cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8114165
title: Transcriptome profile of Carrizo citrange roots in response to <i>Phytophthora parasitica</i> infection

description: <i>Phytophthora parasitica</i> is one of the most widespread <i>Phytophthora</i> species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response to <i>P. parasitica</i> infection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) among <i>P. parasitica</i>-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 h post inoculation and 5521 genes were differentially expressed at 48 h post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. Many <i>R</i> genes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response to <i>P. parasitica</i> infection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks to <i>P. parasitica</i>.
DOI: 10.6084/m9.figshare.8114165.v2
title: Transcriptome profile of Carrizo citrange roots in response to <i>Phytophthora parasitica</i> infection

description: <i>Phytophthora parasitica</i> is one of the most widespread <i>Phytophthora</i> species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response to <i>P. parasitica</i> infection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) among <i>P. parasitica</i>-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 h post inoculation and 5521 genes were differentially expressed at 48 h post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. Many <i>R</i> genes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response to <i>P. parasitica</i> infection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks to <i>P. parasitica</i>.
DOI: 10.6084/m9.figshare.7533761.v1
title: Comparison among ‘Benitaka’ grape, ABA-treated ‘Benitaka’, and its deeper-colored bud mutation revealed the coloring mechanisms on grapes

description: To investigate the deeper coloring mechanism of berry, the ‘Benitaka’ (Be) grape, ABA treatment on ‘Benitaka’ (Be (ABA)), and its deeper coloring bud mutation ‘Brasil’ (Br) grape were compared three weeks post-ABA treatment (11 weeks post-flowering, 200 mg/g ABA). Firstly, the ABA-treated group exhibited a deeper coloring at three weeks post-ABA treatment than the ‘Brasil’. Deeper color in ‘Brasil’ was caused by higher content of peonidin-3-O-monoglucoside, malvidin-3-O-monoglucoside, and malvidin-3-O-coumarylglucoside, while the deeper color in ABA-treated group was mainly caused by higher content of cyanidin-3-O-monoglucoside and peonidin-3-O-monoglucoside. In addition, the results revealed that ‘Brasil’ showed deeper coloring than ‘Benitaka’ was probably due to the higher expression of the <i>VvmybA1</i> and <i>VvmybA1-1</i> genes, similar with ABA-treated group. Compared with ‘Benitaka’, the distinction between the ABA-treated group and ‘Brasil’ was the expression of <i>VvmybA1</i> gene. The gene expression was delayed in the ABA-treated group until three weeks post treatment. The <i>VvmybA1</i> gene and transcription factor play an important role in the anthocyanin biosynthesis, and showed the difference in expressions of the <i>VvmybA1</i> and <i>VvmybA1-1</i> gene during different period of time probably due to different kind of anthocyanins. Based on these results, a possible mechanism of anthocyanins biosynthesis was established to elaborate the reason for the deeper coloring in ABA-treated ‘Benitaka’ and ‘Brasil’ grapes.
DOI: 10.6084/m9.figshare.8114165.v1
title: Transcriptome profile of Carrizo citrange roots in response to <i>Phytophthora parasitica</i> infection

description: <i>Phytophthora parasitica</i> is one of the most widespread <i>Phytophthora</i> species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response to <i>P. parasitica</i> infection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) among <i>P. parasitica</i>-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 h post inoculation and 5521 genes were differentially expressed at 48 h post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. Many <i>R</i> genes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response to <i>P. parasitica</i> infection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks to <i>P. parasitica</i>.
DOI: 10.5281/zenodo.4059542
title: Dataset related to the article "Characteristics of Patients with Arrhythmogenic Left Ventricular Cardiomyopathy - Combining Genetic and Histopathologic Findings"

