cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5127760
title: Supplementary Material for: Sex Chromosome Conservation, <b><i>DMRT1</i></b> Phylogeny and Gonad Morphology in Diploid Palearctic Green Toads (<b><i>Bufo viridis </i></b>Subgroup)

description: Due to the prevailing sex chromosome homomorphy and large genome size, the knowledge on sex determination systems, sex chromosomes and sex-determining genes in amphibians remains scarce. Using 3 cross-amplifying sex-linked microsatellite markers, we uncover sex determination systems and sex chromosomes in purebred, diploid Palearctic green toads (<i>Bufo viridis</i> subgroup), which had so far only been characterized in laboratory-bred hybrids. Our data support an XY system in <i>B. balearicus</i>, <i>B. viridis</i> and <i>B. variabilis</i>. While females show recombination, it is strongly suppressed (or not detectable) in males. Markers corroborate the largest chromosome pair 1 (homologous to linkage group 1 of <i>Xenopus tropicalis</i>) to represent the sex chromosomes in diploid species of the <i>B. viridis</i> subgroup <i>(B. siculus, B. shaartusiensis, B. balearicus, B. turanensis, B. variabilis, B. viridis</i>, and probably <i>B. boulengeri)</i>. This chromosome harbors <i>DMRT1</i>, a key gene of the sexual pathway in deeply divergent animal taxa. However, our phylogenetic analysis of a 600-bp fragment of that gene in diploid green toad taxa reveals that X and Y alleles cluster by species and not by gametolog. This suggests that XY-sequence similarity stems from occasional XY recombination within <i>DMRT1</i>, and we preliminarily reject its role as the master sex determination gene, pending future extension of this evidence to the entire <i>DMRT1 </i>gene. We further create a chain of evidence, which supports the hypothesis that linkage group 1 of <i>X. tropicalis</i> appears to be maintained as the largest chromosome (1), and thus is homologous in anuran karyotype evolution from pipid to hylid, bufonid and ranid anurans.
DOI: 10.6084/m9.figshare.5127751
title: Supplementary Material for: Genetic Variation of <b><i>MT-ND</i></b> Genes in Frontotemporal Lobar Degeneration: Biochemical Phenotype-Genotype Correlation

description: <b><i>Background:</i></b> Frontotemporal lobar degeneration (FTLD) is the second most common early-onset dementia. Over the last few decades, a growing number of evidence suggests mitochondrial involvement in neurodegeneration, namely modifications of mitochondrial DNA (mtDNA) contributing to energy impairment. <b><i>Objective:</i></b> To sequence the 7 mitochondrially encoded complex I <i>(MT-ND)</i> genes in 70 FTLD patients and investigate mitochondrial respiratory chain (MRC) complex I activity. <b><i>Methods:</i></b> A sample of 70 patients was studied (39 females and 31 males; age range: 38-82 years, mean ± SD: 63 ± 11 years) with a probable diagnosis of FTLD. Total DNA was extracted from peripheral blood, and sequencing analysis of 7 <i>MT-ND</i><sub><i>n</i></sub> (1, 2, 3, 4L, 4, 5, 6) genes was performed. Variants identified were submitted to in silico study. Spectrophotometric evaluation of MRC activity in lymphocytes was performed, and results were compared with age-matched controls. <b><i>Results:</i></b> A total of 358 (161 different) alterations were found in 92.9% of patients. According to in silico analysis of nonsynonymous variants, only 5 variations are possibly or probably damaging. Complex I activity is significantly decreased in patients. <b><i>Conclusion:</i></b> To our knowledge, this is the first report of the complete sequence of the <i>MT-ND</i> genes in FTLD patients and correlation with MRC activity. The high number of mtDNA variations identified and a significant decrease in complex I activity suggest a possible involvement of mtDNA alterations in FTLD. Although the majority of these alterations are not primarily pathogenic, an interaction with other mutations may occur, leading to the disease, worsening its expression or influencing age of onset.
DOI: 10.6084/m9.figshare.5127757
title: Supplementary Material for: Evaluation of the Utility of in utero Treatment of Twin Anemia-Polycythemia Sequence

