bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prognostic characteristics in hormone receptor-positive advanced breast cancer and characterization of abemaciclib efficacy
Authors: Di Leo Angelo , O’Shaughnessy Joyce , Sledge George W. , Martin Miguel , Lin Yong , Frenzel Martin , Hardebeck Molly C. , Smith Ian C. , Llombart-Cussac Antonio , Goetz Matthew P. , Johnston Stephen 
Published: December 2018

AbstractCDK4 & 6 inhibitors have enhanced the effectiveness of endocrine therapy (ET) in patients with advanced breast cancer (ABC). This paper presents exploratory analyses examining patient and disease characteristics that may inform in whom and when abemaciclib should be initiated. MONARCH 2 and 3 enrolled women with HR+, HER2- ABC. In MONARCH 2, patients whose disease had progressed while receiving ET were administered fulvestrant+abemaciclib/placebo. In MONARCH 3, patients received a nonsteroidal aromatase inhibitor+abemaciclib/placebo as initial therapy for advanced disease. A combined analysis of the two studies was performed to determine significant prognostic factors. Efficacy results (PFS and ORR in patients with measurable disease) were examined for patient subgroups corresponding to each significant prognostic factor. Analysis of clinical factors confirmed the following to have prognostic value: bone-only disease, liver metastases, tumor grade, progesterone receptor status, performance status, treatment-free interval (TFI) from the end of adjuvant ET, and time from diagnosis to recurrence. Prognosis was poorer in patients with liver metastases, progesterone receptor-negative tumors, high grade tumors, or short TFI (<36 months). Benefit (PFS hazard ratio, ORR increase) from abemaciclib was observed in all patient subgroups. Patients with indicators of poor prognosis had the largest benefit from the addition of abemaciclib. However, in MONARCH 3, for patients with certain good prognostic factors (TFI ≥ 36 months, bone-only disease) ET achieved a median PFS of >20 months. These analyses identified prognostic factors and demonstrated that patients with poor prognostic factors derived the largest benefit from the addition of abemaciclib.
Costs and benefits of Papacarie in pediatric dentistry: a randomized clinical trial
Authors: Bottega Fernanda , Bussadori Sandra Kalil , Battisti Iara Denise Endruweit , Vieira Eusélia Paveglio , Pompeo Tiago Szambelan , Winkelmann Eliane Roseli 
Published: December 2018

AbstractPapacarie gel is an agent that eliminates the need for local anesthesia and reduces the need for using a drill. However, there is no information regarding the cost per procedure. Therefore we analyzed the cost, per procedure, of Papacarie gel compared to the traditional method (drilling), and performed a comparison between these methods of carious tissue removal. A randomized clinical trial was performed with 24 children with an average age of 5.9 years old. Of these children, 12 were boys and 12 were girls, which resulted in a total of 46 restorations. Patients were separated into: Papacarie group (caries removal with the chemical-mechanical method - Papacarie gel) and Drill group (caries removal with the traditional method - drilling). Values of the materials used in the procedures, heart rate (before, 5 minutes during, and after dental treatment), and the total consultation duration were recorded. A level of significance of 5% was adopted. Papacarie had a lower cost per procedure ($ 0.91) when compared to the traditional method ($ 1.58). Papacarie provided a cost reduction of 42% compared to the traditional method. Using local anesthesia ($ 2.17), the cost reduction increased to 58%. In the procedure using drill + Papacarie ($ 1.37), the cost reduction was 33%. Heart rate, consultation duration, and number of restorations were not statistically different. Papacarie shows an excellent cost benefit for minimally invasive removal of carious tissue and is a feasible alternative for public health care.
Health risk stratification based on computed tomography pulmonary artery obstruction index for acute pulmonary embolism
Authors: Guo Fei , Zhu Guanghui , Shen Junjie , Ma Yichuan 
Published: December 2018

