bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi
Authors: Fisher Matthew C. , Ghosh Pria , Shelton Jennifer M. G. , Bates Kieran , Brookes Lola , Wierzbicki Claudia , Rosa Gonçalo M. , Farrer Rhys A. , Aanensen David M. , Alvarado-Rybak Mario , Bataille Arnaud , Berger Lee , Böll Susanne , Bosch Jaime , Clare Frances C. , A. Courtois Elodie , Crottini Angelica , Cunningham Andrew A. , Doherty-Bone Thomas M. , Gebresenbet Fikirte , Gower David J. , Höglund Jacob , James Timothy Y. , Jenkinson Thomas S. , Kosch Tiffany A. , Lambertini Carolina , Laurila Anssi , Lin Chun-Fu , Loyau Adeline , Martel An , Meurling Sara , Miaud Claude , Minting Pete , Ndriantsoa Serge , O’Hanlon Simon J. , Pasmans Frank , Rakotonanahary Tsanta , Rabemananjara Falitiana C. E. , Ribeiro Luisa P. , Schmeller Dirk S. , Schmidt Benedikt R. , Skerratt Lee , Smith Freya , Soto-Azat Claudio , Tessa Giulia , Toledo Luís Felipe , Valenzuela-Sánchez Andrés , Verster Ruhan , Vörös Judit , Waldman Bruce , Webb Rebecca J. , Weldon Che , Wombwell Emma , Zamudio Kelly R. , Longcore Joyce E. , Garner Trenton W. J. 
Published: May 2018

AbstractParasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.
Smooth muscle-like Ca2+-regulation of actin–myosin interaction in adult jellyfish striated muscle
Authors: Tanaka Hiroyuki , Ishimaru Shiori , Nagatsuka Yasuhiro , Ohashi Keisuke 
Published: May 2018

AbstractCnidaria is an animal phylum, whose members probably have the most ancestral musculature. We prepared and characterized, for the first time to our knowledge, native actomyosin from the striated myoepithelium of the adult moon jelly Aurelia sp. The actomyosin contained myosin, paramyosin-like protein, Ser/Thr-kinase, actin, and two isoforms of tropomyosin, but not troponin, which is known to activate contraction dependent on intracellular Ca2+ signaling in almost all striated muscles of bilaterians. Notably, the myosin comprised striated muscle-type heavy chain and smooth muscle-type regulatory light chains. In the presence of Ca2+, the Mg-ATPase activity of actomyosin was stimulated and Ser21 of the regulatory light chain was concomitantly phosphorylated by the addition of calmodulin and myosin light chain kinase prepared from chicken smooth muscle. Collectively, these results suggest that, similar to smooth muscle, the contraction of jellyfish striated muscle is regulated by Ca2+-dependent phosphorylation of the myosin light chain.
Quantitative SUMO proteomics reveals the modulation of several PML nuclear body associated proteins and an anti-senescence function of UBC9
Authors: McManus Francis P. , Bourdeau Véronique , Acevedo Mariana , Lopes-Paciencia Stéphane , Mignacca Lian , Lamoliatte Frédéric , Rojas Pino John W. , Ferbeyre Gerardo , Thibault Pierre 
Published: May 2018

AbstractSeveral regulators of SUMOylation have been previously linked to senescence but most targets of this modification in senescent cells remain unidentified. Using a two-step purification of a modified SUMO3, we profiled the SUMO proteome of senescent cells in a site-specific manner. We identified 25 SUMO sites on 23 proteins that were significantly regulated during senescence. Of note, most of these proteins were PML nuclear body (PML-NB) associated, which correlates with the increased number and size of PML-NBs observed in senescent cells. Interestingly, the sole SUMO E2 enzyme, UBC9, was more SUMOylated during senescence on its Lys-49. Functional studies of a UBC9 mutant at Lys-49 showed a decreased association to PML-NBs and the loss of UBC9’s ability to delay senescence. We thus propose both pro- and anti-senescence functions of protein SUMOylation.
The trimeric solution structure and fucose-binding mechanism of the core fucosylation-specific lectin PhoSL
Authors: Yamasaki Kazuhiko , Yamasaki Tomoko , Tateno Hiroaki 
Published: May 2018

