cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5127964.v1
title: Supplementary Material for: Parameters Used to Discontinue Dialysis in Acute Kidney Injury Recovery: A Survey of United States Nephrologists

description: <b><i>Background:</i></b> Despite advances in the approach to cure acute kidney injury (AKI), including definition, classification and treatment methods, there are no standard criteria to withdraw dialysis in the setting of improving AKI. We conducted this survey to elucidate parameters that United States (US) nephrologists used to determine when to stop dialysis with improving renal function in AKI. We hypothesized that there would be a difference in approach to weaning a patient off dialysis based on years in practice or the number of cases of AKI treated per year. <b><i>Methods:</i></b> This was an anonymous electronic survey of practicing nephrologists who treated AKI. Data was de-identified and analyzed using descriptive statistics. <b><i>Results:</i></b> The commonest criteria used to stop dialysis when renal function improved was, in decreasing order of importance, resolution in oliguria (51%), resolution of volume overload (29%), improvement in serum creatinine (26.7%) and resolution of hyperkalemia (21%). The most common reasons for re-starting dialysis within 28 days did not show a specific trend but respondents (20%) reported re-starting if estimated glomerular filtration rates (eGFR) declined. There was no significant pattern in approach to withdrawing dialysis or resuming dialysis based on the number of years in nephrology practice. However, responses of nephrologists who saw more than 20 AKI patients/year were significantly different in stopping dialysis with clinical stabilization of blood pressure (p &lt; 0.001), improvement in respiratory parameters (p = 0.005), improvement in pre-dialysis blood urea nitrogen (BUN) levels despite the same dose of dialysis (p = 0.05) and resolution of oliguria (p = 0.025) compared to those who saw fewer cases. <b><i>Conclusion:</i></b> Resolution of oliguria was the commonest factor used to help deciding to stop dialysis in improving AKI. However, considerable variation was noted among US nephrologists who participated in this survey, regarding what criteria they used to withdraw dialysis in the setting of improving AKI. These results call for more studies in withdrawing dialysis in the setting of AKI that could lead to guideline formulation.
DOI: 10.6084/m9.figshare.5127967.v1
title: Supplementary Material for: Dialysis Amyloid Deposition in the Aortic Valve and Its Association with Aortic Stenosis

description: <b><i>Background:</i></b> The relationship between dialysis amyloid (DA) deposition in the aortic valve (AV) and aortic stenosis (AS) is unknown. <b><i>Methods:</i></b> This was a cross-sectional study. AV specimens of dialysis patients (median vintage: 8.8 years) consecutively collected from cardiac surgeries (n = 56) or autopsies (n = 13) were examined by a board-certified pathologist blinded to clinical data. DAs were considered to be present if deposits were stained both by Congo red with apple-green birefringence under polarized light and by anti-β2-microblobulin antibody. Degree of deposition was graded as follows: Amyloid (-), no deposit; Amyloid (1+), occasional small deposits; Amyloid (2+), multiple small to large deposits or a single large deposit. Calcification was defined as a calcified deposit with a diameter &gt;1 mm in the specimen. Severe AS (sAS) was defined as a mean gradient &gt;50 mm Hg by echocardiogram. We examined the proportion of DAs and the association between DAs and the sAS. <b><i>Results:</i></b> DAs were present in 71% (n = 49) of specimens and primarily co-localized with calcification. Non-dialysis related amyloid was found in one specimen. After excluding this specimen, sAS was associated with ‘Amyloid (1+) and Calcification &gt;1 mm' and ‘Amyloid (2+) and Calcification &gt;1 mm' (vs. ‘Amyloid (-) and Calcification ≤1 mm', odds ratios (ORs): 13.5 and 34.2, respectively). Furthermore, after adjustment for covariates, sAS was found to be associated with ‘Amyloid (2+) and Calcification &gt;1 mm' (OR: 24.3). <b><i>Conclusions:</i></b> DA deposition in the AV was prevalent among dialysis patients. DA deposition with accompanying calcification might contribute to the severity of AS.
DOI: 10.6084/m9.figshare.5127952
title: Supplementary Material for: Phylogenetic Characterization of a Novel Insect-Specific Flavivirus Detected in a <b><i>Culex </i></b>Pool, Collected from Assam, India

