bluuebunny/crossref_metadata_2025_split huggingface dataset:
Masting and regeneration dynamics of Abies cephalonica, the Greek endemic silver fir
Authors: Daskalakou Evangelia N. , Koutsovoulou Katerina , Ioannidis Kostas , Koulelis Panagiotis P. , Ganatsas Petros , Thanos Costas A. 
Published: November 2019

AbstractMasting and regeneration dynamics were investigated in a long-term perspective using Abies cephalonica as a study tree species. Extensive fieldwork was implemented in Parnitha National Park, Greece, following a large-scale wildfire. Annual cone production was monitored for a 5-year period in 130 tagged trees, in 13 plots with 10 individuals each, established both within the unburned part of the forest and in surviving fragments of the burned area. In the most recent masting year, a high percentage (88%) of cone-bearing trees was recorded, along with a sizeable, average cone production (40.8 cones per tree). In the intermediate, non-masting years, the corresponding values ranged from 2% to 55% and 0.08 to 5.9 cones per tree, respectively. The reproduction process is affected by both tree density and regional climatic conditions, in particular temperature during spring of the maturation year and precipitation during spring and summer of the previous year. For the first time according to our knowledge, natural regeneration was recorded for a 4-year period, in 13 permanent transects within the monitoring plots, in relation with a masting event and the additional implications of a preceding wildfire. Highest mean density of seedlings and saplings (11.4 per m2) was observed during the first spring after masting. In the non-masting years, the corresponding value ranged from 2.1 to 2.9 per m2. Seedling survival during their first summer was considerable (30–76%) but stabilized afterwards (1–3 years) at a lower level (10–20%). The particular post-masting seedling flush was followed by an extremely high mortality rate (88.6%) and cannot represent a major recruitment event.
Genetic Variation in Cytochrome P450 2R1 and Vitamin D Binding Protein Genes are associated with Vitamin D Deficiency in Adolescents
Authors: Kelishadi Roya , Heidari-Beni Motahar , Akbarian Shahab-Aldin , Hasan Tajadini Mohammad , Haghjooy Javanmard Shaghayegh 
Published: November 2019

Abstract. Background: Genome Wide Association Studies (GWAS) have evaluated several genes related to vitamin D synthesis, metabolism and transport. They have proposed a genetic basis for low levels of vitamin D in the blood. The current study aims to investigate the relationship between certain vitamin D-associated gene variants and vitamin D deficiency in Iranian adolescents. Methods: In this case-control study, the genomic DNA was extracted by Real Time PCR High Resolution Melt (HRM). All measurements were carried out with triple repetition. The following factors were assessed: single nucleotide polymorphisms (SNPs) in Vitamin D binding protein ( DBP, rs2282679), 7-Dehydrocholesterol reductase ( DHCR7, rs12785878) and Cytochrome P450 2R1 ( CYP2R1, rs10741657). Results: the genomic DNA of blood samples obtained from 481 adolescents. Participants with hypovitaminosis D were compared with a control group. The average vitamin D level of sufficient subjects (controls) was 44.88±14.01 ng/mL, while subjects who were insufficient (cases) had an average vitamin D level of 7.03±1.24 ng/mL. No statistically significant differences were found in the allelic and genotypic distributions between genders. The SNP frequency in CYP2R1 (rs10741657) and DBP (rs2282679) in the vitamin D deficient group was significantly higher than in the control group (p-values < 0.001 and 0.01 respectively). There were no statistically significant differences in the DHCR7 SNP (rs12785878) distributions between the Vitamin D deficient group and control group. Conclusion: The present study demonstrated evidence of the ability of the SNPs under investigation to predict circulating vitamin D concentration. Further study is needed to better understand if and how genetic factors contribute to vitamin D levels, and certain skeletal-associated disorders in adolescents.
Wind‐Driven Strain Extends Seasonal Stratification
Authors: Ruiz‐Castillo Eugenio , Sharples Jonathan , Hopkins Jo 
Published: November 2019

