cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125507
title: Supplementary Material for: Molecular Pathways and Functional Analysis of miRNA Expression Associated with Paclitaxel-Induced Apoptosis in Hepatocellular Carcinoma Cells

description: <b><i>Background:</i></b> We postulated that microRNAs (miRNAs) might be involved in hepatocellular carcinoma (HCC) targeted chemotherapy with paclitaxel. This study sought to generate a list of potential miRNA-based biomarkers and their potential targets to better understand the response to paclitaxel treatment in HCC. <b><i>Methods:</i></b> Cell viability proliferation assays were conducted to test the sensitivity of the HepG2 cells to paclitaxel. The morphological changes of apoptosis were assessed with 4′,6-diamidino-2-phenylindole staining. Differential expression patterns of miRNA in the HepG2 cells either treated or not treated were analyzed using miRNA microarrays. <b><i>Results:</i></b> The array experiments have identified 54 miRNAs whose basal expression levels differed by &gt;2-fold and p &lt; 0.05 between the two phenotypic groups. The data were validated by a quantitative real-time PCR of 8 selected miRNAs (miR-21, miR-1274a, miR-1260, miR-1290, miR-508-5p, miR-877, miR-1246, miR-183*). The PI3K/Akt, mitogen-activated protein kinase (MAPK), TGF-β, ErbB, p53, cell cycle, mammalian target of rapamycin, and Jak-STAT signaling pathways were involved in paclitaxel-induced apoptosis. <b><i>Conclusions:</i></b> The manipulation of one or more of these miRNAs could be an important approach for the improved management of paclitaxel therapy.
DOI: 10.6084/m9.figshare.5125513.v1
title: Supplementary Material for: Is It Time to Rethink How Neuropsychological Tests Are Used to Diagnose Mild Forms of HIV-Associated Neurocognitive Disorders? Impact of False-Positive Rates on Prevalence and Power

description: <b><i>Background:</i></b> Between 0 and 48% of normal HIV-uninfected individuals score below threshold neuropsychological test scores for HIV-associated neurocognitive disorders (HAND) or are false positives. There has been little effort to understand the effect of varied interpretations of research criteria for HAND on false-positive frequencies, prevalence and analytic estimates. <b><i>Methods:</i></b> The proportion of normal individuals scoring below Z score thresholds drawn from research criteria for HAND, or false-positive frequencies, was estimated in a normal Kenyan population and a simulated normal population using varied interpretations of research criteria for HAND. We calculated the impact of false-positive frequencies on prevalence estimates and statistical power. <b><i>Results:</i></b> False-positive frequencies of 2-74% were observed for asymptomatic neurocognitive impairment/mild neurocognitive disorder and 0-8% for HIV-associated dementia. False-positive frequencies depended on the definition of an abnormal cognitive domain, Z score thresholds and neuropsychological battery size. Misclassification led to clinically important overestimation of prevalence and dramatic decreases in power. <b><i>Conclusions:</i></b> Minimizing false-positive frequencies is critical to decrease bias in prevalence estimates and minimize reductions in power in studies of association, particularly for mild forms of HAND. We recommend changing the Z score threshold to ≤-1.5 for mild impairment, limiting analysis to 3-5 cognitive domains and using the average Z score to define an abnormal domain.
DOI: 10.6084/m9.figshare.5125501
title: Supplementary Material for: Gemcitabine plus Cisplatin versus Capecitabine plus Cisplatin as First-Line Chemotherapy for Advanced Biliary Tract Cancer: A Retrospective Cohort Study

