cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5122387.v1
title: poster-delft_fig4

description: Figure 3 of Poster for Cumulus Parameterization workshop in Delft<br>
DOI: 10.6084/m9.figshare.5122390.v1
title: poster-delft_fig-5

description: Figure 5 of poster fo Cumulus Parameterization workshop in Delft<br>
DOI: 10.6084/m9.figshare.5122369
title: poster-delft_fig-2

description: Figure 2 for Poster at Cumulus Parameterization workshop in Delft<br>
DOI: 10.6084/m9.figshare.5122363
title: BGDMdocker

description: <b>a Docker workflow for data</b><b> </b><b>mi</b><b>ni</b><b>ng and visualization of bacterial pan-genomes and biosynthetic gene clusters </b>
DOI: 10.6084/m9.figshare.5122363.v1
title: BGDMdocker

description: <b>a Docker workflow for data</b><b> </b><b>mi</b><b>ni</b><b>ng and visualization of bacterial pan-genomes and biosynthetic gene clusters </b>
DOI: 10.6084/m9.figshare.5122369.v1
title: poster-delft_fig-2

description: Figure 2 for Poster at Cumulus Parameterization workshop in Delft<br>
DOI: 10.6084/m9.figshare.5122381.v1
title: poster-delft_fig-3

description: Figure 2 for Poster at Cumulus Parameterization workshop in Delft
DOI: 10.6084/m9.figshare.12905855
title: Supplementary Material for: Liraglutide Improves the Kidney Function in a Murine Model of Chronic Kidney Disease

description: <b><i>Background:</i></b> Chronic kidney disease (CKD) is a global health burden, and the current treatment options only slow down the disease progression. GLP-1 receptor agonists (GLP-1 RA) have shown a renal protective effect in models of CKD; however, the mechanism behind the beneficial effect is not understood. In this study, we investigate the effect of the GLP-1 RA liraglutide in the nephrotoxic serum nephritis (NTN) CKD model. Moreover, we compare the gene expression pattern of liraglutide-treated mice to the gene expression pattern of mice treated with the angiotensin converting enzyme inhibitor, enalapril. <b><i>Methods:</i></b> The effect of liraglutide was tested in the NTN model by evaluating the glomerular filtration rate (GFR), albuminuria, mesangial expansion, renal fibrosis, and renal inflammation. Furthermore, the regulation of selected genes involved in CKD and in glomerular, cortical tubulointerstitial, and whole kidney structures was analyzed using a gene expression array on samples following laser capture microdissection. <b><i>Results:</i></b> Treatment with liraglutide improved CKD hallmarks including GFR, albuminuria, mesangial expansion, renal inflammation, and renal fibrosis. The gene expression revealed that both liraglutide and enalapril reversed the regulation of several fibrosis and inflammation associated genes, which are also regulated in human CKD patients. Furthermore, liraglutide and enalapril both regulated genes in the kidney involved in blood pressure control. <b><i>Conclusions:</i></b> Treatment with liraglutide improved the kidney function and diminished renal lesions in NTN-induced mice. Both liraglutide and enalapril reversed the regulation of genes involved in CKD and regulated genes involved in blood pressure control.
DOI: 10.6084/m9.figshare.5121922
title: ReadMe.txt

description: Explanation of the results file naming.
DOI: 10.6084/m9.figshare.5121922.v1
title: ReadMe.txt

description: Explanation of the results file naming.
DOI: 10.6084/m9.figshare.5121898
title: Supplementary Material for: Multifactorial Analysis of a Biomarker Pool for Alzheimer Disease Risk in a North Indian Population

description: <b><i>Background:</i></b> Alzheimer disease (AD) is a progressive neurodegenerative disease with a complex multifactorial etiology. Here, we aim to identify a biomarker pool comprised of genetic variants and blood biomarkers as predictor of AD risk. <b><i>Methods:</i></b> We performed a case-control study involving 108 cases and 159 non-demented healthy controls to examine the association of multiple biomarkers with AD risk. <b><i>Results:</i></b> The <i>APOE</i> genotyping revealed that ε4 allele frequency was significantly high (<i>p</i> value = 0.0001, OR = 2.66, 95% CI 1.58-4.46) in AD as compared to controls, whereas ε2 (<i>p</i> = 0.0430, OR = 0.29, CI 0.07-1.10) was overrepresented in controls. In biochemical assays, significant differences in levels of total copper, free copper, zinc, copper/zinc ratio, iron, epidermal growth factor receptor (EGFR), leptin, and albumin were also observed. The AD risk score (ADRS) as a linear combination of 6 candidate markers involving age, education status, <i>APOE</i> ε4 allele, levels of iron, Cu/Zn ratio, and EGFR was created using stepwise linear discriminant analysis. The area under the ROC curve of the ADRS panel for predicting AD risk was significantly high (AUC = 0.84, <i>p</i> &lt; 0.0001, 95% CI 0.78-0.89, sensitivity = 70.0%, specificity = 83.8%) compared to individual parameters. <b><i>Conclusion:</i></b> These findings support the multifactorial etiology of AD and demonstrate the ability of a panel involving 6 biomarkers to discriminate AD cases from non-demented healthy controls.
DOI: 10.6084/m9.figshare.5121898.v1
title: Supplementary Material for: Multifactorial Analysis of a Biomarker Pool for Alzheimer Disease Risk in a North Indian Population

