bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrical Transition in Isostructural VO2 Thin-Film Heterostructures
Authors: Moatti Adele , Sachan Ritesh , Cooper Valentino R , Narayan Jagdish 
Published: February 2019

AbstractControl over the concurrent occurrence of structural (monoclinic to tetragonal) and electrical (insulator to the conductor) transitions presents a formidable challenge for VO2-based thin film devices. Speed, lifetime, and reliability of these devices can be significantly improved by utilizing solely electrical transition while eliminating structural transition. We design a novel strain-stabilized isostructural VO2 epitaxial thin-film system where the electrical transition occurs without any observable structural transition. The thin-film heterostructures with a completely relaxed NiO buffer layer have been synthesized allowing complete control over strains in VO2 films. The strain trapping in VO2 thin films occurs below a critical thickness by arresting the formation of misfit dislocations. We discover the structural pinning of the monoclinic phase in (10 ± 1 nm) epitaxial VO2 films due to bandgap changes throughout the whole temperature regime as the insulator-to-metal transition occurs. Using density functional theory, we calculate that the strain in monoclinic structure reduces the difference between long and short V-V bond-lengths (ΔV−V) in monoclinic structures which leads to a systematic decrease in the electronic bandgap of VO2. This decrease in bandgap is additionally attributed to ferromagnetic ordering in the monoclinic phase to facilitate a Mott insulator without going through the structural transition.
DGAT1 Inhibitor Suppresses Prostate Tumor Growth and Migration by Regulating Intracellular Lipids and Non-Centrosomal MTOC Protein GM130
Authors: Nardi Francesca , Franco Omar E. , Fitchev Philip , Morales Alejandro , Vickman Renee E. , Hayward Simon W. , Crawford Susan E. 
Published: February 2019

AbstractAcyl-CoA:diacylglycerol acyltransferase I (DGAT1) is a key enzyme in lipogenesis which is increased in metabolically active cells to meet nutrient requirements. DGAT1 has been recognized as an anti-obesity target; however, its role in the tumor microenvironment remains unclear. We postulated that, in prostate cancer (PCa) cells, augmented lipogenesis and growth are due to increased DGAT1 expression leading to microtubule-organizing center (MTOC) amplification. Thus, therapeutic targeting of DGAT1 potentially has tumor suppressive activity. We tested whether blocking DGAT1 in PCa cells altered MTOC and lipid signaling. Western blot and immunofluorescence were performed for MTOC and triglyceride mediators. Treatment with a DGAT1 inhibitor was evaluated. We found a stepwise increase in DGAT1 protein levels when comparing normal prostate epithelial cells to PCa cells, LNCaP and PC-3. Lipid droplets, MTOCs, and microtubule-regulating proteins were reduced in tumor cells treated with a DGAT1 inhibitor. Depletion of the non-centrosomal MTOC protein GM130 reduced PCa cell proliferation and migration. Inhibition of DGAT1 reduced tumor growth both in vitro and in vivo, and a negative feedback loop was discovered between DGAT1, PEDF, and GM130. These data identify DGAT1 as a promising new target for suppressing PCa growth by regulating GM130, MTOC number and disrupting microtubule integrity.
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
Authors: Wilkins Laetitia G. E. , Ettinger Cassandra L. , Jospin Guillaume , Eisen Jonathan A. 
Published: February 2019

AbstractCulture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka.
Probing the Behaviour of Cas1-Cas2 upon Protospacer Binding in CRISPR-Cas Systems using Molecular Dynamics Simulations
Authors: Wan Hua , Li Jianming , Chang Shan , Lin Shuoxin , Tian Yuanxin , Tian Xuhong , Wang Meihua , Hu Jianping 
Published: February 2019

