cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5127487.v1
title: Supplementary Material for: SRS06, a New Semisynthetic Andrographolide Derivative with Improved Anticancer Potency and Selectivity, Inhibits Nuclear Factor-κB Nuclear Binding in the A549 Non-Small Cell Lung Cancer Cell Line

description: <b><i>Background:</i></b> Andrographolide has been reported with anticancer and anti-inflammatory properties through the inhibition of the activity of signaling molecules such as v-Src, nuclear factor-κB (NF-κB), STAT3, and PI3K. NF-κB has been proven to promote cancer cell survival, and targeting this pathway will halt the growth of cancer cells. Efforts have been made to produce semisynthetic derivatives of andrographolide with improved anticancer potency and selectivity. Subsequently, the effect of a selected derivative, 3,14,19-tripropionylandrographolide (SRS06), was tested for its action against NF-κB. <b><i>Methods:</i></b> Screening against 60 US National Cancer Institute (NCI) human cancer cell lines representing leukemia and non-small cell lung (NSCL), colon, CNS, melanoma, ovarian, renal, prostate, and breast cancers was performed to determine the tumor type selectivity and potency of SRS06. Microculture tetrazolium, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide and sulforhodamine B assays were used to determine the in vitro anticancer activity, while Western blot studies were performed to ascertain the inhibitory effect of SRS06 on the NF-κB signaling cascade. The TransAM™ p65 assay kit was used to determine NF-κB p65 DNA binding activity in the NSCL cancer cell line A549. <b><i>Results:</i></b> From the NCI screening, SRS06 was found to exhibit potent growth-inhibitory effects on multiple cancer cell lines with 10-fold lower 50% growth inhibition (GI<sub>50</sub>) compared with andrographolide. It was also discerned that the compound preferentially targeted melanoma, CNS, renal, colon, ovarian, prostate, and NSCL cancer cell lines. The DNA fragmentation assay indicated that the main mode of cell death of SRS06-treated A549 cells was via apoptosis. At 5 µmol/l the compound decreased NF-κB protein expression and caused a significant reduction in the nuclear p65 DNA binding activity. <b><i>Conclusion:</i></b> SRS06 displayed improved anticancer selectivity and potency when compared with andrographolide. We alluded its anticancer activity to its effect of inhibiting NF-κB nuclear binding.
DOI: 10.6084/m9.figshare.5127478.v1
title: Supplementary Material for: Monitoring of Hematopoietic Chimerism by Real-Time Quantitative PCR of Micro Insertions/Deletions in Samples with Low DNA Quantities

description: <b><i>Background:</i></b> Sensitive and accurate methods to detect hematopoietic chimerism after hematopoietic stem cell transplantation (HSCT) are essential to evaluate engraftment and to monitor response to therapeutic procedures such as donor lymphocyte infusion. Continuous long-term follow up, however, requires large amounts of pre-HSCT samples limiting the application of many widely used techniques for sensitive chimerism monitoring. <b><i>Methods: </i></b>DNAs from 42 normal healthy donors and 16 HSCT donor/recipient pairs were employed to validate the use of allele-specific insertion/deletion (indel) quantitative real-time polymerase chain reaction (qPCR) to quantify chimerism in samples with low amounts of DNA. Consequently, indel-qPCR analyses of samples from 16 HSCT patients were compared to short-tandem repeat (STR) specific PCR analyses. <b><i>Results</i></b>: Typing with reduced amounts of input DNA (15 vs. 60 ng) allowed for the reliable distinction of positive (mean threshold cycle (ct) 28.05) and negative (ct &gt;36) signals. The high informativity of primer/probe sets, with 12 out of 19 markers exceeding 20% informativity, was confirmed in our cohort (n = 74). Importantly, a fourfold reduction of input DNA compared to published protocols did not alter PCR efficiencies and allowed for a more sensitive detection of chimerism in 7 of 16 HSCT patients compared to results obtained by STR-PCR. <b><i>Conclusions</i></b>: Our data suggest that indel-qPCR is a more sensitive technique for the detection of hematopoietic chimerism compared to STR-PCR and works efficiently for samples with low amounts of DNA.
DOI: 10.6084/m9.figshare.5127481.v1
title: Supplementary Material for: Prenatal Diagnosis of a Female Fetus with Ring Chromosome 9, 46,XX,r(9)(p24q34), and a de novo Interstitial 9p Deletion

