bluuebunny/crossref_metadata_2025_split huggingface dataset:
The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age
Authors: Szécsényi-Nagy Anna , Roth Christina , Brandt Guido , Rihuete-Herrada Cristina , Tejedor-Rodríguez Cristina , Held Petra , García-Martínez-de-Lagrán Íñigo , Arcusa Magallón Héctor , Zesch Stephanie , Knipper Corina , Bánffy Eszter , Friederich Susanne , Meller Harald , Bueno Ramírez Primitiva , Barroso Bermejo Rosa , de Balbín Behrmann Rodrigo , Herrero-Corral Ana M. , Flores Fernández Raúl , Alonso Fernández Carmen , Jiménez Echevarria Javier , Rindlisbacher Laura , Oliart Camila , Fregeiro María-Inés , Soriano Ignacio , Vicente Oriol , Micó Rafael , Lull Vicente , Soler Díaz Jorge , López Padilla Juan Antonio , Roca de Togores Muñoz Consuelo , Hernández Pérez Mauro S. , Jover Maestre Francisco Javier , Lomba Maurandi Joaquín , Avilés Fernández Azucena , Lillios Katina T. , Silva Ana Maria , Magalhães Ramalho Miguel , Oosterbeek Luiz Miguel , Cunha Claudia , Waterman Anna J. , Roig Buxó Jordi , Martínez Andrés , Ponce Martínez Juana , Hunt Ortiz Mark , Mejías-García Juan Carlos , Pecero Espín Juan Carlos , Cruz-Auñón Briones Rosario , Tomé Tiago , Carmona Ballestero Eduardo , Cardoso João Luís , Araújo Ana Cristina , Liesau von Lettow-Vorbeck Corina , Blasco Bosqued Concepción , Ríos Mendoza Patricia , Pujante Ana , Royo-Guillén José I. , Esquembre Beviá Marco Aurelio , Dos Santos Goncalves Victor Manuel , Parreira Rui , Morán Hernández Elena , Méndez Izquierdo Elena , Vega y Miguel Jorge , Menduiña García Roberto , Martínez Calvo Victoria , López Jiménez Oscar , Krause Johannes , Pichler Sandra L. , Garrido-Pena Rafael , Kunst Michael , Risch Roberto , Rojo-Guerra Manuel A. , Haak Wolfgang , Alt Kurt W. 
Published: November 2017

AbstractAgriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focus on the maternal genetic makeup of the Neolithic (~ 5500–3000 BCE), Chalcolithic (~ 3000–2200 BCE) and Early Bronze Age (~ 2200–1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character.
Hypercholesterolemia Enhances T Cell Receptor Signaling and Increases the Regulatory T Cell Population
Authors: Mailer Reiner K. W. , Gisterå Anton , Polyzos Konstantinos A. , Ketelhuth Daniel F. J. , Hansson Göran K. 
Published: November 2017

AbstractHypercholesterolemia promotes the inflammation against lipoproteins in atherosclerosis. Development of atherosclerosis is affected by the balance between pro-inflammatory effector T cells and anti-inflammatory regulatory T (Treg) cells. However, phenotype and function of T cell subpopulations in hypercholesterolemia remain to be investigated. Here, we found that cholesterol-containing diet increased the expression of the Treg cell lineage-defining transcription factor FoxP3 among thymocytes and splenocytes. Hypercholesterolemia elevated the FoxP3 expression level and population size of peripheral Treg cells, but did not prevent enhanced proliferation of stimulated T cells. Moreover, cholesterol supplementation in diet as well as in cell culture medium promoted T cell antigen receptor (TCR) signaling in CD4+ T cells. Our results demonstrate that hypercholesterolemia enhances TCR stimulation, Treg cell development as well as T cell proliferation. Thus, our findings may help to understand why hypercholesterolemia correlates with altered CD4+ T cell responses.
Robust Segmentation of the Full Cerebral Vasculature in 4D CT of Suspected Stroke Patients
Authors: Meijs Midas , Patel Ajay , van de Leemput Sil C. , Prokop Mathias , van Dijk Ewoud J. , de Leeuw Frank-Erik , Meijer Frederick J. A. , van Ginneken Bram , Manniesing Rashindra 
Published: November 2017