AbstractAdaptation in CRISPR-Cas systems enables the generation of an immunological memory to defend against invading viruses. This process is driven by foreign DNA spacer (termed protospacer) selection and integration mediated by Cas1-Cas2 protein. Recently, different states of Cas1-Cas2, in its free form and in complex with protospacer DNAs, were solved by X-ray crystallography. In this paper, molecular dynamics (MD) simulations are employed to study crystal structures of one free and two protospacer-bound Cas1-Cas2 complexes. The simulated results indicate that the protospacer binding markedly increases the system stability, in particular when the protospacer containing the PAM-complementary sequence. The hydrogen bond and binding free energy calculations explain that PAM recognition introduces more specific interactions to increase the cleavage activity of Cas1. By using principal component analysis (PCA) and intramolecular angle calculation, this study observes two dominant slow motions associated with the binding of Ca1-Cas2 to the protospacer and potential target DNAs respectively. The comparison of DNA structural deformation further implies a cooperative conformational change of Cas1-Cas2 and protospacer for the target DNA capture. We propose that this cooperativity is the intrinsic requirement of the CRISPR integration complex formation. This study provides some new insights into the understanding of CRISPR-Cas adaptation.
Effects of stand age on carbon storage in dragon spruce forest ecosystems in the upper reaches of the Bailongjiang River basin, China
Authors: Cao Jianjun , Gong Yifan , Adamowski Jan F. , Deo Ravinesh C. , Zhu Guofeng , Dong Xiaogang , Zhang Xiaofang , Liu Haibo , Xin Cunlin 
Published: February 2019

AbstractAt an ecosystem level, stand age has a significant influence on carbon storage (CS). Dragon spruce (Picea asperataMast.) situated along the upper reaches of the Bailongjiang River in northwest China were categorized into three age classes (29–32 years, Y1; 34–39 years, Y2; 40–46 years, Y3), and age-related differences in total carbon storage (TCS) of the forest ecosystem were investigated for the first time. Results showed that TCS for the Y1, Y2, and the Y3age groups were 323.64, 240.66 and 174.60 Mg ha−1, respectively. The average TCS of the three age groups was 255.65 Mg C ha−1, with above-ground biomass, below-ground biomass, litter, and soil in the top 0.6 m contributing 15.0%, 3.7%, 12.1%, and 69.2%, respectively. CS in soil and TCS of the Y1age group both significantly exceeded those of the Y3age group (P < 0.05). Contrary to other recent findings, the present study supports the hypothesis that TCS is likely to decrease as stand age increases. This indicates that natural resource managers should rejuvenate forests by routinely thinning older stands, thereby not only achieving vegetation restoration, but also allowing these stands to create a long-term carbon sink for this important eco-region.
Development and validation of a new standardised data collection tool to aid in the diagnosis of canine skin allergies
Authors: Harvey N. D. , Shaw S. C. , Blott S. C. , Vàzquez-Diosdado J. A. , England G. C. W. 
Published: February 2019

AbstractCanine atopic dermatitis (cAD) is a common hereditary clinical syndrome in domestic dogs with no definitive diagnostic tests, which causes marked morbidity and has a high economic impact internationally. We created a novel questionnaire for Labrador (LR) and Golden retriever (GR) owners to evaluate canine skin health with respect to clinical signs of cAD. 4,111 dogs had fully completed questionnaires (2,803 LR; 1,308 GR). ‘Cases’ (793) had a reported veterinary diagnosis of cAD, and ‘controls’ (1652) had no current or past clinical signs of cAD and were aged >3 years. Remaining dogs (1666) were initially categorised as ‘Other’. Simulated annealing was used comparing ‘Cases’ and ‘Others’ to select a novel set of features able to classify a known case. Two feature sets are proposed, one for use on first evaluation and one for dogs with a history of skin problems. A sum for each list when applied to the whole population (including controls) was able to classify ‘Cases’ with a sensitivity of 89% to 94% and specificity of 71% to 69%, respectively, and identify potentially undiagnosed cases. Our findings demonstrate for the first time that owner questionnaire data can be reliably used to aid in the diagnostic process of cAD.
Maize productivity and soil properties in the Loess Plateau in response to ridge-furrow cultivation with polyethylene and straw mulch
Authors: Deng Hao-Liang , Xiong You-Cai , Zhang Heng-Jia , Li Fu-Qiang , Zhou Hong , Wang Yu-Cai , Deng Zhan-Rui 
Published: February 2019

