:</i></b> There were significant differences in performance on free recall for face-name paired associate learning in MCI (<i>n</i> = 22) compared to NC (<i>n</i> = 20) (<i>p</i> &lt; 0.001) and MCI compared to AD (<i>n</i> = 19; <i>p</i> &lt; 0.001). Significant differences were also noted in scores on the famous personalities test between MCI and NC (<i>p</i> = 0.007), and MCI and AD (<i>p</i> = 0.032). The free recall component of face-name pair associative learning significantly correlated with left cuneus (<i>p</i> = 0.005; <i>r</i> = 0.833) and right cuneus (<i>p</i> = 0.003; <i>r</i> = 0.861) volume in AD with no significant correlation among MCI and NC cohorts. <b><i>Conclusions:</i></b> Novel and semantically familiar face-name associative recalls are significantly impaired in MCI, and these potentially predate the MRI volumetric changes in MCI. Our findings expand the spectrum of recall deficits in MCI.
DOI: 10.6084/m9.figshare.7831781.v1
title: Artifact and instructions to generate experimental results for TACAS 2019 paper: Computing the Expected Execution Time of Probabilistic Workflow Nets

description: This is the artifact accompanying the paper "Computing the Expected Execution Time of Probabilistic Workflow Nets", accepted for TACAS 2019. Timed Probabilistic Workflow Nets (TPWN) are a model for business process modeling extended with time and probabilistic information. In the paper, we have shown that computing the excepted execution time of a TPWN is #P-hard, even for simple net structures. We then developed an exponential time algorithm to compute the expected execution time, and evaluated it on a set of real-word workflow net benchmarks. As a result, we obtained that for most nets, the time can be computed efficiently despite the theoretical hardness.<br><br>This artifact can be used to reproduce the results given in Section 6 "Experimental evaluation" of the paper. It includes the workflow and process mining workbench ProM together with the plugin we implemented to compute the expected execution time. Further, this artifact contains a set of 642 workflow nets from IBM, annotated with 3 sets of random times and probabilities, and scripts to compute the expected execution time of all nets and aggregate the results. This can be used to validate the results in Table 1. Also, the workflow net from the BPI Challenge shown in Fig. 4 of the paper is included, in a deterministic and probabilistic version. This net can be analyzed using ProM to validate the results in Table 2.
DOI: 10.6084/m9.figshare.7831544
title: Supplementary Material for: Calbindin-1 Expression in the Hippocampus following Neonatal Hypoxia-Ischemia and Therapeutic Hypothermia and Deficits in Spatial Memory

description: Hippocampal injury following neonatal hypoxia-ischemia (HI) leads to memory impairments despite therapeutic hypothermia (TH). In the hippocampus, the expression of calbindin-1 (Calb1), a Ca<sup>2+</sup>-buffering protein, increases during postnatal development and decreases with aging and neurodegenerative disorders. Since persistent Ca<sup>2+</sup> dysregulation after HI may lead to ongoing injury, persistent changes in hippocampal expression of Calb1 may contribute to memory impairments after neonatal HI. We hypothesized that, despite TH, neonatal HI persistently decreases Calb1 expression in the hippocampus, a change associated with memory deficits in the mouse. We induced cerebral HI in C57BL6 mice at postnatal day 10 (P10) with right carotid ligation and 45 min of hypoxia (FiO<sub>2</sub> = 0.08), followed by normothermia (36°C, NT) or TH (31°C) for 4 h with anesthesia-shams as controls. Nissl staining and glial fibrillary acidic protein (GFAP) immunohistochemistry (IHC) were used to grade brain injury and astrogliosis at P11, P18, and P40 prior to the assessment of Calb1 expression by IHC. The subset of mice followed to P40 also performed a memory behavior task (Y-maze) at P22–P26. Nonparametric statistics stratified by sex were applied. In both anterior and posterior coronal brain sections, hippocampal Calb1 expression doubled between P11 and P40 due to an increase in the cornus ammonis (CA) field (Kruskal-Wallis [KW] <i>p</i> &lt; 0.001) and not the dentate gyrus (DG). Neonatal HI produced delayed (P18) and late (P40) deficits in the expression of Calb1 exclusively in the CA field (KW <i>p</i> = 0.02) in posterior brain sections. TH did not attenuate Calb1 deficits after HI. Thirty days after HI injury (at P40), GFAP scores in the hippocampus (<i>p</i> &lt; 0.001, <i>r</i> = –0.47) and CA field (<i>p</i> &lt; 0.001, <i>r</i> = –0.39) of posterior brain sections inversely correlated with their respective Calb1 expression. Both sexes demonstrated deficits in Y-maze testing, including approximately 40% lower spontaneous alterations performance and twice as much total impairment compared to sham mice (KW <i>p</i> &lt; 0.001), but it was only in females that these deficits correlated with the Calb1 expression in the hippocampal CA field (<i>p</i> &lt; 0.05) of the posterior sections. Hippocampal atrophy after neonatal HI also correlated with worse deficits in Y-maze testing, but it did not predict Calb1 deficits. Neonatal HI produces a long-lasting Calb1 deficit in the hippocampal CA field during development, which is not mitigated by TH. Late Calb1 deficit after HI may be the result of persistent astrogliosis and can lead to memory impairment, particularly in female mice.
DOI: 10.6084/m9.figshare.7831913.v2
title: Cross-strain Reused Growth Medium Experiments Datasets

