bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the genetic variants associated with circulating levels of sgp130. Results from the IMPROVE study
Authors:   on behalf of the IMPROVE study group, Bonomi Alice , Veglia Fabrizio , Baldassarre Damiano , Strawbridge Rona J. , Golabkesh Zahra , Sennblad Bengt , Leander Karin , Smit Andries J. , Giral Philippe , Humphries Steve E. , Tremoli Elena , Hamsten Anders , de Faire Ulf , Gigante Bruna 
Published: January 2020

AbstractThe genes regulating circulating levels of soluble gp130 (sgp130), the antagonist of the inflammatory response in atherosclerosis driven by interleukin 6, are largely unknown. Aims of the present study were to identify genetic loci associated with circulating sgp130 and to explore the potential association between variants associated with sgp130 and markers of subclinical atherosclerosis. The study is based on IMPROVE (n = 3703), a cardiovascular multicentre study designed to investigate the determinants of carotid intima media thickness, a measure of subclinical atherosclerosis. Genomic DNA was genotyped by the CardioMetaboChip and ImmunoChip. About 360,842 SNPs were tested for association with log-transformed sgp130, using linear regression adjusted for age, gender, and population stratification using PLINK v1.07. A p value of 1 × 10−5 was chosen as threshold for significance value. In an exploratory analysis, SNPs associated with sgp130 were tested for association with c-IMT measures. We identified two SNPs significantly associated with sgp130 levels and 24 showing suggestive association with sgp130 levels. One SNP (rs17688225) on chromosome 14 was positively associated with sgp130 serum levels (β = 0.03 SE = 0.007, p = 4.77 × 10−5) and inversely associated with c-IMT (c-IMTmean–maxβ = −0.001 SE = 0.005, p = 0.0342). Our data indicate that multiple loci regulate sgp130 levels and suggest a possible common pathway between sgp130 and c-IMT measures.
Dynamic MAIT cell response with progressively enhanced innateness during acute HIV-1 infection
Authors: Lal Kerri G. , Kim Dohoon , Costanzo Margaret C. , Creegan Matthew , Leeansyah Edwin , Dias Joana , Paquin-Proulx Dominic , Eller Leigh Anne , Schuetz Alexandra , Phuang-ngern Yuwadee , Krebs Shelly J. , Slike Bonnie M. , Kibuuka Hannah , Maganga Lucas , Nitayaphan Sorachai , Kosgei Josphat , Sacdalan Carlo , Ananworanich Jintanat , Bolton Diane L. , Michael Nelson L. , Shacklett Barbara L. , Robb Merlin L. , Eller Michael A. , Sandberg Johan K. 
Published: January 2020

AbstractMucosa-associated invariant T (MAIT) cell loss in chronic HIV-1 infection is a significant insult to antimicrobial immune defenses. Here we investigate the response of MAIT cells during acute HIV-1 infection utilizing the RV217 cohort with paired longitudinal pre- and post-infection samples. MAIT cells are activated and expand in blood and mucosa coincident with peak HIV-1 viremia, in a manner associated with emerging microbial translocation. This is followed by a phase with elevated function as viral replication is controlled to a set-point level, and later by their functional decline at the onset of chronic infection. Interestingly, enhanced innate-like pathways and characteristics develop progressively in MAIT cells during infection, in parallel with TCR repertoire alterations. These findings delineate the dynamic MAIT cell response to acute HIV-1 infection, and show how the MAIT compartment initially responds and expands with enhanced function, followed by progressive reprogramming away from TCR-dependent antibacterial responses towards innate-like functionality.
Heuristic recurrent algorithms for photonic Ising machines
Authors: Roques-Carmes Charles , Shen Yichen , Zanoci Cristian , Prabhu Mihika , Atieh Fadi , Jing Li , Dubček Tena , Mao Chenkai , Johnson Miles R. , Čeperić Vladimir , Joannopoulos John D. , Englund Dirk , Soljačić Marin 
Published: January 2020