AbstractEarly effective identification of high-risk patients for acute pulmonary embolism (APE) contributes to timely treatment. The pulmonary artery obstruction index (PAOI) in computed tomography angiography (CTA) is a semi-quantitative observation index, commonly used to evaluate the severity of a patient’s condition. This study explores the ability of PAOI to assess the risk stratification of APE. Thirty patients with APE were analysed. They were classified according to the guidelines, and the PAOI and cardiovascular parameters were measured in CTA. The difference of PAOI between different risk stratification patients was compared, and the predictive value of the PAOI for high-risk stratification was evaluated by the receiver operating characteristic curve. The correlation between PAOI and cardiovascular parameters was also analysed by Spearman correlation analysis. The PAOI in low- and high-risk patients was (33.2 ± 18.6)% and (68.1 ± 11.8)% respectively, and the difference was statistically significant. The PAOI was strongly predictive for high-risk patients. The cut-off value was 52.5%, with a sensitivity of 100% and specificity of 81.0%. The PAOI was correlated with the main cardiovascular parameters. We conclude that the PAOI in CTA is helpful for assessing risk stratification in patients with APE, which contributes to the selection of both the treatment plan and prognostic evaluation.
In vitro Chondrocyte Responses in Mg-doped Wollastonite/Hydrogel Composite Scaffolds for Osteochondral Interface Regeneration
Authors: Yu Xinning , Zhao Tengfei , Qi Yiying , Luo Jianyang , Fang Jinghua , Yang Xianyan , Liu Xiaonan , Xu Tengjing , Yang Quanming , Gou Zhongru , Dai Xuesong 
Published: December 2018

AbstractThe zone of calcified cartilage (ZCC) is the mineralized region between the hyaline cartilage and subchondral bone and is critical in cartilage repair. A new non-stoichiometric calcium silicate (10% Ca substituted by Mg; CSi-Mg10) has been demonstrated to be highly bioactive in an osteogenic environment in vivo. This study is aimed to systematically evaluate the potential to regenerate osteochondral interface with different amount of Ca-Mg silicate in hydrogel-based scaffolds, and to compare with the scaffolds containing conventional Ca-phosphate biomaterials. Hydrogel-based porous scaffolds combined with 0–6% CSi-Mg10, 6% β-tricalcium phosphate (β-TCP) or 6% nanohydroxyapatite (nHAp) were made with three-dimensional (3D) printing. An increase in CSi-Mg10 content is desirable for promoting the hypertrophy and mineralization of chondrocytes, as well as cell proliferation and matrix deposition. Osteogenic and chondrogenic induction were both up-regulated in a dose-dependent manner. In comparison with the scaffolds containing 6% β-TCP or nHAp, human deep zone chondrocytes (hDZCs) seeded on CSi-Mg10 scaffold of equivalent concentration exhibited higher mineralization. It is noteworthy that the hDZCs in the 6% CSi-Mg10 scaffolds maintained a higher expression of the calcified cartilage zone specific extracellular matrix marker and hypertrophic marker, collagen type X. Immunohistochemical and Alizarin Red staining reconfirmed these findings. The study demonstrated that hydrogel-based hybrid scaffolds containing 6% CSi-Mg10 are particularly desirable for inducing the formation of calcified cartilage.
Complete genome analysis of a Siphoviridae phage TSK1 showing biofilm removal potential against Klebsiella pneumoniae
Authors: Tabassum Rabia , Shafique Muafia , Khawaja Komal Amer , Alvi Iqbal Ahmed , Rehman Yasir , Sheik Cody S. , Abbas Zaigham , Rehman Shafiq ur 
Published: December 2018

AbstractMultidrug-resistant Klebsiella pneumoniae is a nosocomial pathogen, produces septicemia, pneumonia and UTI. Excessive use of antibiotics contributes towards emergence of multidrug-resistance. Bacteriophage-therapy is a potential substitute of antibiotics with many advantages. In this investigation, microbiological and genome characterization of TSK1 bacteriophage and its biofilm elimination capability are presented. TSK1 showed narrow host range and highest stability at pH 7 and 37 °C. TSK1 reduced the growth of K. pneumoniae during the initial 14 hours of infection. Post-treatment with TSK1 against different age K. pneumoniae biofilms reduced 85–100% biomass. Pre-treatment of TSK1 bacteriophage against the biofilm of Klebsiella pneumoniae reduced > 99% biomass in initial 24 hr of incubation. The genome of TSK1 phage comprised 49,836 base pairs with GC composition of 50.44%. Total seventy-five open reading frames (ORFs) were predicted, 25 showed homology with known functional proteins, while 50 were called hypothetical, as no homologs with proved function exists in the genome databases. Blast and phylogenetic analysis put it in the Kp36 virus genus of family Siphoviridae. Proposed packaging strategy of TSK1 bacteriophage genome is headful packaging using the pac sites. The potential of TSK1 bacteriophage could be used to reduce the bacterial load and biofilm in clinical and non-clinical settings.
Free D-amino acids produced by commensal bacteria in the colonic lumen
Authors: Matsumoto Mitsuharu , Kunisawa Akihiro , Hattori Takanari , Kawana Shuichi , Kitada Yusuke , Tamada Hazuki , Kawano Shinichi , Hayakawa Yoshihiro , Iida Junko , Fukusaki Eiichiro 
Published: December 2018