description: <b><i>Background:</i></b> Alzheimer disease (AD) is a progressive neurodegenerative disease with a complex multifactorial etiology. Here, we aim to identify a biomarker pool comprised of genetic variants and blood biomarkers as predictor of AD risk. <b><i>Methods:</i></b> We performed a case-control study involving 108 cases and 159 non-demented healthy controls to examine the association of multiple biomarkers with AD risk. <b><i>Results:</i></b> The <i>APOE</i> genotyping revealed that ε4 allele frequency was significantly high (<i>p</i> value = 0.0001, OR = 2.66, 95% CI 1.58-4.46) in AD as compared to controls, whereas ε2 (<i>p</i> = 0.0430, OR = 0.29, CI 0.07-1.10) was overrepresented in controls. In biochemical assays, significant differences in levels of total copper, free copper, zinc, copper/zinc ratio, iron, epidermal growth factor receptor (EGFR), leptin, and albumin were also observed. The AD risk score (ADRS) as a linear combination of 6 candidate markers involving age, education status, <i>APOE</i> ε4 allele, levels of iron, Cu/Zn ratio, and EGFR was created using stepwise linear discriminant analysis. The area under the ROC curve of the ADRS panel for predicting AD risk was significantly high (AUC = 0.84, <i>p</i> &lt; 0.0001, 95% CI 0.78-0.89, sensitivity = 70.0%, specificity = 83.8%) compared to individual parameters. <b><i>Conclusion:</i></b> These findings support the multifactorial etiology of AD and demonstrate the ability of a panel involving 6 biomarkers to discriminate AD cases from non-demented healthy controls.
DOI: 10.6084/m9.figshare.5121862
title: Supplementary Material for: Mutation Analysis of <i>PAX6</i> in a Chinese Family and a Patient with a Presumed Sporadic Case of Congenital Aniridia

description: <i>Aims:</i> Mutations in the<i> PAX6</i> are the major cause of congenital aniridia. The objective of this study was to analyze genetic mutations in<i> PAX6</i> in Chinese patients with congenital aniridia. <i>Methods:</i> Total genomic DNA was isolated from the peripheral blood of the aniridia patients, all healthy family members and 100 healthy volunteers. The 14 exons (including alternatively spliced exon 5a) of the<i> PAX6</i> gene were amplified by polymerase chain reaction, and the products were sequenced to identify the mutation. <i>Results:</i> Two mutations of<i> PAX6</i> were detected in exon 11 in the congenital aniridia patients. One mutation was caused by the duplication of the 4 nucleic acids CTCC (c.1286insCTCC), which would lead to a frameshift. The other mutation was caused by a transition from C to T (c.1311C → T), which would generate a stop codon. Neither mutation was present in the healthy family members or 100 healthy volunteers. <i>Conclusion:</i> We examined the exon sequence of the <i>PAX6</i> gene in a Chinese family and an unrelated individual with aniridia. The predicted outcome of both mutations is premature termination. The mutation found in the unrelated individual has not previously been reported and represents a new addition to the spectrum of mutations in<i> PAX6.</i>
DOI: 10.6084/m9.figshare.5121865
title: Supplementary Material for: Mineral Metabolism Management in Hemodialysis Patients with Secondary Hyperparathyroidism in Japan: Baseline Data from the MBD-5D

