bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and genetic characterization of a novel Orthobunyavirus species by a straightforward high-throughput sequencing-based approach
Authors: Shifman Ohad , Cohen-Gihon Inbar , Beth-Din Adi , Zvi Anat , Laskar Orly , Paran Nir , Epstein Eyal , Stein Dana , Dorozko Marina , Wolf Dana , Yitzhaki Shmuel , Shapira Shmuel C. , Melamed Sharon , Israeli Ofir 
Published: March 2019

AbstractIdentification and characterization of novel unknown viruses is of great importance. The introduction of high-throughput sequencing (HTS)-based methods has paved the way for genomics-based detection of pathogens without any prior assumptions about the characteristics of the organisms. However, the use of HTS for the characterization of viral pathogens from clinical samples remains limited. Here, we report the identification of a novel Orthobunyavirus species isolated from horse plasma. The identification was based on a straightforward HTS approach. Following enrichment in cell culture, RNA was extracted from the growth medium and rapid library preparation, HTS and primary bioinformatic analyses were performed in less than 12 hours. Taxonomical profiling of the sequencing reads did not reveal sequence similarities to any known virus. Subsequent application of de novo assembly tools to the sequencing reads produced contigs, of which three showed some similarity to the L, M, and S segments of viruses belonging to the Orthobunyavirus genus. Further refinement of these contigs resulted in high-quality, full-length genomic sequences of the three genomic segments (L, M and S) of a novel Orthobunyavirus. Characterization of the genomic sequence, including the prediction of open reading frames and the inspection of consensus genomic termini and phylogenetic analysis, further confirmed that the novel virus is indeed a new species, which we named Ness Ziona virus.
Long-term exercise training improves memory in middle-aged men and modulates peripheral levels of BDNF and Cathepsin B
Authors: De la Rosa Adrián , Solana Elisabeth , Corpas Rubén , Bartrés-Faz David , Pallàs Mercè , Vina Jose , Sanfeliu Coral , Gomez-Cabrera Mari Carmen 
Published: March 2019

AbstractAging is accompanied by a decline in memory and other brain functions. Physical exercise may mitigate this decline through the modulation of factors participating in the crosstalk between skeletal muscle and the brain, such as neurotrophins and oxidative stress parameters. We aimed to determine whether long term exercise training (35 ± 15 years) promotes memory maintenance in middle-aged men, and to characterize the changes in neurotrophic factors and lipid oxidation markers in peripheral blood samples in both middle-aged and young men. The neuropsychological analysis showed significant improvements in memory through the Free and Cued Immediate Recall tests, in the middle-aged trained individuals when compared to the sedentary ones. We found a significant decrease in the resting serum BDNF and plasma Cathepsin B (CTSB) levels in the trained groups at both middle and young ages. BDNF and CTSB levels were inversely correlated with weekly hours of exercise. We also found a significant decrease in plasma malondialdehyde, an index of lipid peroxidation, in middle-aged and young trained subjects. The positive impact of long-term exercise training by delaying the onset of physiological memory loss and the associated neurotrophic and redox peripheral modulation, suggests the effectiveness of exercise as preventive strategy against age-related memory loss and neurodegeneration.
A bio-coupling approach using a dextran-binding domain to immobilize an engineered streptavidin to Sephadex for easy preparation of affinity matrix
Authors: Wu Sau-Ching , Wang Chris , Chin Jonathan , Wong Sui-Lam 
Published: March 2019

AbstractAn engineered streptavidin, SAVSBPM18 with reversible biotin binding capability, has been successfully applied to purify biotinylated and streptavidin-binding peptide (SBP) tagged proteins. To simplify the preparation for the SAVSBPM18 affinity matrix without chemical conjugation, two bio-coupling approaches were developed based on a 14-kDa dextran-binding domain (DBD) from a Leuconostoc mesenteroides dextransucrase. The first approach offers simplicity for bio-coupling by creating a direct fusion, SAVSBPM18-Linker-DBD. Purification of the fusion from crude extract and its immobilization to Sephadex can be consolidated in one-step. The second approach aims at flexibility. A SnoopCatcher (SC) was fused to DBD to create SC-Linker-DBD. This fusion can covalently capture any recombinant proteins tagged with a SnoopTag (ST) including SAVSBPM18-Linker-ST via the formation of an isopeptide bond at the interface through the SnoopCatcher-SnoopTag interaction. Although monomeric DBD binds to dextran with nanomolar affinity, DBD tetramerized via streptavidin (SAVSBPM18-Linker-ST·SC-Linker-DBD) showed an even tighter binding to Sephadex. The majority of the fluorescently labelled DBD tetramers were retained on the Sephadex surface even after four months. Affinity columns generated using either approach effectively purified both SBP-tagged and biotinylated proteins. These columns are reusable and functional even after a year of frequent use.
Hedgehog signaling in the airway epithelium of patients with chronic obstructive pulmonary disease
Authors: Tam A. , Hughes M. , McNagny K. M. , Obeidat M. , Hackett T. L. , Leung J. M. , Shaipanich T. , Dorscheid D. R. , Singhera G. K. , Yang C. W. T. , Paré P. D. , Hogg J. C. , Nickle D. , Sin D. D. 
Published: March 2019