description: <b><i>Background and Aim:</i></b> Gemcitabine plus cisplatin (GP) is a standard chemotherapy option for patients with advanced biliary tract cancer (BTC). We compared the efficacy and safety of capecitabine plus cisplatin (XP) versus GP in advanced BTC. <b><i>Methods:</i></b> The records of all patients treated with GP or XP chemotherapy for unresectable, metastatic, or recurrent BTC at the National Cancer Center between December 2001 and August 2012 were reviewed retrospectively. Patients with histologically confirmed intrahepatic cholangiocarcinoma, gallbladder cancer, or extrahepatic cholangiocarcinoma were enrolled. <b><i>Results:</i></b> Of the 344 patients enrolled, 127 received GP and 217 received XP. At a median follow-up time of 8.9 months, the median time to progression was longer in the GP group than in the XP group (5.6 vs. 4.7 months), but the difference was not statistically significant (p = 0.081). The median overall survival (OS) was 8.4 months (95% CI 6.2-10.7) in the GP group and 7.6 months (95% CI 6.8-8.7) in the XP group (p = 0.024), with statistical significance retained following multivariate analysis (HR 0.72; 95% CI 0.527-0.987; p = 0.004). Grade 3/4 toxicities were significantly more frequent in the GP group than in the XP group (40.9 vs. 24.9%, p = 0.002). <b><i>Conclusions:</i></b> GP was superior to XP in prolonging OS, despite increasing the rate of grade 3/4 adverse events.
DOI: 10.6084/m9.figshare.5125507.v1
title: Supplementary Material for: Molecular Pathways and Functional Analysis of miRNA Expression Associated with Paclitaxel-Induced Apoptosis in Hepatocellular Carcinoma Cells

description: <b><i>Background:</i></b> We postulated that microRNAs (miRNAs) might be involved in hepatocellular carcinoma (HCC) targeted chemotherapy with paclitaxel. This study sought to generate a list of potential miRNA-based biomarkers and their potential targets to better understand the response to paclitaxel treatment in HCC. <b><i>Methods:</i></b> Cell viability proliferation assays were conducted to test the sensitivity of the HepG2 cells to paclitaxel. The morphological changes of apoptosis were assessed with 4′,6-diamidino-2-phenylindole staining. Differential expression patterns of miRNA in the HepG2 cells either treated or not treated were analyzed using miRNA microarrays. <b><i>Results:</i></b> The array experiments have identified 54 miRNAs whose basal expression levels differed by &gt;2-fold and p &lt; 0.05 between the two phenotypic groups. The data were validated by a quantitative real-time PCR of 8 selected miRNAs (miR-21, miR-1274a, miR-1260, miR-1290, miR-508-5p, miR-877, miR-1246, miR-183*). The PI3K/Akt, mitogen-activated protein kinase (MAPK), TGF-β, ErbB, p53, cell cycle, mammalian target of rapamycin, and Jak-STAT signaling pathways were involved in paclitaxel-induced apoptosis. <b><i>Conclusions:</i></b> The manipulation of one or more of these miRNAs could be an important approach for the improved management of paclitaxel therapy.
DOI: 10.6084/m9.figshare.5125510.v1
title: Supplementary Material for: Validity of Discharge Diagnoses in the Surveillance of Stroke

