bluuebunny/crossref_metadata_2025_split huggingface dataset:
GATA-type transcription factors play a vital role in radiation sensitivity of Cryptococcus neoformans by regulating the gene expression of specific amino acid permeases
Authors: Cui Wanchang , Li XiangHong , Hull Lisa , Xiao Mang 
Published: April 2019

AbstractCryptococcus neoformans is a basidiomycete fungus that is highly resistant to ionizing radiation and has been identified in highly radioactive environments. Transcription factors (TFs) are master regulators of gene expression by binding to specific DNA sequences within promoters of target genes. A library of 322 signature-tagged gene deletion strains for 155 C. neoformans TF genes has been established. Previous phenome-based functional analysis of the C. neoformans TF mutant library identified key TFs important for various phenotypes, such as growth, differentiation, virulence-factor production, and stress responses. Here, utilizing the established TF mutant library, we identified 5 TFs that are important for radiation sensitivity, including SRE1, BZP2, GAT5, GAT6, and HCM1. Interestingly, BZP2, GAT5 and GAT6 all belong to the GATA-type transcription factors. These factors regulate transcription of nitrogen catabolite repression (NCR) sensitive genes when preferred nitrogen sources are absent or limiting. In addition to radiation, we found that specific GATA factors are important for other stressors such as rapamycin, fluconazole, and hydroxyurea treatment. Using real-time PCR method, we studied the expression of GATA down-stream genes after radiation exposure and identified that AAP4, AAP5 and URO1 were differentially expressed in the GAT5 and GAT6 mutants compared to the wild type cells. In summary, our data suggest that GATA TFs are important for radiation sensitivity in C. neoformans by regulating specific downstream AAP genes.
Psychological Sleep Interventions for Migraine and Tension-Type Headache: A Systematic Review and Meta-Analysis
Authors: Sullivan Daniel P. , Martin Paul R. , Boschen Mark J. 
Published: April 2019

AbstractDisordered sleep, poor sleep quality, and insufficient or excessive sleep duration are known triggers of primary and secondary headaches. Given this, it is plausible that improving sleep will subsequently reduce headache activity. We report a systematic review of the literature, examining studies utilising psychological sleep interventions for the treatment of migraine and tension-type headache. PubMed, EMBASE, CINAHL, PsycINFO, and Cochrane Central were searched, using terms pertaining to psychological sleep interventions and headaches. Meta-analysis was performed for two outcome measures; headache frequency, and headache intensity. 103 studies were retrieved, of which 55 were duplicates. After completing reviews, three studies were retained. An additional eligible study was published after the initial search, and was found via monthly update searches, resulting in a total of four included studies. The effects of psychological sleep interventions (and in one study, combined with drug therapy) significantly reduced headache frequency and headache intensity. Three studies improved various sleep outcomes such as duration, efficiency, and excessive sleepiness. Psychological sleep interventions improve headache frequency and sleep, however there is conflicting evidence for the effect on headache intensity between studies. Limitations include the small number of studies conducted to date. Despite this, the notable improvements in headaches and sleep achieved after psychological sleep interventions indicates further research on this promising topic is warranted.
The Role of Follow-up Evaluation in the Diagnostic Algorithm of Idiopathic Interstitial Pneumonia: A Retrospective Study
Authors: Han Qian , Wang Hong-yu , Zhang Xiao-xian , Wu Lu-lu , Wang Lu-lin , Jiang Ying , Deng Kui-miao , Mao Meng-meng , Chen Rong-chang , Kolb Martin , Luo Qun 
Published: April 2019

