cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4542955
title: Supplementary Material for: Macrophage-Expressed Perforins Mpeg1 and Mpeg1.2 Have an Anti-Bacterial Function in Zebrafish

description: Macrophage-expressed gene 1 <i>(MPEG1)</i> encodes an evolutionarily conserved protein with a predicted membrane attack complex/perforin domain associated with host defence against invading pathogens. In vertebrates, MPEG1/perforin-2 is an integral membrane protein of macrophages, suspected to be involved in the killing of intracellular bacteria by pore-forming activity. Zebrafish have 3 copies of <i>MPEG1</i>; 2 are expressed in macrophages, whereas the third could be a pseudogene. The <i>mpeg1</i> and <i>mpeg1.2</i> genes show differential regulation during infection of zebrafish embryos with the bacterial pathogens <i>Mycobacterium marinum</i> and <i>Salmonella typhimurium.</i> While <i>mpeg1</i> is downregulated during infection with both pathogens, <i>mpeg1.2</i> is infection inducible. Upregulation of <i>mpeg1.2</i> is partially dependent on the presence of functional Mpeg1 and requires the Toll-like receptor adaptor molecule MyD88 and the transcription factor NFκB. Knockdown of <i>mpeg1</i> alters the immune response to <i>M. marinum</i> infection and results in an increased bacterial burden. In <i>Salmonella typhimurium</i> infection, both <i>mpeg1</i> and <i>mpeg1.2</i> knockdown increase the bacterial burdens, but <i>mpeg1</i> morphants show increased survival times. The combined results of these two in vivo infection models support the anti-bacterial function of the MPEG1/perforin-2 family and indicate that the intricate cross-regulation of the two <i>mpeg1</i> copies aids the zebrafish host in combatting infection of various pathogens.
DOI: 10.6084/m9.figshare.4542958
title: The mesozooplankton of the Patos Lagoon Estuary, Brazil: trends in community structure and secondary production

description: The zooplankton abundance and composition of the Patos Lagoon Estuary (PLE) reflects the local hydrological regime with alternating periods of flood, freshwater run-off and mixing of water. However, little is known about the interannual zooplankton variations and secondary productivity of this community. We sampled zooplankton monthly at two stations within the estuary from April 2009 to March 2013. The brackish/marine calanoid copepod <i>Acartia tonsa</i> was found to play an important role in the PLE, with secondary production values of 1.17 mg C m<sup>−3</sup> day<sup>−1</sup> being comparable with the high values achieved in other estuaries worldwide. During the study period, the greatest change in the community structure was observed in the spring-summer under El Niño influence when the prolonged terrestrial run-off combined with higher temperatures allowed the establishment of a freshwater community that was largely composed of the calanoid copepod <i>Notodiaptomus incompositus</i>, cyclopoids and cladocerans. The freshwater copepod <i>N. incompositus</i>, which replaced <i>A. tonsa</i>, was second in importance with regard to production (mean 0.13 C m<sup>−3</sup> day<sup>−1</sup>). Our work emphasizes the ecological importance of long-term zooplankton monitoring studies and provides the first assessment of <i>N. incompositus</i> production.
DOI: 10.6084/m9.figshare.4542961.v1
title: Jupyter Notebook: Dipteran ortholog search for selected Anopheles stephensi proteins

description: Dipteran ortholog search for selected Anopheles stephensi proteins using orthoDB.
DOI: 10.6084/m9.figshare.4542955.v1
title: Supplementary Material for: Macrophage-Expressed Perforins Mpeg1 and Mpeg1.2 Have an Anti-Bacterial Function in Zebrafish

description: Macrophage-expressed gene 1 <i>(MPEG1)</i> encodes an evolutionarily conserved protein with a predicted membrane attack complex/perforin domain associated with host defence against invading pathogens. In vertebrates, MPEG1/perforin-2 is an integral membrane protein of macrophages, suspected to be involved in the killing of intracellular bacteria by pore-forming activity. Zebrafish have 3 copies of <i>MPEG1</i>; 2 are expressed in macrophages, whereas the third could be a pseudogene. The <i>mpeg1</i> and <i>mpeg1.2</i> genes show differential regulation during infection of zebrafish embryos with the bacterial pathogens <i>Mycobacterium marinum</i> and <i>Salmonella typhimurium.</i> While <i>mpeg1</i> is downregulated during infection with both pathogens, <i>mpeg1.2</i> is infection inducible. Upregulation of <i>mpeg1.2</i> is partially dependent on the presence of functional Mpeg1 and requires the Toll-like receptor adaptor molecule MyD88 and the transcription factor NFκB. Knockdown of <i>mpeg1</i> alters the immune response to <i>M. marinum</i> infection and results in an increased bacterial burden. In <i>Salmonella typhimurium</i> infection, both <i>mpeg1</i> and <i>mpeg1.2</i> knockdown increase the bacterial burdens, but <i>mpeg1</i> morphants show increased survival times. The combined results of these two in vivo infection models support the anti-bacterial function of the MPEG1/perforin-2 family and indicate that the intricate cross-regulation of the two <i>mpeg1</i> copies aids the zebrafish host in combatting infection of various pathogens.
DOI: 10.6084/m9.figshare.4542958.v1
title: The mesozooplankton of the Patos Lagoon Estuary, Brazil: trends in community structure and secondary production