AbstractA robust method is presented for the segmentation of the full cerebral vasculature in 4-dimensional (4D) computed tomography (CT). The method consists of candidate vessel selection, feature extraction, random forest classification and postprocessing. Image features include among others the weighted temporal variance image and parameters, including entropy, of an intensity histogram in a local region at different scales. These histogram parameters revealed to be a strong feature in the detection of vessels regardless of shape and size. The method was trained and tested on a large database of 264 patients with suspicion of acute ischemia who underwent 4D CT in our hospital in the period January 2014 to December 2015. Five subvolumes representing different regions of the cerebral vasculature were annotated in each image in the training set by medical assistants. The evaluation was done on 242 patients. A total of 16 (<8%) patients showed severe under or over segmentation and were reported as failures. One out of five subvolumes was randomly annotated in 159 patients and was used for quantitative evaluation. Quantitative evaluation showed a Dice coefficient of 0.91 ± 0.07 and a modified Hausdorff distance of 0.23 ± 0.22 mm. Therefore, robust vessel segmentation in 4D CT is feasible with good accuracy.
Structural and functional differences in gut microbiome composition in patients undergoing haemodialysis or peritoneal dialysis
Authors: Stadlbauer Vanessa , Horvath Angela , Ribitsch Werner , Schmerböck Bianca , Schilcher Gernot , Lemesch Sandra , Stiegler Philipp , Rosenkranz Alexander R. , Fickert Peter , Leber Bettina 
Published: November 2017

AbstractComplications of end-stage renal disease (ESRD) are critically related to inflammation. The gut microbiome is a key driver of inflammation. Since dialysis modalities may differently influence the gut microbiome, we aimed to compare the effects of haemodialysis (HD) and peritoneal dialysis (PD) on patients’ gut microbiome composition and function. We therefore studied faecal microbiome composition and function as well as inflammation and gut permeability in 30 patients with ESRD (15 HD, 15 PD) and compared to 21 healthy controls. We found an increase in potentially pathogenic species and a decrease in beneficial species in patients on HD and to a lesser extend in patients on PD when compared to controls. These changes in taxonomic composition also resulted in differences in predicted metagenome functions of the faecal microbiome. In HD but not in PD, changes in microbiome composition were associated with an increase in c-reactive protein (CRP) but not with intestinal inflammation or gut permeability. In conclusion microbiome composition in ESRD differs from healthy controls but also between modes of dialysis. These differences are associated with systemic inflammation and cannot completely be explained by dialysis vintage. The mode of renal replacement therapy seems to be an important driver of dysbiosis in ESRD.
Exploring the alpha desynchronization hypothesis in resting state networks with intracranial electroencephalography and wiring cost estimates
Authors: Gómez-Ramírez Jaime , Freedman Shelagh , Mateos Diego , Pérez Velázquez José Luis , Valiante Taufik A. 
Published: November 2017

AbstractThis paper addresses a fundamental question, are eyes closed and eyes open resting states equivalent baseline conditions, or do they have consistently different electrophysiological signatures? We compare the functional connectivity patterns in an eyes closed resting state with an eyes open resting state to investigate the alpha desynchronization hypothesis. The change in functional connectivity from eyes closed to eyes open, is here, for the first time, studied with intracranial recordings. We perform network connectivity analysis in iEEG and we find that phase-based connectivity is sensitive to the transition from eyes closed to eyes open only in interhemispheral and frontal electrodes. Power based connectivity, on the other hand, consistently discriminates between the two conditions in temporal and interhemispheral electrodes. Additionally, we provide a calculation for the wiring cost, defined in terms of the connectivity between electrodes weighted by distance. We find that the wiring cost variation from eyes closed to eyes open is sensitive to the eyes closed and eyes open conditions. We extend the standard network-based approach using the filtration method from algebraic topology which does not rely on the threshold selection problem. Both the wiring cost measure defined here and this novel methodology provide a new avenue for understanding the electrophysiology of resting state.
A Novel Medium for Enhancing Callus Growth of Hazel (Corylus avellana L.)
Authors: Salehi Mina , Moieni Ahmad , Safaie Naser 
Published: November 2017