AbstractGenome-wide association studies have linked gene variants of the receptor patched homolog 1 (PTCH1) with chronic obstructive pulmonary disease (COPD). However, its biological role in the disease is unclear. Our objective was to determine the expression pattern and biological role of PTCH1 in the lungs of patients with COPD. Airway epithelial-specific PTCH1 protein expression and epithelial morphology were assessed in lung tissues of control and COPD patients. PTCH1 mRNA expression was measured in bronchial epithelial cells obtained from individuals with and without COPD. The effects of PTCH1 siRNA knockdown on epithelial repair and mucous expression were evaluated using human epithelial cell lines. Ptch1+/− mice were used to assess the effect of decreased PTCH1 on mucous expression and airway epithelial phenotypes. Airway epithelial-specific PTCH1 protein expression was significantly increased in subjects with COPD compared to controls, and its expression was associated with total airway epithelial cell count and thickness. PTCH1 knockdown attenuated wound closure and mucous expression in airway epithelial cell lines. Ptch1+/− mice had reduced mucous expression compared to wildtype mice following mucous induction. PTCH1 protein is up-regulated in COPD airway epithelium and may upregulate mucous expression. PTCH1 provides a novel target to reduce chronic bronchitis in COPD patients.
Multivariate Optimization of Tenax TA-Thermal Extraction for Determining Gaseous Phase Organophosphate Esters in Air Samples
Authors: Matsiko Julius , Li Honghua , Wang Pu , Sun Huizhong , Zheng Shucheng , Wang Dou , Zhang Weiwei , Hao Yanfen , Zuo Peijie , Li Yingming , Zhang Qinghua , Zhang Jianqing , Jiang Guibin 
Published: March 2019

AbstractSuitable conditions for thermal extraction of semi-volatile organic compounds have largely been arrived at by univariate optimization or based on the recommendations provided by the manufacturers of the extraction equipment. Herein, we demonstrated the multivariate optimization of Tenax TA–thermal extraction for determining organophosphate esters in the gas phase fraction of air samples. Screening and refining experiments were performed using the eighth fraction factorial and Box-Behnken designs, respectively, and satisfactory models were obtained. Subsequently, the process was optimized by Derringer’s desirability function and the global desirability was 0.7299. Following optimization, the analytes were desorbed at 290 °C for 10 minutes at a helium flow of 95 mL min−1, with the transfer line set at 290 °C. The analytes were then cryofocused at 20 °C and then cryodesorbed into the chromatographic column at 295 °C for 6 minutes. Method validation exhibited high linearity coefficients (>0.99), good precision (CV < 14%) and low detection limits (0.1–0.5 ng m−3). The method was tested by pumping 0.024 m3 of real indoor environment air through Tenax TA sorbent tubes. Furthermore, with multivariate optimization, analysis time and other resources were significantly reduced, and information about experimental factor interaction effects was investigated, as compared to the univariate optimization and other traditional methods.
Density of bulk trap states of hybrid lead halide perovskite single crystals: temperature modulated space-charge-limited-currents
Authors: Pospisil Jan , Zmeskal Oldrich , Nespurek Stanislav , Krajcovic Jozef , Weiter Martin , Kovalenko Alexander 
Published: March 2019

AbstractTemperature-modulated space-charge-limited-current spectroscopy (TMSCLC) is applied to quantitatively evaluate the density of trap states in the band-gap with high energy resolution of semiconducting hybrid lead halide perovskite single crystals. Interestingly multicomponent deep trap states were observed in the pure perovskite crystals, which assumingly caused by the formation of nanodomains due to the presence of the mobile species in the perovskites.
In Vivo Flow Cytometry of Extremely Rare Circulating Cells
Authors: Tan Xuefei , Patil Roshani , Bartosik Peter , Runnels Judith M. , Lin Charles P. , Niedre Mark 
Published: March 2019