description: The zooplankton abundance and composition of the Patos Lagoon Estuary (PLE) reflects the local hydrological regime with alternating periods of flood, freshwater run-off and mixing of water. However, little is known about the interannual zooplankton variations and secondary productivity of this community. We sampled zooplankton monthly at two stations within the estuary from April 2009 to March 2013. The brackish/marine calanoid copepod <i>Acartia tonsa</i> was found to play an important role in the PLE, with secondary production values of 1.17 mg C m<sup>−3</sup> day<sup>−1</sup> being comparable with the high values achieved in other estuaries worldwide. During the study period, the greatest change in the community structure was observed in the spring-summer under El Niño influence when the prolonged terrestrial run-off combined with higher temperatures allowed the establishment of a freshwater community that was largely composed of the calanoid copepod <i>Notodiaptomus incompositus</i>, cyclopoids and cladocerans. The freshwater copepod <i>N. incompositus</i>, which replaced <i>A. tonsa</i>, was second in importance with regard to production (mean 0.13 C m<sup>−3</sup> day<sup>−1</sup>). Our work emphasizes the ecological importance of long-term zooplankton monitoring studies and provides the first assessment of <i>N. incompositus</i> production.
DOI: 10.6084/m9.figshare.4542949
title: Villanueva-Cañas_etal_supTables

description: Supplementary tables for the manuscript "New genes and functional innovation in mammals" by Villanueva-Cañas et al.<br>
DOI: 10.6084/m9.figshare.4542952
title: Supplementary Material for: Effects of Cerebellothalamic Tractotomy on Cognitive and Emotional Functioning in Essential Tremor: A Preliminary Study in 5 Essential Tremor Patients

description: <b><i>Background:</i></b> Subthalamic stereotactic interventions have recently caught renewed interest as a treatment for essential tremor (ET). However, it is not clear whether these interventions are associated with neurocognitive, mood or personality changes. <b><i>Objective:</i></b> To investigate neurocognition, neuropsychiatric functions and personality variables in patients with ET and to explore the neurocognitive and neuropsychiatric effects of cerebellothalamic tractotomy (CTT), a form of subthalamotomy. <b><i>Methods:</i></b> In our study, we investigated cognitive functions, frontal functions, mood and personality variables in 5 patients with intractable ET. Patients were tested before and 3 months after surgery using neuropsychological tests, clinical scales for depression, anxiety, anger regulation and a personality test. <b><i>Results:</i></b> Before surgery, ET patients showed normal neurocognitive function, a slightly elevated frontal lobe score in the dimensions mental control and memory, without being indicative of a frontal lesion, and no elevated depression or anxiety scores compared to norm values. After surgery, there was no change in neurocognitive function and no increase in depression or anxiety scores. <b><i>Conclusion:</i></b> In this exploratory study on 5 ET patients, CTT was not associated with alterations of mood or neurocognitive functions.
DOI: 10.6084/m9.figshare.4542913
title: Supplementary Material for: Differences in Physicians' and Patients' Perception of Acute Hypothyroid Symptoms Induced by Thyroid Hormone Withdrawal in Thyroid Cancer Patients: A Multicenter Survey in Korea