AbstractD-amino acids (D-AAs) have various biological activities, such as activation ofN-methyl-D-aspartic acid (NMDA) receptor as a co-agonist byD-Ser. Since several freeD-AAs are released in the broth monocultured with bacterium andD-AAs are probably utilized for bacterial communication, we presume that intestinal microbiota releases several kinds of freeD-AAs, which may be involved in the hosts’ health. However, presently, only four freeD-AAs have been found in the ceacal lumen, but not in the colonic lumen. Here, we showed, by simultaneous analysis of chiral AAs using high-sensitivity liquid chromatography-tandem mass spectrometry (LC-MS/MS), that 12 freeD-AAs (D-Ala,D-Arg,D-Asp,D-Gln,D-Glu,D-allo-Ile,D-Leu,D-Lys,D-Met,D-Phe,D-Ser, andD-Trp) are produced by intestinal microbiota and identified bacterial groups belonging to Firmicutes as the relevant bacterial candidates.
Fermi surface topology in a metallic phase of VO2 thin films grown on TiO2(001) substrates
Authors: Muraoka Yuji , Nagao Hiroki , Yao Yuichiro , Wakita Takanori , Terashima Kensei , Yokoya Takayoshi , Kumigashira Hiroshi , Oshima Masaharu 
Published: December 2018

AbstractSince the first observation of the metal-to-insulator transition (MIT), VO2 has attracted substantial attention in terms of whether this transition is impelled by electron–phonon interaction (Peierls transition) or electron–electron interaction. Regarding Peierls transition, it has been theoretically predicted that the Fermi surface (FS) cross-section exhibits certain nesting features for a metallic phase of VO2. Various experimental studies related to the nesting feature have been reported. Nevertheless, there is no experimental result on FS topology. In this work, we determine the FS topology of the metallic phase of VO2 through studies of VO2 epitaxial thin films on TiO2(001) substrates, using synchrotron radiation angle-resolved photoemission spectroscopy (ARPES). Three electron pockets around Γ are observed in band structures along the Γ–X direction. These three bands form electron surfaces around Γ in the ΓXRZ plane. Furthermore, the lowest energy band FS exhibits the nesting feature corresponding to a nesting vector $$\overrightarrow{q}$$

q
→

= ΓR, as predicted by the calculation. Our results strongly indicate the formation of the charge-density wave with $$\overrightarrow{q}$$

q
→

= ΓR and thus, the importance of Peierls transition for the mechanism of the MIT in VO2.
Decomposer diversity increases biomass production and shifts aboveground-belowground biomass allocation of common wheat
Authors: Eisenhauer Nico , Vogel Anja , Jensen Britta , Scheu Stefan 
Published: December 2018

AbstractBiodiversity is well known to enhance many ecosystem functions, but empirical evidence for the role of soil biodiversity for plant biomass production and allocation is scarce. Here we studied the effects of animal decomposer diversity (1, 2, and 4 species as well as a control without any decomposers) on the biomass production and aboveground-belowground biomass allocation of common wheat using two earthworm and two Collembola species using an additive design in two soil management types (organic and mineral fertilizer treatments) in a microcosm experiment. Shoot (+11%), spike (+7%), and root biomass (+56%), increased significantly with increasing decomposer diversity, and these effects were consistent across the two soil management types. Notably, decomposer diversity effects were stronger on root than on shoot biomass, significantly decreasing the shoot-to-root ratio (−27%). Increased plant biomass production was positively correlated with a decomposer richness-induced increase in soil water nitrate concentrations five weeks after the start of the experiment. However, elevated soil nitrate concentrations did not cause significantly higher plant tissue nitrogen concentrations and nitrogen amounts, suggesting that additional mechanisms might be at play. Consistent decomposer diversity effects across soil management types indicate that maintaining soil biodiversity is a robust and sustainable strategy to enhance crop yield.
Transcriptome and protein interaction profiling in cancer cells with mutations in histone H3.3
Authors: Lim Jinyeong , Park Joo Hyun , Baude Annika , Fellenberg Jörg , Zustin Jozef , Haller Florian , Krücken Irene , Kang Hyun Guy , Park Yoon Jung , Plass Christoph , Lindroth Anders M. 
Published: December 2018