description: <b><i>Background:</i></b> Hospital administrative data have been suggested as a valuable cost-effective tool for providing information about the stroke burden. Nevertheless, the choice of the diagnosis codes has been a critical issue in the development of case ascertainment algorithms. <b><i>Methods:</i></b> In this study, the Minimum Basic Data Set administrative database was used to analyze the accuracy of different ICD-9-CM algorithms based on the neurologist's clinical judgement as the ‘gold standard'. <b><i>Results:</i></b> The most accurate algorithm observed in our study involved the selection of ICD-9-CM codes 430-438 in the primary diagnosis. It yielded a sensitivity of 96.1%, a specificity of 87.5% and a positive predictive value of 82.5%. <b><i>Conclusions:</i></b> The Minimum Basic Data Set is a valuable source to evaluate stroke frequency when using an accurate algorithm to select events.
DOI: 10.6084/m9.figshare.5125492
title: Supplementary Material for: The Role of Mechanical Bowel Preparation before Ileal Urinary Diversion: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Although the use of mechanical bowel preparation (MBP) is still widely promoted as the dogma before patients undergo ileal urinary diversion, an increasing number of clinical trials have suggested that there is no benefit. Thus, we performed a meta-analysis to evaluate the efficacy of MBP in ileal urinary diversion surgery. <b><i>Methods:</i></b> A literature search was performed in electronic databases, including PubMed, Embase, Science Citation Index Expanded as well as the Cochrane Library and the Cochrane Clinical Trials Registry, from 1966 to January 1, 2013. Clinical trials comparing outcomes of MBP versus no MBP for ileal urinary diversion surgery were included in the meta-analysis. Pooled odds ratios with 95% confidence intervals were calculated using the fixed- or random-effects models. <b><i>Results:</i></b> In total, two randomized controlled trials and five cohort studies were included in this meta-analysis. The primary outcomes, such as bowel leak and bowel obstruction, showed no statistical difference between the two groups. Additionally, the overall mortality rate and death rate related to operation also manifested that MBP does not offer an advantage over the no MBP. <b><i>Conclusion:</i></b> This meta-analysis suggests that MBP does not reduce the incidence of perioperative complications in urinary diversion compared with no MBP. However, large randomized controlled clinical trials are needed to confirm this finding.
DOI: 10.6084/m9.figshare.5125495
title: Supplementary Material for: Role of p66shc in Renal Toxicity of Oleic Acid

description: <b><i>Background/Aims:</i></b> Adult and childhood obesity is an independent risk factor in development of chronic kidney disease (CKD) and its progression to end-stage kidney disease. Pathologic consequences of obesity include non-esterified fatty acid-induced oxidative stress and consequent injury. Since the serine36-phosphorylated p66shc is a newly recognized mediator of oxidative stress and kidney injury, we studied its role in oleic acid (OA)-induced production of reactive oxygen species (ROS), mitochondrial depolarization and injury in cultured renal proximal tubule cells. <b><i>Methods:</i></b> Renal proximal tubule cells were used and treated with OA: ROS production, mitochondrial depolarization as well as injury were determined. Transcriptional effects of OA on the p66shc gene were determined in a reporter luciferase assay. The role of p66shc in adverse effects of OA was determined using knockdown, p66shc serine36 phosphorylation and cytochrome <i>c </i>binding-deficient cells. <b><i>Results:</i></b> We found that OA increased ROS production via the mitochondria - and to a less extent via the NADPH oxidase - resulting in ROS-dependent mitochondrial depolarization and consequent injury. Interestingly, OA also stimulated the promoter of p66shc. Hence, knockdown of p66shc, impairment its Ser36 phosphorylation (mutation of Ser36 residue to alanine) or cytochrome <i>c</i> binding (W134F mutation) significantly attenuated OA-dependent lipotoxicity. <b><i>Conclusion:</i></b> These results offer a novel mechanism by which obesity may lead to renal tubular injury and consequently development of CKD. Manipulation of this pathway may offer therapeutic means to ameliorate obesity-dependent renal lipotoxicity.
DOI: 10.6084/m9.figshare.5125498
title: Supplementary Material for: 5-Hydroxytryptamine 1A and 2B Serotonin Receptors in Neurite Outgrowth: Involvement of Early Growth Response Protein 1