description: Ring chromosomes are circular structures formed as a result of breaks in the chromosome arms and the fusion of the proximal broken ends with a loss of distal material, or by fusion of dysfunctional telomeres without any loss. The mechanism underlying this process has not yet been sufficiently explained. Commonly, rings occur as acquired genetic abnormalities; however, sometimes they are found as constitutional aberrations with a prevalence of around 1:50,000 live births. Here, we present a new case of r(9) in a female fetus with intrauterine growth retardation and slight craniofacial dysmorphisms. Both parents had a normal phenotype. Amniotic fluid karyotype showed r(9)(p24q34). An array CGH revealed 3 deletion segments: a ring chromosome with a 2.57-Mb deletion at 9pterp24.2 (chr9:163,131-2,729,722), a 2.60-Mb deletion at 9q34.3qter (chr9:138,523,302-141,122,055), and also a 0.15-Mb interstitial deletion at 9p24.1 (chr9:5,090,443-5,235,765). These deletions overlap with proposed regions for the 9p24.3 deletion and Kleefstra syndrome. Segregation analysis revealed a maternal origin of the rearranged chromosome. We conclude that both the ring chromosome and the interstitial deletion occurred de novo<i>. </i>This last deletion has not been reported before. Prenatal array CGH, combined with fine mapping of breakpoints contributes to the assessment of genotype-phenotype correlations.
DOI: 10.6084/m9.figshare.5127466
title: Supplementary Material for: Treatment of Organic Livestock with Medicinal Plants: A Systematic Review of European Ethnoveterinary Research

description: <b><i>Background:</i></b> The EC Regulation for Organic Farming states that organic livestock should be treated preferably with phytotherapeutic products. In spite of the high importance of organic livestock in Europe, primarily ruminants, today almost no phytotherapeutic product is registered for livestock. Also, information regarding veterinary phytotherapy is rare. The aim of this paper is to find approaches to cope with health problems of organic ruminants in Europe on the basis of findings from the European ethnoveterinary medicine (EuEVM). <b><i>Methods:</i></b> A systematic review of ethno-biomedicinal papers was conducted with the aid of the Scopus database, and 75 papers, from European countries were analyzed regarding ethnoveterinary information. <b><i>Results:</i></b> A total of 590 plant species referring to 102 different plant families are reported to be used for animal treatment, with <i>Asteraceae</i>, <i>Fabaceae</i> and <i>Lamiaceae</i> being the most important families. The traditional use of some plant species (e.g. mallow, chamomile, wormwood) corresponds with findings from recent scientific literature. The large number of less studied plant species, such as white lupin as an antiparasitic herb, and <i>Helleborus</i> spp. as potential immunostimulatory agent, opens an interesting field for future research. <b><i>Conclusions:</i></b> In general, EuEVM provides interesting treatment approaches for gastrointestinal and dermatological disorders as well as parasitosis. Findings regarding disorders of female genital or respiratory tract are less consistent. Nevertheless, EuEVM offers a solid basis for stimulating research in veterinary phytotherapy in Europe with a perspective to solve animal health problems in organic or even nonorganic ruminant production.
DOI: 10.6084/m9.figshare.5127469
title: Supplementary Material for: Anti-Tumour Necrosis Factor-Induced Visceral and Cutaneous Leishmaniasis: Case Report and Review of the Literature

description: <b><i>Background:</i></b> Leishmaniasis is a chronic protozoan disease in which organisms are found within phagolysosomes of the mononuclear phagocyte system. There are three major forms: cutaneous, mucocutaneous and visceral. We report the first case of visceral leishmaniasis with cutaneous involvement in a patient with rheumatoid arthritis treated with the anti-tumour necrosis factor (anti-TNF) adalimumab. <b><i>Objective:</i></b> To highlight cutaneous leishmaniasis as the first indicator of a kala-azar disease in a patient treated with anti-TNF and to review the literature on leishmaniasis in the context of anti-TNF therapy. <b><i>Case Report:</i></b> A 59-year-old woman presented with a crusted plaque on the right elbow 34 months after the initiation of adalimumab. A cutaneous biopsy showed intracellular amastigotes. No <i>Leishmania</i> parasites were observed in a bone marrow aspirate, but laboratory tests showed anaemia and impaired liver function, abdominal ultrasonography showed hepatomegaly, and ELISA serology was strongly positive for <i>Leishmania</i> antibodies in serum and urine. Adalimumab was withdrawn and treatment combining intralesional pentavalent antimonials and liposomal amphotericin was started. Eight weeks later, the leishmaniasis had resolved. <b><i>Conclusion:</i></b> A skin biopsy disclosing leishmaniasis should prompt tests to rule out visceral leishmaniasis, especially in an area such as the Mediterranean where the prevalence of latent <i>Leishmania</i> infection is high.
DOI: 10.6084/m9.figshare.5127475
title: Supplementary Material for: Factors Influencing Lymph Node Metastasis in Patients with Ampullary Adenocarcinoma