description: <b><i>Background:</i></b> Acute short-term hypothyroidism induced by thyroid hormone withdrawal (THW) for follow-up surveillance or therapeutic radioiodine causes patients with differentiated thyroid cancer to suffer from a myriad of deleterious symptoms. <b><i>Objectives:</i></b> To know how patient recognition of hypothyroid symptoms compares to physician perception of patient symptoms. <b><i>Methods:</i></b> The survey was performed in 10 referral hospitals throughout Korea from December 2010 to May 2011 and targeted patients with total thyroidectomy and remnant ablation. The survey consisted of questions regarding the effect of THW on patient symptoms, the duration of symptoms, impact on social life, and patient complaints. The physicians treating thyroid cancer patients also responded to the survey and provided their perceptions of patient symptoms and treatment decisions. <b><i>Results:</i></b> About 70% of the patients responded that they experienced a negative physical or psychological impact on their life and work due to hypothyroid symptoms. However, 76% of doctors thought hypothyroidism could negatively impact a patient's daily life but would be endurable. Two thirds of physicians do not routinely recommend recombinant human TSH (rhTSH) to their patients. Multivariate analysis showed patients with female sex, stronger educational background, emotionally negative experiences of hypothyroidism, and younger age were more willing to pay for therapy that could prevent hypothyroidism symptoms. <b><i>Conclusions:</i></b> There was a substantial gap in the perception of hypothyroid symptoms during THW between physicians and patients. Physicians who are aware of the seriousness of hypothyroidism in their patients were more likely to recommend the use of rhTSH for their patients.
DOI: 10.6084/m9.figshare.4542856
title: Supplementary Material for: A Porcine Reproductive and Respiratory Syndrome Virus Vaccine Candidate Based on PRRSV Glycoprotein 5 and the Toll-Like Receptor 5 Agonist Salmonella typhimurium Flagellin

description: Glycoprotein 5 (GP5) from porcine reproductive and respiratory syndrome virus (PRRSV) is a key inducer of neutralizing antibodies. A truncated GP5 gene lacking the signal peptide and transmembrane sequences was amplified via an overlap PCR method and inserted into prokaryotic expression vectors, pET32a or pGEX-6p-1, to add an His or GST tag, respectively. His-tagged GP5 was induced with IPTG, verified by SDS-PAGE and Western blotting, and purified to serve as an immunogen accompanied with the <i>Salmonella typhimurium</i> flagellin (FliC), a Toll-like receptor 5 (TLR5) agonist. Levels of TLR5 and cytokine mRNAs in spleens of mice following injection with FliC were detected by qRT-PCR to verify the activation of innate immunity. FliC was used as an adjuvant and administered with the GP5 to C57BL/6 mice via intraperitoneal injection. Coadministration of GP5 with FliC induced a significantly enhanced GP5-specific IgG and IFN-γ response compared with administration of GP5 alone, and the GP5-specific titer in the GP5 + FliC coadministration group was elevated almost twofold after the third immunization. These results indicate that FliC is an effective adjuvant, increasing the induction of antibodies against GP5 with the induction of both humoral and cellular immune responses.
DOI: 10.6084/m9.figshare.4542871
title: Supplementary Material for: Increased Rate of Deleterious Variants in Long Runs of Homozygosity of an Inbred Population from Qatar

description: <b><i>Objective:</i></b> The aim of this study is to evaluate the fraction of putatively deleterious variants within genomic runs of homozygosity (ROH) regions in an inbred and selected cohort of Qatari individuals. <b><i>Methods:</i></b> High-density SNP array analysis was performed in 36 individuals, and for 14 of them whole-exome sequencing (WES) was also carried out. <b><i>Results:</i></b> In all individuals, regions characterized by a high (hotspot) or low (coldspot) degree of homozygosity in all the analysed individuals were mapped, and the most frequent hotspot regions were selected. WES data were exploited to identify the single nucleotide variations (SNVs) harboured by genes located within both regions in each individual. Evolutionary conservation-based algorithms were employed to predict the potential deleteriousness of SNVs. The amount of in silico predicted deleterious SNVs was significantly different (p &lt; 0.05) between homozygosity hotspot and coldspot regions. <b><i>Conclusion:</i></b> Genes located within ROH hotspot regions contain a significant burden of predicted putatively deleterious variants compared to genes located outside these regions, suggesting inbreeding as a possible mechanism allowing an enrichment of putatively deleterious variants at the homozygous state.
DOI: 10.6084/m9.figshare.4542871.v1
title: Supplementary Material for: Increased Rate of Deleterious Variants in Long Runs of Homozygosity of an Inbred Population from Qatar

