cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4246298.v1
title: Supplementary Material for: The House Dust Mite Major Allergen Der p 23 Displays O-Glycan-Independent IgE Reactivities but No Chitin-Binding Activity

description: <b><i>Background:</i></b> The in-depth characterization of the recently identified house dust mite (HDM) major allergen Der p 23 requires the production of its recombinant counterpart because the natural allergen is poorly extractable from fecal pellets. This study aimed to provide a detailed physico-chemical characterization of recombinant Der p 23 (rDer p 23) as well as to investigate its IgE reactivity in a cohort of HDM-allergic patients from Thailand. <b><i>Methods:</i></b> Purified rDer p 23, secreted from recombinant <i>Pichia pastoris</i>, was characterized by mass spectrometry and circular dichroism analyses as well as for its chitin-binding activity. The IgE-binding frequency and allergenicity of Der p 23 were determined by ELISA and RBL-SX38 degranulation assays, respectively. <b><i>Results:</i></b> Purified intact rDer p 23 carried O-mannosylation and mainly adopted a random coil structure. Polyclonal antibodies to rDer p 23 can detect the corresponding natural allergen (nDer p 23) in aqueous fecal pellet extracts, suggesting that both forms of Der p 23 share common B-cell epitopes. Despite its homologies with chitin-binding proteins, both natural Der p 23 and rDer p 23 were unable to interact in vitro with chitin matrices. Of 222 Thai HDM-allergic patients tested, 54% displayed Der p 23-specific IgE responses. Finally, the allergenicity of rDer p 23 was confirmed by the degranulation of rat basophil leukemia cells. <b><i>Conclusion:</i></b> Our findings highlighted important levels of Der p 23 sensitizations in Thailand. Our study clearly suggested that rDer p 23 is likely more appropriate for HDM allergy component-resolved diagnosis than HDM extracts.
DOI: 10.6084/m9.figshare.4246265
title: Supplementary Material for: Maternal Diet Enriched with α-Linolenic or Saturated Fatty Acids Differentially Regulates Gene Expression in the Liver of Mouse Offspring

description: <b><i>Background/Aims:</i></b> Lipid metabolic disarray in the liver of young and adult mice offspring is induced by saturated fatty acids (SFA) but prevented by α-linolenic acid (ALA, 18:3 ω-3) in the maternal diet during pregnancy and lactation. The aim of the present study was to analyze the impact of maternal dietary ALA compared to an SFA diet on the liver gene expression in the newborn offspring. <b><i>Methods:</i></b> C57Bl6/J dams were fed with diets normal in calories but rich in ALA or SFA before mating and during pregnancy. Pups were sacrificed at birth and liver parameters were assessed. Gene expression was characterized by microarray analysis and validated by real-time quantitative PCR. <b><i>Results:</i></b> ALA, compared to SFA, in maternal diets during pregnancy increased polyunsaturated fatty acids, while it differentially modified fatty acid desaturase activities in offspring liver. Overall, 474 and 662 genes from the liver of newborn pups were differentially regulated by ALA and SFA compared to control diet (p &lt; 0.05; fold change 2), respectively. Notably, Per3 was upregulated by ALA, whereas it was downregulated by SFA, compared to control diet. <b><i>Conclusions:</i></b> ALA- and SFA-enriched diets differentially affect the gene expression pattern in the offspring's liver. ALA, in particular, upregulates genes associated with low adiposity.
DOI: 10.6084/m9.figshare.4246295.v1
title: Supplementary Material for: Laser Speckle Contrast Imaging for Monitoring Changes in Microvascular Blood Flow

