bluuebunny/crossref_metadata_2025_split huggingface dataset:
Universal behavior of the apparent fragility in ultraslow glass forming systems
Authors: Drozd-Rzoska Aleksandra 
Published: May 2019

AbstractDespite decades of studies on the grand problem of the glass transition the question of well-defined universal patterns, including the key problem of the previtreous behavior of the primary (structural) relaxation time, remains elusive. This report shows the universal previtreous behavior of the apparent fragility, i.e. the steepness index mP (T > Tg) = d log10τ(T)/d( Tg/T). It is evidenced that mP(T) = 1(T − T*), for T → Tg and  T*= Tg − Δ T*. Basing on this finding, the new 3-parameter dependence for portraying the previtreous behavior of the primary relaxation time has been derived: τ(T) = CΩ((T − T*)/T)−Ω × [exp((T − T*)/T)]Ω. The universality of obtained relations is evidenced for glass formers belonging to low molecular weight liquids, polymers (melt and solid), plastic crystals, liquid crystals, resins and relaxors. They exhibit clear preferences either for the VFT or for the critical-like descriptions, if recalled already used modeling. The novel relation can obey even above the dynamic crossover temperature, with the power exponent Ω ranging between ~17 (liquid crystals) to ~57 (glycerol), what may indicate the impact of symmetry on the previtreous effect. Finally, the emerging similarity to the behavior in the isotropic phase of nematic liquid crystals is recalled.
Immunoprofiling of Colitis-associated and Sporadic Colorectal Cancer and its Clinical Significance
Authors: Soh Jae Seung , Jo Su In , Lee Hyejin , Do Eun-ju , Hwang Sung Wook , Park Sang Hyoung , Ye Byong Duk , Byeon Jeong-Sik , Yang Suk-Kyun , Kim Ji Hun , Yang Dong-Hoon , Kim Sang-Yeob , Myung Seung-Jae 
Published: May 2019

AbstractImmunoprofiling is useful for predicting prognosis in various malignancies and provides targets for immunotherapy. Quantitative multispectral imaging system, which allows simultaneous detection of multiple immune markers, is a novel method for examining the tumor immune environment. We compared the expression levels of various surface markers in immune cells between colitis-associated cancer (CAC) and sporadic colorectal cancer (CRC) and evaluated the clinical usefulness of immunoprofiling in CRC. Tumor specimens from 24 CAC patients and 48 sporadic CRC patients, matched by age, sex, and tumor location to CAC, were included in the analysis. The expression levels of CD3, CD8, Foxp3, and programmed death-ligand 1 (PD-L1) in immune cells at the invasive margins of tumor tissues were evaluated by quantitative multispectral imaging. The CAC group had significantly less levels of cells expressing CD3, CD8, Foxp3, or PD-L1 (all, p < 0.01). In the CAC group, patients whose immune cells had high expression of CD3+ and CD8+ had better overall survival. The immune profiling patterns of CAC patients were significantly distinct from those of sporadic CRC patients, suggesting that CAC and sporadic CRC have distinct disease phenotypes. Immunoprofiling can be helpful for evaluation of clinical prognosis in CAC.
Untargeted metabolomics reveals N, N, N-trimethyl-L-alanyl-L-proline betaine (TMAP) as a novel biomarker of kidney function
Authors: Velenosi Thomas J. , Thomson Benjamin K. A. , Tonial Nicholas C. , RaoPeters Adrien A. E. , Mio Megan A. , Lajoie Gilles A. , Garg Amit X. , House Andrew A. , Urquhart Bradley L. 
Published: May 2019

AbstractThe diagnosis and prognosis of chronic kidney disease (CKD) currently relies on very few circulating small molecules, which can vary by factors unrelated to kidney function. In end-stage renal disease (ESRD), these same small molecules are used to determine dialysis dose and dialytic clearance. Therefore, we aimed to identify novel plasma biomarkers to estimate kidney function in CKD and dialytic clearance in ESRD. Untargeted metabolomics was performed on plasma samples from patients with a single kidney, non-dialysis CKD, ESRD and healthy controls. For ESRD patients, pre- and post-dialysis plasma samples were obtained from several dialysis modalities. Metabolomics analysis revealed over 400 significantly different features in non-dialysis CKD and ESRD plasma compared to controls while less than 35 features were significantly altered in patients with a single kidney. N,N,N-trimethyl-L-alanyl-L-proline betaine (TMAP, AUROC = 0.815) and pyrocatechol sulfate (AUROC = 0.888) outperformed creatinine (AUROC = 0.745) in accurately identifying patients with a single kidney. Several metabolites accurately predicted ESRD; however, when comparing pre-and post-hemodialysis, TMAP was the most robust biomarker of dialytic clearance for all modalities (AUROC = 0.993). This study describes TMAP as a novel potential biomarker of kidney function and dialytic clearance across several hemodialysis modalities.
Laser-PIXE using laser-accelerated proton beams
Authors: Barberio M. , Antici P. 
Published: May 2019