AbstractThe onset and breakdown of stratification are key physical drivers of phytoplankton growth in shelf seas and the open ocean. We show how in the Celtic Sea, where seasonality in stratification is generally viewed as controlled by heat input, a cross‐shelf salinity gradient horizontally strained by the wind prolonged the stratified period by 5–6 days in autumn prior to full winter mixing, while in spring caused seasonal stratification to begin 7 days early. Salinity straining has important implications for setting light conditions during the start of the spring bloom and for the timing of bottom‐water ventilation in winter. Analysis of winds around the time of likely onset of spring stratification between 1979 and 2016 showed that in 60% of the years' wind conditions were favorable for salinity straining. Accurate knowledge of the horizontal salinity field and wind stress are required to correctly determine the onset and breakdown of stratification.
Water Permeability Evolution With Faulting for Unconsolidated Turbidite Sand in a Gas‐Hydrate Reservoir in the Eastern Nankai Trough Area of Japan
Authors: Kimura Sho , Ito Takuma , Noda Shohei , Kaneko Hiroaki , Suzuki Kiyofumi , Yasuda Hisato , Minagawa Hideki 
Published: November 2019

AbstractGas hydrates in sediments are forecast to become an unconventional natural gas resource. In 2013 and 2017, an offshore natural gas production test in subseabed gas hydrate‐bearing sand layers was carried out in the eastern Nankai Trough area of Japan. However, permeability evolution with progressive shearing of these faulted reservoirs has remained enigmatic. It is necessary to understand fault behavior under shear, as well as how normal stress affects permeability evolution. Here, we examine the relationship between fault development and permeability reduction in unconsolidated turbidite sandy sediment from Japan's eastern Nankai Trough area using a laboratory ring‐shear experiments. At each stress condition, the permeability decreased significantly following shear displacements of ~0.2–0.5 m, gradually decreasing further with shear displacements up to 10 m. Permeability after shearing was reduced by 3 to 4 orders of magnitude compared to that before shearing. Grain crushing and compaction within the shear zone and surrounding host sediment are dependent on stress and mineralogy. The findings of the role of shear zone development in modifying fault permeability for turbidite sand are expected to contribute directly to rational evaluation of gas‐hydrate reservoir, production simulations, and development strategies in future studies.
THEMIS Observations of the 2018 Mars Global Dust Storm
Authors: Smith Michael D. 
Published: November 2019

AbstractWe present Thermal Imaging System (THEMIS) infrared observations taken during the recent global dust storm that occurred during the summer of 2018 (Mars Year 34). THEMIS observations of the dust storm show the distinct thermal signature of the storm and the spatial and temporal variation of column dust optical depth before, during, and after the storm. Dust optical depth was observed by THEMIS to increase in two stages, initially at Ls = 185° and then again after Ls = 195°. Peak globally average dust optical depth was attained at Ls = 205°, which was followed by a relatively rapid decrease in dust loading. Evening atmospheric temperatures warmed by more than 20 K at all observed latitudes and by as much as 40 K at high southern latitudes. Morning atmospheric temperatures were also observed to warm but by a smaller amount (~15 K) and with a different latitude dependence. A comparison to global dust storms that occurred in Mars Years 25 and 28 shows similarities in the thermal response but differences in the details of the time history of dust optical depth. Each global dust storm is unique, and the new observations of this most recent storm will provide important new clues to the physical processes that govern these storms.
Unifying machine learning and quantum chemistry with a deep neural network for molecular wavefunctions
Authors: Schütt K. T. , Gastegger M. , Tkatchenko A. , Müller K.-R. , Maurer R. J. 
Published: November 2019

AbstractMachine learning advances chemistry and materials science by enabling large-scale exploration of chemical space based on quantum chemical calculations. While these models supply fast and accurate predictions of atomistic chemical properties, they do not explicitly capture the electronic degrees of freedom of a molecule, which limits their applicability for reactive chemistry and chemical analysis. Here we present a deep learning framework for the prediction of the quantum mechanical wavefunction in a local basis of atomic orbitals from which all other ground-state properties can be derived. This approach retains full access to the electronic structure via the wavefunction at force-field-like efficiency and captures quantum mechanics in an analytically differentiable representation. On several examples, we demonstrate that this opens promising avenues to perform inverse design of molecular structures for targeting electronic property optimisation and a clear path towards increased synergy of machine learning and quantum chemistry.
MDC1 PST-repeat region promotes histone H2AX-independent chromatin association and DNA damage tolerance
Authors: Salguero Israel , Belotserkovskaya Rimma , Coates Julia , Sczaniecka-Clift Matylda , Demir Mukerrem , Jhujh Satpal , Wilson Marcus D. , Jackson Stephen P. 
Published: November 2019