description: Neurotransmitters play important roles in neurogenesis; in particular, acetylcholine and serotonin may regulate neurite elongation. Acetylcholine may also activate transcription factors such as early growth response protein 1 (EGR-1), which plays a role in neurite extension. N18TG2 neuroblastoma cells (which do not produce neurotransmitters and constitutively express muscarinic acetylcholine receptors) were transfected with constructs containing the cDNA for choline acetyltransferase, 5-hydroxytryptamine 1A (5-HT<sub>1A</sub>) and 5-HT<sub>2B</sub> serotonin receptors to study acetylcholine and serotonin interplay in neurite outgrowth. 5-HT<sub>1A</sub> receptor stimulation causes a decrease in EGR-1 levels and inhibition of neurite outgrowth; 5-HT<sub>2B</sub> stimulation, however, has no effect. Muscarinic cholinergic stimulation, on the other end, increases EGR-1 levels and fiber outgrowth. Inhibition of EGR-1 binding reduces fiber outgrowth activity. When both cholinergic and 5-HT<sub>1A</sub> receptors are stimulated, fiber outgrowth is restored; therefore, acetylcholine counterbalances the inhibitory effect of serotonin on neurite outgrowth. These results suggest that EGR-1 plays a role in the interplay of acetylcholine and serotonin in the regulation of neurite extension during development.
DOI: 10.6084/m9.figshare.5125504.v1
title: Supplementary Material for: Shan Virus: A New Mimivirus Isolated from the Stool of a Tunisian Patient with Pneumonia

description: <b><i>Objective:</i></b> Following the isolation of a Marseillevirus from the stool of a healthy young Senegalese and a Mimivirus from a Tunisian patient with pneumonia, we attempted to isolate other giant viruses of amoebae from a large human stool collection. <b><i>Methods: </i></b>During the period 2010-2011, a total of 1,605 stool samples, including 115 from Tunisian patients with pneumonia, were cultured on amoebae. We used a recently developed high-throughput isolation system to detect amoebae plaque lysis on agar plates; this method allows for the testing of 100 samples per plate per week. The giant virus was identified by sequencing of genes conserved in Megavirales. <b><i>Results:</i></b> A single giant virus, called Shan, was isolated from the stool of a Tunisian patient with pneumonia who responded poorly to antibiotics. This virus has an icosahedral shape typical of members of the family Mimiviridae and a size of 640 ± 10 nm. Phylogenetic analyses showed that Shan virus was classified as a member of Mimivirus lineage C that infects amoebae. <b><i>Conclusion:</i></b> Only one isolate was obtained in this study, suggesting that giant viruses of amoebae are rare in human stool. The isolation of Shan virus from a patient with pneumonia brings into question the etiological role of this virus and its subsequent release in stool.
DOI: 10.6084/m9.figshare.5125495.v1
title: Supplementary Material for: Role of p66shc in Renal Toxicity of Oleic Acid

description: <b><i>Background/Aims:</i></b> Adult and childhood obesity is an independent risk factor in development of chronic kidney disease (CKD) and its progression to end-stage kidney disease. Pathologic consequences of obesity include non-esterified fatty acid-induced oxidative stress and consequent injury. Since the serine36-phosphorylated p66shc is a newly recognized mediator of oxidative stress and kidney injury, we studied its role in oleic acid (OA)-induced production of reactive oxygen species (ROS), mitochondrial depolarization and injury in cultured renal proximal tubule cells. <b><i>Methods:</i></b> Renal proximal tubule cells were used and treated with OA: ROS production, mitochondrial depolarization as well as injury were determined. Transcriptional effects of OA on the p66shc gene were determined in a reporter luciferase assay. The role of p66shc in adverse effects of OA was determined using knockdown, p66shc serine36 phosphorylation and cytochrome <i>c </i>binding-deficient cells. <b><i>Results:</i></b> We found that OA increased ROS production via the mitochondria - and to a less extent via the NADPH oxidase - resulting in ROS-dependent mitochondrial depolarization and consequent injury. Interestingly, OA also stimulated the promoter of p66shc. Hence, knockdown of p66shc, impairment its Ser36 phosphorylation (mutation of Ser36 residue to alanine) or cytochrome <i>c</i> binding (W134F mutation) significantly attenuated OA-dependent lipotoxicity. <b><i>Conclusion:</i></b> These results offer a novel mechanism by which obesity may lead to renal tubular injury and consequently development of CKD. Manipulation of this pathway may offer therapeutic means to ameliorate obesity-dependent renal lipotoxicity.
DOI: 10.6084/m9.figshare.5125498.v1
title: Supplementary Material for: 5-Hydroxytryptamine 1A and 2B Serotonin Receptors in Neurite Outgrowth: Involvement of Early Growth Response Protein 1