AbstractLaser-driven proton acceleration is a field of growing interest, in particular for its numerous applications, including in the field of materials science. A benefit of these laser-based particle sources is their potential for a relative compactness in addition to some characteristics at the source that differ from those of conventional, radio-frequency based proton sources. These features include, e.g., a higher brilliance, a shorter duration, and a larger energy spread. Recently, the use of laser-accelerated protons has been proposed in the field of Cultural Heritage, as alternative source for the Particle Induced X-ray Emission diagnostic (“laser-PIXE”), a particular ion beam analysis (IBA) technique that allows to precisely analyse the chemical composition of the material bulk. In this paper we study the feasibility of the laser-PIXE using laser-accelerated proton beams. We focus on materials specifically of interest for the Cultural Heritage domain. Using Geant4 simulations, we show that the laser-PIXE allows analysing a larger volume than conventional PIXE, profiting from the large energy spread of laser-accelerated protons. Furthermore, for specific materials, the large energy spread allows investigating multilayer materials, providing an advantage compared to conventional PIXE technologies.
Node centrality measures are a poor substitute for causal inference
Authors: Dablander Fabian , Hinne Max 
Published: May 2019

AbstractNetwork models have become a valuable tool in making sense of a diverse range of social, biological, and information systems. These models marry graph and probability theory to visualize, understand, and interpret variables and their relations as nodes and edges in a graph. Many applications of network models rely on undirected graphs in which the absence of an edge between two nodes encodes conditional independence between the corresponding variables. To gauge the importance of nodes in such a network, various node centrality measures have become widely used, especially in psychology and neuroscience. It is intuitive to interpret nodes with high centrality measures as being important in a causal sense. Using the causal framework based on directed acyclic graphs (DAGs), we show that the relation between causal influence and node centrality measures is not straightforward. In particular, the correlation between causal influence and several node centrality measures is weak, except for eigenvector centrality. Our results provide a cautionary tale: if the underlying real-world system can be modeled as a DAG, but researchers interpret nodes with high centrality as causally important, then this may result in sub-optimal interventions.
Immunogenicity profiling of protein antigens from capsular group B Neisseria meningitidis
Authors: Awanye Amaka M. , Chang Chun-Mien , Wheeler Jun X. , Chan Hannah , Marsay Leanne , Dold Christina , Rollier Christine S. , Bird Louise E. , Nettleship Joanne E. , Owens Raymond J. , Pollard Andrew J. , Derrick Jeremy P. 
Published: May 2019

AbstractOuter membrane vesicle (OMV)- based vaccines have been used to provide strain-specific protection against capsular group B Neisseria meningitidis infections, but the full breadth of the immune response against the components of the OMV has not been established. Sera from adults vaccinated with an OMV vaccine were used to screen 91 outer membrane proteins (OMPs) incorporated in an antigen microarray panel. Antigen-specific IgG levels were quantified pre-vaccination, and after 12 and 18 weeks. These results were compared with IgG levels from mice vaccinated with the same OMV vaccine. The repertoires of highly responding antigens in humans and mice overlapped, but were not identical. The highest responding antigens to human IgG comprised four integral OMPs (PorA, PorB, OpcA and PilQ), a protein which promotes the stability of PorA and PorB (RmpM) and two lipoproteins (BamC and GNA1162). These observations will assist in evaluating the role of minor antigen components within OMVs in providing protection against meningococcal infection. In addition, the relative dominance of responses to integral OMPs in humans emphasizes the importance of this subclass and points to the value of maintaining conformational epitopes from integral membrane proteins in vaccine formulations.
Giant bowing of the band gap and spin-orbit splitting energy in GaP1−xBix dilute bismide alloys
Authors: Bushell Zoe L. , Broderick Christopher A. , Nattermann Lukas , Joseph Rita , Keddie Joseph L. , Rorison Judy M. , Volz Kerstin , Sweeney Stephen J. 
Published: May 2019

AbstractUsing spectroscopic ellipsometry measurements on GaP1−xBix/GaP epitaxial layers up to x = 3.7% we observe a giant bowing of the direct band gap ($${E}_{g}^{{\rm{\Gamma }}}$$