description: <b><i>Aim:</i></b> In cases of ampullary carcinoma, lymph node involvement affects the selection of treatment strategies. This study aimed to identify clinicopathologic features of ampullary carcinoma with lymph node metastases. <b><i>Methods:</i></b> The records of 74 consecutive patients with ampullary adenocarcinoma who underwent pancreaticoduodenectomy (PD) with regional lymph node dissection were retrospectively analyzed. <b><i>Results:</i></b> Twenty-two patients (30%) with lymph node metastasis had significantly worse survival after resection than those without lymph node metastasis (p = 0.017). Univariate analyses revealed that preoperative biliary drainage; elevated serum carbohydrate antigen 19-9 (≥36 U/ml); moderate-to-poor pathologic grade (G2/3); perineural, vascular, lymphatic, pancreas, and duodenal invasion; and T category were significantly associated with lymph node metastasis. In multivariate analysis, only pathologic grade (G2/3) remained significantly associated with lymph node metastasis (hazard ratio, 6.51; p = 0.035). In sub-classified analysis for T category, lymph node metastasis was found in 5 of 22 cases (22.7%) of T1 tumors. Four of five cases with lymph node metastases had a dominant G2/3 component, whereas only 2 of 17 cases without lymph node metastases had a G2/3 component in T1 tumors (p = 0.0036). <b><i>Conclusions:</i></b> Pathologic grade (G2/3) was significantly and independently associated with lymph node metastasis and was also a significant predictor in T1 tumor cases.
DOI: 10.6084/m9.figshare.5127463
title: Supplementary Material for: Patients' Perspective on Day Case Breast Surgery

description: <b><i>Background: </i></b>This study assessed the views of patients undergoing breast surgery for breast cancer with a planned overnight stay, asking whether they would be happy to be discharged home on the same day of surgery. <b><i>Methods:</i></b> A structured questionnaire sent out in the 6 weeks following surgery was used to ascertain the patients' views. <b><i>Results:</i></b> The majority of patients undergoing mastectomy and axillary node clearance preferred an overnight stay, primarily for psychological reasons. <b><i>Conclusions:</i></b> Patients undergoing breast-conserving surgery were more prepared to go home on the day of surgery.
DOI: 10.6084/m9.figshare.5127472
title: Supplementary Material for: High Phosphorus Level Leads to Aortic Calcification via β-Catenin in Chronic Kidney Disease

description: <b><i>Aims:</i></b> Vascular calcification is a risk factor for causing cardiovascular events and has a high prevalence among chronic kidney disease (CKD) patients. However, the molecular mechanism underlying this pathogenic process is still obscure. <b><i>Methods:</i></b> Vascular smooth muscle cells (VSMCs) were induced by a concentration of phosphorus (Pi) of 2.5 mM, and were subjected to cell calcification analyses. The effect of high Pi on the Wnt/β-catenin pathway was measured using a TOP/FOP-Flash reporter assay. The transcriptional regulation of β-catenin on PIT1 (a type III sodium-dependent phosphate cotransporter) was confirmed by promoter reporter and chromatin immunoprecipitation assays. The 5/6 nephrectomized rat was used as an in vivo model and was fed a high Pi diet to induce aortic calcification. Serum levels of phosphate, calcium, creatine, and blood urea nitrogen were measured, and abdominal aortic calcification was examined. <b><i>Results:</i></b> High Pi induced VSMC calcification, downregulated expression levels of VSMC markers, and upregulated levels of osteogenic markers. High Pi activated the Wnt/β-catenin pathway and β-catenin activity. β-Catenin was involved in the process of high Pi-induced VSMC calcification. Further investigation revealed that β-catenin transcriptionally regulated <i>Pit1</i>, a necessary player in VSMC osteogenic phenotype change and calcification. The in vivo study showed that β-catenin was involved in rat abdominal aortic calcification induced by high Pi. When knockdown expression of β-catenin in the rat model was investigated, we found that aortic calcification was reduced. <b><i>Conclusion:</i></b> These results suggest that β-catenin is an important player in high phosphorus level-induced aortic calcification in CKD.
DOI: 10.6084/m9.figshare.5127460
title: Supplementary Material for: Development and Mapping of CL-Repeat Display Markers on the Maize B Chromosome