AbstractWe aimed to evaluate the alteration of diagnosis of individual expert and multidisciplinary discussion (MDD) team in the longitudinal diagnostic assessment of idiopathic interstitial pneumonia (IIP). The retrospective analysis included 56 patients diagnosed as IIP by The First Affiliated Hospital of Guangzhou Medical University with follow-up visits during Jan 1st to Aug 31st 2014. Each expert was provided information in a sequential manner and was asked to assign an individual diagnosis and an MDD diagnosis after group discussion. The level of agreement among individual experts and between different visits was calculated by kappa and the agreement between individual specialist and MDD team with different consensus levels was measured by weighted-kappa coefficients. Follow-up data changed the original clinical diagnosis and MDD diagnosis in 24.1% and 10.7% of all cases, respectively, and clinician and MDD consensus level in 55.4% and 25.0%, respectively. The diagnostic performance of individual clinicians or radiologist was closer to that of the MDD compared with the pathologist, and follow-up further increased the agreement. The longitudinal evaluation of patients with IIP improved the inter-observer agreement in a multidisciplinary team. The performance of individual clinicians or radiologist was approaching the accuracy of multidisciplinary team when provided with follow-up data.
Mesenchymal Stem Cells Increase Alveolar Differentiation in Lung Progenitor Organoid Cultures
Authors: Leeman Kristen T. , Pessina Patrizia , Lee Joo-Hyeon , Kim Carla F. 
Published: April 2019

AbstractLung epithelial cell damage and dysfunctional repair play a role in the development of lung disease. Effective repair likely requires the normal functioning of alveolar stem/progenitor cells. For example, we have shown in a mouse model of bronchopulmonary dysplasia (BPD) that mesenchymal stem cells (MSC) protect against hyperoxic lung injury at least in part by increasing the number of Epcam+ Sca-1+ distal lung epithelial cells. These cells are capable of differentiating into both small airway (CCSP+) and alveolar (SPC+) epithelial cells in three-dimensional (3D) organoid cultures. To further understand the interactions between MSC and distal lung epithelial cells, we added MSC to lung progenitor 3D cultures. MSC stimulated Epcam+ Sca-1+ derived organoid formation, increased alveolar differentiation and decreased self-renewal. MSC-conditioned media was sufficient to promote alveolar organoid formation, demonstrating that soluble factors secreted by MSC are likely responsible for the response. This work provides strong evidence of a direct effect of MSC-secreted factors on lung progenitor cell differentiation.
Contrasting latitudinal patterns in phylogenetic diversity between woody and herbaceous communities
Authors: Massante Jhonny C. , Götzenberger Lars , Takkis Krista , Hallikma Tiit , Kaasik Ants , Laanisto Lauri , Hutchings Michael J. , Gerhold Pille 
Published: April 2019

AbstractAlthough many studies have shown that species richness decreases from low to high latitudes (the Latitudinal Diversity Gradient), little is known about the relationship between latitude and phylogenetic diversity. Here we examine global latitudinal patterns of phylogenetic diversity using a dataset of 459 woody and 589 herbaceous plant communities. We analysed the relationships between community phylogenetic diversity, latitude, biogeographic realm and vegetation type. Using the most recent global megaphylogeny for seed plants and the standardised effect sizes of the phylogenetic diversity metrics ‘mean pairwise distance’ (SESmpd) and ‘mean nearest taxon distance’ (SESmntd), we found that species were more closely-related at low latitudes in woody communities. In herbaceous communities, species were more closely-related at high latitudes than at intermediate latitudes, and the strength of this effect depended on biogeographic realm and vegetation type. Possible causes of this difference are contrasting patterns of speciation and dispersal. Most woody lineages evolved in the tropics, with many gymnosperms but few angiosperms adapting to high latitudes. In contrast, the recent evolution of herbaceous lineages such as grasses in young habitat types may drive coexistence of closely-related species at high latitudes. Our results show that high species richness commonly observed at low latitudes is not associated with high phylogenetic diversity.
New Approach in Ulcer Prevention and Wound Healing Treatment using Doxycycline and Amoxicillin/LDH Nanocomposites
Authors: El-Ela Fatma I. Abo , Farghali Ahmed A. , Mahmoud Rehab K. , Mohamed Nada A. , Moaty S. A. Abdel 
Published: April 2019