E

g

Γ

) and valence band spin-orbit splitting energy (ΔSO). $${E}_{g}^{{\rm{\Gamma }}}$$

E

g

Γ

(ΔSO) is measured to decrease (increase) by approximately 200 meV (240 meV) with the incorporation of 1% Bi, corresponding to a greater than fourfold increase in ΔSO in going from GaP to GaP0.99Bi0.01. The evolution of $${E}_{g}^{{\rm{\Gamma }}}$$

E

g

Γ

and ΔSO with x is characterised by strong, composition-dependent bowing. We demonstrate that a simple valence band-anticrossing model, parametrised directly from atomistic supercell calculations, quantitatively describes the measured evolution of $${E}_{g}^{{\rm{\Gamma }}}$$

E

g

Γ

and ΔSO with x. In contrast to the well-studied GaAs1−xBix alloy, in GaP1−xBix substitutional Bi creates localised impurity states lying energetically within the GaP host matrix band gap. This leads to the emergence of an optically active band of Bi-hybridised states, accounting for the overall large bowing of $${E}_{g}^{{\rm{\Gamma }}}$$

E

g

Γ

and ΔSO and in particular for the giant bowing observed for x ≲ 1%. Our analysis provides insight into the action of Bi as an isovalent impurity, and constitutes the first detailed experimental and theoretical analysis of the GaP1−xBix alloy band structure.
Computational prediction and in vitro validation of VEGFR1 as a novel protein target for 2,3,7,8-tetrachlorodibenzo-p-dioxin
Authors: Chitrala Kumaraswamy Naidu , Yang Xiaoming , Busbee Brandon , Singh Narendra P. , Bonati Laura , Xing Yongna , Nagarkatti Prakash , Nagarkatti Mitzi 
Published: May 2019

AbstractThe toxic manifestations of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an environmental contaminant, primarily depend on its ability to activate aryl hydrocarbon receptor (AhR), which is a ligand-dependent transcription factor belonging to the superfamily of basic-helix-loop-helix DNA-binding proteins. In the present study, we aimed to identify novel protein receptor targets for TCDD using computational and in vitro validation experiments. Interestingly, results from computational methods predicted that Vascular Endothelial Growth Factor Receptor 1 (VEGFR1) could be one of the potential targets for TCDD in both mouse and humans. Results from molecular docking studies showed that human VEGFR1 (hVEGFR1) has less affinity towards TCDD compared to the mouse VEGFR1 (mVEGFR1). In vitro validation results showed that TCDD can bind and phosphorylate hVEGFR1. Further, results from molecular dynamic simulation studies showed that hVEGFR1 interaction with TCDD is stable throughout the simulation time. Overall, the present study has identified VEGFR1 as a novel target for TCDD, which provides the basis for further elucidating the role of TCDD in angiogenesis.
Large apparent growth increases in boreal forests inferred from tree-rings are an artefact of sampling biases
Authors: Duchesne Louis , Houle Daniel , Ouimet Rock , Caldwell Liam , Gloor Manuel , Brienen Roel 
Published: May 2019

AbstractTree rings are thought to be a powerful tool to reconstruct historical growth changes and have been widely used to assess tree responses to global warming. Demographic inferences suggest, however, that typical sampling procedures induce spurious trends in growth reconstructions. Here we use the world’s largest single tree-ring dataset (283,536 trees from 136,621 sites) from Quebec, Canada, to assess to what extent growth reconstructions based on these - and thus any similar - data might be affected by this problem. Indeed, straightforward growth rate reconstructions based on these data suggest a six-fold increase in radial growth of black spruce (Picea mariana) from ~0.5 mm yr−1 in 1800 to ~2.5 mm yr−1 in 1990. While the strong correlation (R2 = 0.98) between this increase and that of atmospheric CO2 could suggest a causal relationship, we here unambiguously demonstrate that this growth trend is an artefact of sampling biases caused by the absence of old, fast-growing trees (cf. “slow-grower survivorship bias”) and of young, slow-growing trees (cf. “big-tree selection bias”) in the dataset. At the moment, we cannot envision how to remedy the issue of incomplete representation of cohorts in existing large-scale tree-ring datasets. Thus, innovation will be needed before such datasets can be used for growth rate reconstructions.
Acidic Stress Triggers Sodium-Coupled Bicarbonate Transport and Promotes Survival in A375 Human Melanoma Cells
Authors: Yang Oscar C. Y. , Loh Shih-Hurng 
Published: May 2019