AbstractMutations of histone variant H3.3 are highly recurrent in childhood glioblastoma and in young adults with Giant Cell Tumor of the Bone (GCTB). The heterozygotic representation of the mutations in the tumors, and with potential histone H3 and H3.3 redundancy, suggest that the mutations are gain-of-function by nature. To address common H3.3 point mutations, we have generated data from GCTB patient samples with H3.3 G34W substitutions and engineered human GFP-tagged H3.3-mutated isogenic cell lines for high throughput data comparisons. First, a total of thirty-six patient samples and cell lines were used to acquire gene expression transcriptome data using microarray and RNA-sequencing. The expression data were validated with the orthogonal nCounter assay. Second, to uncover the H3.3-GFP interaction proteomes from the isogenic cell lines, immunoprecipitation of unmutated wild type, K27M, G34R, and G34W substitutions were performed. The RNA-sequencing data and the H3.3 interaction proteome enable potentially important functional insight into the tumorigenic process and should spur further detailed analysis.
The metabolic regimes of 356 rivers in the United States
Authors: Appling Alison P. , Read Jordan S. , Winslow Luke A. , Arroita Maite , Bernhardt Emily S. , Griffiths Natalie A. , Hall Robert O. , Harvey Judson W. , Heffernan James B. , Stanley Emily H. , Stets Edward G. , Yackulic Charles B. 
Published: December 2018

AbstractA national-scale quantification of metabolic energy flow in streams and rivers can improve understanding of the temporal dynamics of in-stream activity, links between energy cycling and ecosystem services, and the effects of human activities on aquatic metabolism. The two dominant terms in aquatic metabolism, gross primary production (GPP) and aerobic respiration (ER), have recently become practical to estimate for many sites due to improved modeling approaches and the availability of requisite model inputs in public datasets. We assembled inputs from the U.S. Geological Survey and National Aeronautics and Space Administration for October 2007 to January 2017. We then ran models to estimate daily GPP, ER, and the gas exchange rate coefficient for 356 streams and rivers across the continental United States. We also gathered potential explanatory variables and spatial information for cross-referencing this dataset with other datasets of watershed characteristics. This dataset offers a first national assessment of many-day time series of metabolic rates for up to 9 years per site, with a total of 490,907 site-days of estimates.
Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach
Authors: Shao Chenghua , Liu Zonghong , Yang Huanwang , Wang Sijian , Burley Stephen K. 
Published: December 2018

AbstractOutlier analyses are central to scientific data assessments. Conventional outlier identification methods do not work effectively for Protein Data Bank (PDB) data, which are characterized by heavy skewness and the presence of bounds and/or long tails. We have developed a data-driven nonparametric method to identify outliers in PDB data based on kernel probability density estimation. Unlike conventional outlier analyses based on location and scale, Probability Density Ranking can be used for robust assessments of distance from other observations. Analyzing PDB data from the vantage points of probability and frequency enables proper outlier identification, which is important for quality control during deposition-validation-biocuration of new three-dimensional structure data. Ranking of Probability Density also permits use of Most Probable Range as a robust measure of data dispersion that is more compact than Interquartile Range. The Probability-Density-Ranking approach can be employed to analyze outliers and data-spread on any large data set with continuous distribution.
Taenia solium glutathione transferase fraction activates macrophages and favors the development of Th1-type response
Authors: Vega-Angeles Vera Teresa , Terrazas Luis I. , Ledesma-Soto Yadira , Jiménez Lucía , Landa Abraham 
Published: December 2018