AbstractThe core α1–6 fucosylation-specific lectin from a mushroom Pholiota squarrosa (PhoSL) is a potential tool for precise diagnosis of cancers. This lectin consists of only 40 amino acids and can be chemically synthesized. We showed here that a synthesized PhoSL peptide formed a trimer by gel filtration and chemical cross-linking assays, and determined a structure of the PhoSL trimer by NMR. The structure possesses a β-prism motif with a three-fold rotational symmetry, where three antiparallel β-sheets are tightly connected by swapping of β-strands. A triad of Trp residues comprises the structural core, forming NH–π electrostatic interactions among the indole rings. NMR analysis with an excess amount of fucose revealed the structural basis for the molecular recognition. Namely, fucose deeply enters a pocket formed at a junction of β-sheet edges, with the methyl group placed at the bottom. It forms a number of hydrophobic and hydrogen-bonding interactions with PhoSL residues. In spite of partial similarities to the structures of other functionally related lectins, the arrangement of the antiparallel β-sheets in the PhoSL trimer is novel as a structural scaffold, and thus defines a novel type of lectin structure.
Perlecan, a heparan sulfate proteoglycan, regulates systemic metabolism with dynamic changes in adipose tissue and skeletal muscle
Authors: Yamashita Yuri , Nakada Satoshi , Yoshihara Toshinori , Nara Takeshi , Furuya Norihiko , Miida Takashi , Hattori Nobutaka , Arikawa-Hirasawa Eri 
Published: May 2018

AbstractPerlecan (HSPG2), a heparan sulfate proteoglycan, is a component of basement membranes and participates in a variety of biological activities. Here, we show physiological roles of perlecan in both obesity and the onset of metabolic syndrome. The perinatal lethality-rescued perlecan knockout (Hspg2−/−-Tg) mice showed a smaller mass and cell size of white adipose tissues than control (WT-Tg) mice. Abnormal lipid deposition, such as fatty liver, was not detected in the Hspg2−/−-Tg mice, and those mice also consumed more fat as an energy source, likely due to their activated fatty acid oxidation. In addition, the Hspg2−/−-Tg mice demonstrated increased insulin sensitivity. Molecular analysis revealed the significantly relatively increased amount of the muscle fiber type IIA (X) isoform and a larger quantity of mitochondria in the skeletal muscle of Hspg2−/−-Tg mice. Furthermore, the perlecan-deficient skeletal muscle also had elevated levels of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α) protein. PGC1α expression is activated by exercise, and induces mitochondrial biosynthesis. Thus, perlecan may act as a mechano-regulator of catabolism of both lipids and glucose by shifting the muscle fiber composition to oxidative fibers. Our data suggest that downregulation of perlecan is a promising strategy to control metabolic syndrome.
Strain induced electronic structure variation in methyl-ammonium lead iodide perovskite
Authors: Zhang Le , Geng Wei , Tong Chuan-jia , Chen Xueguang , Cao Tengfei , Chen Mingyang 
Published: May 2018

AbstractMethyl-ammonium lead iodide perovskite (CH3NH3PbI3) has drawn great attention due to its excellent photovoltaic properties. Because of its loosely compacted structure, the structural, electronic and optical properties of CH3NH3PbI3 are sensitive to external modulations. Strain effects on CH3NH3PbI3 are fully investigated by the first principles calculations. The results indicate that the inorganic framework deforms under compression or stretch and the embedded organic CH3NH3+ molecules rotate correspondingly. A band gap oscillation and a new structural phase in response to the external strain were observed for the first time. These phenomena are explained with the nonlinear structural deformation and phase transition under the external strains. The semi-quantitative relationship between the band gap variation and geometry change under the external strain is obtained. We found that the shift of valence band maximum under the external strain is mostly determined by the most stretched or compressed Pb-I bond of CH3NH3PbI3, and the shift of the conduction band minimum under the external strain is likely to be determined by the largest Pb-I-Pb bond angle in the system. These results are important for understanding of strain effects on semiconductors and guiding the experiments to improve the performance of the perovskite solar cells.
Coherent control schemes for the photoionization of neon and helium in the Extreme Ultraviolet spectral region
Authors: Giannessi Luca , Allaria Enrico , Prince Kevin C. , Callegari Carlo , Sansone Giuseppe , Ueda Kiyoshi , Morishita Toru , Liu Chien Nan , Grum-Grzhimailo Alexei N. , Gryzlova Elena V. , Douguet Nicolas , Bartschat Klaus 
Published: May 2018