description: This dataset includes data collected during an experiment designed to test the growth response of three marine microalgae strains to the growth medium derived conditioned by a single algae strain. Bacteria communities in the algae cultures were also sequenced and identified. Metadata includes descriptions of variables in each data table. More information about the experiments and data collection methods are available in the publication that will accompany this dataset.
DOI: 10.6084/m9.figshare.7831502
title: Supplementary Material for: Prenatal Diagnosis, Management, and Outcome of Fetal Subdural Haematoma: A Case Report and Systematic Review

description: <b><i>Background:</i></b> Fetal subdural haematoma (SDH) is associated with poor prognosis. <b><i>Objective:</i></b> The conflicting evidence from the literature presents a challenge in prenatal counselling. We present a case study and systematic review of the literature for the management and outcome of fetal SDH. <b><i>Methods:</i></b> Systematic search of electronic database. <b><i>Results:</i></b> A total 45 cases were extracted from 39 papers. Prenatal ultrasonographic features were intracranial echogenicity (42%), lateral ventriculomegaly (38%), presence of an intracranial mass (31%), macrocephaly (24%), midline deviation of cerebral falx (20%), and intracranial fluid collection (11%). Further secondary features were noted including reversed diastolic flow in the middle cerebral artery (11%), echogenic bowel (4%), hydrops fetalis (2%), and elevated middle cerebral artery peak systolic velocity (2%) (all highly likely to be associated with fetal anaemia). The rates of termination of pregnancy, stillbirth, and neonatal death were 18% (8/45), 16% (7/45), and 11% (5/45), respectively. Overall, therefore, the fetal and perinatal mortality was 32% (12/37). Amongst the 24 survivors with available neurological outcome, 42% (10/24) and 58% (14/24) had abnormal and normal neurological outcome, respectively. Underlying aetiology of fetal SDH was not identified in 47% (21/45). Fetal SDH with an identifiable underlying aetiology was the only factor associated with a higher chance of normal neurological outcome when compared to fetal SDH without a detectable cause (78.5 vs. 21.4%, <i>p</i> = 0.035). <b><i>Conclusions:</i></b> Stillbirth and neonatal death occurred in a significant proportion of fetal SDH. 58% of survivors had normal neurological outcome, and better prognosis was seen in SDH with identifiable underlying aetiology.
DOI: 10.6084/m9.figshare.7831526
title: DMI Qaanaaq Ice Observatory AWS observations (2015-2017)

description: Automated Weather Station (AWS) Observations from the DMI Qaanaaq ice observatory from 2015-2017 winter campaigns. Observations from the site include e.g. T1m, T2m, Tskin, wind speed, shortwave and longwave radiation. The data used here are snapshot measurements every 10 minute. <br><br><br>
DOI: 10.6084/m9.figshare.7831502.v1
title: Supplementary Material for: Prenatal Diagnosis, Management, and Outcome of Fetal Subdural Haematoma: A Case Report and Systematic Review