AbstractThe inability of conventional electronic architectures to efficiently solve large combinatorial problems motivates the development of novel computational hardware. There has been much effort toward developing application-specific hardware across many different fields of engineering, such as integrated circuits, memristors, and photonics. However, unleashing the potential of such architectures requires the development of algorithms which optimally exploit their fundamental properties. Here, we present the Photonic Recurrent Ising Sampler (PRIS), a heuristic method tailored for parallel architectures allowing fast and efficient sampling from distributions of arbitrary Ising problems. Since the PRIS relies on vector-to-fixed matrix multiplications, we suggest the implementation of the PRIS in photonic parallel networks, which realize these operations at an unprecedented speed. The PRIS provides sample solutions to the ground state of Ising models, by converging in probability to their associated Gibbs distribution. The PRIS also relies on intrinsic dynamic noise and eigenvalue dropout to find ground states more efficiently. Our work suggests speedups in heuristic methods via photonic implementations of the PRIS.
Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis
Authors: Schafflick David , Xu Chenling A. , Hartlehnert Maike , Cole Michael , Schulte-Mecklenbeck Andreas , Lautwein Tobias , Wolbert Jolien , Heming Michael , Meuth Sven G. , Kuhlmann Tanja , Gross Catharina C. , Wiendl Heinz , Yosef Nir , Meyer zu Horste Gerd 
Published: January 2020

AbstractCerebrospinal fluid (CSF) protects the central nervous system (CNS) and analyzing CSF aids the diagnosis of CNS diseases, but our understanding of CSF leukocytes remains superficial. Here, using single cell transcriptomics, we identify a specific location-associated composition and transcriptome of CSF leukocytes. Multiple sclerosis (MS) – an autoimmune disease of the CNS – increases transcriptional diversity in blood, but increases cell type diversity in CSF including a higher abundance of cytotoxic phenotype T helper cells. An analytical approach, named cell set enrichment analysis (CSEA) identifies a cluster-independent increase of follicular (TFH) cells potentially driving the known expansion of B lineage cells in the CSF in MS. In mice, TFH cells accordingly promote B cell infiltration into the CNS and the severity of MS animal models. Immune mechanisms in MS are thus highly compartmentalized and indicate ongoing local T/B cell interaction.
Synaptic density marker SV2A is reduced in schizophrenia patients and unaffected by antipsychotics in rats
Authors: Onwordi Ellis Chika , Halff Els F. , Whitehurst Thomas , Mansur Ayla , Cotel Marie-Caroline , Wells Lisa , Creeney Hannah , Bonsall David , Rogdaki Maria , Shatalina Ekaterina , Reis Marques Tiago , Rabiner Eugenii A. , Gunn Roger N. , Natesan Sridhar , Vernon Anthony C. , Howes Oliver D. 
Published: January 2020

AbstractSynaptic dysfunction is hypothesised to play a key role in schizophrenia pathogenesis, but this has not been tested directly in vivo. Here, we investigated synaptic vesicle glycoprotein 2A (SV2A) levels and their relationship to symptoms and structural brain measures using [11C]UCB-J positron emission tomography in 18 patients with schizophrenia and 18 controls. We found significant group and group-by-region interaction effects on volume of distribution (VT). [11C]UCB-JVTwas significantly lower in the frontal and anterior cingulate cortices in schizophrenia with large effect sizes (Cohen’sd = 0.8-0.9), but there was no significant difference in the hippocampus. We also investigated the effects of antipsychotic drug administration on SV2A levels in Sprague-Dawley rats using western blotting, [3H]UCB-J autoradiography and immunostaining with confocal microscopy, finding no significant effects on any measure. These findings indicate that there are lower synaptic terminal protein levels in schizophrenia in vivo and that antipsychotic drug exposure is unlikely to account for them.
Haspin-dependent and independent effects of the kinase inhibitor 5-Iodotubercidin on self-renewal and differentiation
Authors: Karanika Eleftheria , Soupsana Katerina , Christogianni Anastasia , Stellas Dimitris , Klinakis Apostolos , Politou Anastasia S. , Georgatos Spyros 
Published: January 2020