description: This record contains raw data related to the article “Characteristics of Patients with Arrhythmogenic Left Ventricular Cardiomyopathy - Combining Genetic and Histopathologic Findings”. <strong>Abstract</strong> <strong>Background: </strong>Arrhythmogenic left ventricular cardiomyopathy (ALVC) is an under-characterized phenotype of arrhythmogenic cardiomyopathy involving the LV ab initio. ALVC was not included in the 2010 International Task Force Criteria (ITFC) for arrhythmogenic right ventricular cardiomyopathy diagnosis and data regarding this phenotype are scarce. <strong>Methods: </strong>clinical characteristics were reported from all consecutive patients diagnosed with ALVC, defined as a LV isolated late gadolinium enhancement (LGE) and fibro-fatty replacement (FFR) at cardiac magnetic resonance (CMR) plus genetic variants associated with ARVC and/or of an endomyocardial biopsy (EMB) showing FFR complying with the 2010 ITFC in the LV. <strong>Results: </strong>twenty-five ALVC patients (53 [48–59] years, 60% male) were enrolled. T-wave inversion in infero-lateral and left precordial leads were the most common ECG abnormalities. Overall arrhythmic burden at study inclusion was 56%. CMR showed LV LGE in the LV lateral and/or posterior basal segments in all patients. In 72% of the patients an invasive evaluation was performed, in which electroanatomical voltage mapping (EVM) and EVM-guided EMB showed low endocardial voltages and FFR in areas of LGE presence. Genetic variants in desmosomal genes (desmoplakin and desmoglein-2) were identified in 12/25 of the cohort presenting pathogenic/likely-pathogenic variants. A definite/borderline 2010 ITFC ARVC diagnosis was reached only in 11/25 patients. <strong>Conclusion: </strong>ALVC presents with a preferential involvement of the lateral and/or postero-lateral basal LV and is associated mostly with variants in desmoplakin and<em> </em>desmoglein-2 genes. An amendment to the current ITFC is reasonable to better diagnose ALVC patients.
DOI: 10.6084/m9.figshare.7533761
title: Comparison among ‘Benitaka’ grape, ABA-treated ‘Benitaka’, and its deeper-colored bud mutation revealed the coloring mechanisms on grapes

description: To investigate the deeper coloring mechanism of berry, the ‘Benitaka’ (Be) grape, ABA treatment on ‘Benitaka’ (Be (ABA)), and its deeper coloring bud mutation ‘Brasil’ (Br) grape were compared three weeks post-ABA treatment (11 weeks post-flowering, 200 mg/g ABA). Firstly, the ABA-treated group exhibited a deeper coloring at three weeks post-ABA treatment than the ‘Brasil’. Deeper color in ‘Brasil’ was caused by higher content of peonidin-3-O-monoglucoside, malvidin-3-O-monoglucoside, and malvidin-3-O-coumarylglucoside, while the deeper color in ABA-treated group was mainly caused by higher content of cyanidin-3-O-monoglucoside and peonidin-3-O-monoglucoside. In addition, the results revealed that ‘Brasil’ showed deeper coloring than ‘Benitaka’ was probably due to the higher expression of the <i>VvmybA1</i> and <i>VvmybA1-1</i> genes, similar with ABA-treated group. Compared with ‘Benitaka’, the distinction between the ABA-treated group and ‘Brasil’ was the expression of <i>VvmybA1</i> gene. The gene expression was delayed in the ABA-treated group until three weeks post treatment. The <i>VvmybA1</i> gene and transcription factor play an important role in the anthocyanin biosynthesis, and showed the difference in expressions of the <i>VvmybA1</i> and <i>VvmybA1-1</i> gene during different period of time probably due to different kind of anthocyanins. Based on these results, a possible mechanism of anthocyanins biosynthesis was established to elaborate the reason for the deeper coloring in ABA-treated ‘Benitaka’ and ‘Brasil’ grapes.
DOI: 10.6084/m9.figshare.9822719
title: The influence of resistant soybean cultivars on the biological development of <i>Euschistus heros</i> (Hemiptera: Pentatomidae)

description: Two stink bug-resistant soybean cultivars, Dowling and IAC 100, and one sucepible, Silvânia were selected to evaluate their influence on <i>Euschistus heros</i> development. Evaluation of the biology of <i>E. heros</i> was conducted on nymph development, adult longevity, female fecundity and egg fertility in seeds of each cultivar. The results showed that <i>E. heros</i> nymphs reared on cv Dowling did not complete their biological cycle, but it was completed on cvs Silvânia and IAC 100. The total amount of six isoflavonoids identified and one flavonol was higher in cv Silvânia compared to the levels quantified in cv Dowling. The results showed that cvs Dowling and IAC 100 have constitutive resistance affecting <i>E. heros</i> development and that the major falvonoids quantified in these cultivars are not involved in soybean antibiotic effect observed in this study.
DOI: 10.6084/m9.figshare.9822719.v1
title: The influence of resistant soybean cultivars on the biological development of <i>Euschistus heros</i> (Hemiptera: Pentatomidae)