AbstractPaclitaxel is a powerful antimitotic agent with excellent activity against a range of cancers. Hazel has been described as a paclitaxel-producing species among angiosperms. Fast-growing callus is a prerequisite for the success of callus production and then paclitaxel production. Therefore, optimizing the medium culture for enhancing callus growth is a crucial step for paclitaxel production. In this research, Murashige and Skoog (1962) (MS) medium was optimized for improving callus growth of hazel (Corylus avellana L.). The M10 medium (MS medium with pH 6.0 and supplemented with 1000 mg l−1 spirulina powder, 1000 mg l−1 casein hydrolysate and 3 g l−1 gelrite) significantly improved hazel callus growth. This modified MS medium increased callus fresh weight (55.8%) as compared to the control. M10 medium increased fatty acids yield of callus (66.7%) as compared to the control. Liquid M10 medium maintained growth over a longer period of time and also increased slightly, the paclitaxel production as compared to the control. This novel medium is promising for facilitating the mass production of hazel callus as a source of valuable metabolites including paclitaxel, linoleic and oleic acids.
Crystal structure of the N-terminal domain of human CDC73 and its implications for the hyperparathyroidism-jaw tumor (HPT-JT) syndrome
Authors: Sun Wei , Kuang Xiao-Lin , Liu Yan-Ping , Tian Li-Fei , Yan Xiao-Xue , Xu Wenqing 
Published: November 2017

AbstractCDC73/Parafibromin is a critical component of the Paf1 complex (PAF1C), which is involved in transcriptional elongation and histone modifications. Mutations of the human CDC73/HRPT2 gene are associated with hyperparathyroidism-jaw tumor (HPT-JT) syndrome, an autosomal dominant disorder. CDC73/parafibromin was initially recognized as a tumor suppressor by inhibiting cell proliferation via repression of cyclin D1 and c-myc genes. In recent years, it has also shown oncogenic features by activating the canonical Wnt/β-catenin signal pathway. Here, through limited proteolysis analysis, we demonstrate that the evolutionarily conserved human CDC73 N-terminal 111 residues form a globularly folded domain (hCDC73-NTD). We have determined a crystal structure of hCDC73-NTD at 1.02 Å resolution, which reveals a novel protein fold. CDC73-NTD contains an extended hydrophobic groove on its surface that may be important for its function. Most pathogenic CDC73 missense mutations associated with the HPT-JT syndrome are located in the region encoding CDC73-NTD. Our crystal and biochemical data indicate that most CDC73 missense mutations disrupt the folding of the hydrophobic core of hCDC73-NTD, while others such as the K34Q mutant reduce its thermostability. Overall, our results provide a solid structural basis for understanding the structure and function of CDC73 and its association with the HPT-JT syndrome and other diseases.
Sex-specific association between asthma and hypertension in nationally representative young Korean adults
Authors: Lee Hong Seok , Park Yong-Moon , Han Kyungdo , Pekler Gerald , Lee Seong-Su , Yoo Soonjib , Kim Sung Rae 
Published: November 2017

AbstractIt has been reported that people with asthma have an increased risk of hypertension. However, little is known about the specific relationship between asthma and hypertension in young adults. Among subjects who participated in the Korea National Health and Nutrition Examination Survey conducted in 2008–2013, a total of 10,138 young adults (4,226 men and 5,912 women) aged 19–39 years were analyzed. Multiple logistic regression analysis was used to estimate adjusted odds ratios (ORs) and 95% confidence intervals (CIs). The prevalence of ever asthma was 11.1% in men and 8.4% in women. The mean diastolic blood pressure (DBP) was lower in men with asthma than in men without asthma (p = 0.03), whereas the mean DBP was higher in women with asthma than in women without asthma (p = 0.04). Having asthma was inversely associated with hypertension in men (OR: 0.62, 95% CI: 0.41–0.91). In contrast, having asthma was positively associated with hypertension in women (OR: 2.19, 95% CI: 1.19–4.02). Our results suggest that asthma pathophysiology might be differentially associated with hypertension in young adults depending on sex.
Differential overexpression of SERPINA3 in human prion diseases
Authors: Vanni S. , Moda F. , Zattoni M. , Bistaffa E. , De Cecco E. , Rossi M. , Giaccone G. , Tagliavini F. , Haïk S. , Deslys J. P. , Zanusso G. , Ironside J. W. , Ferrer I. , Kovacs G. G. , Legname G. 
Published: November 2017