AbstractHistone H2AX and MDC1 are key DNA repair and DNA-damage signalling proteins. When DNA double-strand breaks (DSBs) occur, H2AX is phosphorylated and then recruits MDC1, which in turn serves as a docking platform to promote the localization of other factors, including 53BP1, to DSB sites. Here, by using CRISPR-Cas9 engineered human cell lines, we identify a hitherto unknown, H2AX-independent, function of MDC1 mediated by its PST-repeat region. We show that the PST-repeat region directly interacts with chromatin via the nucleosome acidic patch and mediates DNA damage-independent association of MDC1 with chromatin. We find that this region is largely functionally dispensable when the canonical γH2AX-MDC1 pathway is operative but becomes critical for 53BP1 recruitment to DNA-damage sites and cell survival following DSB induction when H2AX is not available. Consequently, our results suggest a role for MDC1 in activating the DDR in areas of the genome lacking or depleted of H2AX.
Nematic fluctuations in the cuprate superconductor Bi2Sr2CaCu2O8+δ
Authors: Auvray N. , Loret B. , Benhabib S. , Cazayous M. , Zhong R. D. , Schneeloch J. , Gu G. D. , Forget A. , Colson D. , Paul I. , Sacuto A. , Gallais Y. 
Published: November 2019

AbstractEstablishing the presence and the nature of a quantum critical point in their phase diagram is a central enigma of the high-temperature superconducting cuprates. It could explain their pseudogap and strange metal phases, and ultimately their high superconducting temperatures. Yet, while solid evidences exist in several unconventional superconductors of ubiquitous critical fluctuations associated to a quantum critical point, in the cuprates they remain undetected until now. Here using symmetry-resolved electronic Raman scattering in the cuprate $${\mathrm{Bi}}_2{\mathrm{Sr}}_2{\mathrm{CaCu}}_2{\mathrm{O}}_{8+\delta}$$

Bi

2

Sr

2

CaCu

2

O

8
+
δ

, we report the observation of enhanced electronic nematic fluctuations near the endpoint of the pseudogap phase. While our data hint at the possible presence of an incipient nematic quantum critical point, the doping dependence of the nematic fluctuations deviates significantly from a canonical quantum critical scenario. The observed nematic instability rather appears to be tied to the presence of a van Hove singularity in the band structure.
Toll-like receptor 2 expression on c-kit+ cells tracks the emergence of embryonic definitive hematopoietic progenitors
Authors: Balounová Jana , Šplíchalová Iva , Dobešová Martina , Kolář Michal , Fišer Karel , Procházka Jan , Sedlacek Radislav , Jurisicova Andrea , Sung Hoon-ki , Kořínek Vladimír , Alberich-Jorda Meritxell , Godin Isabelle , Filipp Dominik 
Published: November 2019

AbstractHematopoiesis in mammalian embryos proceeds through three successive waves of hematopoietic progenitors. Since their emergence spatially and temporally overlap and phenotypic markers are often shared, the specifics regarding their origin, development, lineage restriction and mutual relationships have not been fully determined. The identification of wave-specific markers would aid to resolve these uncertainties. Here, we show that toll-like receptors (TLRs) are expressed during early mouse embryogenesis. We provide phenotypic and functional evidence that the expression of TLR2 on E7.5 c-kit+ cells marks the emergence of precursors of erythro-myeloid progenitors (EMPs) and provides resolution for separate tracking of EMPs from primitive progenitors. Using in vivo fate mapping, we show that at E8.5 the Tlr2 locus is already active in emerging EMPs and in progenitors of adult hematopoietic stem cells (HSC). Together, this data demonstrates that the activation of the Tlr2 locus tracks the earliest events in the process of EMP and HSC specification.
Myosin 1b is an actin depolymerase
Authors: Pernier Julien , Kusters Remy , Bousquet Hugo , Lagny Thibaut , Morchain Antoine , Joanny Jean-François , Bassereau Patricia , Coudrier Evelyne 
Published: November 2019