description: <b><i>Objective:</i></b> The aim of this study is to evaluate the interest in the in utero treatment of twin anemia-polycythemia sequence (TAPS). <b><i>Methods:</i></b> The obstetrical and neonatal data on all cases of TAPS followed up in our institution between 2006 and 2013 were reviewed. Statistical analyses were conducted using Bayesian methods. <b><i>Results:</i></b> Twenty cases of TAPS were included. Laser therapy or intrauterine transfusion (IUT) was performed on the donor twin in 9 cases. Eleven cases were included in the ‘nontreated' group (managed expectantly or diagnosed at birth). The gestational age at diagnosis was lower in the group with treated TAPS [difference (diff) = -22.20 days (-57.13, 14.28), probability (Pr) (diff &gt;0) = 10.6%]. The rate of preterm premature rupture of membranes was higher in the group with treated TAPS [diff = 22.5% (-14, 57), Pr (diff &gt;0) = 89%], but overall mortality was similar. The interval between diagnosis and delivery was longer [diff = 44.37 days (9.41, 77.90), Pr (diff &gt;0) = 99.2%], the TAPS resolution rate was higher [diff = 49.9% (12, 81), Pr (diff &gt;0) = 99.4%], and the neonatal transfusion rate was lower [diff = -30.5% (-60, 0), Pr (diff &gt;0) = 2.6%] in the treated group. <b><i>Conclusion:</i></b> In utero treatment for TAPS is associated with a higher resolution rate of TAPS and a longer time between diagnosis and birth, but overall mortality is the same as with expectant management.
DOI: 10.6084/m9.figshare.5127757.v1
title: Supplementary Material for: Evaluation of the Utility of in utero Treatment of Twin Anemia-Polycythemia Sequence

description: <b><i>Objective:</i></b> The aim of this study is to evaluate the interest in the in utero treatment of twin anemia-polycythemia sequence (TAPS). <b><i>Methods:</i></b> The obstetrical and neonatal data on all cases of TAPS followed up in our institution between 2006 and 2013 were reviewed. Statistical analyses were conducted using Bayesian methods. <b><i>Results:</i></b> Twenty cases of TAPS were included. Laser therapy or intrauterine transfusion (IUT) was performed on the donor twin in 9 cases. Eleven cases were included in the ‘nontreated' group (managed expectantly or diagnosed at birth). The gestational age at diagnosis was lower in the group with treated TAPS [difference (diff) = -22.20 days (-57.13, 14.28), probability (Pr) (diff &gt;0) = 10.6%]. The rate of preterm premature rupture of membranes was higher in the group with treated TAPS [diff = 22.5% (-14, 57), Pr (diff &gt;0) = 89%], but overall mortality was similar. The interval between diagnosis and delivery was longer [diff = 44.37 days (9.41, 77.90), Pr (diff &gt;0) = 99.2%], the TAPS resolution rate was higher [diff = 49.9% (12, 81), Pr (diff &gt;0) = 99.4%], and the neonatal transfusion rate was lower [diff = -30.5% (-60, 0), Pr (diff &gt;0) = 2.6%] in the treated group. <b><i>Conclusion:</i></b> In utero treatment for TAPS is associated with a higher resolution rate of TAPS and a longer time between diagnosis and birth, but overall mortality is the same as with expectant management.
DOI: 10.6084/m9.figshare.5127760.v1
title: Supplementary Material for: Sex Chromosome Conservation, <b><i>DMRT1</i></b> Phylogeny and Gonad Morphology in Diploid Palearctic Green Toads (<b><i>Bufo viridis </i></b>Subgroup)

description: Due to the prevailing sex chromosome homomorphy and large genome size, the knowledge on sex determination systems, sex chromosomes and sex-determining genes in amphibians remains scarce. Using 3 cross-amplifying sex-linked microsatellite markers, we uncover sex determination systems and sex chromosomes in purebred, diploid Palearctic green toads (<i>Bufo viridis</i> subgroup), which had so far only been characterized in laboratory-bred hybrids. Our data support an XY system in <i>B. balearicus</i>, <i>B. viridis</i> and <i>B. variabilis</i>. While females show recombination, it is strongly suppressed (or not detectable) in males. Markers corroborate the largest chromosome pair 1 (homologous to linkage group 1 of <i>Xenopus tropicalis</i>) to represent the sex chromosomes in diploid species of the <i>B. viridis</i> subgroup <i>(B. siculus, B. shaartusiensis, B. balearicus, B. turanensis, B. variabilis, B. viridis</i>, and probably <i>B. boulengeri)</i>. This chromosome harbors <i>DMRT1</i>, a key gene of the sexual pathway in deeply divergent animal taxa. However, our phylogenetic analysis of a 600-bp fragment of that gene in diploid green toad taxa reveals that X and Y alleles cluster by species and not by gametolog. This suggests that XY-sequence similarity stems from occasional XY recombination within <i>DMRT1</i>, and we preliminarily reject its role as the master sex determination gene, pending future extension of this evidence to the entire <i>DMRT1 </i>gene. We further create a chain of evidence, which supports the hypothesis that linkage group 1 of <i>X. tropicalis</i> appears to be maintained as the largest chromosome (1), and thus is homologous in anuran karyotype evolution from pipid to hylid, bufonid and ranid anurans.
DOI: 10.6084/m9.figshare.5127769.v1
title: Supplementary Material for: Microhabitat Use Affects Brain Size and Structure in Intertidal Gobies