description: The CL-repeat is a repetitive sequence that is unique to the maize B chromosome, where it resides in the centromeric knob and the first 3 distal heterochromatic regions of the long arm. Given this organization, it would be desirable to identify molecular markers that are specifically distributed in the B chromosome. In this report, the CL-repeat has been used to develop a class of molecular markers for the maize B chromosome. To this end, a modified transposon display procedure designated as CL-repeat display was used to generate and display 26 genomic fragments that are specific to the B chromosome, all of which were cloned and sequenced. The sequences of 19 fragments were highly homologous to the 5′ or 3′ terminus of the CL-repeat. Five of these fragments also contained sequences that were homologous to sequences of the B chromosome centromere. Four of the other 7 fragments shared homology with B chromosome centromere sequences, and the remaining 3 were of unidentified sequences. Using 13 B-10L translocations with various breakpoints along the B chromosome long arm, the 26 CL-repeat display markers were mapped to definite regions of the B chromosome. This strategy should be feasible for the development of molecular markers for the B chromosome in maize and in other species where B chromosome-specific repeats have been identified.
DOI: 10.6084/m9.figshare.5127463.v1
title: Supplementary Material for: Patients' Perspective on Day Case Breast Surgery

description: <b><i>Background: </i></b>This study assessed the views of patients undergoing breast surgery for breast cancer with a planned overnight stay, asking whether they would be happy to be discharged home on the same day of surgery. <b><i>Methods:</i></b> A structured questionnaire sent out in the 6 weeks following surgery was used to ascertain the patients' views. <b><i>Results:</i></b> The majority of patients undergoing mastectomy and axillary node clearance preferred an overnight stay, primarily for psychological reasons. <b><i>Conclusions:</i></b> Patients undergoing breast-conserving surgery were more prepared to go home on the day of surgery.
DOI: 10.6084/m9.figshare.5127469.v1
title: Supplementary Material for: Anti-Tumour Necrosis Factor-Induced Visceral and Cutaneous Leishmaniasis: Case Report and Review of the Literature

description: <b><i>Background:</i></b> Leishmaniasis is a chronic protozoan disease in which organisms are found within phagolysosomes of the mononuclear phagocyte system. There are three major forms: cutaneous, mucocutaneous and visceral. We report the first case of visceral leishmaniasis with cutaneous involvement in a patient with rheumatoid arthritis treated with the anti-tumour necrosis factor (anti-TNF) adalimumab. <b><i>Objective:</i></b> To highlight cutaneous leishmaniasis as the first indicator of a kala-azar disease in a patient treated with anti-TNF and to review the literature on leishmaniasis in the context of anti-TNF therapy. <b><i>Case Report:</i></b> A 59-year-old woman presented with a crusted plaque on the right elbow 34 months after the initiation of adalimumab. A cutaneous biopsy showed intracellular amastigotes. No <i>Leishmania</i> parasites were observed in a bone marrow aspirate, but laboratory tests showed anaemia and impaired liver function, abdominal ultrasonography showed hepatomegaly, and ELISA serology was strongly positive for <i>Leishmania</i> antibodies in serum and urine. Adalimumab was withdrawn and treatment combining intralesional pentavalent antimonials and liposomal amphotericin was started. Eight weeks later, the leishmaniasis had resolved. <b><i>Conclusion:</i></b> A skin biopsy disclosing leishmaniasis should prompt tests to rule out visceral leishmaniasis, especially in an area such as the Mediterranean where the prevalence of latent <i>Leishmania</i> infection is high.
DOI: 10.6084/m9.figshare.5127454
title: Supplementary Material for: Clinical and Molecular Heterogeneity in Brazilian Patients with Sotos Syndrome