description: <b><i>Objective:</i></b> We report the phylogenetic characterization of a unique flavivirus sequence detected in a wild <i>Culex tritaeniorhynchus</i> mosquito pool, collected from the northeast Indian state of Assam. <b><i>Methods:</i></b> DNA and RNA were extracted from field-collected mosquito pools. Extracts were subjected to PCR and reverse transcriptase PCR amplification using universal and type-specific primers for direct detection of flavivirus-specific viral nucleic acids. An amplified flavivirus nonstructural protein 5 (NS5) genetic region was sequenced and BLAST searched, and phylogenetic analyses performed with reference sequences retrieved from GenBank. <b><i>Results:</i></b> Phylogenetic analyses revealed the sequence to be related to insect-specific flaviviruses (ISFs) of the genus Flavivirus, family Flaviviridae. Despite being related to the Palm Creek virus (PCV; an ISF very recently reported from Northern Australia), the present sequence (provisionally named Assam virus) was found to be highly divergent from PCV and other ISF sequences available in GenBank. The partial NS5 sequence analysis demonstrated low nucleotide sequence identity (66-77%) with known ISFs reported from other parts of the globe. <b><i>Conclusion:</i></b> Findings of this study suggest the presence of a candidate novel ISF - the first to be reported from India.
DOI: 10.6084/m9.figshare.5127961.v1
title: Supplementary Material for: Outcomes of Systemic Therapy for Patients with Metastatic Angiosarcoma

description: <b><i>Background:</i></b> Angiosarcomas (AS) are rare tumors of vascular origin with a variable behavior and overall poor prognosis. We sought to assess the outcomes of patients treated for metastatic disease. <b><i>Methods:</i></b> We performed a retrospective analysis of 119 patients treated for metastatic AS. Outcomes and efficacy measurements of the first and subsequent lines of treatment were analyzed. <b><i>Results:</i></b> Median age was 61 years, and the most frequent primary sites were chest wall/breast (31%), viscera (22%) and head/neck (20%). Seventy-three (61%) and 46 (39%) patients received ≥2 and ≥3 lines of therapy, respectively. The most commonly used agents included taxanes and anthracyclines. Median overall survival was 12.1 months. Median times to tumor progression were 3.5 months for first line, 3.7 months for second line and 2.7 months for third line. Among 48 patients evaluable per RECIST, the overall response rate to first line was 30% and &lt;10% in subsequent lines. Doxorubicin, liposomal doxorubicin and taxanes resulted in similar response rates and survival, and there was no apparent benefit for combination chemotherapy. <b><i>Conclusion:</i></b> Despite reasonable response rates in the first-line setting, benefit from systemic therapy is short-lived in metastatic AS, and outcomes are poor. Doxorubicin, liposomal doxorubicin and taxanes are reasonable and appropriate choices for monotherapy.
DOI: 10.6084/m9.figshare.5127946
title: Supplementary Material for: NextGen Brain Microdialysis: Applying Modern Metabolomics Technology to the Analysis of Extracellular Fluid in the Central Nervous System