AbstractPrion diseases are fatal neurodegenerative disorders with sporadic, genetic or acquired etiologies. The molecular alterations leading to the onset and the spreading of these diseases are still unknown. In a previous work we identified a five-gene signature able to distinguish intracranially BSE-infected macaques from healthy ones, with SERPINA3 showing the most prominent dysregulation. We analyzed 128 suitable frontal cortex samples, from prion-affected patients (variant Creutzfeldt-Jakob disease (vCJD) n = 20, iatrogenic CJD (iCJD) n = 11, sporadic CJD (sCJD) n = 23, familial CJD (gCJD) n = 17, fatal familial insomnia (FFI) n = 9, Gerstmann–Sträussler–Scheinker syndrome (GSS)) n = 4), patients with Alzheimer disease (AD, n = 14) and age-matched controls (n = 30). Real Time-quantitative PCR was performed for SERPINA3 transcript, and ACTB, RPL19, GAPDH and B2M were used as reference genes. We report SERPINA3 to be strongly up-regulated in the brain of all human prion diseases, with only a mild up-regulation in AD. We show that this striking up-regulation, both at the mRNA and at the protein level, is present in all types of human prion diseases analyzed, although to a different extent for each specific disorder. Our data suggest that SERPINA3 may be involved in the pathogenesis and the progression of prion diseases, representing a valid tool for distinguishing different forms of these disorders in humans.
Impact of deforestation and climate on the Amazon Basin’s above-ground biomass during 1993–2012
Authors: Exbrayat Jean-François , Liu Yi Y. , Williams Mathew 
Published: November 2017

AbstractSince the 1960s, large-scale deforestation in the Amazon Basin has contributed to rising global CO2 concentrations and to climate change. Recent advances in satellite observations enable estimates of gross losses of above-ground biomass (AGB) stocks due to deforestation. However, because of simultaneous regrowth, the net contribution of deforestation emissions to rising atmospheric CO2 concentrations is poorly quantified. Climate change may also reduce the potential for forest regeneration in previously disturbed regions. Here, we address these points of uncertainty with a machine-learning approach that combines satellite observations of AGB with climate data across the Amazon Basin to reconstruct annual maps of potential AGB during 1993–2012, the above-ground C storage potential of the undisturbed landscape. We derive a 2.2 Pg C loss of AGB over the study period, and, for the regions where these losses occur, we estimate a 0.7 Pg C reduction in potential AGB. Thus, climate change has led to a decline of ~1/3 in the capacity of these disturbed forests to recover and recapture the C lost in disturbances during 1993–2012. Our approach further shows that annual variations in land use change mask the natural relationship between the El Niño/Southern Oscillation and AGB stocks in disturbed regions.
Spatial distribution of tree species in evergreen-deciduous broadleaf karst forests in southwest China
Authors: Du Hu , Hu Fang , Zeng Fuping , Wang Kelin , Peng Wanxia , Zhang Hao , Zeng Zhaoxia , Zhang Fang , Song Tongqing 
Published: November 2017

AbstractUnderstanding the spatial distribution of tree species in subtropical evergreen-deciduous broadleaf karst forest is fundamental to studying species coexistence and karst species diversity. Here, complete spatial randomness and heterogeneous Poisson process models were used to analyze the spatial distribution patterns of 146 species with at least one individual per ha in a 25-ha plot in southwest China. We used canonical correspondence analysis (CCA) and the torus-translation test (TTT) to explain the distributions of observed species. Our results show that an aggregated distribution was the dominant pattern in Mulun karst forests; the percentage and intensity of aggregated decreased with increasing spatial scale, abundance, mean diameter at breast height (DBH), and maximum DBH. Rare species were more aggregated than intermediately abundant and abundant species. However, functional traits (e.g., growth form and phenological guild) had no significant effects on the distributions of species. The CCA revealed that the four analyzed topographic variables (elevation, slope, aspect, and convexity) had significant influences on species distributions. The TTT showed that not all species have habitat preferences and that 68.5% (100 out of 146 species) show a strongly positive or negative association with at least one habitat. Most species were inclined to grow on slopes and hilltops.
Sociospatial structure explains marked variation in brucellosis seroprevalence in an Alpine ibex population
Authors: Marchand Pascal , Freycon Pauline , Herbaux Jean-Philippe , Game Yvette , Toïgo Carole , Gilot-Fromont Emmanuelle , Rossi Sophie , Hars Jean 
Published: November 2017