description: The ecological cognition hypothesis poses that the brains and behaviours of individuals are largely shaped by the environments in which they live and the associated challenges they must overcome during their lives. Here we examine the effect of environmental complexity on relative brain size in 4 species of intertidal gobies from differing habitats. Two species were rock pool specialists that lived on spatially complex rocky shores, while the remainder lived on dynamic, but structurally simple, sandy shores. We found that rock pool-dwelling species had relatively larger brains and telencephalons in particular, while sand-dwelling species had a larger optic tectum and hypothalamus. In general, it appears that various fish species trade off neural investment in specific brain lobes depending on the environment in which they live. Our previous research suggests that rock pool species have greater spatial learning abilities, enabling them to navigate their spatially complex environment, which may account for their enlarged telencephalon, while sand-dwelling species likely have a reduced need for spatial learning, due to their spatially simple habitat, and a greater need for visual acuity. The dorsal medulla and cerebellum size was unaffected by the habitat in which the fish lived, but there were differences between species indicative of species-specific trade-offs in neural investment.
DOI: 10.6084/m9.figshare.5127745
title: Supplementary Material for: Multidisciplinary Proactive Psychiatric Consultation Service: Impact on Length of Stay for Medical Inpatients

description: <b><i>Background:</i></b> Mental illness correlates with an increased length of stay (LOS) for patients hospitalized for medical conditions. While psychiatric consultations help manage mental illness among those hospitalized for medical conditions, consultations initiated by nonpsychiatric mental disease may lack maximum effectiveness. <b><i>Methods:</i></b> In a before-and-after design, in 2 contiguous years LOS for internist-initiated, conventional consultation (CC) as usual treatment was compared to LOS of a proactive, mental health professional-initiated, multidisciplinary intervention delivered by the behavioral intervention team (BIT) on the same units. The patient populations included general medical patients with a variety of illnesses. Patients were treated in 3 different inpatient settings with a total capacity of 92 beds serving 15,858 patient visits over 3 comparison years. BIT comprised a psychiatrist, a nurse, and a social worker, each of whom performed the specific tasks of their professional discipline, while collaborating among themselves and their health-care colleagues. BIT provided timely, appropriate, and effective patient care alongside consultative advice and education to their corresponding professional peers. BIT was compared to CC on the outcome of LOS. <b><i>Results:</i></b> There was a statistically significant reduction of LOS favoring BIT over CC for patients with an LOS of &lt;31 days which persisted while controlling for multiple co-morbid factors. Also, a statistically significant spillover effect was suggested by the overall improvement of LOS on units implementing BIT. <b><i>Conclusion:</i></b> BIT is a promising means of lowering LOS on general medical units while providing a high level of care and staff support.
DOI: 10.6084/m9.figshare.5127748
title: Supplementary Material for: Low-Frequency Electromagnetic Field Exposure Enhances Extracellular Trap Formation by Human Neutrophils through the NADPH Pathway

description: Low-frequency (LF) electromagnetic fields (EMFs) are abundantly present in modern society, and the potential biological consequences of exposure to these fields are under intense debate. Immune cells are suggested as possible target cells, though a clear mechanism is lacking. Considering their crucial role in innate immune activation, we selected an ex vivo exposure set-up with human neutrophils to investigate a possible correlation between neutrophil extracellular trap (NET) formation and LF EMF exposure. Our study shows that formation of NETs is enhanced by LF EMF exposure<i>. </i>Enhanced NET formation leads to increased antimicrobial properties as well as damage to surrounding cells. We found that LF-EMF-induced NET formation is dependent on the NADPH oxidase pathway and production of reactive oxygen species. Additionally, LF EMF exposure does not influence autophagy and PAD4 activity. Our study provides a mechanism by which exposure to LF EMFs could influence the innate immune system.
DOI: 10.6084/m9.figshare.5127751.v1
title: Supplementary Material for: Genetic Variation of <b><i>MT-ND</i></b> Genes in Frontotemporal Lobar Degeneration: Biochemical Phenotype-Genotype Correlation