description: Microdialysis is a powerful method for in vivo neurochemical analyses. It allows fluid sampling in a dynamic manner in specific brain regions over an extended period of time. A particular focus has been the neurochemical analysis of extracellular fluids to explore central nervous system functions. Brain microdialysis recovers neurotransmitters, low-molecular-weight neuromodulators and neuropeptides of special interest when studying behavior and drug effects. Other small molecules, such as central metabolites, are typically not assessed despite their potential to yield important information related to brain metabolism and activity in selected brain regions. We have implemented a liquid chromatography online mass spectrometry metabolomics platform for an expanded analysis of mouse brain microdialysates. The method is sensitive and delivers information for a far greater number of analytes than commonly used electrochemical and fluorescent detection or biochemical assays. The metabolomics platform was applied to the analysis of microdialysates in a foot shock-induced mouse model of posttraumatic stress disorder (PTSD). The rich metabolite data information was then used to delineate affected prefrontal molecular pathways that reflect individual susceptibility for developing PTSD-like symptoms. We demonstrate that hypothesis-free metabolomics can be adapted to the analysis of microdialysates for the discovery of small molecules with functional significance.
DOI: 10.6084/m9.figshare.5127949
title: Supplementary Material for: Mortality of Testicular Cancer in East and West Germany 20 Years after Reunification: A Gap Not Closed Yet

description: <b><i>Background:</i></b> The decline of testicular cancer mortality in East Germany began in the 1980s, about 10 years later than that recorded in West Germany. We aimed at providing up-to-date time trends of testicular cancer mortality rates in Germany. <b><i>Material and Methods:</i></b> Mortality data from East Germany (1971-2010) and West Germany (1954-2010) were provided by the Federal Bureau of Statistics. We estimated age-specific and age-standardized mortality rates using the World Standard Population. <b><i>Results:</i></b> Despite the declining trend in the 2000s, the mortality rates of testicular cancer remained higher in East than in West Germany. These rates were 5.5 and 2.6 per million person-years in 2010, respectively. Age-specific mortality trends by period and birth cohort showed that the mortality decline was larger among younger (15-44 years) than elderly men. <b><i>Conclusion:</i></b> The mortality of testicular cancer is still higher in East than West Germany. Despite very similar densities of hospital beds, urologists and oncologist per million male population in both parts of Germany, we hypothesized that a paucity of centers of expertise for treating testicular cancers in the East could account for this particular pattern.
DOI: 10.6084/m9.figshare.5127940
title: Supplementary Material for: Molecular and Cytological Comparisons of Chromosomes 7el<sub>1</sub>, 7el<sub>2</sub>, 7E<sup>e</sup>, and 7E<sup>i</sup> Derived from <b><i>Thinopyrum</i></b>

description: <i>Thinopyrum</i> chromosomes 7el<sub>1</sub>, 7el<sub>2</sub>, 7E<sup>e</sup>, and 7E<sup>i</sup>, homoeologous to group 7 chromosomes of common wheat <i>(Triticum aestivum)</i>, were determined to have many useful agronomical traits for wheat improvement. To analyze the genetic relationships among the 4 <i>Thinopyrum</i> 7E chromosomes, the conserved orthologous set markers, genomic in situ hybridization (GISH), and meiotic chromosome pairing were used in this study. The unweighted pair-group method with arithmetical averages (UPGMA) analysis indicated that 7el<sub>1</sub>, derived from <i>T. ponticum</i>, and 7E<sup>i</sup>, derived from <i>T. intermedium</i>, were the most closely related. 7el<sub>2</sub>, derived from <i>T. ponticum</i>, was relatively distant from the 7el<sub>1</sub>-7E<sup>i</sup> complex. While 7E<sup>e</sup>, derived from <i>T. elongatum</i>, was more distantly related to 7el<sub>1</sub>, 7el<sub>2</sub>, and 7E<sup>i</sup>. This is the first report showing that 7el<sub>1</sub> and 7E<sup>i</sup> may be similar, which could be explained by the similar chromosome signal distribution revealed by GISH as well as UPGMA analysis revealed by both molecular markers and the highest frequency of meiotic pairing. The newly developed genome-specific molecular markers may be useful for marker-assisted selection of <i>Lr19</i>, <i>Bdv3</i>, and <i>Fhblop</i>.
DOI: 10.6084/m9.figshare.5127943
title: Supplementary Material for: The Aldosterone/Renin Ratio as a Diagnostic Tool for the Diagnosis of Primary Hypoaldosteronism in Newborns and Infants