Abstract
Glutathione (GSH) transferase (GST) is an essential enzyme in cestodes for the detoxification of xenobiotics. In Taenia solium, two GSTs (Ts25GST and Ts26GST kDa) were isolated as a fraction (SGSTF) by GSH-Sepharose-4B. Both are located on the tegument. Immunization assays with SGSTF reduced up to 90% of the parasitic load in a murine model of cysticercosis. It prompted us to investigate how SGSTF induces this protective immune response. To test it, we exposed peritoneal macrophages to SGSTF for 24 h; such exposure favored the production of IL-12, TNF, and IL-10 as well as the expression of nitric oxide synthase 2 inducible (Nos2) and CD86, but did not induce the expression of chitinase-like 3 (Chil3). Confocal microscopy showed that the macrophages internalize the SGSTF which co-localized after 1 h with MHC-II in their plasma membranes. Macrophages exposed to SGSTF and co-cultured with anti-CD3 pre-activated T CD4+ cells, enhanced the proliferation of CD4+ cells, induced high interferon-γ (IFN-γ) secretion, and elevated the expression of CD25 and CD69, molecules associated with cell activation. Similar assay using T CD4+ cells from DO11.10 mice and ovalbumin (OVA) peptide+SGSTF as stimuli, showed enhanced cell proliferation and OVA-specific IFN-γ secretion. These data are in-line with those indicating that the P1, P5, and P6 peptides of Schistosoma japonicum 28GST highly promote T-cell proliferation and Th1 response in vitro. We found that such peptides are also present on Ts25GST and Ts26GST. It suggests that SGSTF activates peritoneal macrophages to a classically activated-like phenotype, and that these macrophages induce the differentiation of T CD4+ cells toward a Th1-type response.
Investigating ULX accretion flows and cyclotron resonance in NGC 300 ULX1
Authors: Koliopanos F. , Vasilopoulos G. , Buchner J. , Maitra C. , Haberl F. 
Published: December 2018

Aims. We investigate accretion models for the newly discovered pulsating ultraluminous X-ray source (ULX) NGC 300 ULX1.
Methods. We analyzed broadband XMM-Newton and NuSTAR observations of NGC 300 ULX1, performing phase-averaged and phase-resolved spectroscopy. Using the Bayesian framework, we compared two physically motivated models for the source spectrum: Non-thermal accretion column emission modeled by a power law with a high-energy exponential roll-off (AC model), and multicolor thermal emission from an optically thick accretion envelope plus a hard power-law tail (MCAE model). The AC model is an often used phenomenological model for the emission of X-ray pulsars, while the MCAE model has recently been proposed for the emission of the optically thick accretion envelope that is expected to form in ultraluminous (LX >  1039 erg s−1), highly magnetized accreting neutron stars. We combined the findings of our Bayesian analysis with qualitative physical considerations to evaluate the suitability of each model.
Results. The low-energy part (< 2 keV) of the source spectrum is dominated by non-pulsating, multicolor thermal emission. The (pulsating) high-energy continuum is more ambiguous. If modeled with the AC model, a residual structure is detected that can be modeled using a broad Gaussian absorption line centered at ∼12 keV. However, the same residuals can be successfully modeled using the MCAE model, without the need for the absorption-like feature. Model comparison using the Bayesian approach strongly indicates that the MCAE model without the absorption line is the preferred model.
Conclusions. The spectro-temporal characteristics of NGC 300 ULX1 are consistent with previously reported traits for X-ray pulsars and (pulsating) ULXs. All models considered strongly indicate the presence of an accretion disk that is truncated at a large distance from the central object, as has recently been suggested for a large portion of both pulsating and non-pulsating ULXs. The hard, pulsed emission is not described by a smooth spectral continuum. If modeled by a broad Gaussian absorption line, the fit residuals can be interpreted as a cyclotron scattering feature (CRSF) compatible with a ∼1012 G magnetic field. However, the MCAE model can successfully describe the spectral and temporal characteristics of the source emission, without the need for an additional absorption feature, and it yields physically meaningful parameter values. Therefore strong doubts are cast on the presence of a CRSF in NGC 300 ULX1.
Global distribution center number of some graphs and an algorithm
Authors: Durgut Rafet , Kutucu Hakan , Turaci Tufan 
Published: December 2018

The global center is a newly proposed graph concept. For a graph G = (V(G), E(G)), a set S ⊆ V(G) is a global distribution center if every vertex v ∈ V(G)\S is adjacent to a vertex u ∈ S with |N[u] ∩ S| ≥ |N[v] ∩ (V(G)\S)|, where N(v) = {u ∈ V(G)|uv ∈ E(G)} and N[v] = N(v) ∪ {v}. The global distribution center number of a graph G is the minimum cardinality of a global distribution center of G. In this paper, we investigate the global distribution center number for special families of graphs. Furthermore, we develop a polynomial time heuristic algorithm to find the set of the global distribution center for general graphs.