description: <b><i>Background/Aims:</i></b> Microvascular blood flow is essential for healing and predicts surgical outcome. The aim of the current study was to investigate the relation between fluxes measured with the laser speckle contrast imaging (LSCI) technique and changes in absolute blood flow. In addition, we studied the reproducibility of the LSCI technique when assessing the intra-abdominal microcirculation of the pig. <b><i>Methods:</i></b> During trial 1, a fish gill arch was mechanically perfused with heparinized fish blood under controlled stepwise-altered flow rates alongside mechanically induced movement artefacts. The microcirculation of the fish gill was simultaneously assessed with the LSCI technique. In trial 2, microcirculation was measured in the stomach, liver, and small intestine of 10 pigs by two observers. <b><i>Results:</i></b> A linear correlation was observed between flux and volumetric flow. During conditions of no volumetric flow, the high recording speed with the LSCI technique registered the movement artefacts as flow signals. The LSCI measurements showed good correlation and agreement between the two observers when assessing microcirculation in the stomach, liver, and small intestine (r<sup>2</sup> = 0.857, 0.956, and 0.946; coefficients of variation = 6.0, 3.2, and 6.4%, respectively). <b><i>Conclusion:</i></b> Due to the non-contact and real-time assessment over large areas, LSCI is a promising technique for the intraoperative assessment of intra-abdominal microcirculation. A linear correlation between flux and volumetric flow was found, in accordance with previous experimental studies. However, movement artefacts affect flux measurements, and the choice of the sampling speed must be made with care, depending on the given setting.
DOI: 10.6084/m9.figshare.4246265.v1
title: Supplementary Material for: Maternal Diet Enriched with α-Linolenic or Saturated Fatty Acids Differentially Regulates Gene Expression in the Liver of Mouse Offspring

description: <b><i>Background/Aims:</i></b> Lipid metabolic disarray in the liver of young and adult mice offspring is induced by saturated fatty acids (SFA) but prevented by α-linolenic acid (ALA, 18:3 ω-3) in the maternal diet during pregnancy and lactation. The aim of the present study was to analyze the impact of maternal dietary ALA compared to an SFA diet on the liver gene expression in the newborn offspring. <b><i>Methods:</i></b> C57Bl6/J dams were fed with diets normal in calories but rich in ALA or SFA before mating and during pregnancy. Pups were sacrificed at birth and liver parameters were assessed. Gene expression was characterized by microarray analysis and validated by real-time quantitative PCR. <b><i>Results:</i></b> ALA, compared to SFA, in maternal diets during pregnancy increased polyunsaturated fatty acids, while it differentially modified fatty acid desaturase activities in offspring liver. Overall, 474 and 662 genes from the liver of newborn pups were differentially regulated by ALA and SFA compared to control diet (p &lt; 0.05; fold change 2), respectively. Notably, Per3 was upregulated by ALA, whereas it was downregulated by SFA, compared to control diet. <b><i>Conclusions:</i></b> ALA- and SFA-enriched diets differentially affect the gene expression pattern in the offspring's liver. ALA, in particular, upregulates genes associated with low adiposity.
DOI: 10.6084/m9.figshare.4246214
title: Supplementary Material for: A Risk Score to Guide Cystatin C Testing to Detect Occult-Reduced Estimated Glomerular Filtration Rate

description: <strong><em>Background/Aims:</em></strong> Persons with occult-reduced estimated glomerular filtration rate (eGFR &lt;60 ml/min/1.73 m<sup>2</sup> detected by serum cystatin C but missed by creatinine) have high risk for complications. Among persons with preserved kidney function by creatinine-based eGFR (eGFRcreat &gt;60 ml/min/1.73 m<sup>2</sup>), tools to guide cystatin C testing are needed. <b><i>Methods:</i></b> We developed a risk score to estimate an individual's probability of reduced eGFR by cystatin C (eGFRcys &lt;60 ml/min/1.73 m<sup>2</sup>) in The Reasons for Geographic and Racial Differences in Stroke (REGARDS) study and externally validated in the Third National Health and Nutrition Examination Survey (NHANES III). We used logistic regression with Bayesian model averaging and variables available in practice. We assessed performance characteristics using calibration and discrimination measures. <b><i>Results:</i></b> Among 24,877 adults with preserved kidney function by creatinine, 13.5% had reduced eGFRcys. Older and Black participants, current smokers and those with higher body mass index, lower eGFRcreat, diabetes, hypertension and history of cardiovascular disease were more likely to have occult-reduced eGFR (p &lt; 0.001). The final risk function had a c-statistic of 0.87 in REGARDS and 0.84 in NHANES. By risk score, 72% of occult-reduced eGFR cases were detected by screening only 22% of participants. <b><i>Conclusions:</i></b> A risk score using characteristics readily accessible in clinical practice can identify the majority of persons with reduced eGFRcys, which is missed by creatinine.<br>
DOI: 10.6084/m9.figshare.4246193
title: Supplementary Material for: The Expression of CCAT2, a Novel Long Noncoding RNA Transcript, and rs6983267 Single-Nucleotide Polymorphism Genotypes in Colorectal Cancers