AbstractThe regulation of actin dynamics is essential for various cellular processes. Former evidence suggests a correlation between the function of non-conventional myosin motors and actin dynamics. Here we investigate the contribution of myosin 1b to actin dynamics using sliding motility assays. We observe that sliding on myosin 1b immobilized or bound to a fluid bilayer enhances actin depolymerization at the barbed end, while sliding on myosin II, although 5 times faster, has no effect. This work reveals a non-conventional myosin motor as another type of depolymerase and points to its singular interactions with the actin barbed end.
Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in mice
Authors: Wang Zhengpin , Xu Xiaojiang , Li Jian-Liang , Palmer Cameron , Maric Dragan , Dean Jurrien 
Published: November 2019

AbstractSpermatogonial stem cells (SSCs) have the dual capacity to self-renew and differentiate into progenitor spermatogonia that develop into mature spermatozoa. Here, we document that preferentially expressed antigen of melanoma family member 12 (PRAMEF12) plays a key role in maintenance of the spermatogenic lineage. In male mice, genetic ablation ofPramef12arrests spermatogenesis and results in sterility which can be rescued by transgenic expression ofPramef12.Pramef12deficiency globally decreases expression of spermatogenic-related genes, and single-cell transcriptional analysis of post-natal male germline cells identifies four spermatogonial states. In the absence ofPramef12expression, there are fewer spermatogonial stem cells which exhibit lower expression of SSC maintenance-related genes and are defective in their ability to differentiate. The disruption of the first wave of spermatogenesis in juvenile mice results in agametic seminiferous tubules. These observations mimic a Sertoli cell-only syndrome in humans and may have translational implications for reproductive medicine.
Virus-borne mini-CRISPR arrays are involved in interviral conflicts
Authors: Medvedeva Sofia , Liu Ying , Koonin Eugene V. , Severinov Konstantin , Prangishvili David , Krupovic Mart 
Published: November 2019

AbstractCRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome—all spacers contained in a microbiome—associated with hyperthermophilic archaea of the order Sulfolobales recovered directly from an environmental sample and from enrichment cultures established in the laboratory. The 25 million CRISPR spacers sequenced from a single sampling site dwarf the diversity of spacers from all available Sulfolobales isolates and display complex temporal dynamics. Comparison of closely related virus strains shows that CRISPR targeting drives virus genome evolution. Furthermore, we show that some archaeal viruses carry mini-CRISPR arrays with 1–2 spacers and preceded by leader sequences but devoid ofcasgenes. Closely related viruses present in the same population carry spacers against each other. Targeting by these virus-borne spacers represents a distinct mechanism of heterotypic superinfection exclusion and appears to promote archaeal virus speciation.
Observation of a topological nodal surface and its surface-state arcs in an artificial acoustic crystal
Authors: Yang Yihao , Xia Jian-ping , Sun Hong-xiang , Ge Yong , Jia Ding , Yuan Shou-qi , Yang Shengyuan A. , Chong Yidong , Zhang Baile 
Published: November 2019

AbstractThree-dimensional (3D) gapless topological phases can be classified by the dimensionality of the band degeneracies, including zero-dimensional (0D) nodal points, one-dimensional (1D) nodal lines, and two-dimensional (2D) nodal surfaces. Both nodal points and nodal lines have been realized recently in photonics and acoustics. However, a nodal surface has never been observed in any classical-wave system. Here, we report on the experimental observation of a twofold symmetry-enforced nodal surface in a 3D chiral acoustic crystal. In particular, the demonstrated nodal surface carries a topological charge of 2, constituting the first realization of a higher-dimensional topologically-charged band degeneracy. Using direct acoustic field measurements, we observe the projected nodal surface and its Fermi-arc-like surface states and demonstrate topologically-induced robustness of the surface states against disorders. This discovery of a higher-dimensional topologically-charged band degeneracy paves the way toward further explorations of the physics and applications of new topological semimetal phases.
A rationale for surgical debulking to improve anti-PD1 therapy outcome in non small cell lung cancer
Authors: Guisier Florian , Cousse Stephanie , Jeanvoine Mathilde , Thiberville Luc , Salaun Mathieu 
Published: November 2019