AbstractDoxycycline (DOX) and amoxicillin (AMOX) are important Broad-spectrum antibiotics used in treating multiple human and animal diseases. For the sake of exploring novel medical applications, both antibiotics were loaded into magnesium aluminium layer double hydroxide (Mg-Al)/LDH nanocomposite through the co-precipitation method. The synthesized materials were characterized by XRD, FT-IR, particle size analysis, FESEM and HRTEM. Acute toxicological studies were conducted using median lethal dose LD50, where a total number of 98 rats (200–150 gm) of both sexes were used. An experimental wound was aseptically incised on the anterior-dorsal side of each rat, while 98% of pure medical ethanol was used for ulcer induction. Acute toxicity, wound closure rate, healing percentages, ulcer index, protective rate and histopathological studies were investigated. Antibiotic Nanocomposites has significantly prevented ulcer formation and improved wound healing process to take shorter time than that of the typical processes, when compared with that of same drugs in microscale systems or commercial standard drugs. These results were confirmed by the histopathological findings. By converting it into the Nanoform, which is extremely important, especially with commonly used antibiotics, novel pharmacological properties were acquired from the antibiotics. The safe uses of DOX/LDH and AMOX/LDH Nanocomposites in this study were approved for biomedical applications.
Detection and manipulation of methylation in blood cancer DNA using terahertz radiation
Authors: Cheon Hwayeong , Paik Jin Ho , Choi Moran , Yang Hee-Jin , Son Joo-Hiuk 
Published: April 2019

AbstractDNA methylation is a pivotal epigenetic modification of DNA that regulates gene expression. Abnormal regulation of gene expression is closely related to carcinogenesis, which is why the assessment of DNA methylation is a key factor in cancer research. Terahertz radiation may play an important role in active demethylation for cancer therapy because the characteristic frequency of the methylated DNA exists in the terahertz region. Here, we present a novel technique for the detection and manipulation of DNA methylation using terahertz radiation in blood cancer cell lines. We observed the degree of DNA methylation in blood cancer at the characteristic resonance of approximately 1.7 THz using terahertz time-domain spectroscopy. The terahertz results were cross-checked with global DNA methylation quantification using an enzyme-linked immunosorbent assay. We also achieved the demethylation of cancer DNA using high-power terahertz radiation at the 1.7-THz resonance. The demethylation degrees ranged from 10% to 70%, depending on the type of cancer cell line. Our results show the detection of DNA methylation based on the terahertz molecular resonance and the manipulation of global DNA methylation using high-power terahertz radiation. Terahertz radiation may have potential applications as an epigenetic inhibitor in cancer treatment, by virtue of its ability to induce DNA demethylation, similarly to decitabine.
CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing
Authors: Markham John F. , Yerneni Satwica , Ryland Georgina L. , Leong Huei San , Fellowes Andrew , Thompson Ella R. , De Silva Wasanthi , Kumar Amit , Lupat Richard , Li Jason , Ellul Jason , Fox Stephen , Dickinson Michael , Papenfuss Anthony T. , Blombery Piers 
Published: April 2019

AbstractNext Generation Sequencing is now routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and germline sequence variations in patient samples. However, clinical assessment of copy number variations (CNVs) and large-scale structural variations (SVs) is still challenging. While tools exist to estimate both, their results are typically presented separately in tables or static plots which can be difficult to read and are unable to show the context needed for clinical interpretation and reporting. We have addressed this problem with CNspector, a multi-scale interactive browser that shows CNVs in the context of other relevant genomic features to enable fast and effective clinical reporting. We illustrate the utility of CNspector at different genomic scales across a variety of sample types in a range of case studies. We show how CNspector can be used for diagnosis and reporting of exon-level deletions, focal gene-level amplifications, chromosome and chromosome arm level amplifications/deletions and in complex genomic rearrangements. CNspector is a web-based clinical variant browser tailored to the clinical application of next generation sequencing for CNV assessment. We have demonstrated the utility of this interactive software in typical applications across a range of tissue types and disease contexts encountered in the context of diagnostic pathology. CNspector is written in R and the source code is available for download under the GPL3 Licence from https://github.com/PapenfussLab/CNspector.
Spiking Neural Network Modelling Approach Reveals How Mindfulness Training Rewires the Brain
Authors: Doborjeh Zohreh , Doborjeh Maryam , Taylor Tamasin , Kasabov Nikola , Wang Grace Y. , Siegert Richard , Sumich Alex 
Published: April 2019