description: Neurotransmitters play important roles in neurogenesis; in particular, acetylcholine and serotonin may regulate neurite elongation. Acetylcholine may also activate transcription factors such as early growth response protein 1 (EGR-1), which plays a role in neurite extension. N18TG2 neuroblastoma cells (which do not produce neurotransmitters and constitutively express muscarinic acetylcholine receptors) were transfected with constructs containing the cDNA for choline acetyltransferase, 5-hydroxytryptamine 1A (5-HT<sub>1A</sub>) and 5-HT<sub>2B</sub> serotonin receptors to study acetylcholine and serotonin interplay in neurite outgrowth. 5-HT<sub>1A</sub> receptor stimulation causes a decrease in EGR-1 levels and inhibition of neurite outgrowth; 5-HT<sub>2B</sub> stimulation, however, has no effect. Muscarinic cholinergic stimulation, on the other end, increases EGR-1 levels and fiber outgrowth. Inhibition of EGR-1 binding reduces fiber outgrowth activity. When both cholinergic and 5-HT<sub>1A</sub> receptors are stimulated, fiber outgrowth is restored; therefore, acetylcholine counterbalances the inhibitory effect of serotonin on neurite outgrowth. These results suggest that EGR-1 plays a role in the interplay of acetylcholine and serotonin in the regulation of neurite extension during development.
DOI: 10.6084/m9.figshare.5125501.v1
title: Supplementary Material for: Gemcitabine plus Cisplatin versus Capecitabine plus Cisplatin as First-Line Chemotherapy for Advanced Biliary Tract Cancer: A Retrospective Cohort Study

description: <b><i>Background and Aim:</i></b> Gemcitabine plus cisplatin (GP) is a standard chemotherapy option for patients with advanced biliary tract cancer (BTC). We compared the efficacy and safety of capecitabine plus cisplatin (XP) versus GP in advanced BTC. <b><i>Methods:</i></b> The records of all patients treated with GP or XP chemotherapy for unresectable, metastatic, or recurrent BTC at the National Cancer Center between December 2001 and August 2012 were reviewed retrospectively. Patients with histologically confirmed intrahepatic cholangiocarcinoma, gallbladder cancer, or extrahepatic cholangiocarcinoma were enrolled. <b><i>Results:</i></b> Of the 344 patients enrolled, 127 received GP and 217 received XP. At a median follow-up time of 8.9 months, the median time to progression was longer in the GP group than in the XP group (5.6 vs. 4.7 months), but the difference was not statistically significant (p = 0.081). The median overall survival (OS) was 8.4 months (95% CI 6.2-10.7) in the GP group and 7.6 months (95% CI 6.8-8.7) in the XP group (p = 0.024), with statistical significance retained following multivariate analysis (HR 0.72; 95% CI 0.527-0.987; p = 0.004). Grade 3/4 toxicities were significantly more frequent in the GP group than in the XP group (40.9 vs. 24.9%, p = 0.002). <b><i>Conclusions:</i></b> GP was superior to XP in prolonging OS, despite increasing the rate of grade 3/4 adverse events.
DOI: 10.6084/m9.figshare.5125489
title: Supplementary Material for: Analysis of the Complete Genomes of Acholeplasma brassicae, A. palmae and A. laidlawii and Their Comparison to the Obligate Parasites from ‘Candidatus Phytoplasma'