AbstractThe seeded Free-Electron Laser (FEL) FERMI is the first source of short-wavelength light possessing the full coherence of optical lasers, together with the extreme power available from FELs. FERMI provides longitudinally coherent radiation in the Extreme Ultraviolet and soft x-ray spectral regions, and therefore opens up wide new fields of investigation in physics. We first propose experiments exploiting this property to provide coherent control of the photoionization of neon and helium, carry out numerical calculations to find optimum experimental parameters, and then describe how these experiments may be realized. The approach uses bichromatic illumination of a target and measurement of the products of the interaction, analogous to previous Brumer-Shapiro-type experiments in the optical spectral range. We describe operational schemes for the FERMI FEL, and simulate the conditions necessary to produce light at the fundamental and second or third harmonic frequencies, and to control the phase with respect to the fundamental. We conclude that a quantitative description of the phenomena is extremely challenging for present state-of-the-art theoretical and computational methods, and further development is necessary. Furthermore, the intensity available may already be excessive for the experiments proposed on helium. Perspectives for further development are discussed.
Risk factors associated with HTLV-1 vertical transmission in Brazil: longer breastfeeding, higher maternal proviral load and previous HTLV-1-infected offspring
Authors: Paiva Arthur M. , Assone Tatiane , Haziot Michel E. J. , Smid Jerusa , Fonseca Luiz Augusto M. , Luiz Olinda do Carmo , de Oliveira Augusto Cesar Penalva , Casseb Jorge 
Published: May 2018

AbstractHTLV-1 is transmitted primarily either through sexual intercourse or from mother to child. The mother/child pairs were classified as seroconcordant or serodiscordant. We analyzed mother to child transmission (MTCT) according to sociodemographic, clinical and epidemiological characteristics of the mother, child’s gender and duration of breastfeeding. Between June 2006 and August 2016 we followed 192 mothers with HTLV-1 infection (mean age 41 years old), resulting in 499 exposed offspring, 288 (57.7%) of whom were tested for HTLV-1, making up the final sample for the study, along with their 134 respective mothers. Among the tested mother/child pairs, 41 (14.2%) were HTLV-1 positive, highlighted that seven of 134 family clusters concentrated 48.8% of positive cases. Variables associated with a positive child: breastfeeding duration ≥12 months, maternal PVL ≥100 copies/104 PBMC, mother’s age at delivery >26 years old, and HTLV-1 in more than one child of the same mother. In a multiple logistic regression, breastfeeding ≥12 months, higher maternal PVL and ≥2 previous HTLV-1-infected children remained independently associated with the outcome. Thus, high maternal PVL and breastfeeding beyond 12 months were independently associated with MTCT of the HTLV-1 infection. Our results reinforce the need for both prenatal HTLV screening in endemic areas and for advising mothers on breastfeeding.
Sequential immunizations with a panel of HIV-1 Env virus-like particles coach immune system to make broadly neutralizing antibodies
Authors: Mohan Teena , Berman Zachary , Kang Sang-Moo , Wang Bao-Zhong 
Published: May 2018