AbstractThere has been substantial interest in Mindfulness Training (MT) to understand how it can benefit healthy individuals as well as people with a broad range of health conditions. Research has begun to delineate associated changes in brain function. However, whether measures of brain function can be used to identify individuals who are more likely to respond to MT remains unclear. The present study applies a recently developed brain-inspired Spiking Neural Network (SNN) model to electroencephalography (EEG) data to provide novel insight into: i) brain function in depression; ii) the effect of MT on depressed and non-depressed individuals; and iii) neurobiological characteristics of depressed individuals who respond to mindfulness. Resting state EEG was recorded from before and after a 6 week MT programme in 18 participants. Based on self-report, 3 groups were formed: non-depressed (ND), depressed before but not after MT (responsive, D+) and depressed both before and after MT (unresponsive, D−). The proposed SNN, which utilises a standard brain-template, was used to model EEG data and assess connectivity, as indicated by activation levels across scalp regions (frontal, frontocentral, temporal, centroparietal and occipitoparietal), at baseline and follow-up. Results suggest an increase in activation following MT that was site-specific as a function of the group. Greater initial activation levels were seen in ND compared to depressed groups, and this difference was maintained at frontal and occipitoparietal regions following MT. At baseline, D+ had great activation than D−. Following MT, frontocentral and temporal activation reached ND levels in D+ but remained low in D−. Findings support the SNN approach in distinguishing brain states associated with depression and responsiveness to MT. The results also demonstrated that the SNN approach can be used to predict the effect of mindfulness on an individual basis before it is even applied.
Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations
Authors: Di Muccio Giovanni , Rossini Aldo Eugenio , Di Marino Daniele , Zollo Giuseppe , Chinappi Mauro 
Published: April 2019

AbstractSingle molecule protein sequencing would represent a disruptive burst in proteomic research with important biomedical impacts. Due to their success in DNA sequencing, nanopore based devices have been recently proposed as possible tools for the sequencing of peptide chains. One of the open questions in nanopore protein sequencing concerns the ability of such devices to provide different signals for all the 20 standard amino acids. Here, using equilibrium all-atom molecular dynamics simulations, we estimated the pore clogging in α-Hemolysin nanopore associated to 20 different homopeptides, one for each standard amino acid. Our results show that pore clogging is affected by amino acid volume, hydrophobicity and net charge. The equilibrium estimations are also supported by non-equilibrium runs for calculating the current blockades for selected homopeptides. Finally, we discuss the possibility to modify the α-Hemolysin nanopore, cutting a portion of the barrel region close to the trans side, to reduce spurious signals and, hence, to enhance the sensitivity of the nanopore.
A novel series of high-efficiency vectors for TA cloning and blunt-end cloning of PCR products
Authors: Motohashi Ken 
Published: April 2019

AbstractAn efficient PCR cloning method is indispensable in modern molecular biology, as it can greatly improve the efficiency of DNA cloning processes. Here, I describe the development of three vectors for TA cloning and blunt-end cloning. Specifically, pCRT and pCRZeroT were designed to improve the efficiency of TA cloning. pCRZeroT can also be used with pCRZero to facilitate blunt-end cloning using the ccdB gene. Using pCRZero and pCRZeroT and applying the Golden Gate reaction, I developed a direct PCR cloning protocol with non-digested circular vectors and PCR products. This direct PCR cloning protocol yielded colony-formation rates and cloning efficiencies that are comparable with those obtained by conventional PCR cloning with pre-digested vectors and PCR products. The three plasmids I designed are available from Addgene (https://www.addgene.org/).
Modelling Highly Biodiverse Areas in Brazil
Authors: Oliveira Ubirajara , Soares-Filho Britaldo Silveira , Santos Adalberto J. , Paglia Adriano Pereira , Brescovit Antonio D. , de Carvalho Claudio J. B. , Silva Daniel Paiva , Rezende Daniella T. , Leite Felipe Sá Fortes , Batista João Aguiar Nogueira , Barbosa João Paulo Peixoto Pena , Stehmann João Renato , Ascher John S. , Vasconcelos Marcelo F. , Marco Paulo De , Löwenberg-Neto Peter , Ferro Viviane Gianluppi 
Published: April 2019