description: Two stink bug-resistant soybean cultivars, Dowling and IAC 100, and one sucepible, Silvânia were selected to evaluate their influence on <i>Euschistus heros</i> development. Evaluation of the biology of <i>E. heros</i> was conducted on nymph development, adult longevity, female fecundity and egg fertility in seeds of each cultivar. The results showed that <i>E. heros</i> nymphs reared on cv Dowling did not complete their biological cycle, but it was completed on cvs Silvânia and IAC 100. The total amount of six isoflavonoids identified and one flavonol was higher in cv Silvânia compared to the levels quantified in cv Dowling. The results showed that cvs Dowling and IAC 100 have constitutive resistance affecting <i>E. heros</i> development and that the major falvonoids quantified in these cultivars are not involved in soybean antibiotic effect observed in this study.
DOI: 10.5281/zenodo.4059541
title: Dataset related to the article "Characteristics of Patients with Arrhythmogenic Left Ventricular Cardiomyopathy - Combining Genetic and Histopathologic Findings"

description: This record contains raw data related to the article “Characteristics of Patients with Arrhythmogenic Left Ventricular Cardiomyopathy - Combining Genetic and Histopathologic Findings”. <strong>Abstract</strong> <strong>Background: </strong>Arrhythmogenic left ventricular cardiomyopathy (ALVC) is an under-characterized phenotype of arrhythmogenic cardiomyopathy involving the LV ab initio. ALVC was not included in the 2010 International Task Force Criteria (ITFC) for arrhythmogenic right ventricular cardiomyopathy diagnosis and data regarding this phenotype are scarce. <strong>Methods: </strong>clinical characteristics were reported from all consecutive patients diagnosed with ALVC, defined as a LV isolated late gadolinium enhancement (LGE) and fibro-fatty replacement (FFR) at cardiac magnetic resonance (CMR) plus genetic variants associated with ARVC and/or of an endomyocardial biopsy (EMB) showing FFR complying with the 2010 ITFC in the LV. <strong>Results: </strong>twenty-five ALVC patients (53 [48–59] years, 60% male) were enrolled. T-wave inversion in infero-lateral and left precordial leads were the most common ECG abnormalities. Overall arrhythmic burden at study inclusion was 56%. CMR showed LV LGE in the LV lateral and/or posterior basal segments in all patients. In 72% of the patients an invasive evaluation was performed, in which electroanatomical voltage mapping (EVM) and EVM-guided EMB showed low endocardial voltages and FFR in areas of LGE presence. Genetic variants in desmosomal genes (desmoplakin and desmoglein-2) were identified in 12/25 of the cohort presenting pathogenic/likely-pathogenic variants. A definite/borderline 2010 ITFC ARVC diagnosis was reached only in 11/25 patients. <strong>Conclusion: </strong>ALVC presents with a preferential involvement of the lateral and/or postero-lateral basal LV and is associated mostly with variants in desmoplakin and<em> </em>desmoglein-2 genes. An amendment to the current ITFC is reasonable to better diagnose ALVC patients.
DOI: 10.6084/m9.figshare.8248088
title: An expanded role of the SNARE-containing regulon as it relates to the defense process that <i>Glycine max</i> has to <i>Heterodera glycines</i>