AbstractAnti-PD1 immunotherapy has emerged as a gold-standard treatment for first- or second-line treatment of stage IV NSCLC, with response rates ranging from 10 to 60%. Strategies to improve the disease control rate are needed. Several reports suggested that debulking surgery enhances anti-tumor immunity. We aimed at examining tumor burden as a predictive factor of anti-PD1 tretment efficacy and to evaluate the role of cytoreductive surgery in anti-PD1 treated NSCLC. Immunocompetent DBA/2 mice engrafted with various amount of allogeneic lung squamous cancer KLN-205 cells were treated with anti-PD1 monoclonal antibody. Mice engrafted with two tumors also underwent a debulking surgery or a sham procedure. Tumor volume was monitored to assess treatment efficacy. Tumor infiltrating lymphocytes were assessed by flow cytometry. In a retrospective study of 48 stage IV NSCLC patients treated with Nivolumab who underwent a 18-FDG PETscan before treatment onset, the prognostic role of metabolic tumor volume was analysed. Anti-PD1 treatment effect was greater in mice bearing smaller tumors. Treatment with higher doses of anti-PD1 antibody did not improve the outcome, independently of the size of the tumor. In mice bearing 2 tumors, excision of 1 tumor improved the anti-PD1 treatment effect on the remaining tumor. In 48 NSCLC patients receiving anti-PD1 treatment, high metabolic tumor volume was associated with poor overall survival and the absence of clinical benefit. Treg infiltration, but not effector T cells, was positively correlated to tumor volume. Taken together, our results suggest that tumor volume is a predictive factor of anti-PD1 efficacy in NSCLC. Additionally, an experimental murine model suggests that tumor debulking may improve control of residual tumor.
Aspirin suppresses chemoresistance and enhances antitumor activity of 5-Fu in 5-Fu-resistant colorectal cancer by abolishing 5-Fu-induced NF-κB activation
Authors: Fu Jinbo , Xu Yiming , Yang Yushan , Liu Yun , Ma Lulu , Zhang Yiyao 
Published: November 2019

AbstractChemoresistance to 5-fluorouracil (5-Fu)-based chemotherapy is a leading obstacle in achieving effective treatment for colorectal cancer (CRC). Typically, NF-κB activation induced by the chemotherapeutics themselves is an important cause resulting in chemoresistance. Specifically, NF-κB activation can inhibit tumor cell apoptosis and induce chemoresistance. Drugs that can prevent NF-κB activation induced by chemotherapeutics are urgently needed to overcome chemoresistance. Obviously, aspirin is one of these agents, which has been demonstrated to possess antitumor activities and as an inhibitor of NF-κB. The current study aimed to investigate whether aspirin was able to overcome the chemoresistance to 5-Fu in CRC, together with the potential synergistic mechanisms. Our results suggested that aspirin remarkably potentiated the inhibitory effect of 5-Fu on the growth and invasion of resistant cells in vitro. In vivo, aspirin markedly enhanced the antitumor activity of 5-Fu in suppressing tumor growth and metastasis, and down-regulating the expression of NF-κB-regulated genes in the 5-Fu-resistant cells. Obviously, aspirin completely eradicated the 5-Fu-induced NF-κB activation, without inducing pronounced adverse effects. Taken together, findings in this study suggest that aspirin can reverse chemoresistance and potentiate the antitumor effect of 5-Fu, which is achieved through abolishing the 5-Fu-induced NF-κB activation, suggesting that aspirin may be a promising adjuvant therapeutic agent for CRC.
Evidence of CPV2c introgression into Croatia and novel insights into phylogeny and cell tropism
Authors: Novosel Dinko , Tuboly Tamas , Balka Gyula , Szeredi Levente , Lojkic Ivana , Jungic Andreja , Acinger-Rogic Zaklin , Ait-Ali Tahar , Csagola Attila 
Published: November 2019

AbstractCanine parvovirus type 2 (CPV2) emerged for the first time in 1978 and evolved into two antigenic variants CPV2a and CPV2b and the third new antigenic variant CPV2c reported in 2000 in Italy. During 2014 unexplained outbreaks of gastroenteritis were observed in kennels where an extensive vaccination program was ongoing and where vaccinated animals showed pathologic lesions consistent with typical parvovirosis. The aim of this study was to investigate whether CPV2 could have played a role in the emergence of these cases and to evaluate genetic or pathological specificities of the virus and the disease. Using PCR and phylogenetic analysis we showed that the CPV2c variant is circulating in Croatia and is in close relationships with isolates from North and South America. Histopathological lesions and cell tropism that are known for CPV2 we are reporting the identification of the virus in glial cells and ovaries. It seems that evolution of CPV and CPV2a-c and adaptation to dogs are two independent events. Croatian isolates had specific and some unique amino acid mutations under positive selection. The effect of the alterations on the immunoglobulin binding cannot be excluded.