description: <b><i>Background:</i></b> Frontotemporal lobar degeneration (FTLD) is the second most common early-onset dementia. Over the last few decades, a growing number of evidence suggests mitochondrial involvement in neurodegeneration, namely modifications of mitochondrial DNA (mtDNA) contributing to energy impairment. <b><i>Objective:</i></b> To sequence the 7 mitochondrially encoded complex I <i>(MT-ND)</i> genes in 70 FTLD patients and investigate mitochondrial respiratory chain (MRC) complex I activity. <b><i>Methods:</i></b> A sample of 70 patients was studied (39 females and 31 males; age range: 38-82 years, mean ± SD: 63 ± 11 years) with a probable diagnosis of FTLD. Total DNA was extracted from peripheral blood, and sequencing analysis of 7 <i>MT-ND</i><sub><i>n</i></sub> (1, 2, 3, 4L, 4, 5, 6) genes was performed. Variants identified were submitted to in silico study. Spectrophotometric evaluation of MRC activity in lymphocytes was performed, and results were compared with age-matched controls. <b><i>Results:</i></b> A total of 358 (161 different) alterations were found in 92.9% of patients. According to in silico analysis of nonsynonymous variants, only 5 variations are possibly or probably damaging. Complex I activity is significantly decreased in patients. <b><i>Conclusion:</i></b> To our knowledge, this is the first report of the complete sequence of the <i>MT-ND</i> genes in FTLD patients and correlation with MRC activity. The high number of mtDNA variations identified and a significant decrease in complex I activity suggest a possible involvement of mtDNA alterations in FTLD. Although the majority of these alterations are not primarily pathogenic, an interaction with other mutations may occur, leading to the disease, worsening its expression or influencing age of onset.
DOI: 10.6084/m9.figshare.5127754.v1
title: Supplementary Material for: Vascular Endothelial Growth Factor-C Expression as a Biomarker of Poor Prognosis in Esophageal Squamous Cell Carcinoma: A Meta-Analysis

description: <b><i>Background:</i></b> Vascular endothelial growth factor C (VEGF-C) is involved in the development and progression of tumor angio-/lymphangiogenesis. The purpose of this study is to evaluate whether VEGF-C expression is an indicator of aggressiveness and poor prognosis of esophageal squamous cell carcinoma (ESCC). <b><i>Method:</i></b> A meta-analysis was conducted to investigate the association between VEGF-C expression with clinicopathological characteristics and survival of ESCC patients. The dataset was defined by searching PubMed, Embase, Google Scholar, and the Cochrane database for appropriate articles published until April 2014. <b><i>Result:</i></b> The final analysis was made from 9 studies, including 656 ESCC patients. Positive VEGF-C expression was defined by immunohistochemistry (IHC) or mRNA expression analysis. The results demonstrated that VEGF-C expression was significantly associated with advanced-stage disease (odds ratio (OR) = 2.29, 95% confidence interval (CI) = 1.37-3.84, P = 0.002), deeper tumor invasion, lymph node metastasis, and lymphatic invasion. The 5-year survival of VEGF-C expression-negative patients was found to be better than that of VEGF-C expression-positive patients (OR = 0.35, 95% CI = 0.21-0.58, P &lt; 0.0001). However, there was no significant association between the VEGF-C expression levels and either poorer tumor differentiation or vascular invasion. <b><i>Conclusion:</i></b> The results of the meta-analysis strongly indicate that VEGF-C expression could function as a marker for predicting the aggressiveness and prognosis of ESCC.
DOI: 10.6084/m9.figshare.5127742
title: Supplementary Material for: Differential Phonological and Semantic Modulation of Neurophysiological Responses to Visual Word Recognition