AbstractCirculating tumor cells (CTCs) are of great interest in cancer research, but methods for their enumeration remain far from optimal. We developed a new small animal research tool called “Diffuse in vivo Flow Cytometry” (DiFC) for detecting extremely rare fluorescently-labeled circulating cells directly in the bloodstream. The technique exploits near-infrared diffuse photons to detect and count cells flowing in large superficial arteries and veins without drawing blood samples. DiFC uses custom-designed, dual fiber optic probes that are placed in contact with the skin surface approximately above a major vascular bundle. In combination with a novel signal processing algorithm, DiFC allows counting of individual cells moving in arterial or venous directions, as well as measurement of their speed and depth. We show that DiFC allows sampling of the entire circulating blood volume of a mouse in under 10 minutes, while maintaining a false alarm rate of 0.014 per minute. In practice, this means that DiFC allows reliable detection of circulating cells below 1 cell per mL. Hence, the unique capabilities of DiFC are highly suited to biological applications involving very rare cell types such as the study of hematogenous cancer metastasis.
Evidence for the homogeneous ferromagnetic phase in (Ga,Mn)(Bi,As) epitaxial layers from muon spin relaxation spectroscopy
Authors: Levchenko K. , Prokscha T. , Sadowski J. , Radelytskyi I. , Jakiela R. , Trzyna M. , Andrearczyk T. , Figielski T. , Wosinski T. 
Published: March 2019

AbstractFerromagnetic semiconductor thin layers of the quaternary (Ga,Mn)(Bi,As) and reference, ternary (Ga,Mn)As compounds, epitaxially grown under either compressive or tensile strain, have been characterized from a perspective of structural and magnetization homogeneity. The quality and composition of the layers have been confirmed by secondary-ion mass spectrometry (SIMS). A thorough evaluation of the magnetic properties as a function of temperature and applied magnetic field has been performed by means of SQUID magnetometry and low-energy muon spin relaxation (µSR) spectroscopy, which enables studying local (on the nanometer scale) magnetic properties of the layers. The results testify that the ferromagnetic order builds up almost homogeneously below the Curie temperature in the full volume fraction of both the (Ga,Mn)As and (Ga,Mn)(Bi,As) layers. Incorporation of a small amount of heavy Bi atoms into (Ga,Mn)As, which distinctly enhances the strength of spin-orbit coupling in the quaternary (Ga,Mn)(Bi,As) layers, does not deteriorate noticeably their magnetic properties.
The changes of microbial community and flavor compound in the fermentation process of Chinese rice wine using Fagopyrum tataricum grain as feedstock
Authors: Ren Qing , Sun Leping , Wu Huijun , Wang Yousheng , Wang Zhiwei , Zheng Fuping , Lu Xin , Xu Jialiang 
Published: March 2019

AbstractChinese rice wine (CRW), a unique wine species, has a long history in China. Fagopyrum tataricum grain is a kind of high-quality grain with function in health care. The production of CRW wine with F. tataricum grain is beneficial to the development of new rice wine products. The flavor compounds and microorganisms in F. tataricum grain rice wine were studied. One hundred and seven volatile compounds (including 11 kinds of pyrazines that were rarely detected in wine) were detected and eight organic acids were measured. The microecological diversity in the fermentation process of F. tataricum rice wine was studied. It was found that Bacillus was the main bacterial genus, and the unclassfied_O_Saccharomycetales was the main fungi. Correlation analysis between microorganism and flavor compound shown there are 838 correlations. A total of 108 microbial genera maybe participate in the formation of flavor compounds. In addition, fourteen genera included unclassified_O_Saccharomycetales, Lactococcus, Pediococcus, Aspergillus, Cladosporium, Cochliobolus, Sporidiobolus, Pichia and Saccharomycopsis et al. were screened as functional significant microbiota and built correlation with flavor compounds. This work provides a perspective for bridging the gap between flavor compound and microbial community, and advances our understanding of mechanisms in F. tataricum rice wine fermentation.
Association between TP53 rs1042522 gene polymorphism and the risk of malignant bone tumors: a meta-analysis
Authors: Huang Xin , Wu Fashuai , Zhang Zhicai , Shao Zengwu 
Published: March 2019