AbstractIn a context of (re)emerging infectious diseases with wildlife reservoirs, understanding how animal ecology shapes epidemiology is a key issue, particularly in wild ungulates that share pathogens with domestic herbivores and have similar food requirements. For the first time in Europe, brucellosis (Brucella melitensis), a virulent zoonosis, persisted in an Alpine ibex (Capra ibex) population and was transmitted to cattle and humans. To better understand disease dynamics, we investigated the relationships between the spatial ecology of ibex and the epidemiology of brucellosis. Combining home range overlap between 37 GPS-collared individuals and visual observations of 148 visually-marked individuals monitored during the 2013–2016 period, we showed that females were spatially segregated in at least 4 units all year round, whereas males were more prone to move between female units, in particular during the rutting period. In addition to ibex age, the spatial structure in females largely contributed to variation in seroprevalence in the whole population. These results suggest that non-sexual routes are the most likely pathways of intraspecific transmission, crucial information for management. Accounting for wildlife spatial ecology was hence decisive in improving our ability to better understand this health challenge involving a wildlife reservoir.
Genomic mosaicism in paternal sperm and multiple parental tissues in a Dravet syndrome cohort
Authors: Yang Xiaoxu , Liu Aijie , Xu Xiaojing , Yang Xiaoling , Zeng Qi , Ye Adam Yongxin , Yu Zhe , Wang Sheng , Huang August Yue , Wu Xiru , Wu Qixi , Wei Liping , Zhang Yuehua 
Published: November 2017

AbstractGenomic mosaicism in parental gametes and peripheral tissues is an important consideration for genetic counseling. We studied a Chinese cohort affected by a severe epileptic disorder, Dravet syndrome (DS). There were 56 fathers who donated semen and 15 parents who donated multiple peripheral tissue samples. We used an ultra-sensitive quantification method, micro-droplet digital PCR (mDDPCR), to detect parental mosaicism of the proband’s pathogenic mutation in SCN1A, the causal gene of DS in 112 families. Ten of the 56 paternal sperm samples were found to exhibit mosaicism of the proband’s mutations, with mutant allelic fractions (MAFs) ranging from 0.03% to 39.04%. MAFs in the mosaic fathers’ sperm were significantly higher than those in their blood (p = 0.00098), even after conditional probability correction (p’ = 0.033). In three mosaic fathers, ultra-low fractions of mosaicism (MAF < 1%) were detected in the sperm samples. In 44 of 45 cases, mosaicism was also observed in other parental peripheral tissues. Hierarchical clustering showed that MAFs measured in the paternal sperm, hair follicles and urine samples were clustered closest together. Milder epileptic phenotypes were more likely to be observed in mosaic parents (p = 3.006e-06). Our study provides new insights for genetic counseling.
Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm
Authors: Soorni Aboozar , Fatahi Reza , Haak David C. , Salami Seyed Alireza , Bombarely Aureliano 
Published: November 2017

AbstractCannabis sativa has a complex history reflected in both selection on naturally occurring compounds and historical trade routes among humans. Iran is a rich resource of natural populationswhich hold the promise to characterize historical patterns of population structure and genetic diversity within Cannabis. Recent advances in high-throughput DNA sequencing technologies have dramatically increased our ability to produce information to the point that it is now feasible to inexpensively obtain population level genotype information at a large scale. In the present investigation, we have explored the use of Genotyping-By-Sequencing (GBS) in Iranian cannabis. We genotyped 98 cannabis samples 36 from Iranian locations and 26 accessions from two germplasm collections. In total, 24,710 high-quality Single Nucleotide Polymorphisms (SNP) were identified. Clustering analysis by Principal Component Analysis (PCA) identified two genetic clusters among Iranian populations and fineSTRUCTURE analysis identified 19 populations with some geographic partitioning. We defined Iranian cannabis in two main groups using the results of the PCA and discovered some strong signal to define some locations as population according to fineSTRUCTURE analyses. However, single nucleotide variant analysis uncovered a relatively moderate level of variation among Iranian cannabis.