AbstractRidge-furrow with full film mulching (RFFM) is widely used in the Loess Plateau (LP) to increase maize yield. However, continuous RFFM application may cause excessive depletion of soil organic carbon (SOC) and soil water storage (SWS). The present study tested four production systems, namely, (1) RFFM; (2) ridge-furrow with polyethylene film and straw mulching (RFFSM); (3) non-contoured seedbed with film mulching (FFM); and (4) non-contoured seedbed without mulching (CK) in 2013 and 2014 to identify an optimal technique to increase maize yield yet minimizing the negative effects. SWS under RFFSM was significantly higher by 5.4% and 13.4% compared to RFFM and CK, respectively. The changes in SOC were −0.2, −0.2, and −0.4 g·kg−1 for RFFM, FFM, and CK, respectively, and 0.3 g·kg−1 for RFFSM. Increased root residue and extra external carbon input to soil under RFFSM directly contributed to SOC recovery. RFFSM had a comparable grain yield but higher water use efficiency compared to RFFM. The combination of RFFSM is promising for improving SOC stocks, water storage, and maize productivity.
Protein tyrosine phosphatase 4A3 (PTP4A3/PRL-3) promotes the aggressiveness of human uveal melanoma through dephosphorylation of CRMP2
Authors: Duciel Laura , Anezo Océane , Mandal Kalpana , Laurent Cécile , Planque Nathalie , Coquelle Frédéric M. , Gentien David , Manneville Jean-Baptiste , Saule Simon 
Published: February 2019

AbstractUveal melanoma (UM) is an aggressive tumor in which approximately 50% of patients develop metastasis. Expression of the PTP4A3 gene, encoding a phosphatase, is predictive of poor patient survival. PTP4A3 expression in UM cells increases their migration in vitro and invasiveness in vivo. Here, we show that CRMP2 is mostly dephosphorylated on T514 in PTP4A3 expressing cells. We also demonstrate that inhibition of CRMP2 expression in UM cells expressing PTP4A3 increases their migration in vitro and invasiveness in vivo. This phenotype is accompanied by modifications of the actin microfilament network, with shortened filaments, whereas cells with a inactive mutant of the phosphatase do not show the same behavior. In addition, we showed that the cell cytoplasm becomes stiffer when CRMP2 is downregulated or PTP4A3 is expressed. Our results suggest that PTP4A3 acts upstream of CRMP2 in UM cells to enhance their migration and invasiveness and that a low level of CRMP2 in tumors is predictive of poor patient survival.
Bovine colostrum and product intervention associated with relief of childhood infectious diarrhea
Authors: Li Ji , Xu Yi-Wen , Jiang Jing-Jing , Song Qing-Kun 
Published: February 2019

AbstractThis meta-analysis aimed to investigate the protective effects of bovine colostrum against childhood infectious diarrhea. A systematic search was conducted using PubMed, Cochrane Library databases and clinicaltrial.gov. Among 166 research articles, only five RCTs were included into final analysis. Review manager (version 5.2) was used to pool the effect-size across studies. Sensitivity and risk of bias were estimated accordingly. Under a pooled analysis, bovine colostrum consumption correlated with a significant reduction in stool frequency of infectious diarrhea, by 1.42 times per day (95% CI: −2.70, −0.14). Bovine colostrum intervention also reduced occurrence of diarrhea by 71% (pooled OR = 0.29, 95%CI 0.16, 0.52). The OR of positive detection of pathogen in the stool was 0.29 (95%CI 0.08, 0.71) in bovine colostrum treated group, compared with placebo group. In the sensitivity analysis of studies with low risk of biases, bovine colostrum significantly reduced stool frequency, occurrence of diarrhea and pathogen detection. BC and related products have a significant benefit in reducing the frequency and relieving the symptoms of childhood infectious diarrhea.
Comparative analysis of differentially secreted proteins in serum-free and serum-containing media by using BONCAT and pulsed SILAC
Authors: Shin Jihye , Rhim Jiheon , Kwon Yumi , Choi Sun Young , Shin Sungho , Ha Chul-Won , Lee Cheolju 
Published: February 2019