Abstract
TP53 is a tumor suppressor gene which is essential for regulating cell division and preventing tumor formation. Several studies have assessed the associations of TP53 single-nucleotide polymorphisms (SNP) with susceptibility of malignant bone tumors, including osteosarcoma and Ewing sarcoma, but the results are inconsistent. In the present meta-analysis, we aimed to elucidate the associations of TP53 rs1042522 genetic polymorphism with the risk of osteosarcoma or Ewing sarcoma. We systematically searched Medline, PubMed, Web of Science, Embase, and the Cochrane Library databases. Eligible studies assessing the polymorphisms in the TP53 rs1042522 gene and risk of malignant bone tumors were incorporated. The pooled odds ratio (OR) with its 95% confidence intervals (95% CIs) were used to assess these possible associations. Five studies with a total of 567 cases and 935 controls were finally included the meta-analysis. Meta-analysis of TP53 rs1042522 polymorphism was significantly associated with an increased risk of malignant bone tumors (G versus C: OR = 1.27, 95% CI 1.08–1.50, P=0.005; GG versus GC/CC: OR = 1.55, 95% CI 1.21–2.00, P=0.001). Moreover, in a stratified analysis, a statistically significant correlation between this SNP and osteosarcoma risk was also observed. Our results suggest that there are significant associations of TP53 rs1042522 polymorphism with malignant bone tumors risk. More studies based on larger sample sizes and homogeneous samples are warranted to confirm these findings.
New view of the corona of classical T Tauri stars: Effects of flaring activity in circumstellar disks
Authors: Colombo S. , Orlando S. , Peres G. , Reale F. , Argiroffi C. , Bonito R. , Ibgui L. , Stehlé C. 
Published: March 2019

Context. Classical T Tauri stars (CTTSs) are young low-mass stellar objects that accrete mass from their circumstellar disks. They are characterized by high levels of coronal activity, as revealed by X-ray observations. This activity may affect the disk stability and the circumstellar environment.
Aims. Here we investigate if an intense coronal activity due to flares that occur close to the accretion disk may perturb the stability of the inner disk, disrupt the inner part of the disk, and might even trigger accretion phenomena with rates comparable with those observed.
Methods. We modeled a magnetized protostar surrounded by an accretion disk through 3D magnetohydrodinamic simulations. The model takes into account the gravity from the central star, the effects of viscosity in the disk, the thermal conduction (including the effects of heat flux saturation), the radiative losses from optically thin plasma, and a parameterized heating function to trigger the flares. We explored cases characterized by a dipole plus an octupole stellar magnetic field configuration and different density of the disk or by different levels of flaring activity.
Results. As a result of the simulated intense flaring activity, we observe the formation of several loops that link the star to the disk; all these loops build up a hot extended corona with an X-ray luminosity comparable with typical values observed in CTTSs. The intense flaring activity close to the disk can strongly perturb the disk stability. The flares trigger overpressure waves that travel through the disk and modify its configuration. Accretion funnels may be triggered by the flaring activity and thus contribute to the mass accretion rate of the star. Accretion rates synthesized from the simulations are in a range between 10−10 and 10−9 M⊙ yr−1. The accretion columns can be perturbed by the flares, and they can interact with each other; they might merge into larger streams. As a result, the accretion pattern can be rather complex: the streams are highly inhomogeneous, with a complex density structure, and clumped.
The shape of (7) Iris as evidence of an ancient large impact?
Authors: Hanuš J. , Marsset M. , Vernazza P. , Viikinkoski M. , Drouard A. , Brož M. , Carry B. , Fetick R. , Marchis F. , Jorda L. , Fusco T. , Birlan M. , Santana-Ros T. , Podlewska-Gaca E. , Jehin E. , Ferrais M. , Grice J. , Bartczak P. , Berthier J. , Castillo-Rogez J. , Cipriani F. , Colas F. , Dudziński G. , Dumas C. , Ďurech J. , Kaasalainen M. , Kryszczynska A. , Lamy P. , Le Coroller H. , Marciniak A. , Michalowski T. , Michel P. , Pajuelo M. , Tanga P. , Vachier F. , Vigan A. , Witasse O. , Yang B. 
Published: March 2019