description: <b><i>Background:</i></b> Fetal subdural haematoma (SDH) is associated with poor prognosis. <b><i>Objective:</i></b> The conflicting evidence from the literature presents a challenge in prenatal counselling. We present a case study and systematic review of the literature for the management and outcome of fetal SDH. <b><i>Methods:</i></b> Systematic search of electronic database. <b><i>Results:</i></b> A total 45 cases were extracted from 39 papers. Prenatal ultrasonographic features were intracranial echogenicity (42%), lateral ventriculomegaly (38%), presence of an intracranial mass (31%), macrocephaly (24%), midline deviation of cerebral falx (20%), and intracranial fluid collection (11%). Further secondary features were noted including reversed diastolic flow in the middle cerebral artery (11%), echogenic bowel (4%), hydrops fetalis (2%), and elevated middle cerebral artery peak systolic velocity (2%) (all highly likely to be associated with fetal anaemia). The rates of termination of pregnancy, stillbirth, and neonatal death were 18% (8/45), 16% (7/45), and 11% (5/45), respectively. Overall, therefore, the fetal and perinatal mortality was 32% (12/37). Amongst the 24 survivors with available neurological outcome, 42% (10/24) and 58% (14/24) had abnormal and normal neurological outcome, respectively. Underlying aetiology of fetal SDH was not identified in 47% (21/45). Fetal SDH with an identifiable underlying aetiology was the only factor associated with a higher chance of normal neurological outcome when compared to fetal SDH without a detectable cause (78.5 vs. 21.4%, <i>p</i> = 0.035). <b><i>Conclusions:</i></b> Stillbirth and neonatal death occurred in a significant proportion of fetal SDH. 58% of survivors had normal neurological outcome, and better prognosis was seen in SDH with identifiable underlying aetiology.
DOI: 10.6084/m9.figshare.7831355
title: Supplementary Material for: Premature Lambs Exhibit Normal Mitochondrial Respiration after Long-Term Extrauterine Support

description: <b><i>Background:</i></b> In an effort to mitigate the major morbidities and mortality associated with extreme prematurity, we have developed an EXTrauterine Environment for Neonatal Development (EXTEND) designed to provide physiologic support of extremely premature infants. <b><i>Objectives:</i></b> We have previously shown that long-term, physiologic support of premature fetal lambs is possible with EXTEND, but in this study, we sought to demonstrate bioenergetic equipoise at the tissue level. <b><i>Methods:</i></b> Four premature fetal lambs were delivered by hysterotomy at gestational ages (GA) of 105–107 days (term ∼145 days), cannulated via the umbilical vessels, and transitioned to support on EXTEND for 3–4 weeks. Five control fetuses were age-matched to the GA of experimental fetuses at the time of study end (128–134 days GA) and immediately sacrificed after hysterotomy. Mitochondria were isolated from the heart, liver, kidney, and skeletal muscle of fetuses at the time of sacrifice, and oxygen consumption rates (OCRs) were measured. <b><i>Results:</i></b> There were no differences in basal mitochondrial OCR between EXTEND and control fetuses for heart, kidney, or skeletal muscle. For liver, the basal OCR was higher in EXTEND fetuses compared to controls. There were no differences in physiologic maximal OCR or reserve capacity for any tissue analyzed. <b><i>Conclusions:</i></b> Fetal lambs supported by EXTEND demonstrate physiologic mitochondrial function as evidenced by adequate basal and physiologic maximal cellular respiration as well as preserved reserve capacity.
DOI: 10.6084/m9.figshare.7831526.v2
title: DMI Qaanaaq Ice Observatory AWS observations (2015-2017)

description: Automated Weather Station (AWS) Observations from the DMI Qaanaaq ice observatory from 2015-2017 winter campaigns. Observations from the site include e.g. T1m, T2m, Tskin, wind speed, shortwave and longwave radiation. The data used here are snapshot measurements every 10 minute. <br><br><br>
DOI: 10.6084/m9.figshare.7831259
title: Frequent birth of de novo genes in the compact yeast genome