description: Colon cancer-associated transcription 2 (<i>CCAT2</i>) was recently identified as a novel long noncoding RNA transcript encompassing the single-nucleotide polymorphism rs6983267. <i>CCAT2</i> is overexpressed in colorectal cancer (CRC) where it promotes tumor growth, metastasis, and chromosomal instability, although the clinical relevance of this enhanced expression is unknown. In this retrospective study, <i>CCAT2</i> expression was evaluated using real-time polymerase chain reaction in 149 CRC patients, and its associations with clinicopathological characteristics, outcome, rs6983267 genotypes, microsatellite status, DNA ploidy, and <i>BubR1</i> expression were analyzed. <i>CCAT2</i> expression in cancer tissue was significantly higher than in noncancer tissue (<i>p </i>&lt; 0.001), particularly in cases of metastatic cancer (<i>p </i>&lt; 0.001). However, relative <i>CCAT2</i> expression levels and rs6983267 genotypes were not correlated with clinicopathological features or patient prognosis. CRC cases demonstrating high <i>CCAT2</i> expression were all microsatellite stable (<i>p </i>&lt; 0.005). Together, this indicates that <i>CCAT2</i> expression was associated with microsatellite-stable CRC.
DOI: 10.6084/m9.figshare.4246214.v1
title: Supplementary Material for: A Risk Score to Guide Cystatin C Testing to Detect Occult-Reduced Estimated Glomerular Filtration Rate

description: <strong><em>Background/Aims:</em></strong> Persons with occult-reduced estimated glomerular filtration rate (eGFR &lt;60 ml/min/1.73 m<sup>2</sup> detected by serum cystatin C but missed by creatinine) have high risk for complications. Among persons with preserved kidney function by creatinine-based eGFR (eGFRcreat &gt;60 ml/min/1.73 m<sup>2</sup>), tools to guide cystatin C testing are needed. <b><i>Methods:</i></b> We developed a risk score to estimate an individual's probability of reduced eGFR by cystatin C (eGFRcys &lt;60 ml/min/1.73 m<sup>2</sup>) in The Reasons for Geographic and Racial Differences in Stroke (REGARDS) study and externally validated in the Third National Health and Nutrition Examination Survey (NHANES III). We used logistic regression with Bayesian model averaging and variables available in practice. We assessed performance characteristics using calibration and discrimination measures. <b><i>Results:</i></b> Among 24,877 adults with preserved kidney function by creatinine, 13.5% had reduced eGFRcys. Older and Black participants, current smokers and those with higher body mass index, lower eGFRcreat, diabetes, hypertension and history of cardiovascular disease were more likely to have occult-reduced eGFR (p &lt; 0.001). The final risk function had a c-statistic of 0.87 in REGARDS and 0.84 in NHANES. By risk score, 72% of occult-reduced eGFR cases were detected by screening only 22% of participants. <b><i>Conclusions:</i></b> A risk score using characteristics readily accessible in clinical practice can identify the majority of persons with reduced eGFRcys, which is missed by creatinine.<br>
DOI: 10.6084/m9.figshare.4246181
title: Supplementary Material for: Eccentric Left Ventricular Hypertrophy and Sudden Death in Patients with End-Stage Kidney Disease