Context. Asteroid (7) Iris is an ideal target for disk-resolved imaging owing to its brightness (V ~ 7–8) and large angular size of 0.33′′ during its apparitions. Iris is believed to belong to the category of large unfragmented asteroids that avoided internal differentiation, implying that its current shape and topography may record the first few 100 Myr of the solar system’s collisional evolution.
Aims. We recovered information about the shape and surface topography of Iris from disk-resolved VLT/SPHERE/ZIMPOL images acquired in the frame of our ESO large program.
Methods. We used the All-Data Asteroid Modeling (ADAM) shape reconstruction algorithm to model the 3D shape of Iris, using optical disk-integrated data and disk-resolved images from SPHERE and earlier AO systems as inputs. We analyzed the SPHERE images and our model to infer the asteroid’s global shape and the morphology of its main craters.
Results. We present the 3D shape, volume-equivalent diameter Deq = 214 ± 5 km, and bulk density ρ = 2.7 ± 0.3 g cm−3 of Iris. Its shape appears to be consistent with that of an oblate spheroid with a large equatorial excavation. We identified eight putative surface features 20–40 km in diameter detected at several epochs, which we interpret as impact craters, and several additional crater candidates. Craters on Iris have depth-to-diameter ratios that are similar to those of analogous 10 km craters on Vesta.
Conclusions. The bulk density of Iris is consistent with that of its meteoritic analog based on spectroscopic observations, namely LL ordinary chondrites. Considering the absence of a collisional family related to Iris and the number of large craters on its surface, we suggest that its equatorial depression may be the remnant of an ancient (at least 3 Gyr) impact. Iris’s shape further opens the possibility that large planetesimals formed as almost perfect oblate spheroids. Finally, we attribute the difference in crater morphology between Iris and Vesta to their different surface gravities, and the absence of a substantial impact-induced regolith on Iris.
Analysis of Inherited Optic Neuropathies
Authors: Lazdinyte Simona , Schorderet Daniel , Schaller André , Valmaggia Christophe , Todorova Margarita 
Published: March 2019

Abstract
Background Inherited optic neuropathies (IONs) cover a spectrum of clinically and genetically heterogenic conditions. Genetic evaluation of patients with IONs may enable their better clinico-diagnostic assessment and management of the disease. The aim of the present study was to determine the genetic condition related to the phenotype in patients with diverse inherited optic neuropathies.
Patients and Methods A retrospective study was performed in 12 adults and 8 children of 8 non-related families. Clinical phenotyping, supported by color fundus, FAF, and OCT imaging, was performed. Genetic testing was obtained for all family members suspected for ION.
Results Identification of pathogenic mutations in eight non-related families helped to confirm the diagnosis of ION. Affected from ION were ten patients (eight adults and two children; four women and six men). Bilateral Leberʼs hereditary optic neuropathy (LHON) was linked to the m.11778G>A mutation in two families (two affected and five carriers). Secondary homoplasmic LHON mutations in MT-ND1 (m.4216T>C) and MT-CO3 genes (m.9804G>A) were confirmed in two families (each one subject, three eyes affected), without detection of a primary LHON mutation. One member presented a picture of right-sited optic neuropathy associated with a c.220C>G mutation in the ACO2 gene and a heterozygous c.185C>T mutation in the LDLR gene. Autosomal dominant optic atrophy was confirmed in three non-related families (five subjects with bilateral ION), where molecular genetic analyses confirmed four different heterozygous mutations in OPA1: c.1847+1G>T; c.2497-1G>A, 297A>G and c.(2983+1_2984-1)_(c.*3211) (2 splicing mutations, 1 missense mutation, and 1 gross deletion encompassing exons 30 and 31).
Conclusions Combining clinics and molecular genetics when evaluating patients with IONs helps in characterizing disease and, therefore, is strongly recommended for such patients.
Herpes Simplex Infection During Pregnancy, Results of a Tertiary Referral Center in Turkey
Authors: Sert Umit Yasemin , Ozgu-Erdinc A. Seval , Saygan Sibel , Engin-Ustun Yaprak 
Published: March 2019

Abstract
Objective The present study aimed to determine herpes simplex virus (HSV) infection during pregnancy, serologic status of symptomatic patients, and the frequency of PCR and culture positivity and neonatal disease in an obstetric population.
Materials and methods Sera of 1,690 women with genital lesions were tested for HSV IgM and/or HSV IgG between 2008 and 2017. All the patients were evaluated by PCR and viral culture to demonstrate genital herpes infection.
Results The frequency of HSV IgG and IgM seropositivity was 73.8% (1245/1685) and 28.6% (484/1690). The number with a positive viral culture was 288, whereas positive PCR was 305. Five infants had localized skin lesions of HSV infection at the time of birth.
Conclusion This study shows the serologic status, viral culture and PCR testing results of pregnant women who had a symptomatic genital HSV infection and efficacy of management strategies to prevent neonatal herpes infection.