description: Analysis of the completely determined genomes of the plant-derived <i>Acholeplasma brassicae</i> strain O502 and <i>A. palmae</i> strain J233 revealed that the circular chromosomes are 1,877,792 and 1,554,229 bp in size, have a G + C content of 36 and 29%, and encode 1,690 and 1,439 proteins, respectively. Comparative analysis of these sequences and previously published genomes of <i>A. laidlawii</i> strain PG-8, ‘<i>Candidatus</i> Phytoplasma asteris' strains, ‘<i>Ca</i>. P. australiense' and ‘<i>Ca</i>. P. mali' show a limited shared basic genetic repertoire. The acholeplasma genomes are characterized by a low number of rearrangements, duplication and integration events. Exceptions are the unusual duplication of rRNA operons in <i>A. brassicae</i> and an independently introduced second gene for a single-stranded binding protein in both genera. In contrast to phytoplasmas, the acholeplasma genomes differ by encoding the cell division protein FtsZ, a wide variety of ABC transporters, the F₀F<sub>1</sub> ATP synthase, the <i>Rnf</i>-complex, SecG of the <i>Sec</i>-dependent secretion system, a richly equipped repertoire for carbohydrate metabolism, fatty acid, isoprenoid and partial amino acid metabolism. Conserved metabolic proteins encoded in phytoplasma genomes such as the malate dehydrogenase SfcA, several transporters and proteins involved in host-interaction, and virulence-associated effectors were not predicted for the acholeplasmas.
DOI: 10.6084/m9.figshare.5125480
title: Supplementary Material for: Analysis of Turner Syndrome Patients within the Jordanian Population, with a Focus on Four Patients with Y Chromosome Abnormalities

description: This study presents findings in Turner syndrome (TS) patients from the Jordanian population, with focus on 4 patients with Y chromosomal abnormalities. From 1989 to 2011, 504 patients with TS stigmata were referred to our institute for karyotyping, resulting in 142 positive TS cases. Of these, 62 (43.7%) had the typical 45,X karyotype and the remaining individuals (56.3%) were found to be mosaics. Fifteen TS patients (10.5%) carried a structural abnormality of the Y chromosome and presented with the mosaic 45,X/46,XY karyotype. From these, 4 TS cases were investigated further. Karyotyping revealed that 1 patient carried a small supernumerary marker chromosome, whereas cytogenetic and molecular analyses showed that 3 patients carried 2 copies of the <i>SRY </i>gene. Further analysis by <i>SRY</i> sequencing revealed no mutations within the gene. The analyzed patients were found to be phenotypically either females or males, depending on the predominance of the cell line carrying the Y chromosome. This study demonstrates the importance of detailed cytogenetic analysis (such as FISH) in TS patients, and it also emphasizes the need for molecular analysis (such as PCR and sequencing) when fragments of the Y chromosome are present.
DOI: 10.6084/m9.figshare.5125483
title: Supplementary Material for: Transcriptional Repressor HipB Regulates the Multiple Promoters in <b><i>Escherichia coli</i></b>

description: HipB is a DNA-binding protein in <i>Escherichia coli</i> and negatively regulates its own promoter by binding to the palindromic sequences [TATCCN<sub>8</sub>GGATA (N represents any nucleotides)] on the <i>hipBA</i> promoter. For such sequences, bioinformatic analysis revealed that there are a total of 39 palindromic sequences (TATCCN<sub>(x)</sub>GGATA: N is any nucleotides and x is the number of nucleotides from 1 to 30) in the promoter regions of 33 genes on the <i>E. coli</i> genome. Notably, <i>eutH</i> and <i>fadH</i> have two and three TATCCN<sub>(x)</sub>GGATA palindromic sequences located in their promoters, respectively. Another significant finding was that a palindromic sequence was also identified in the promoter region of <i>hipAB</i> locus, known to be involved in the RelA-dependent persister cell formation in bacteria. Here, we demonstrated that HipB binds to the palindromic structures in the <i>eutH</i>,<i> fadH</i>, as well as the <i>relA</i> promoter regions and represses their expressions. We further demonstrated that HipA enhances the repression of the <i>relA</i> promoter activity by HipB. This effect was not observed with D291A HipA mutant which was previously shown to lack an ability to interact with HipB, indicating that HipA enhances the HipB's repressor activity through direct interaction with HipB.