description: <b><i>Objective:</i></b> The aim of this study is to evaluate the fraction of putatively deleterious variants within genomic runs of homozygosity (ROH) regions in an inbred and selected cohort of Qatari individuals. <b><i>Methods:</i></b> High-density SNP array analysis was performed in 36 individuals, and for 14 of them whole-exome sequencing (WES) was also carried out. <b><i>Results:</i></b> In all individuals, regions characterized by a high (hotspot) or low (coldspot) degree of homozygosity in all the analysed individuals were mapped, and the most frequent hotspot regions were selected. WES data were exploited to identify the single nucleotide variations (SNVs) harboured by genes located within both regions in each individual. Evolutionary conservation-based algorithms were employed to predict the potential deleteriousness of SNVs. The amount of in silico predicted deleterious SNVs was significantly different (p &lt; 0.05) between homozygosity hotspot and coldspot regions. <b><i>Conclusion:</i></b> Genes located within ROH hotspot regions contain a significant burden of predicted putatively deleterious variants compared to genes located outside these regions, suggesting inbreeding as a possible mechanism allowing an enrichment of putatively deleterious variants at the homozygous state.
DOI: 10.6084/m9.figshare.4542949.v1
title: Villanueva-Cañas_etal_supTables

description: Supplementary tables for the manuscript "New genes and functional innovation in mammals" by Villanueva-Cañas et al.<br>
DOI: 10.6084/m9.figshare.4542817
title: Real Instances

description: Real Instances
DOI: 10.6084/m9.figshare.4542817.v1
title: Real Instances

description: Real Instances
DOI: 10.6084/m9.figshare.4542745
title: Supplementary Material for: Does ß-Catenin Cross-Regulate NFκB Signalling in Pancreatic Cancer and Chronic Pancreatitis?

description: <b><i>Background:</i></b> It is not clear by which mechanism nuclear factor-kappaB (NFκB) induces cell proliferation and escapes from the apoptotic pathway in pancreatic carcinogenesis. This study aimed to investigate ß<i>-</i>catenin and NFκB signalling in chronic pancreatitis and pancreatic cancer. <b><i>Materials and Methods:</i></b> On tissue samples of chronic pancreatitis and pancreatic cancer, we performed immunohistochemistry for detecting the expression of tumour necrosis factor alpha (TNFa), ß<i>-</i>catenin and NFκB, Western blot for TNFa, NFκB, ß-catenin, c-Myc and FasL, co-immunoprecipitation for ß-catenin with NFκB and RT-PCR for cyclin D1, c-Myc and Fas. <b><i>Results:</i></b> TNFa and NFκB expression was increased in chronic pancreatitis and pancreatic cancer. ß-Catenin and cyclin D1 expression was intense in pancreatic cancer and moderate in chronic pancreatitis. Of the NFκB response elements, the expression of pro-proliferative c-Myc is intense in pancreatic cancer and moderate in chronic pancreatitis, but the pro-apoptotic factors, Fas and FasL were down-regulated in pancreatic cancer and moderately expressed in chronic pancreatitis. The co-immunoprecipitation results showed a significant interaction of ß-catenin with NFκB in pancreatic cancer and a non-significant interaction in chronic pancreatitis. <b><i>Conclusions:</i></b> ß<i>-</i>Catenin might cross-regulate NFκB by interrupting the balance of cell death and cell survival via recruiting NFκB into the cell survival pathway alone in most cases of pancreatic cancer and some cases of chronic pancreatitis.
DOI: 10.6084/m9.figshare.4542706
title: 128x128 Random Instances

description: 128x128 Random Instances
DOI: 10.6084/m9.figshare.4542700
title: 64x64 Random Instances

description: 64x64 Random Instances
DOI: 10.6084/m9.figshare.4542706.v1
title: 128x128 Random Instances

description: 128x128 Random Instances
DOI: 10.6084/m9.figshare.4542694
title: Supplementary Material for: Antipathy of Trichoderma against Sclerotium rolfsii Sacc.: Evaluation of Cell Wall-Degrading Enzymatic Activities and Molecular Diversity Analysis of Antagonists

description: The fungus <i>Trichoderma</i> is a teleomorph of the <i>Hypocrea</i> genus and associated with biological control of plant diseases. The microscopic, biochemical, and molecular characterization of <i>Trichoderma </i>was carried out and evaluated for in vitro antagonistic activity against the fungal pathogen <i>Sclerotium rolfsii</i> causing stem rot disease in groundnut. In total, 11 isolates of <i>Trichoderma</i> were examined for antagonism at 6 and 12 days after inoculation (DAI). Out of 11, <i>T. virens </i>NBAII Tvs12 evidenced the highest (87.91%) growth inhibition of the test pathogen followed by <i>T. koningii</i> MTCC 796 (67.03%), <i>T. viride </i>NBAII Tv23 (63.74%), and <i>T. harzianum </i>NBAII Th1 (60.44%). Strong mycoparasitism was observed in the best antagonist Tvs12 strain during 6-12 DAI. The specific activity of cell wall-degrading enzymes - chitinase and β-1,3-glucanase - was positively correlated with growth inhibition of the test pathogen. In total, 18 simple sequence repeat (SSR) polymorphisms were reported to amplify 202 alleles across 11 <i>Trichoderma </i>isolates. The average polymorphism information content for SSR markers was found to be 0.80. The best antagonist Tvs 12 was identified with 7 unique SSR alleles amplified by 5 SSR markers. Clustering patterns of 11 <i>Trichoderma </i>strains showed the best antagonist <i>T. virens</i> NBAII Tvs 12 outgrouped with a minimum 3% similarity from the rest of <i>Trichoderma.</i>
DOI: 10.6084/m9.figshare.4542700.v1
title: 64x64 Random Instances