AbstractDespite the increased interest in secretomes associated with paracrine/autocrine mechanisms, the majority of mass spectrometric cell secretome studies have been performed using serum-free medium (SFM). On the other hand, serum-containing medium (SCM) is not recommended very much because the secretome obtained with SCM is easily contaminated with fetal bovine serum (FBS) proteins. In this study, through the combination of bioorthogonal non-canonical amino acid tagging (BONCAT) and pulsed-SILAC (pSILAC), we analyzed differentially secreted proteins between SFM and SCM in a cancer-derived human cell, U87MG, and a mesenchymal stem cell derived from human Wharton’s jelly (hWJ-MSCs). In most cases, the bioinformatic tools predicted a protein to be truly secretory when the secretion level of the protein was more in SCM than in SFM. In the case of hWJ-MSCs, the amount of proteins secreted in SCM for 24 hours was larger than that of SFM (log2 fold change = 0.96), even considering different cell proliferation rates. hWJ-MSCs proteins secreted more in SCM included several positive markers of MSC paracrine factors implicated in angiogenesis, neurogenesis and osteogenesis, and upstream regulators of cell proliferation. Our study suggests the analysis of the secretome should be processed in SCM that promotes cell proliferation and secretion.
Climate and landscape changes as driving forces for future range shift in southern populations of the European badger
Authors: Rosalino Luís M. , Guedes Diana , Cabecinha Diogo , Serronha Ana , Grilo Clara , Santos-Reis Margarida , Monterroso Pedro , Carvalho João , Fonseca Carlos , Pardavila Xosé , Virgós Emílio , Hipólito Dário 
Published: February 2019

AbstractHuman-Induced Rapid Environmental Change (HIREC), particularly climate change and habitat conversion, affects species distributions worldwide. Here, we aimed to (i) assess the factors that determine range patterns of European badger (Meles meles) at the southwestern edge of their distribution and (ii) forecast the possible impacts of future climate and landcover changes on those patterns. We surveyed 272 cells of 5 × 5 km, to assess badger presence and confirmed its occurrence in 95 cells (35%). Our models estimate that badger’s presence is promoted by the occurrence of herbaceous fields and shrublands (5%–10%), and low proportions of Eucalyptus plantations (<~15%). Regions with >50% of podzols and eruptive rocks, higher sheep/goat density (>4 ind/km2), an absence of cattle, intermediate precipitation regimes (800–1000 mm/year) and mild mean temperatures (15–16 °C) are also more likely to host badgers. We predict a decrease in favourability of southern areas for hosting badgers under forecasted climate and landcover change scenarios, which may lead to a northwards retraction of the species southern distribution limit, but the overall landscape favourability is predicted to slightly increase. The forecasted retraction may affect community functional integrity, as its role in southern ecological networks will be vacant.
CD271-selected mesenchymal stem cells from adipose tissue enhance cartilage repair and are less angiogenic than plastic adherent mesenchymal stem cells
Authors: Kohli Nupur , Al-Delfi Ibtesam R. T. , Snow Martyn , Sakamoto Takumi , Miyazaki Tsuyoshi , Nakajima Hideaki , Uchida Kenzo , Johnson William E. B. 
Published: February 2019

AbstractCD271 is a marker of bone marrow MSCs with enhanced differentiation capacity for bone or cartilage repair. However, the nature of CD271+ MSCs from adipose tissue (AT) is less well understood. Here, we investigated the differentiation, wound healing and angiogenic capacity of plastic adherent MSCs (PA MSCs) versus CD271+ MSCs from AT. There was no difference in the extent to which PA MSCs and CD271+ MSCs formed osteoblasts, adipocytes or chondrocytesin vitro. In contrast, CD271+ MSCs transplanted into athymic rats significantly enhanced osteochondral wound healing with reduced vascularisation in the repair tissue compared to PA MSCs and control animals; there was little histological evidence of mature articular cartilage formation in all animals. Conditioned medium from CD271+ MSC cultures was less angiogenic than PA MSC conditioned medium, and had little effect on endothelial cell migration or endothelial tubule formationin vitro. The low angiogenic activity of CD271+ MSCs and improved early stage tissue repair of osteochondral lesions when transplanted, along with a comparable differentiation capacity along mesenchymal lineages when induced, suggests that these selected cells are a better candidate than PA MSCs for the repair of cartilaginous tissue.
Protecting maize from rootworm damage with the combined application of arbuscular mycorrhizal fungi, Pseudomonas bacteria and entomopathogenic nematodes
Authors: Jaffuel Geoffrey , Imperiali Nicola , Shelby Kent , Campos-Herrera Raquel , Geisert Ryan , Maurhofer Monika , Loper Joyce , Keel Christoph , Turlings Ted C. J. , Hibbard Bruce E. 
Published: February 2019