description: <i>Background/Aims:</i> The Mineral and Bone Disorder Outcomes Study for Japanese CKD Stage 5D Patients (MBD-5D) is a multicenter, prospective observational study of hemodialysis patients with secondary hyperparathyroidism (SHPT) in Japan, where the national guideline recommends targets for serum calcium (8.4–10.0 mg/dl), phosphorus (3.5–6.0 mg/dl), and intact parathyroid hormone (PTH) (60–180 pg/ml). <i>Methods:</i> The MBD-5D involved patients who were receiving hemodialysis for more than 3 months and met at least one of the following conditions: having intact PTH levels &gt;180 pg/ml, or receiving intravenous vitamin D receptor activators (VDRAs) or oral VDRA analog. This report describes the baseline characteristics of the study participants and examines factors associated with mineral metabolism controllability. <i>Results:</i> A total of 8,229 patients were registered from 86 facilities as the whole cohort, and 3,276 patients were randomly selected as the subcohort. The severity of SHPT was associated with a lower likelihood of achieving the targets for calcium and phosphorus, whereas patients with a history of parathyroidectomy were more likely to achieve these targets as compared with those who had not undergone surgery despite high PTH levels. The use of 2.5 mEq/l calcium dialysate was also associated with a higher likelihood of achieving the targets compared with the use of 3.0 mEq/l calcium dialysate. <i>Conclusion:</i> The severity of SHPT and the use of dialysate with higher calcium concentration are associated with practical difficulty in managing mineral metabolism in dialysis patients. Further prospective follow-up is needed to confirm our findings and to examine their impact on patient-level outcomes.
DOI: 10.6084/m9.figshare.5121880
title: Male nutritional history affects female fecundity in a male-dimorphic mite.xlsx

description: Mass changes, fecundity and mortality data of males and females of the male-dimorphic bulb mite <i>Rhizoglyphus robini</i>.<br>
DOI: 10.6084/m9.figshare.5121850
title: Supplementary Material for: Activation of KCNQ2/3 Potassium Channels by Novel Pyrazolo[1,5-a]pyrimidin-7(4H)-One Derivatives

description: The voltage-gated M-type potassium channel, encoded mainly by the KCNQ2/3 genes, plays an important role in the control of neuronal excitability. Mutations in the KCNQ2 gene lead to a form of neonatal epilepsy in humans termed ‘benign familial neonatal convulsions’, which is characterized by hyperexcitability of neurons. KCNQ openers or activators are expected to decrease the firing of overactive neurons and are thus conducive to the treatment of epilepsy and pain. Here, we report that four novel synthesized derivatives of pyrazolo[1,5-a]pyrimidin-7(4H)-one (PPO) named QO-26, QO-28, QO-40 and QO-41 potently augmented KCNQ2/3 channels expressed in Chinese hamster ovary cells and shifted the half-maximal activation voltage (V<sub>1/2</sub>) in the hyperpolarizing direction. The V<sub>1/2</sub> was negatively shifted in a concentration-dependent manner. The compounds markedly slowed both KCNQ2/3 channel activation and deactivation kinetics. Structure-activity relationship studies suggest that trifluoromethyl at the C-2 position, phenyl or naphthyl at the C-3 position, and trifluoromethyl or chloromethyl at the C-5 position are essential for the activity. These results suggest the four PPO derivatives act as KCNQ2/3 channel openers, providing a new dimension for the design and development of more potent channel openers.
DOI: 10.6084/m9.figshare.5121859
title: Supplementary Material for: <i>TGFBR3</i> Polymorphisms and Its Haplotypes Associated with Chronic Hepatitis B Virus Infection and Age of Hepatocellular Carcinoma Occurrence

description: <i>Objective:</i> Hepatocellular carcinoma (HCC) is one of the most common cancers and is mainly caused by viral infections including hepatitis B virus (HBV). Recently, the decreased expression level of the <i>transforming growth factor, beta receptor III</i> (<i>TGFBR3</i>) gene, has been implicated in HCC and other human cancers. This study investigated whether <i>TGFBR3</i> polymorphisms might be associated with HBV clearance and HCC occurrence. <i>Methods:</i> This study identified 27 single nucleotide polymorphisms (SNPs) in the exon, promoter, and exon-intron boundary regions of <i>TGFBR3</i> by resequencing in 24 individuals. Then, 9 SNPs in the promoter and exons of the gene were genotyped from 1,065 Koreans composed of 637 chronic carriers (CC) and 428 spontaneously recovered (SR) subjects. <i>Results:</i> Two SNPs, <i>rs1805113</i> (Phe676Phe) in exon 13 and <i>rs1805117</i> in 3′-UTR (p = 0.009 and p = 0.008, respectively) were significantly associated with HBV clearance. In addition, Cox relative hazards analyses revealed that haplotype<i> BL2_ht2 </i>showed a significant association with the age of HCC occurrence among chronic HBV patients (relative hazard = 1.38; p = 0.007). <i>Conclusion:</i> Our findings suggest that <i>TGFBR3</i> polymorphisms and its haplotypes might be associated with HBV clearance and age of HCC occurrence.
DOI: 10.6084/m9.figshare.5121865.v1
title: Supplementary Material for: Mineral Metabolism Management in Hemodialysis Patients with Secondary Hyperparathyroidism in Japan: Baseline Data from the MBD-5D