AbstractThe kinase Haspin phosphorylates histone H3 at threonine-3 (H3T3ph), creating a docking site for the Chromosomal Passenger Complex (CPC). CPC plays a pivotal role in preventing chromosome misalignment. Here, we have examined the effects of 5-Iodotubercidin (5-ITu), a commonly used Haspin inhibitor, on self-renewal and differentiation of mouse embryonic stem cells (ESCs). Treatment with low concentrations of 5-ITu eliminates the H3T3ph mark during mitosis, but does not affect the mode or the outcome of self-renewal divisions. Interestingly, 5-ITu causes sustained accumulation of p53, increases markedly the expression of histone genes and results in reversible upregulation of the pluripotency factor Klf4. However, the properties of 5-ITu treated cells are distinct from those observed in Haspin-knockout cells generated by CRISPR/Cas9 genome editing, suggesting “off-target” effects. Continuous exposure to 5-ITu allows modest expansion of the ESC population and growth of embryoid bodies, but release from the drug after an initial treatment aborts embryoid body or teratoma formation. The data reveal an unusual robustness of ESCs against mitotic perturbants and suggest that the lack of H3T3ph and the “off-target” effects of 5-ITu can be partially compensated by changes in expression program or accumulation of suppressor mutations.
Challenges in reporting pathogenic/potentially pathogenic variants in 94 cancer predisposing genes - in pediatric patients screened with NGS panels
Authors: Chirita-Emandi Adela , Andreescu Nicoleta , Zimbru Cristian G. , Tutac Paul , Arghirescu Smaranda , Serban Margit , Puiu Maria 
Published: January 2020

AbstractThe benefit of reporting unsolicited findings in Next Generation Sequencing (NGS) related to cancer genes in children may have implications for family members, nevertheless, could also cause distress. We aimed to retrospectively investigate germline variants in 94 genes implicated in oncogenesis, in patients referred to NGS testing for various rare genetic diseases and reevaluate the utility of reporting different classes of pathogenicity. We used in silico prediction software to classify variants and conducted manual review to examine unsolicited findings frequencies in 145 children with rare diseases, that underwent sequencing - using a 4813 gene panel. The anonymized reanalysis revealed 18250 variants, of which 126 were considered after filtering. Six pathogenic variants (in BRCA1,BMPR1A,FANCA,FANCC,NBN genes) with cancer related phenotype and three unsolicited variants (in BRCA2,PALB2,RAD50 genes) were reported to patients. Additionally, three unsolicited variants in ATR, BLM (in two individuals), and FANCB genes presented potential cancer susceptibility, were not reported to patients. In retrospect, 4.8% (7/145) of individuals in our cohort had unsolicited NGS findings related to cancer. More efforts are needed to create an updatable consensus in reporting variants in cancer predisposing genes, especially for children. Consent process is crucial to inform of both value and risk of additional genetic information.
Sublethal and transgenerational effects of dinotefuran on biological parameters and behavioural traits of the mirid bug Apolygus lucorum
Authors: Lu Zengbin , Dong Song , Li Chao , Li Lili , Yu Yi , Men Xingyuan , Yin Shuyan 
Published: January 2020

AbstractThe mirid bug, Apolygus lucorum, has become a major pest of many crops and fruit trees since the widespread adoption of Bt cotton in northern China. Neonicotinoid insecticides, such as dinotefuran, applied to control this pest may show sublethal effects, but evidence for such effects is lacking. Here, we investigated the sublethal and transgenerational effects of dinotefuran on biological parameters and feeding behavioural traits of A. lucorum using the age-stage, two-sex life table and electrical penetration graphs (EPGs), respectively. The LC10 and LC30 of dinotefuran against 3rd-instar nymphs of A. lucorum were 14.72 and 62.95 mg L−1, respectively. These two concentrations significantly extended the development duration from 3rd-instar nymph to adult in parent generation (F0). LC30 also increased the oviposition period and male adult longevity and reduced nymphal survival rate in the F0. For offspring generation (F1), the egg duration, preadult duration, and total preoviposition period were significantly lower at LC10 than in the control, and the egg duration, duration of 4th-instar nymphs, preadult duration, oviposition period, and fecundity were also decreased at LC30. However, the four demographic parameters of F1 generation, namely, net reproductive rate (R0), intrinsic rate of increase (r), finite rate of increase (λ), and mean generation time (T), were not affected by dinotefuran. The significant differences in the number of probes and duration of each of four feeding waveforms failed to be detected when A. lucorum nymphs treated by dinotefuran feed on Bt cotton plants without insecticide exposure. Overall, the dinotefuran concentrations tested here have sublethal, but no transgenerational impacts on A. lucorum.
Biopolymers as a sustainable solution for the enhancement of soil mechanical properties
Authors: Soldo Antonio , Miletić Marta , Auad Maria L. 
Published: January 2020