AbstractBroadly neutralizing antibodies (bnAbs) are correlated with passive HIV/SHIV protection and are desirable components of a HIV protective immunity. In the current study, we have designed a sequential-immunization strategy with a panel of envelope glycoprotein (Env)-enriched virus-like particles (VLPs) from various HIV-1 clades (A-E) to elicit bnAbs with high breadth and potency of neutralization in rabbits. We have compared this regimen with repetitive immunizations of individual Env (subtype B) VLPs or a mixture of various Env VLPs. Our results demonstrate that the sequential immunization group of animals induced significantly higher IgG endpoint titers against respective HIV Env (autologous) antigen than other control groups. Animals vaccinated sequentially showed an increase in the antibody endpoint titers and IgG antibody secreting cells (ASCs) against Con-S Env protein. Sequential immunizations with various Env VLPs promoted antibody avidity indices and enhanced bnAb responses against a panel of HIV pseudotyped virions including some of the tier 3 pseudostrains. Sequential immunizations with various VLPs displaying “native-like” HIV-1 Envs elicited bnAb responses with increased breadth and potency of neutralization.
Comparison of conventional sonographic signs and magnetic resonance imaging proton density fat fraction for assessment of hepatic steatosis
Authors: Kim Mimi , Kang Bo-Kyeong , Jun Dae Won 
Published: May 2018

AbstractThis study correlated conventional ultrasonography (US) signs with the magnetic resonance imaging (MRI) proton density fat fraction (PDFF) to evaluate the diagnostic performance of US signs (alone or combined) to predict presence and degree of hepatic steatosis (HS). Overall, 182 subjects met the study inclusion criteria between February 2014 and October 2016. Four US signs were evaluated independently by two radiologists. MRI PDFF was defined as the average of 24 non-overlapping regions of interest (ROIs) within eight liver segments obtained by drawing three ROIs within each segment. The latter acted as the reference standard to evaluate diagnostic accuracy of the US signs and their combinations. Diagnostic performance of US for HS was assessed using receiver operating characteristic (ROC) curve analyses. There was a strongly positive correlation between some combinations of US signs and PDFF (σ = 0.780, p < 0.001). The sensitivity, specificity, PPV, and NPV were 96.6%, 74.8%, 64.8%, and 97.9%, respectively, determined using abnormal hepatorenal echoes to detect grade 1 or higher HS (area under the ROC curve = 0.875). The sensitivity and NPV for detecting HS with US were good and US may be considered a suitable screening tool for exclusion of HS.
Genetic diversity of PRRSV 1 in Central Eastern Europe in 1994–2014: origin and evolution of the virus in the region
Authors: Balka Gyula , Podgórska Katarzyna , Brar Manreetpal Singh , Bálint Ádám , Cadar Daniel , Celer Vladimir , Dénes Lilla , Dirbakova Zuzana , Jedryczko Anna , Márton Lázár , Novosel Dinko , Petrović Tamaš , Sirakov Ivo , Szalay Dóra , Toplak Ivan , Leung Frederick Chi-Ching , Stadejek Tomasz 
Published: May 2018

AbstractMore than 20 years after the first outbreaks, the phylogenetic picture of PRRSV is still incomplete and full of gaps, especially in regards of PRRSV 1. Due to the exceptional diversity observed at the eastern borders of Europe and the low number of available sequences from Central Eastern European countries, the authors collected and analyzed both recent as well as already submitted sequences comparing them to a large backbone set of available ORF5 sequences representing the full spectrum of PRRSV 1 Subtype 1 diversity to conduct a systematic phylogenetic analysis and reclassification elucidating the diversity of the virus in these countries. Moreover, further analyses of the EUROSTAT data regarding the live pig movement trends revealed their influence of virus diversity and evolution. The results indicate that besides the effect of local, isolated divergent evolution and the use of modified live vaccines, the most important factor influencing a given country’s virus diversity is the transboundary movement of live, infected animals.
Non-predictive online spatial coding in the posterior parietal cortex when aiming ahead for catching
Authors: Reid Sinéad A. , Dessing Joost C. 
Published: May 2018

AbstractCatching movements must be aimed ahead of the moving ball, which may require predictions of when and where to catch. Here, using repetitive Transcranial Magnetic Stimulation we show for the first time that the Superior Parietal Occipital Cortex (SPOC) displays non-predictive online spatial coding at the moment the interception movements were already aimed at the predicted final target position. The ability to aim ahead for catching must thus arise downstream within the parietofrontal network for reaching.
Transcriptome and miRNA analyses of the response to Corynespora cassiicola in cucumber
Authors: Wang Xiangyu , Zhang Di , Cui Na , Yu Yang , Yu Guangchao , Fan Haiyan 
Published: May 2018