description: Supplementary data from the paper "Frequent birth of de novo genes in the compact yeast genome" (Blevins et al., bioRxiv 2019)<br>Blevins_etal_data.xls: information for the S.cerevisiae transcripts (annotated and novel), including expression level in rich media and oxidative conditions and phylogenetic conservation level.<br>Blevins_transcriptome_Scerevisiae_over15TPM.gtf: annotation file for S.cerevisiae transcripts expressed over 15 transcripts per million (TPM) in normal and/or oxidative stress conditions.<br>Files with extension .fa: protein sequences in fasta format for the three groups of genes (expressed at &gt; 15 TPM). The files contain a combination of ORFs with evidence of translation using ribosome profling data and annotated coding sequences (CDS). Please note that in some cases a start codon other than ATG was detected. Some transcripts had more than one translated ORF (indicated with sufixes -1, -3, etc.).<br>
DOI: 10.6084/m9.figshare.7831259.v2
title: Frequent birth of de novo genes in the compact yeast genome

description: Supplementary data from the paper "Frequent birth of de novo genes in the compact yeast genome" (Blevins et al., bioRxiv 2019)<br>Blevins_etal_data.xls: information for the S.cerevisiae transcripts (annotated and novel), including expression level in rich media and oxidative conditions and phylogenetic conservation level.<br>Blevins_transcriptome_Scerevisiae_over15TPM.gtf: annotation file for S.cerevisiae transcripts expressed over 15 transcripts per million (TPM) in normal and/or oxidative stress conditions.<br>Files with extension .fa: protein sequences in fasta format for the three groups of genes (expressed at &gt; 15 TPM). The files contain a combination of ORFs with evidence of translation using ribosome profling data and annotated coding sequences (CDS). Please note that in some cases a start codon other than ATG was detected. Some transcripts had more than one translated ORF (indicated with sufixes -1, -3, etc.).<br>
DOI: 10.6084/m9.figshare.7831259.v1
title: Frequent birth of de novo genes in the compact yeast genome

description: Blevins_etal_data.xls: information for S.cerevisiae transcripts, including expression level in rich media and oxidative conditions and phylogenetic conservation level.Blevins_transcriptome_Scerevisiae_over15TPM.gt: annotation file for S.cerevisiae transcripts expressed over 15 transcripts per million (TPM) in normal and/or oxidative stress conditions.<br>
DOI: 10.25345/c58471
title: MassIVE MSV000086033 - Co-cultivation_of_anaerobic_fungi_with_rumen_bacteria_establishes_an_antagonistic_relationship
title: Raw spectra supporting Swift et al. "Co-cultivation of anaerobic fungi with rumen bacteria establishes an antagonistic relationship"
DOI: 10.6084/m9.figshare.7830800
title: Supplementary Material for: Cytochrome <b><i>bcc-aa3</i></b> Oxidase Supercomplexes in the Aerobic Respiratory Chain of <b><i>Streptomyces coelicolor</i></b> A3(2)

description: <i>Streptomyces coelicolor</i> A3(2), an obligately aerobic, oxidase-positive, and filamentous soil bacterium, lacks a soluble cytochrome <i>c</i> in its respiratory chain, having instead a membrane-associated diheme <i>c</i>-type cytochrome, QcrC. This necessitates complex formation to allow electron transfer between the cytochrome <i>bcc</i> and <i>aa3</i> oxidase respiratory complexes. Combining genetic complementation studies with in-gel cytochrome oxidase activity staining, we demonstrate that the complete <i>qcrCAB-ctaCDFE</i> gene locus on the chromosome, encoding, respectively, the <i>bcc</i> and <i>aa3</i> complexes, is required to manifest a cytochrome oxidase enzyme activity in both spores and mycelium of a <i>qcr-cta</i> deletion mutant. Blue-native-PAGE identified a cytochrome <i>aa3</i> oxidase complex of approximately 270 kDa, which catalyzed oxygen-dependent diaminobenzidine oxidation without the requirement for exogenously supplied cytochrome <i>c</i>, indicating association with QcrC. Furthermore, higher molecular mass complexes were identified upon addition of soluble cytochrome <i>c</i>, suggesting the supercomplex is unstable and readily dissociates into subcomplexes lacking QcrC. Immunological and mass spectrometric analyses of active, high-molecular mass oxidase-containing complexes separated by clear-native PAGE identified key<i></i> subunits of both the <i>bcc</i> complex and the <i>aa3</i> oxidase, supporting supercomplex formation. Our data also indicate that the cytochrome <i>b</i> QcrB of the <i>bcc</i> complex is less abundant in spores compared with mycelium.
DOI: 10.6084/m9.figshare.7830767
title: Supplementary Material for: Cerebrospinal Fluid Biomarkers for the Diagnosis of Prodromal Alzheimer’s Disease in Amnestic Mild Cognitive Impairment