AbstractImproving soil engineering properties is an inevitable process before construction on soft soil. Increasing soil strength with chemical stabilizing agents, such as cement, raises environmental concerns. Therefore, sustainable solutions are in high demand. One of the promising solutions is the usage of biopolymers. Five biopolymer types were investigated in this study: Xanthan Gum, Beta 1,3/1,6 Glucan, Guar Gum, Chitosan, and Alginate. Their effect on the soil strength improvement was experimentally investigated by performing unconfined compression, splitting tensile, triaxial, and direct shear tests. All tests were performed with different biopolymer concentrations and curing periods. Additionally, in order to have an insight on the susceptibility to natural elements, plain soil, and biopolymer-treated specimens were exposed to real atmospheric conditions. The extensive experimental results showed that the soil strength tends to increase with the increase of biopolymer concentration and with the curing time. However, it was shown that the soil strength does not considerably change after a certain biopolymer concentration level and curing time. Furthermore, it has been observed that the biopolymer-treated specimens showed better resistance to the influence of the environmental conditions. In general, Xanthan Gum, Guar Gum, and Beta 1,3/1,6 Glucan showed the most dominant effect and potential for the future of sustainable engineering.
The clock gene Gigantea 1 from Petunia hybrida coordinates vegetative growth and inflorescence architecture
Authors: Brandoli Claudio , Petri César , Egea-Cortines Marcos , Weiss Julia 
Published: January 2020

AbstractThe gene GIGANTEA (GI) appeared early in land plants. It is a single copy gene in most plants and is found in two to three copies in Solanaceae. We analyzed the silencing of one GI copy, Petunia hybrida GI1 (PhGI1), by hairpin RNAs in Petunia in order to gain knowledge about its range of functions. Decreased transcript levels of PhGI1 were accompanied also by a reduction of PhGI2. They were further associated with increased time period between two consecutive peaks for PhGI1 and CHANEL (PhCHL), the orthologue of the blue light receptor gene ZEITLUPE (ZTL), confirming its role in maintaining circadian rhythmicity. Silenced plants were bigger with modified internode length and increased leaf size while flowering time was not altered. We uncovered a new function for PhGI1 as silenced plants showed reduction of flower bud number and the appearance of two flower buds in the bifurcation point, were normally one flower bud and the inflorescence meristem separate. Furthermore, one of the flower buds consistently showed premature flower abortion. Flowers that developed fully were significantly smaller as a result of decreased cell size. Even so the circadian pattern of volatile emission was unchanged in the silenced lines, flowers emitted 20% less volatiles on fresh weight basis over 24 hours and showed changes in the scent profile. Our results indicate a novel role of PhGI1 in the development of reproductive organs in Petunia. PhGI1 therefore represses growth in vegetative plant parts, maintains the typical cymose inflorescence structure, and inhibits premature flower abortion.
Observations of the warm-tongue circulation in the northern East China Sea
Authors: Lee Hojun , Lee Kyungjae , Nam SungHyun , Lee Jae-Hak 
Published: January 2020

AbstractA subsurface thermohaline front semi-permanently formed in association with near-bottom cyclonic circulation in the northern East China Sea was newly found from detailed hydrographic data collected during two cruises in February 2017 (winter) and April 2018 (spring) along with supplementary satellite remote sensing and historical hydrographic data. An alternate intruding frontal structure in water properties was observed across the cyclonic circulation in both seasons as formed by two contrasting water masses—low-temperature and low-salinity (i.e., low spiciness) water transported by the East China Sea Current and high-temperature and high-salinity (i.e., high spiciness) water transported by the Tsushima Warm Current. Consistent structures were confirmed from current observations during the two cruises, historical hydrographic observations, and satellite altimetry-derived sea surface height and surface frontal structure, indicative of retroflection of the Cheju Warm Current as deemed by the seasonal development of thermal stratification in spring. Our results reveal significant heat and material exchanges between the open Pacific and the broad shelf, particularly via diapycnal mixing and cross-front transports associated with across-front flow and cyclonic circulation, in the northern East China Sea.
Cysteine-silver-gold Nanocomposite as potential stable green corrosion inhibitor for mild steel under acidic condition
Authors: Basik Megha , Mobin Mohammad , Shoeb Mohd 
Published: January 2020