description: <strong><em>Background/Aims:</em></strong> Both all-cause and cardiovascular mortality risks are extremely high in patients with end-stage kidney disease (ESKD). Sudden death accounts for approximately one-quarter of all fatal events. Left ventricular hypertrophy (LVH) is a known risk factor for mortality and can be divided in 2 types: concentric and eccentric. This study evaluated possible differences in all-cause mortality, cardiovascular mortality and sudden death between prevalent ESKD patients with concentric and eccentric LVH. <b><i>Methods:</i></b> Participants of the CONvective TRAnsport STudy (CONTRAST) who underwent transthoracic echocardiography (TTE) at baseline were analyzed. In patients with LVH, a relative wall thickness of ≤0.42 was considered eccentric and &gt;0.42 was considered concentric hypertrophy. Cox proportional hazards models, adjusted for potential confounders, were used to calculate hazard ratios (HRs) of patients with eccentric LVH versus patients with concentric LVH for all-cause mortality, cardiovascular mortality and sudden death. <b><i>Results:</i></b> TTE was performed in 328 CONTRAST participants. LVH was present in 233 participants (71%), of which 87 (37%) had concentric LVH and 146 (63%) eccentric LVH. The HR for all-cause mortality of eccentric versus concentric LVH was 1.14 (p = 0.52), 1.79 (p = 0.12) for cardiovascular mortality and 4.23 (p = 0.02) for sudden death in crude analyses. Propensity score-corrected HR for sudden death in patients with eccentric LVH versus those with concentric LVH was 5.22 (p = 0.03). <b><i>Conclusions:</i></b> (1) The hazard for all-cause mortality, cardiovascular mortality and sudden death is markedly increased in patients with LVH. (2) The sudden death risk is significantly higher in ESKD patients with eccentric LVH compared to subjects with concentric LVH.<br>
DOI: 10.6084/m9.figshare.4246181.v1
title: Supplementary Material for: Eccentric Left Ventricular Hypertrophy and Sudden Death in Patients with End-Stage Kidney Disease

description: <strong><em>Background/Aims:</em></strong> Both all-cause and cardiovascular mortality risks are extremely high in patients with end-stage kidney disease (ESKD). Sudden death accounts for approximately one-quarter of all fatal events. Left ventricular hypertrophy (LVH) is a known risk factor for mortality and can be divided in 2 types: concentric and eccentric. This study evaluated possible differences in all-cause mortality, cardiovascular mortality and sudden death between prevalent ESKD patients with concentric and eccentric LVH. <b><i>Methods:</i></b> Participants of the CONvective TRAnsport STudy (CONTRAST) who underwent transthoracic echocardiography (TTE) at baseline were analyzed. In patients with LVH, a relative wall thickness of ≤0.42 was considered eccentric and &gt;0.42 was considered concentric hypertrophy. Cox proportional hazards models, adjusted for potential confounders, were used to calculate hazard ratios (HRs) of patients with eccentric LVH versus patients with concentric LVH for all-cause mortality, cardiovascular mortality and sudden death. <b><i>Results:</i></b> TTE was performed in 328 CONTRAST participants. LVH was present in 233 participants (71%), of which 87 (37%) had concentric LVH and 146 (63%) eccentric LVH. The HR for all-cause mortality of eccentric versus concentric LVH was 1.14 (p = 0.52), 1.79 (p = 0.12) for cardiovascular mortality and 4.23 (p = 0.02) for sudden death in crude analyses. Propensity score-corrected HR for sudden death in patients with eccentric LVH versus those with concentric LVH was 5.22 (p = 0.03). <b><i>Conclusions:</i></b> (1) The hazard for all-cause mortality, cardiovascular mortality and sudden death is markedly increased in patients with LVH. (2) The sudden death risk is significantly higher in ESKD patients with eccentric LVH compared to subjects with concentric LVH.<br>
DOI: 10.6084/m9.figshare.4246169
title: Supplementary Material for: Characterisation of Prognosis and Invasion of Cutaneous Squamous Cell Carcinoma by Podoplanin and E-Cadherin Expression