description: <b><i>Background/Aims:</i></b> Disease-modifying therapy for Alzheimer’s disease (AD) has led to a need for biomarkers to identify prodromal AD and very early stage of AD dementia. We aimed to identify the cutoff values of cerebrospinal fluid (CSF) biomarkers for detecting prodromal AD. <b><i>Methods:</i></b> We assessed 56 patients with amnestic mild cognitive impairment (aMCI) who underwent lumbar puncture. Additionally, 87 healthy elderly individuals and 34 patients with AD dementia served as controls. Positron emission tomography was performed using florbetaben as a probe. We analyzed the concentration of Aβ<sub>1–42</sub>, total tau protein (t-Tau), and tau protein phosphorylated at threonine 181 (p-Tau<sup>181</sup>) in CSF with INNOTEST enzyme-linked immunosorbent assay. <b><i>Results:</i></b> For the detection of prodromal AD in patients with aMCI, the cutoff values of CSF Aβ<sub>1–42</sub>, t-Tau, and p-Tau<sup>181</sup> were 749.5 pg/mL, 225.6 pg/mL, and 43.5 pg/mL, respectively. To discriminate prodromal AD in patients with aMCI, the t-Tau/Aβ<sub>1–42</sub> and ­p-Tau<sup>181</sup>/Aβ<sub>1–42</sub> ratios defined cutoff values at 0.298 and 0.059, respectively. <b><i>Conclusions:</i></b> CSF biomarkers are very useful tools for the differential diagnosis of prodromal AD in aMCI patients. The concentration of CSF biomarkers is well correlated with the stages of the AD spectrum.
DOI: 10.6084/m9.figshare.7830767.v1
title: Supplementary Material for: Cerebrospinal Fluid Biomarkers for the Diagnosis of Prodromal Alzheimer’s Disease in Amnestic Mild Cognitive Impairment

description: <b><i>Background/Aims:</i></b> Disease-modifying therapy for Alzheimer’s disease (AD) has led to a need for biomarkers to identify prodromal AD and very early stage of AD dementia. We aimed to identify the cutoff values of cerebrospinal fluid (CSF) biomarkers for detecting prodromal AD. <b><i>Methods:</i></b> We assessed 56 patients with amnestic mild cognitive impairment (aMCI) who underwent lumbar puncture. Additionally, 87 healthy elderly individuals and 34 patients with AD dementia served as controls. Positron emission tomography was performed using florbetaben as a probe. We analyzed the concentration of Aβ<sub>1–42</sub>, total tau protein (t-Tau), and tau protein phosphorylated at threonine 181 (p-Tau<sup>181</sup>) in CSF with INNOTEST enzyme-linked immunosorbent assay. <b><i>Results:</i></b> For the detection of prodromal AD in patients with aMCI, the cutoff values of CSF Aβ<sub>1–42</sub>, t-Tau, and p-Tau<sup>181</sup> were 749.5 pg/mL, 225.6 pg/mL, and 43.5 pg/mL, respectively. To discriminate prodromal AD in patients with aMCI, the t-Tau/Aβ<sub>1–42</sub> and ­p-Tau<sup>181</sup>/Aβ<sub>1–42</sub> ratios defined cutoff values at 0.298 and 0.059, respectively. <b><i>Conclusions:</i></b> CSF biomarkers are very useful tools for the differential diagnosis of prodromal AD in aMCI patients. The concentration of CSF biomarkers is well correlated with the stages of the AD spectrum.