description: <b><i>Background/Aims:</i></b> Primary hypoaldosteronism is a rare inborn disorder with life-threatening symptoms in newborns and infants due to an aldosterone synthase defect. Diagnosis is often difficult as the plasma aldosterone concentration (PAC) can remain within the normal range and thus lead to misinterpretation and delayed initiation of life-saving therapy. We aimed to test the eligibility of the PAC/plasma renin concentration (PRC) ratio as a tool for the diagnosis of primary hypoaldosteronism in newborns and infants. <b><i>Meth</i></b><b><i>ods:</i></b> Data of 9 patients aged 15 days to 12 months at the time of diagnosis were collected. The diagnosis of primary hypoaldosteronism was based on clinical and laboratory findings over a period of 12 years in 3 different centers in Switzerland. To enable a valid comparison, the values of PAC and PRC were correlated to reference methods. <b><i>Results:</i></b> In 6 patients, the PAC/PRC ratio could be determined and showed constantly decreased values &lt;1 (pmol/l)/(mU/l). In 2 patients, renin was noted as plasma renin activity (PRA). PAC/PRA ratios were also clearly decreased. The diagnosis was subsequently genetically confirmed in 8 patients. <b><i>Conclusion:</i></b> A PAC/PRC ratio &lt;1 pmol/mU and a PAC/PRA ratio &lt;28 (pmol/l)/(ng/ml × h) are reliable tools to identify primary hypoaldosteronism in newborns and infants and help to diagnose this life-threatening disease faster.
DOI: 10.6084/m9.figshare.5127937
title: Supplementary Material for: Cerebrospinal Fluid Biomarkers in Familial Forms of Alzheimer's Disease and Frontotemporal Dementia

description: As dementia is a fast-growing health care problem, it is becoming an increasingly urgent need to provide an early diagnosis in order to offer patients the best medical treatment and care. Validated biomarkers which reflect the pathology and disease progression are essential for diagnosis and are important when developing new therapies. Today, the core protein biomarkers amyloid-β<sub>42</sub>, total tau and phosphorylated tau in the cerebrospinal fluid (CSF) are used to diagnose Alzheimer's disease (AD), because these biomarkers have shown to reflect the underlying amyloid and tau pathology. However, the biomarkers have proved insufficient predictors of dementias with a different pathology, e.g. frontotemporal dementia (FTD); furthermore, the biomarkers are not useful for early AD diagnosis. Familial dementias with a known disease-causing mutation can be extremely valuable to study; yet the biomarker profiles in patients with familial dementias are not clear. This review summarizes CSF biomarker findings from studies on symptomatic and presymptomatic individuals carrying a mutation in one of the genes known to cause early-onset familial AD or FTD. In conclusion, the biomarker profile of inherited AD is quite similar between carriers of different mutations as well as similar to the profile found in sporadic AD, whereas familial FTD does not seem to have a clear biomarker profile. Hence, new biomarkers are needed for FTD.
DOI: 10.6084/m9.figshare.5127949.v1
title: Supplementary Material for: Mortality of Testicular Cancer in East and West Germany 20 Years after Reunification: A Gap Not Closed Yet