description: Sotos syndrome (SoS) is a multiple anomaly, congenital disorder characterized by overgrowth, macrocephaly, distinctive facial features and variable degree of intellectual disability. Haploinsufficiency of the <i>NSD1</i> gene at 5q35.3, arising from 5q35 microdeletions, point mutations, and partial gene deletions, accounts for a majority of patients with SoS. Recently, mutations and possible pathogenetic rare CNVs, both affecting a few candidate genes for overgrowth, have been reported in patients with Sotos-like overgrowth features. To estimate the frequency of <i>NSD1</i> defects in the Brazilian SoS population and possibly reveal other genes implicated in the etiopathogenesis of this syndrome, we collected a cohort of 21 Brazilian patients, who fulfilled the diagnostic criteria for SoS, and analyzed the <i>NSD1</i> and <i>PTEN</i> genes by means of multiplex ligation-dependent probe amplification and mutational screening analyses. We identified a classical <i>NSD1</i> microdeletion, a novel missense mutation (p.C1593W), and 2 previously reported truncating mutations: p.R1984X and p.V1760Gfs*2. In addition, we identified a novel de novo <i>PTEN</i> gene mutation (p.D312Rfs*2) in a patient with a less severe presentation of SoS phenotype, which did not include pre- and postnatal overgrowth. For the first time, our study implies <i>PTEN</i> in the pathogenesis of SoS and further emphasizes the existence of ethno-geographical differences in <i>NSD1</i> molecular alterations between patients with SoS from Europe/North America (70-93%) and those from South America (10-19%).
DOI: 10.6084/m9.figshare.5127457
title: Supplementary Material for: Genome-Wide Analysis of the WRKY Transcription Factors in <b><i>Aegilops tauschii</i></b>

description: The WRKY transcription factors (TFs) play important roles in responding to abiotic and biotic stress in plants. However, due to its unfinished genome sequencing, relatively few WRKY TFs with full-length coding sequences (CDSs) have been identified in wheat. Instead, the <i>Aegilops tauschii</i> genome, which is the D-genome progenitor of the hexaploid wheat genome, provides important resources for the discovery of new genes. In this study, we performed a bioinformatics analysis to identify WRKY TFs with full-length CDSs from the <i>A. tauschii</i> genome. A detailed evolutionary analysis for all these TFs was conducted, and quantitative real-time PCR was carried out to investigate the expression patterns of the abiotic stress-related WRKY TFs under different abiotic stress conditions in <i>A. tauschii</i> seedlings. A total of 93 WRKY TFs were identified from <i>A. tauschii</i>, and 79 of them were found to be newly discovered genes compared with wheat. Gene phylogeny, gene structure and chromosome location of the 93 WRKY TFs were fully analyzed. These studies provide a global view of the WRKY TFs from <i>A. tauschii</i> and a firm foundation for further investigations in both <i>A. tauschii</i> and wheat.
DOI: 10.6084/m9.figshare.5127472.v1
title: Supplementary Material for: High Phosphorus Level Leads to Aortic Calcification via β-Catenin in Chronic Kidney Disease

description: <b><i>Aims:</i></b> Vascular calcification is a risk factor for causing cardiovascular events and has a high prevalence among chronic kidney disease (CKD) patients. However, the molecular mechanism underlying this pathogenic process is still obscure. <b><i>Methods:</i></b> Vascular smooth muscle cells (VSMCs) were induced by a concentration of phosphorus (Pi) of 2.5 mM, and were subjected to cell calcification analyses. The effect of high Pi on the Wnt/β-catenin pathway was measured using a TOP/FOP-Flash reporter assay. The transcriptional regulation of β-catenin on PIT1 (a type III sodium-dependent phosphate cotransporter) was confirmed by promoter reporter and chromatin immunoprecipitation assays. The 5/6 nephrectomized rat was used as an in vivo model and was fed a high Pi diet to induce aortic calcification. Serum levels of phosphate, calcium, creatine, and blood urea nitrogen were measured, and abdominal aortic calcification was examined. <b><i>Results:</i></b> High Pi induced VSMC calcification, downregulated expression levels of VSMC markers, and upregulated levels of osteogenic markers. High Pi activated the Wnt/β-catenin pathway and β-catenin activity. β-Catenin was involved in the process of high Pi-induced VSMC calcification. Further investigation revealed that β-catenin transcriptionally regulated <i>Pit1</i>, a necessary player in VSMC osteogenic phenotype change and calcification. The in vivo study showed that β-catenin was involved in rat abdominal aortic calcification induced by high Pi. When knockdown expression of β-catenin in the rat model was investigated, we found that aortic calcification was reduced. <b><i>Conclusion:</i></b> These results suggest that β-catenin is an important player in high phosphorus level-induced aortic calcification in CKD.