AbstractDiabrotica virgifera virgifera LeConte, the western corn rootworm (WCR), is the most destructive pest of maize in North America, and has recently spread across central Europe. Its subterranean larval stages are hard to reach with pesticides and it has evolved resistance to conventional management practices. The application of beneficial soil organisms is being considered as a sustainable and environmental friendly alternative. In a previous study, the combined application in wheat fields of arbuscular mycorrhizal fungi, entomopathogenic Pseudomonas bacteria, and entomopathogenic nematodes was found to promote growth and protection against a natural pest infestation, without negative cross effects. Because of the insect-killing capacity of the bacteria and nematodes, we hypothesized that the application of these organisms would have similar or even greater beneficial effects in WCR-infested maize fields. During three consecutive years (2015–2017), we conducted trials in Missouri (USA) in which we applied the three organisms, alone or in combinations, in plots that were artificially infested with WCR and in non-infested control plots. For two of the three trials, we found that in plots treated with entomopathogenic nematodes and/or entomopathogenic Pseudomonas bacteria, roots were less damaged than the roots of plants in control plots. During one year, WCR survival was significantly lower in plots treated with Pseudomonas than in control plots, and the surviving larvae that were recovered from these plots were lighter. The bacterial and nematodes treatments also enhanced yield, assessed as total grain weight, in one of the trials. The effects of the treatments varied considerable among the three years, but they were always positive for the plants.
The CDR1 and Other Regions of Immunoglobulin Light Chains are Hot Spots for Amyloid Aggregation
Authors: Ruiz-Zamora Robin Axel , Guillaumé Simon , Al-Hilaly Youssra K. , Al-Garawi Zahraa , Rodríguez-Alvarez Francisco Javier , Zavala-Padilla Guadalupe , Pérez-Carreón Julio I. , Rodríguez-Ambriz Sandra L. , Herrera Guillermo A. , Becerril-Luján Baltazar , Ochoa-Leyva Adrián , Melendez-Zajgla Jorge , Serpell Louise , del Pozo-Yauner Luis 
Published: February 2019

AbstractImmunoglobulin light chain-derived (AL) amyloidosis is a debilitating disease without known cure. Almost nothing is known about the structural factors driving the amyloidogenesis of the light chains. This study aimed to identify the fibrillogenic hotspots of the model protein 6aJL2 and in pursuing this goal, two complementary approaches were applied. One of them was based on several web-based computational tools optimized to predict fibrillogenic/aggregation-prone sequences based on different structural and biophysical properties of the polypeptide chain. Then, the predictions were confirmed with an ad-hoc synthetic peptide library. In the second approach, 6aJL2 protein was proteolyzed with trypsin, and the products incubated in aggregation-promoting conditions. Then, the aggregation-prone fragments were identified by combining standard proteomic methods, and the results validated with a set of synthetic peptides with the sequence of the tryptic fragments. Both strategies coincided to identify a fibrillogenic hotspot located at the CDR1 and β-strand C of the protein, which was confirmed by scanning proline mutagenesis analysis. However, only the proteolysis-based strategy revealed additional fibrillogenic hotspots in two other regions of the protein. It was shown that a fibrillogenic hotspot associated to the CDR1 is also encoded by several κ and λ germline variable domain gene segments. Some parts of this study have been included in the chapter “The Structural Determinants of the Immunoglobulin Light Chain Amyloid Aggregation”, published in Physical Biology of Proteins and Peptides, Springer 2015 (ISBN 978-3-319-21687-4).