description: <b><i>Background:</i></b> Around 5% of all cutaneous squamous cell carcinoma (cSCC) metastasise. Metastases usually locate in regional skin and lymph nodes, suggesting collective cancer invasion. The cellular level of tumour invasion and prognostic parameters remain to be characterised. <b><i>Methods:</i></b> We performed immunohistochemical analyses of E-cadherin (marker for collective cancer invasion) and podoplanin (marker for epithelial-mesenchymal transition [EMT], single-cell invasion) expression in 102 samples of metastatic and non-metastatic cSCC and 18 corresponding skin and lymph node metastases to characterise the invasion of cSCC. Immunohistochemical results were retrospectively correlated with clinical data. <b><i>Results:</i></b> E-cadherin was highly expressed in metastatic and non-metastatic cSCC and skin metastases. This suggests collective cancer invasion. However, E-cadherin was downregulated in poorly differentiated cSCC and lymph node metastases, suggesting partial EMT. Podoplanin was significantly upregulated in metastatic (<i>p</i> = 0.002) and poorly differentiated (<i>p</i> = 0.003) cSCC. Overexpression of podoplanin represented a statistically independent prognostic factor for disease-free survival (<i>p</i> = 0.014). <b><i>Conclusion:</i></b> Collective cancer invasion is likely in cSCC. In lymph node metastases and poorly differentiated cSCC, partial EMT is possible. Podoplanin is an independent prognostic parameter for metastasis.
DOI: 10.6084/m9.figshare.4246178
title: Supplementary Material for: Alternative to LRRK2-IN-1 for Pharmacological Studies of Parkinson's Disease

description: <br><strong><em>Background/Aims:</em></strong> LRRK2 (leucine-rich repeat protein kinase 2) is one of the most commonly accepted genes associated with Parkinson's disease (PD). The overexpression of disease-associated mutations in LRRK2 is toxic to the cells, while reduction or elimination of LRRK2 expression promotes cell health and growth. Thus, the identification of an LRRK2 inhibitor with good physiochemical and pharmacokinetic properties is of great interest for the treatment of PD. <b><i>Methods:</i></b> In this study, we have investigated LRRK2 compounds, LRRK2-IN-1 and Compound 1, in vitro and in vivo to determine how suitable they are as a selective LRRK2 tool compound. <b><i>Results:</i></b> We report that Compound 1, patented by GSK, is a potent and selective LRRK2 inhibitor with good blood-brain barrier permeability as reflected by its high brain to plasma ratio in rats. In addition, Compound 1 can significantly promote neurite outgrowth in a primary cortical culture, indicating an optimistic cellular function of this compound in a biological system. In contrast, LRRK2-IN-1 is a less selective LRRK2 inhibitor and has low brain penetration. Furthermore, LRRK2-IN-1 is cyto- and genotoxic, while Compound 1 does not exhibit any toxicity. <b><i>Conclusions:</i></b> These results suggest that Compound 1 may be a superior tool compound than LRRK2-IN-1 to advance future pharmacological research on LRRK2.
DOI: 10.6084/m9.figshare.4246169.v1
title: Supplementary Material for: Characterisation of Prognosis and Invasion of Cutaneous Squamous Cell Carcinoma by Podoplanin and E-Cadherin Expression