description: <i>Background/Aims:</i> The Mineral and Bone Disorder Outcomes Study for Japanese CKD Stage 5D Patients (MBD-5D) is a multicenter, prospective observational study of hemodialysis patients with secondary hyperparathyroidism (SHPT) in Japan, where the national guideline recommends targets for serum calcium (8.4–10.0 mg/dl), phosphorus (3.5–6.0 mg/dl), and intact parathyroid hormone (PTH) (60–180 pg/ml). <i>Methods:</i> The MBD-5D involved patients who were receiving hemodialysis for more than 3 months and met at least one of the following conditions: having intact PTH levels &gt;180 pg/ml, or receiving intravenous vitamin D receptor activators (VDRAs) or oral VDRA analog. This report describes the baseline characteristics of the study participants and examines factors associated with mineral metabolism controllability. <i>Results:</i> A total of 8,229 patients were registered from 86 facilities as the whole cohort, and 3,276 patients were randomly selected as the subcohort. The severity of SHPT was associated with a lower likelihood of achieving the targets for calcium and phosphorus, whereas patients with a history of parathyroidectomy were more likely to achieve these targets as compared with those who had not undergone surgery despite high PTH levels. The use of 2.5 mEq/l calcium dialysate was also associated with a higher likelihood of achieving the targets compared with the use of 3.0 mEq/l calcium dialysate. <i>Conclusion:</i> The severity of SHPT and the use of dialysate with higher calcium concentration are associated with practical difficulty in managing mineral metabolism in dialysis patients. Further prospective follow-up is needed to confirm our findings and to examine their impact on patient-level outcomes.
DOI: 10.6084/m9.figshare.5121880.v1
title: Male nutritional history affects female fecundity in a male-dimorphic mite.xlsx

description: Mass changes, fecundity and mortality data of males and females of the male-dimorphic bulb mite <i>Rhizoglyphus robini</i>.<br>
DOI: 10.6084/m9.figshare.5121841
title: Supplementary Material for: Chromosomal Variants in Klinefelter Syndrome

description: Klinefelter syndrome (KS) describes the phenotype of the most common sex chromosome abnormality in humans and occurs in one of every 600 newborn males. The typical symptoms are a tall stature, narrow shoulders, broad hips, sparse body hair, gynecomastia, small testes, absent spermatogenesis, normal to moderately reduced Leydig cell function, increased secretion of follicle-stimulating hormone, androgen deficiency, and normal to slightly decreased verbal intelligence. Apart from that, amongst others, osteoporosis, varicose veins, thromboembolic disease, or diabetes mellitus are observed. Some of the typical features can be very weakly pronounced so that the affected men often receive the diagnosis only at the adulthood by their infertility. With a frequency of 4%, KS is described to be the most common genetic reason for male infertility. The most widespread karyotype in affected patients is 47,XXY. Apart from that, various other karyotypes have been described, including 46,XX in males, 47,XXY in females, 47,XX,der(Y), 47,X,der(X),Y, or other numeric sex chromosome abnormalities (48,XXXY, 48,XXYY, and 49,XXXXY). The focus of this review was to abstract the different phenotypes, which come about by the various karyotypes and to compare them to those with a ‘normal’ KS karyotype. For that the patients have been divided into 6 different groups: Klinefelter patients with an additional isochromosome Xq, with additional rearrangements on 1 of the 2 X chromosomes or accordingly on the Y chromosome, as well as XX males and true hermaphrodites, 47,XXY females and Klinefelter patients with other numeric sex chromosome abnormalities. In the latter, an almost linear increase in height and developmental delay was observed. Men with an additional isochromosome Xq show infertility and other minor features of ‘normal’ KS but not an increased height. Aside from the infertility, in male patients with other der(X) as well as der(Y) rearrangements and in XXY women no specific phenotype is recognizable amongst others due to the small number of cases. The phenotype of XX males depends on the presence of <i>SRY</i> (sex-determining region Y) and the level of X inactivation at which <i>SRY</i>-negative patients are generally rarely observed.
DOI: 10.6084/m9.figshare.5121844
title: Supplementary Material for: Impact of a Mechanical Massage on Gene Expression Profile and Lipid Mobilization in Female Gluteofemoral Adipose Tissue