description: 64x64 Random Instances
DOI: 10.6084/m9.figshare.4542709.v1
title: Toward a Smell-aware Bug Prediction Model

description: Code smells are symptoms of poor design and implementation choices. Previous studies empirically assessed the impact of smells on code quality and clearly indicate their negative impact on maintainability, including a higher bug-proneness of components affected by code smells. In this paper, we capture previous findings on bug-proneness to build a specialized bug prediction model for smelly classes. Specifically, we evaluate the contribution of a measure of the severity of code smells (i.e., code smell intensity) by adding it to existing bug prediction models based on both product and process metrics, and comparing the results of the new model against the baseline models. Results indicate that the accuracy of a bug prediction model increases by adding the code smell intensity as predictor. We also compare the results achieved by the proposed model with the ones of an alternative technique which considers metrics about the history of code smells in files, finding that our model works generally better. However, we observed interesting complementarities between the set of buggy and smelly classes correctly classified by the two models. By evaluating the actual information gain provided by the intensity index with respect to the other metrics in the model, we found that the intensity index is a relevant feature for both product and process metrics-based models. At the same time, the metric counting the average number of code smells in previous versions of a class considered by the alternative model is also able to reduce the entropy of the model. On the basis of this result, we devise and evaluate a smell-aware combined bug prediction model that included product, process, and smell-related features. We demonstrate how such model classifies bug-prone code components with an F-Measure at least 13% higher than the existing state-of-the-art models.
DOI: 10.6084/m9.figshare.4542691
title: 32x32 Random Instances

description: Files for 32x32 Random Instances.<br>
DOI: 10.6084/m9.figshare.4542691.v1
title: 32x32 Random Instances

description: Files for 32x32 Random Instances.<br>
DOI: 10.6084/m9.figshare.4542640
title: Supplementary Material for: Diverse Patterns of Perilymphatic Space Enhancement in the Rat Inner Ear after Intratympanic Injection of Two Different Types of Gadolinium: A 9.4-Tesla Magnetic Resonance Study

description: <b><i>Objective:</i></b> To compare the quality of perilymphatic enhancement in the rat inner ear after intratympanic injection of two types of gadolinium with a 9.4-tesla micro-MRI. <b><i>Materials and Methods:</i></b> Gadolinium was injected into the middle ear in 6 Sprague-Dawley rats via the transtympanic route. The left ear was injected with Gd-DO3A-butrol first, and then the right ear was injected with Gd-DOTA. MR images of the inner ear were acquired 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, and 4 h after intratympanic (IT) injection using an Agilent MRI system 9.4T/160/AS. The normalized signal intensity was quantitatively analyzed at the scala vestibuli (SV), scala media, and scala tympani (ST) using a Marosis M-view system. Then the normalized signal intensities (SIs) were compared between the two contrast agents. <b><i>Results:</i></b> For Gd-DO3A-butrol, the SI was as low as 1.0-1.5 throughout 1-4 h at the SV and ST of the basal turn. The maximum SI was 1.5 ± 0.5 at the SV (2 h) and 1.3 ± 0.5 at the ST (2 h). For Gd-DOTA, the 1-hour postinjection SI at the basal turn was 2.5 ± 0.5 at the SV, 1.6 ± 0.3 at the ST, and 1.2 ± 0.3 at the scala media. In the apical turn, the maximum SI was reached after 2.5 h. The maximum SI in the apical turn was 1.8 ± 0.4 at the SV (3.5 h), 1.8 ± 0.4 at the ST (4 h), and 1.4 ± 0.3 at the scala media (4 h). <b><i>Conclusions:</i></b> We were able to clearly visualize and separate the ST and SV using IT Gd and 9.4-tesla micro-MRI. We recommend using Gd-DO3A-butrol over Gd-DOTA and to perform the MRI 2.5 h after using IT Gd in the rat inner ear.