description: <b><i>Background:</i></b> Around 5% of all cutaneous squamous cell carcinoma (cSCC) metastasise. Metastases usually locate in regional skin and lymph nodes, suggesting collective cancer invasion. The cellular level of tumour invasion and prognostic parameters remain to be characterised. <b><i>Methods:</i></b> We performed immunohistochemical analyses of E-cadherin (marker for collective cancer invasion) and podoplanin (marker for epithelial-mesenchymal transition [EMT], single-cell invasion) expression in 102 samples of metastatic and non-metastatic cSCC and 18 corresponding skin and lymph node metastases to characterise the invasion of cSCC. Immunohistochemical results were retrospectively correlated with clinical data. <b><i>Results:</i></b> E-cadherin was highly expressed in metastatic and non-metastatic cSCC and skin metastases. This suggests collective cancer invasion. However, E-cadherin was downregulated in poorly differentiated cSCC and lymph node metastases, suggesting partial EMT. Podoplanin was significantly upregulated in metastatic (<i>p</i> = 0.002) and poorly differentiated (<i>p</i> = 0.003) cSCC. Overexpression of podoplanin represented a statistically independent prognostic factor for disease-free survival (<i>p</i> = 0.014). <b><i>Conclusion:</i></b> Collective cancer invasion is likely in cSCC. In lymph node metastases and poorly differentiated cSCC, partial EMT is possible. Podoplanin is an independent prognostic parameter for metastasis.
DOI: 10.6084/m9.figshare.4246178.v1
title: Supplementary Material for: Alternative to LRRK2-IN-1 for Pharmacological Studies of Parkinson's Disease

description: <br><strong><em>Background/Aims:</em></strong> LRRK2 (leucine-rich repeat protein kinase 2) is one of the most commonly accepted genes associated with Parkinson's disease (PD). The overexpression of disease-associated mutations in LRRK2 is toxic to the cells, while reduction or elimination of LRRK2 expression promotes cell health and growth. Thus, the identification of an LRRK2 inhibitor with good physiochemical and pharmacokinetic properties is of great interest for the treatment of PD. <b><i>Methods:</i></b> In this study, we have investigated LRRK2 compounds, LRRK2-IN-1 and Compound 1, in vitro and in vivo to determine how suitable they are as a selective LRRK2 tool compound. <b><i>Results:</i></b> We report that Compound 1, patented by GSK, is a potent and selective LRRK2 inhibitor with good blood-brain barrier permeability as reflected by its high brain to plasma ratio in rats. In addition, Compound 1 can significantly promote neurite outgrowth in a primary cortical culture, indicating an optimistic cellular function of this compound in a biological system. In contrast, LRRK2-IN-1 is a less selective LRRK2 inhibitor and has low brain penetration. Furthermore, LRRK2-IN-1 is cyto- and genotoxic, while Compound 1 does not exhibit any toxicity. <b><i>Conclusions:</i></b> These results suggest that Compound 1 may be a superior tool compound than LRRK2-IN-1 to advance future pharmacological research on LRRK2.
DOI: 10.6084/m9.figshare.4246160
title: Data for Ru aerobic oxidation caatalyst

description: Data for Ru-catalysed aerobic oxidation of benzyl alcohol recorded under continuous flow at different temperatures and pressures.
DOI: 10.6084/m9.figshare.4246160.v1
title: Data for Ru aerobic oxidation caatalyst

description: Data for Ru-catalysed aerobic oxidation of benzyl alcohol recorded under continuous flow at different temperatures and pressures.
DOI: 10.17608/k6.auckland.4246091
title: seismic data from RU of the 2016 Rotorua earthquake

description: <br><br>sac files from school seismometers in the RU network used in our EJP publication to create figure 6.<br>
DOI: 10.17608/k6.auckland.4246091.v1
title: data from the 2016 Rotorua earthquake on RU stations

description: <br>sac files from school seismometers in the RU network used in our EJP publication to create figure 6.<br>
DOI: 10.17608/k6.auckland.4246091.v3
title: seismic data from RU of the 2016 Rotorua earthquake

description: <br><br>sac files from school seismometers in the RU network used in our EJP publication to create figure 6.<br>
DOI: 10.17608/k6.auckland.4246091.v2
title: data from the 2016 Rotorua earthquake on RU stations

description: <br><br>sac files from school seismometers in the RU network used in our EJP publication to create figure 6.<br>