description: <b><i>Background:</i></b> The decline of testicular cancer mortality in East Germany began in the 1980s, about 10 years later than that recorded in West Germany. We aimed at providing up-to-date time trends of testicular cancer mortality rates in Germany. <b><i>Material and Methods:</i></b> Mortality data from East Germany (1971-2010) and West Germany (1954-2010) were provided by the Federal Bureau of Statistics. We estimated age-specific and age-standardized mortality rates using the World Standard Population. <b><i>Results:</i></b> Despite the declining trend in the 2000s, the mortality rates of testicular cancer remained higher in East than in West Germany. These rates were 5.5 and 2.6 per million person-years in 2010, respectively. Age-specific mortality trends by period and birth cohort showed that the mortality decline was larger among younger (15-44 years) than elderly men. <b><i>Conclusion:</i></b> The mortality of testicular cancer is still higher in East than West Germany. Despite very similar densities of hospital beds, urologists and oncologist per million male population in both parts of Germany, we hypothesized that a paucity of centers of expertise for treating testicular cancers in the East could account for this particular pattern.
DOI: 10.6084/m9.figshare.5127931
title: Supplementary Material for: A Prospective Investigation of Graves' Disease and Selenium: Thyroid Hormones, Auto-Antibodies and Self-Rated Symptoms

description: <b><i>Background:</i></b> In Graves' thyrotoxicosis tachycardia, weight loss and mental symptoms are common. Recovery takes time and varies between patients. Treatment with methimazole reduces thyroid hormone levels. According to previous research, this reduction has been faster if selenium (Se) is added. <b><i>Objective:</i></b> The objective was to investigate whether supplementing the pharmacologic treatment with Se could change the immune mechanisms, hormone levels and/or depression and anxiety. <b><i>Methods:</i></b> We prospectively investigated 38 patients with initially untreated thyrotoxicosis by measuring the thyroid-stimulating hormone (TSH), free thyroxine (FT<sub>4</sub>), free triiodothyronine (FT<sub>3</sub>), thyroid receptor antibodies and thyroid peroxidase auto-antibodies before medication and at 6, 18 and 36 weeks after commencing treatment with methimazole and levo-thyroxine, with a randomized blinded oral administration of 200 µg Se/day or placebo. The selenoprotein P concentration was determined in plasma at inclusion and after 36 weeks. The patients were also assessed with questionnaires about depression, anxiety and self-rated symptoms before medication was started and after 36 weeks. <b><i>Results:</i></b> FT<sub>4</sub> decreased more in the Se group at 18 weeks (14 vs. 17 pmol/l compared to the placebo group, p = 0.01) and also at 36 weeks (15 vs. 18 pmol/l, p = 0.01). The TSH increased more in the Se group at 18 weeks (0.05 vs. 0.02 mIU/l, p = 0.04). The depression and anxiety scores were similar in both groups. In the Se group, the depression rates correlated negatively with FT<sub>3</sub> and positively with TSH. This was not seen in the placebo group. <b><i>Conclusions:</i></b> Se supplementation can enhance biochemical restoration of hyperthyroidism, but whether this could shorten clinical symptoms of thyrotoxicosis and reduce mental symptoms must be investigated further.
DOI: 10.6084/m9.figshare.5127934
title: Supplementary Material for: DNA Methylation Changes Induced by a High-Fat Diet and Fish Oil Supplementation in the Skeletal Muscle of Mice

description: <b><i>Background/Aims:</i></b> To investigate the global changes in DNA methylation and methylation of the promoter region of the peroxisome proliferator-activated receptor gamma transcript variant 2 <i>(Pparg2)</i> gene resulting from a high-fat diet (HFD) and/or fish oil supplementation. <b><i>Methods:</i></b> Fish oil, rich in omega-3 polyunsaturated fatty acids, or water was orally administered to male mice for 12 weeks. After the first 4 weeks, the animals were fed a control diet or an HFD until the end of the experimental protocol, when the epididymal fat, gastrocnemius muscle and liver were excised. <b><i>Results:</i></b><i>Pparg2</i> mRNA expression was upregulated by obesity and downregulated by fish oil supplementation in the liver. In the gastrocnemius muscle, diet-induced obesity increased global DNA methylation. Fish oil prevented the decrease in <i>Pparg2</i> promoter methylation induced by obesity in the gastrocnemius muscle. Regardless of the diet given, fish oil supplementation increased <i>Pparg2</i> promoter methylation at CpG-263 in muscle and adipose tissue. <b><i>Conclusion:</i></b> HFD and fish oil modified global and <i>Pparg2</i> promoter DNA methylation in a tissue-specific manner. Fish oil supplementation attenuated body weight gain, abolished the increase in <i>Pparg2</i> expression in the liver and prevented the decrease in <i>Pparg2</i> promoter methylation in the muscle induced by the HFD.
DOI: 10.6084/m9.figshare.5127940.v1
title: Supplementary Material for: Molecular and Cytological Comparisons of Chromosomes 7el<sub>1</sub>, 7el<sub>2</sub>, 7E<sup>e</sup>, and 7E<sup>i</sup> Derived from <b><i>Thinopyrum</i></b>