description: The defense regulon has been defined genetically in <i>Arabidopsis thaliana</i> to involve the syntaxin <i>PENETRATION1</i> (<i>PEN1</i>), the secreted glucosidase (<i>PEN2</i>) and an ATP-binding cassette (ABC) transporter (<i>PEN3</i>). Experiments in <i>Glycine max</i> (soybean) have identified homologous genes being expressed in root cells undergoing defense processes to <i>Heterodera glycines</i> parasitism. These experiments have not examined proteins involved in cargo delivery to the infection site. A good candidate fulfilling this role would be myosin XI. In related studies, prior microscopic analyses have shown the accumulation of callose at these defense sites. Experiments presented here show that callose synthase expression impairs <i>H. glycines</i> parasitism. The experiments presented here have expanded on prior results demonstrating the central defense role of the plant vesicular trafficking apparatus and callose synthase to the defense process that <i>G. max</i> has toward <i>H. glycines</i> parasitism.
DOI: 10.6084/m9.figshare.8248088.v2
title: An expanded role of the SNARE-containing regulon as it relates to the defense process that <i>Glycine max</i> has to <i>Heterodera glycines</i>

description: The defense regulon has been defined genetically in <i>Arabidopsis thaliana</i> to involve the syntaxin <i>PENETRATION1</i> (<i>PEN1</i>), the secreted glucosidase (<i>PEN2</i>) and an ATP-binding cassette (ABC) transporter (<i>PEN3</i>). Experiments in <i>Glycine max</i> (soybean) have identified homologous genes being expressed in root cells undergoing defense processes to <i>Heterodera glycines</i> parasitism. These experiments have not examined proteins involved in cargo delivery to the infection site. A good candidate fulfilling this role would be myosin XI. In related studies, prior microscopic analyses have shown the accumulation of callose at these defense sites. Experiments presented here show that callose synthase expression impairs <i>H. glycines</i> parasitism. The experiments presented here have expanded on prior results demonstrating the central defense role of the plant vesicular trafficking apparatus and callose synthase to the defense process that <i>G. max</i> has toward <i>H. glycines</i> parasitism.
DOI: 10.6084/m9.figshare.8248088.v1
title: An expanded role of the SNARE-containing regulon as it relates to the defense process that <i>Glycine max</i> has to <i>Heterodera glycines</i>

description: The defense regulon has been defined genetically in <i>Arabidopsis thaliana</i> to involve the syntaxin <i>PENETRATION1</i> (<i>PEN1</i>), the secreted glucosidase (<i>PEN2</i>) and an ATP-binding cassette (ABC) transporter (<i>PEN3</i>). Experiments in <i>Glycine max</i> (soybean) have identified homologous genes being expressed in root cells undergoing defense processes to <i>Heterodera glycines</i> parasitism. These experiments have not examined proteins involved in cargo delivery to the infection site. A good candidate fulfilling this role would be myosin XI. In related studies, prior microscopic analyses have shown the accumulation of callose at these defense sites. Experiments presented here show that callose synthase expression impairs <i>H. glycines</i> parasitism. The experiments presented here have expanded on prior results demonstrating the central defense role of the plant vesicular trafficking apparatus and callose synthase to the defense process that <i>G. max</i> has toward <i>H. glycines</i> parasitism.
DOI: 10.6084/m9.figshare.14186243
title: Supplementary Material for: Improved Formula for Predicting Hemodialyzability of Intravenous and Oral Drugs

description: <b><i>Background:</i></b> The rate of drug removal by hemodialysis needs to be considered when designing drug dosage regimens for patients on hemodialysis. We previously developed a simplified equation to predict the removal rates of intravenously administered drugs by hemodialysis. Here, we addressed shortcomings of this equation and developed a more accurate equation that can also predict the removal rates of orally administered drugs. <b><i>Methods:</i></b> A total of 70 drugs with known pharmacokinetic and physical parameters and drug removal rates that were measured during hemodialysis in clinical cases were randomly assigned at a 4:1 ratio to a training data group or a test data group. A prediction equation was developed by performing stepwise multiple regression analyses using the training data (i.e., the removal rate by hemodialysis) as the objective variable and pharmacokinetic parameters as the explanatory variables. The equation was validated using the test data. <b><i>Results:</i></b> Multiple regression analyses revealed that molecular weight (MW), protein binding rate, and fraction excreted unchanged in urine relative to the volume of distribution (Vd) were independently correlated with the drug clearance rate (adjusted coefficient of determination, 0.83; <i>p</i> = 2.2e−16). The following equation was obtained: drug removal rate by hemodialysis (%) = −17.32 × [log (MW)] – 0.39 × [protein binding rate (%)] + 0.06 × [fraction excreted unchanged in urine (%)/Vd (L/kg)] + 83.34. Validation of the equation using the test data showed a very high correlation between predicted and measured reduction rate (<i>R</i> = 0.93, <i>p</i> = 1.87e−6). Mean error was −3.34 (95% confidence interval: −10.03, 3.35), mean absolute error was 9.59, and root mean square error was 16.48. <b><i>Conclusion:</i></b> The modified equation derived in this study using pharmacokinetic and physical parameters as variables precisely predicted the removal rates of both intravenous and oral drugs by hemodialysis.
DOI: 10.5255/ukda-sn-854637
title: Childhood Adaptations to Negative Life Experiences: the Role of Cognitive Traits, 2020