AbstractCysteine based silver-gold nanocomposite (Cys/Ag-Au NCz) was synthesized, this was followed by its characterization using Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Ultraviolet-visible spectroscopy (UV-Vis), Scanning electron microscopy (SEM), Energy-dispersive X-ray spectroscopy (EDAX), Thermogravimetric analysis (TGA) and Transmission electron microscopy (TEM). Cys/Ag-Au NCz was studied as novel green corrosion inhibitor for mild steel in 1M HCl solution at varying concentration and temperature using gravimetric, Potentiodynamic polarization (PDP), Electrochemical impedance spectroscopy (EIS), SEM, EDAX and FTIR. Weight loss, PDP and EIS studies confirmed Cys/Ag-Au NCz as efficient corrosion inhibitor at moderately low concentration. The maximum inhibition efficiency of 96 % was observed at 303 K at 300 ppm. Cys/Ag-Au NCz acted by affecting both anodic and cathodic processes and its adsorption on steel surface followed the Langmuir adsorption isotherm. EIS data displayed the existence of protective film at mild steel/solution interface in Cys/Ag-Au NCz inhibited system. SEM micrograph in presence of Cys/Ag-Au NCz inhibited acid solution displayed better morphology as compared to blank solution. The UV-Vis and FTIR data indicates good interaction between the Cys/Ag-Au NCz and steel surface.
Color and genesis of californite from Pakistan: insights from μ-XRF mapping, optical spectra and X-ray photoelectron spectroscopy
Authors: Lu Zhiyun , He Xuemei , Lin Chenlu , Liang Lin , Jin Xinyu , Guo Qingfeng 
Published: January 2020

AbstractFour californite samples from Pakistan with yellowish-green, green and reddish-brown colors were investigated by combining the methods of μ-XRF mapping, XRD, Raman spectra, optical spectra, EPMA and XPS. The results show that the californite is composed mainly of microcrystalline vesuvianite and smaller amounts of clinochlore. Based on the distribution of the clinochlore, the californite can be divided into three types. The gem-quality californite is composed of microcrystalline vesuvianite and has a translucent appearance. The ordinary-quality californite contains microcrystalline vesuvianite as well as clinochlore, and it has an opaque appearance. The transitional-type has properties that are intermediate between those of gem- and ordinary-quality californite. Octahedrally coordinated iron and chromium in the clinochlore reduce the transparency and contribute to the opaque green and yellowish-green colors of the californite. At sites where there is no clinochlore, Cr3+ in the octahedrally coordinated site Y3 of the vesuvianite is mainly responsible for the green tone of the californite, Fe3+ and Mn3+ at the Y3 site contribute mainly to the yellowish-green and reddish-brown colors, respectively. The Fe2+ → Fe3+ charge transfer also occurs in vesuvianite and partly influences the appearance of the californite. The actual color of californite that lacks clinochlore is due to the synergy of Cr3+, Fe3+ and Mn3+ crystal field transfers at the octahedral site Y3 as well as the Fe2+ → Fe3+ charge transfer in the vesuvianite. Vesuvianite in the californite can be assigned to the P4/n space group, and the occurrence of clinochlore reflects the fact that the californite from Pakistan formed under medium-grade metamorphic conditions at temperatures of ~300–500 °C. The content of clinochlore provides a basis for grading the quality of the californite.
Endoplasmic reticulum-derived bodies enable a single-cell chemical defense in Brassicaceae plants
Authors: Yamada Kenji , Goto-Yamada Shino , Nakazaki Akiko , Kunieda Tadashi , Kuwata Keiko , Nagano Atsushi J. , Nishimura Mikio , Hara-Nishimura Ikuko 
Published: January 2020

AbstractBrassicaceae plants have a dual-cell type of chemical defense against herbivory. Here, we show a novel single-cell defense involving endoplasmic reticulum (ER)-derived organelles (ER bodies) and the vacuoles. We identify various glucosinolates as endogenous substrates of the ER-body β-glucosidases BGLU23 and BGLU21. Woodlice strongly prefer to eat seedlings of bglu23 bglu21 or a glucosinolate-deficient mutant over wild-type seedlings, confirming that the β-glucosidases have a role in chemical defense: production of toxic compounds upon organellar damage. Deficiency of the Brassicaceae-specific protein NAI2 prevents ER-body formation, which results in a loss of BGLU23 and a loss of resistance to woodlice. Hence, NAI2 that interacts with BGLU23 is essential for sequestering BGLU23 in ER bodies and preventing its degradation. Artificial expression of NAI2 and BGLU23 in non-Brassicaceae plants results in the formation of ER bodies, indicating that acquisition of NAI2 by Brassicaceae plants is a key step in developing their single-cell defense system.