description: <b><i>Background:</i></b> Reading words for meaning relies on orthographic, phonological and semantic processing. The triangle model implicates a direct orthography-to-semantics pathway and a phonologically mediated orthography-to-semantics pathway, which interact with each other. The temporal evolution of processing in these routes is not well understood, although theoretical evidence predicts early phonological processing followed by interactive phonological and semantic processing. <b><i>Method:</i></b> This study used electroencephalography-event-related potential (ERP) analysis and magnetoencephalography (MEG) source localisation to identify temporal markers and the corresponding neural generators of these processes in early (∼200 ms) and late (∼400 ms) neurophysiological responses to visual words, pseudowords and consonant strings. <b><i>Results:</i></b> ERP showed an effect of phonology but not semantics in both time windows, although at ∼400 ms there was an effect of stimulus familiarity. Phonological processing at ~200 ms was localised to the left occipitotemporal cortex and the inferior frontal gyrus. At 400 ms, there was continued phonological processing in the inferior frontal gyrus and additional semantic processing in the anterior temporal cortex. There was also an area in the left temporoparietal junction which was implicated in both phonological and semantic processing. In ERP, the semantic response at ∼400 ms appeared to be masked by concurrent processes relating to familiarity, while MEG successfully differentiated these processes. <b><i>Discussion:</i></b> The results support the prediction of early phonological processing followed by an interaction of phonological and semantic processing during word recognition. Neuroanatomical loci of these processes are consistent with previous neuropsychological and functional magnetic resonance imaging studies. The results also have implications for the classical interpretation of N400-like responses as markers for semantic processing.
DOI: 10.6084/m9.figshare.5127739
title: Supplementary Material for: DuOx2 Promoter Regulation by Hormones, Transcriptional Factors and the Coactivator TAZ

description: The production of H<sub>2</sub>O<sub>2</sub>, which is essential to thyroid hormone synthesis, involves two NADPH oxidases: dual oxidases 1 and 2 (DuOx1 and DuOx2). A functional study with human DuOx genes and their 5′-flanking regions showed that DuOx1 and -2 promoters are different from thyroid-specific gene promoters. Furthermore, their transcriptional activities are not restricted to thyroid cells. While regulation of Tg (thyroglobulin) and TPO (thyroperoxidase) expression have been extensively studied, DuOx2 promoter regulation by hormones and transcriptional factors need to be more explored. Herein we investigated the role of TSH, insulin and insulin-like growth factor 1 (IGF-1), as well as the cAMP effect on DuOx2 promoter (ptx41) activity in transfected rat thyroid cell lines (PCCL3). We also assessed DuOx2 promoter activity in the presence of transcriptional factors crucial to thyroid development such as TTF-1 (thyroid transcription factor 1), PAX8, CREB, DREAM, Nkx2.5 and the coactivator TAZ in HeLa and HEK 293T-transfected cells. Our results show that TSH and forskolin, which increase cAMP in thyroid cells, stimulated DuOx2 promoter activity. IGF-1 led to pronounced stimulation, while insulin induction was not statistically different from DuOx2 promoter basal activity. All transcriptional factors selected for this work and coactivator TAZ, except DREAM, stimulated DuOx2 promoter activity. Moreover, Nkx2.5 and TAZ synergistically increased DuOx2 promoter activity. In conclusion, we show that DuOx2 expression is regulated by hormones and transcription factors involved in thyroid organogenesis and carcinogenesis, reinforcing the importance of the control of H<sub>2</sub>O<sub>2</sub> generation in the thyroid.
DOI: 10.6084/m9.figshare.5127736
title: Supplementary Material for: Fucose-Mediated Transcriptional Activation of the <b><i>fcs</i></b> Operon by FcsR in <b><i>Streptococcus pneumoniae</i></b>

description: In this study, we explore the impact of fucose on the transcriptome of <i>S. pneumoniae</i> D39. The expression of various genes and operons, including the fucose uptake PTS and utilization operon (<i>fcs</i> operon) was altered in the presence of fucose. By means of quantitative RT-PCR and β-galactosidase analysis, we demonstrate the role of the transcriptional regulator FcsR, present upstream of the <i>fcs</i> operon, as a transcriptional activator of the <i>fcs</i> operon. We also predict a 19-bp putative FcsR regulatory site (5′-ATTTGAACATTATTCAAGT-3′) in the promoter region of the <i>fcs</i> operon. The functionality of this predicted FcsR regulatory site was further confirmed by promoter-truncation experiments, where deletion of half of the FscR regulatory site or full deletion led to the abolition of expression of the <i>fcs</i> operon.