AbstractCucumber (Cucumis sativus L.) target leaf spot (TLS), which is caused by the fungus Corynespora cassiicola (C. cassiicola), seriously endangers the production of cucumber. In this assay, we performed comprehensive sequencing of the transcriptome and microRNAs (miRNAs) of a resistant cucumber (Jinyou 38) during C. cassiicola inoculation using the Illumina NextSeq 500 platform. The possible genes related to the response to C. cassiicola were associated with plant hormones, transcription factors, primary metabolism, Ca2+ signaling pathways, secondary metabolism and defense genes. In total, 150 target genes of these differentially expressed miRNAs were predicted by the bioinformatic analysis. By analyzing the function of the target genes, several candidate miRNAs that may be related to the response to C. cassiicola stress were selected. We also predicted 7 novel miRNAs and predicted their target genes. Moreover, the expression patterns of the candidate genes and miRNAs were tested by quantitative real-time RT-PCR. According to the analysis, genes and miRNAs associated with secondary metabolism, particularly the phenylpropanoid biosynthesis pathway, may play a major role in the resistance to C. cassiicola stress in cucumber. These results offer a foundation for future studies exploring the mechanism and key genes of resistance to cucumber TLS.
Computational identification of specific genes for glioblastoma stem-like cells identity
Authors: Fiscon Giulia , Conte Federica , Licursi Valerio , Nasi Sergio , Paci Paola 
Published: May 2018

AbstractGlioblastoma, the most malignant brain cancer, contains self-renewing, stem-like cells that sustain tumor growth and therapeutic resistance. Identifying genes promoting stem-like cell differentiation might unveil targets for novel treatments. To detect them, here we apply SWIM – a software able to unveil genes (named switch genes) involved in drastic changes of cell phenotype – to public datasets of gene expression profiles from human glioblastoma cells. By analyzing matched pairs of stem-like and differentiated glioblastoma cells, SWIM identified 336 switch genes, potentially involved in the transition from stem-like to differentiated state. A subset of them was significantly related to focal adhesion and extracellular matrix and strongly down-regulated in stem-like cells, suggesting that they may promote differentiation and restrain tumor growth. Their expression in differentiated cells strongly correlated with the down-regulation of transcription factors like OLIG2, POU3F2, SALL2, SOX2, capable of reprogramming differentiated glioblastoma cells into stem-like cells. These findings were corroborated by the analysis of expression profiles from glioblastoma stem-like cell lines, the corresponding primary tumors, and conventional glioma cell lines. Switch genes represent a distinguishing feature of stem-like cells and we are persuaded that they may reveal novel potential therapeutic targets worthy of further investigation.
Coexistence of Nerve Enlargement and Neuratrophy Detected by Ultrasonography in Leprosy Patients
Authors: Chen Xiaohua , Zhang Liangfu , Huang Meiying , Zhai Xiuli , Wen Yan , Pan Chunzhi 
Published: May 2018

AbstractThe purpose of this study was to evaluate peripheral neural impairment in leprosy patients by ultrasonography (US). The cross-sectional areas (CSAs) of the median (M), ulnar (U) and common fibular (CF) nerves were compared in 71 leprosy patients and 29 healthy controls, and the data were analyzed between the leprosy, multibacillary (MB)/paucibacillary (PB), reaction (R)/no reaction (NR), disability (D)/no disability (ND), and longer/shorter duration groups after treatment. We found that for the nerves located in upper limbs, the CSAs were significantly increased in the leprosy patients vs the controls; the PB group vs the MB group; the R group vs the NR group; the ND group vs the D group; and the longer duration group vs the shorter duration group at some positions of the M nerve and U nerve. In contrast, for the nerves located in lower limbs, the CSAs were significantly reduced in the leprosy patients vs the controls and in the longer duration group vs the shorter duration group at some positions of the CF nerve. This result indicated that nerve enlargement and neuratrophy coexist in leprosy patients.