description: <i>Background:</i> Gluteofemoral adipose tissue areas are known to be poorly metabolically reactive. Mechanical massage has previously been reported to show morphological and functional impact on this tissue. The present study was carried out to delve more deeply into the mechanistic considerations regarding the incidence of a mechanical massage technique on gene expression profile and β-adrenergic-mediated lipid mobilization in female femoral adipose tissue. <i>Methods:</i> Twelve premenopausal healthy women were included and received 12 sessions of calibrated mechanical massage (Endermologie®). Total RNA was extracted from femoral adipose tissue biopsies for gene expression studies. Microdialysis was carried out in the femoral adipose tissue in order to assess lipolytic responsiveness (via glycerol determination) and changes in local blood flow following perfusion of a lipolytic agent, isoproterenol. Evaluations were performed before and after the 6-week experimental period. <i>Results:</i> Mechanical massage initiated important modifications in gene expression profile. The lipid-mobilizing effect of isoproterenol was enhanced after the experimental period. Basal local blood flow and isoproterenol-induced vasodilatation were also improved. <i>Conclusion:</i> The protocol of mechanical massage used in the study promoted noticeable changes in the expression of genes involved in metabolic pathways. The lipolytic and local adipose tissue blood flow responses initiated by isoproterenol were significantly enhanced.
DOI: 10.6084/m9.figshare.5121847
title: Supplementary Material for: Knock-Out of β-Glucosidase 2 Has No Influence on Dextran Sulfate Sodium-Induced Colitis

description: <i>Background/Aims:</i> The non-lysosomal glucosylceramidase, β-glucosidase (Gba2), hydrolyzes glucosylceramide to glucose and ceramide (Cer). Cer is a potent second-messenger lipid that plays an important role in signaling cascades involved in apoptosis. The aim of this study was to investigate whether Gba2 knock-out (Gba2<sup>–/–</sup>) affects the extent of dextran sulfate sodium (DSS)-induced colitis in mice. <i>Methods:</i> Acute colitis was induced in wild-type (WT) and Gba2<sup>–/–</sup> mice by administration of 2% DSS in drinking water. After 7 days, mice underwent colonoscopy and were sacrificed. <i>Results:</i> Both DSS-treated WT (n = 10) and Gba2<sup>–/–</sup> (n = 12) mice showed elevated histological and endoscopic scores compared to respective H<sub>2</sub>O controls (n = 9 each). However, no significant differences between the DSS groups were detected. Flow cytometric analysis of propidium iodide staining, cleavage of caspases-3 and -8, indicative for apoptosis, as well as Cer levels were not altered in DSS-treated WT or Gba2<sup>–/–</sup> mice. Gba2<sup>–/–</sup> resulted in slightly decreased expression of glucocerebrosidase (Gba1) as well as in upregulation of proteins being involved in cellular regeneration, such as STAT3 (signal transducer and activator of transcription), JNK and iNOS, upon DSS treatment. <i>Conclusion:</i> We demonstrate that Gba2<sup>–/–</sup> does not affect the extent of DSS-induced inflammation in mice, however, it might be involved in tissue regeneration in response to toxic agents.
DOI: 10.6084/m9.figshare.5121859.v1
title: Supplementary Material for: <i>TGFBR3</i> Polymorphisms and Its Haplotypes Associated with Chronic Hepatitis B Virus Infection and Age of Hepatocellular Carcinoma Occurrence

description: <i>Objective:</i> Hepatocellular carcinoma (HCC) is one of the most common cancers and is mainly caused by viral infections including hepatitis B virus (HBV). Recently, the decreased expression level of the <i>transforming growth factor, beta receptor III</i> (<i>TGFBR3</i>) gene, has been implicated in HCC and other human cancers. This study investigated whether <i>TGFBR3</i> polymorphisms might be associated with HBV clearance and HCC occurrence. <i>Methods:</i> This study identified 27 single nucleotide polymorphisms (SNPs) in the exon, promoter, and exon-intron boundary regions of <i>TGFBR3</i> by resequencing in 24 individuals. Then, 9 SNPs in the promoter and exons of the gene were genotyped from 1,065 Koreans composed of 637 chronic carriers (CC) and 428 spontaneously recovered (SR) subjects. <i>Results:</i> Two SNPs, <i>rs1805113</i> (Phe676Phe) in exon 13 and <i>rs1805117</i> in 3′-UTR (p = 0.009 and p = 0.008, respectively) were significantly associated with HBV clearance. In addition, Cox relative hazards analyses revealed that haplotype<i> BL2_ht2 </i>showed a significant association with the age of HCC occurrence among chronic HBV patients (relative hazard = 1.38; p = 0.007). <i>Conclusion:</i> Our findings suggest that <i>TGFBR3</i> polymorphisms and its haplotypes might be associated with HBV clearance and age of HCC occurrence.