description: <i>Thinopyrum</i> chromosomes 7el<sub>1</sub>, 7el<sub>2</sub>, 7E<sup>e</sup>, and 7E<sup>i</sup>, homoeologous to group 7 chromosomes of common wheat <i>(Triticum aestivum)</i>, were determined to have many useful agronomical traits for wheat improvement. To analyze the genetic relationships among the 4 <i>Thinopyrum</i> 7E chromosomes, the conserved orthologous set markers, genomic in situ hybridization (GISH), and meiotic chromosome pairing were used in this study. The unweighted pair-group method with arithmetical averages (UPGMA) analysis indicated that 7el<sub>1</sub>, derived from <i>T. ponticum</i>, and 7E<sup>i</sup>, derived from <i>T. intermedium</i>, were the most closely related. 7el<sub>2</sub>, derived from <i>T. ponticum</i>, was relatively distant from the 7el<sub>1</sub>-7E<sup>i</sup> complex. While 7E<sup>e</sup>, derived from <i>T. elongatum</i>, was more distantly related to 7el<sub>1</sub>, 7el<sub>2</sub>, and 7E<sup>i</sup>. This is the first report showing that 7el<sub>1</sub> and 7E<sup>i</sup> may be similar, which could be explained by the similar chromosome signal distribution revealed by GISH as well as UPGMA analysis revealed by both molecular markers and the highest frequency of meiotic pairing. The newly developed genome-specific molecular markers may be useful for marker-assisted selection of <i>Lr19</i>, <i>Bdv3</i>, and <i>Fhblop</i>.
DOI: 10.6084/m9.figshare.5127928
title: Supplementary Material for: Different Preference of Degradome in Invasion versus Angiogenesis

description: Proteases are required for a multitude of cellular processes including homeostatic tissue remodelling, invasion and angiogenesis. The physiological function of a cell or tissue is reflected by the set of proteases expressed, also termed degradome. The role of proteases in invasion and angiogenesis has been studied intensively, mostly in cancer. We aimed to compare the set of proteases required for physiological invasion versus physiological angiogenesis from cells deriving from the same organ, and to identify the proteases specific for each process. The human placenta comprises trophoblasts that invade the maternal uterus in a regulated, physiological manner, and it is the source of primary endothelial cells. We isolated the trophoblasts and endothelial cells and verified their invasive phenotype and angiogenic properties, respectively. We then performed gene expression analysis of the degradome, e.g. cysteine, metallo, serine, threonine and aspartic proteases, identified the differentially expressed proteases among the trophoblasts and endothelial cells, and clustered them hierarchically. The results revealed that the set of proteases in trophoblasts versus in endothelial cells overlaps, with a total of 69% in common. Nevertheless, 42% of the studied degradomes differed, with a fold change ≥2. For instance, metalloproteinases were predominantly expressed in trophoblasts, and 31% of the proteases were exclusively expressed in either trophoblasts or endothelial cells; this suggests particular roles for these proteases in either invasion or angiogenesis. Our data identify common and distinct proteases in cells capable of performing invasion and angiogenesis, and may provide basic information for the design of techniques to specifically investigate invasion or angiogenesis.