AbstractTraditional conservation techniques for mapping highly biodiverse areas assume there to be satisfactory knowledge about the geographic distribution of biodiversity. There are, however, large gaps in biological sampling and hence knowledge shortfalls. This problem is even more pronounced in the tropics. Indeed, the use of only a few taxonomic groups or environmental surrogates for modelling biodiversity is not viable in mega-diverse countries, such as Brazil. To overcome these limitations, we developed a comprehensive spatial model that includes phylogenetic information and other several biodiversity dimensions aimed at mapping areas with high relevance for biodiversity conservation. Our model applies a genetic algorithm tool for identifying the smallest possible region within a unique biota that contains the most number of species and phylogenetic diversity, as well as the highest endemicity and phylogenetic endemism. The model successfully pinpoints small highly biodiverse areas alongside regions with knowledge shortfalls where further sampling should be conducted. Our results suggest that conservation strategies should consider several taxonomic groups, the multiple dimensions of biodiversity, and associated sampling uncertainties.
Treatment of Common Sunflower (Helianthus annus L.) Seeds with Radio-frequency Electromagnetic Field and Cold Plasma Induces Changes in Seed Phytohormone Balance, Seedling Development and Leaf Protein Expression
Authors: Mildažienė Vida , Aleknavičiūtė Vesta , Žūkienė Rasa , Paužaitė Giedrė , Naučienė Zita , Filatova Irina , Lyushkevich Veronika , Haimi Perttu , Tamošiūnė Inga , Baniulis Danas 
Published: April 2019

AbstractTreatment of plant seeds with electromagnetic fields or non-thermal plasmas aims to take advantage of plant functional plasticity towards stimulation of plant agricultural performance. In this study, the effects of pre-sowing seed treatment using 200 Pa vacuum (7 min), 5.28 MHz radio-frequency cold plasma (CP −2, 5, and 7 min) and electromagnetic field (EMF −5, 10, 15 min) on seed germination kinetics, content of phytohormones, morphometric parameters of seedlings and leaf proteome were assessed. CP 7 min and EMF 15 min treatments caused 19–24% faster germination in vitro; germination in the substrate was accelerated by vacuum (9%) and EMF 15 min (17%). The stressors did not change the seed germination percentage, with exception of EMF 5 min treatment that caused a decrease by 7.5%. Meanwhile both CP 7 min and EMF 15 min treatments stimulated germination, but the EMF treatment resulted in higher weight of leaves. Stressor-specific changes in phytohormone balance were detected in seeds: vacuum treatment decreased zeatin amount by 39%; CP treatments substantially increased gibberellin content, but other effects strongly varied with the treatment duration; the abscisic acid content was reduced by 55–60% after the EMF treatment. Analysis of the proteome showed that short exposure of seeds to the EMF or CP induced a similar long-term effect on gene expression in leaves, mostly stimulating expression of proteins involved in photosynthetic processes and their regulation.
Levodopa does not affect expression of reinforcement learning in older adults
Authors: Grogan J. P. , Isotalus H. K. , Howat A. , Irigoras Izagirre N. , Knight L. E. , Coulthard E. J. 
Published: April 2019

AbstractDopamine has been implicated in learning from rewards and punishment, and in the expression of this learning. However, many studies do not fully separate retrieval and decision mechanisms from learning and consolidation. Here, we investigated the effects of levodopa (dopamine precursor) on choice performance (isolated from learning or consolidation). We gave 31 healthy older adults 150 mg of levodopa or placebo (double-blinded, randomised) 1 hour before testing them on stimuli they had learned the value of the previous day. We found that levodopa did not affect the overall accuracy of choices, nor the relative expression of positively or negatively reinforced values. This contradicts several studies and suggests that overall dopamine levels may not play a role in the choice performance for values learned through reinforcement learning in older adults.