description: Child maltreatment has been one of the strongest predictors for future psychopathology. It is assumed that child maltreatment disrupts brain circuits adversely affecting the development of cognitive and behavioural domains and functioning. The neurobiological alterations impair several important cognitive functions, including autobiographical memory and reward processing. The present study examines the effect of child maltreatment on autobiographical memory and in turn its impact on emotional regulation and social functioning. Further the study explores the effect on child maltreatment on reward processing and in turn its impact on impulsivity. The number of participants was 139 (non-maltreated=76, maltreated=63). Participants were recruited online and through support groups and were assessed through a set of questionnaires. Participants were grouped based on the severity of maltreatment they had experienced when young: none, low, moderate, and severe. Results indicated no significant differences on autobiographical memory and reward processing of the maltreated group in comparison to the control group. However, the study found that the interaction between child maltreatment and cognitive traits predict adulthood behavioural problems. The results suggest that child maltreatment can disrupt cognitive functions which in turn have a negative impact on behaviour that might persist through life.
DOI: 10.6084/m9.figshare.12124158
title: Mayfly community and habitat condition metadata from the Luvuvhu catchment

description: Mayfly community data collected in the Luvuvhu catchment, RSA. Data was collected at 23 sites for 12 months. At each sites, one biotope 'stones-in-current' was sampled with six samples collected from six different stones. Other environmental variables were also measured.
DOI: 10.6084/m9.figshare.12124158.v1
title: Mayfly and Habitat condition data

description: Mayfly community data collected in the Luvuvhu catchment, RSA. Data was collected at 23 sites for 12 months. At each sites, one biotope 'stones-in-current' was sampled with six samples collected from six different stones. Other environmental variables were also measured.
DOI: 10.6084/m9.figshare.14186274.v1
title: Raw data from tetrad experiments from Light environment influences mating behaviours during the early stages of divergence in tropical butterflies

description: Raw data underlying Results section b)
DOI: 10.6084/m9.figshare.14186277
title: Raw data from mounted female experiments from Light environment influences mating behaviours during the early stages of divergence in tropical butterflies

description: Raw data underlying Results sections a) and c)
DOI: 10.6084/m9.figshare.14186274
title: Raw data from tetrad experiments from Light environment influences mating behaviours during the early stages of divergence in tropical butterflies

description: Raw data underlying Results section b)
DOI: 10.6084/m9.figshare.14186277.v1
title: Raw data from mounted female experiments from Light environment influences mating behaviours during the early stages of divergence in tropical butterflies

description: Raw data underlying Results sections a) and c)
DOI: 10.5281/zenodo.4573897
title: Nanoscale Dynamics of Peptidoglycan Assembly during the Cell Cycle of Streptococcus pneumoniae

description: Raw phase contrast images to analyze the shape of <em>Streptococcus pneumoniae</em> cells in the presence of aDA-DA. Raw phase contrast and diffraction-limited images to determine the aDA-DA concentration to use for peptidoglycan labeling in <em>S. pneumoniae</em>. Raw phase contrast and diffraction-limited images to determine the effect of D-cycloserine on aDA and aDA-DA incorporation in <em>S. pneumoniae</em>. Raw bright field, diffraction-limited and dSTORM images to determine the duration of the incubation period with aDA-DA for peptidoglycan labeling in <em>S. pneumoniae</em>. Raw western blot images to analyze the depletion level of PBP2b in <em>S. pneumoniae</em>. Raw bright field, diffraction-limited and dSTORM images to analyze peptidoglycan synthesis in <em>S. pneumoniae</em>.