AbstractMelanoma cells preserve intracellular pH (pHi) within a viable range despite an acidic ambient pH that typically falls below pH 7.0. The molecular mechanisms underlying this form of acidic preservation in melanoma remain poorly understood. Previous studies had demonstrated that proton transporters including the monocarboxylate transporter (MCT), the sodium hydrogen exchanger (NHE), and V-Type ATPase mediate acid extrusion to counter intracellular acidification in melanoma cells. In this report, the expression and function of the Sodium-Coupled Bicarbonate Transporter (NCBT) family of base loaders were further characterized in melanoma cell lines. NCBT family members were found to be expressed in three different melanoma cell lines – A375, MeWo, and HS695T – and included the electrogenic sodium-bicarbonate cotransporter isoforms 1 and 2 (NBCe1 and NBCe2), the electroneutral sodium-bicarbonate cotransporter (NBCn1), and the sodium-dependent chloride-bicarbonate exchanger (NDCBE). These transporters facilitated 4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid (DIDS)-dependent pHirecovery in melanoma cells, in response to intracellular acidification induced by ammonium chloride prepulse. Furthermore, the expression of NCBTs were upregulated via chronic exposure to extracellular acidification. Given the current research interest in the NCBTs as a molecular driver of tumourigenesis, characterising NCBT in melanoma provides impetus for developing novel therapeutic targets for melanoma treatment.
Cisplatin Pharmacodynamics Following Endobronchial Ultrasound-Guided Transbronchial Needle Injection into Lung Tumors
Authors: Mori Vitor , Roy Gregory S. , Bates Jason H. T. , Kinsey C. Matthew 
Published: May 2019

AbstractIntratumoral delivery of cisplatin by endobronchial ultrasound-guided transbronchial needle injection (EBUS-TBNI) has recently emerged as a therapy for treating peribronchial lung cancers. It remains unclear, however, where best to inject drug into a tumor, and at how many sites, so current cisplatin delivery strategies remain empirical. Motivated by the need to put EBUS-TBNI treatment of lung cancer on a more objective footing, we developed a computational model of cisplatin pharmacodynamics following EBUS-TBNI. The model accounts for diffusion of cisplatin within and between the intracellular and extracellular spaces of a tumor, as well as clearance of cisplatin from the tumor via the vasculature and clearance from the body via the kidneys. We matched the tumor model geometry to that determined from a thoracic CT scan of a patient with lung cancer. The model was calibrated by fitting its predictions of cisplatin blood concentration versus time to measurements made up to 2 hrs following EBUS-TBNI of cisplatin into the patient’s lung tumor. This gave a value for the systemic volume of distribution for cisplatin of 12.2 L and a rate constant of clearance from the tumor into the systemic compartment of 1.46 × 10−4 s−1. Our model indicates that the minimal dose required to kill all cancerous cells in a lung tumor can be reduced by roughly 3 orders of magnitude if the cisplatin is apportioned between 5 optimally spaced locations throughout the tumor rather than given as a single bolus to the tumor center. Our findings suggest that optimizing the number and location of EBUS-TBNI sites has a dramatic effect on the dose of cisplatin required for efficacious treatment of lung cancer.
Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome
Authors: Maher Rebecca L. , Rice Mallory M. , McMinds Ryan , Burkepile Deron E. , Vega Thurber Rebecca 
Published: May 2019

AbstractPerturbations in natural systems generally are the combination of multiple interactions among individual stressors. However, methods to interpret the effects of interacting stressors remain challenging and are biased to identifying synergies which are prioritized in conservation. Therefore we conducted a multiple stressor experiment (no stress, single, double, triple) on the coralPocillopora meandrinato evaluate how its microbiome changes compositionally with increasing levels of perturbation. We found that effects of nutrient enrichment, simulated predation, and increased temperature are antagonistic, rather than synergistic or additive, for a variety of microbial community diversity measures. Importantly, high temperature and scarring alone had the greatest effect on changing microbial community composition and diversity. Using differential abundance analysis, we found that the main effects of stressors increased the abundance of opportunistic taxa, and two-way interactions among stressors acted antagonistically on this increase, while three-way interactions acted synergistically. These data suggest that: (1) multiple statistical analyses should be conducted for a complete assessment of microbial community dynamics, (2) for some statistical metrics multiple stressors do not necessarily increase the disruption of microbiomes over single stressors in this coral species, and (3) the observed stressor-induced community dysbiosis is characterized by a proliferation of opportunists rather than a depletion of a proposed coral symbiont of the genusEndozoicomonas.
Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota
Authors: Lee Sangwon , La Tae-Min , Lee Hong-Jae , Choi In-Soo , Song Chang-Seon , Park Seung-Yong , Lee Joong-Bok , Lee Sang-Won 
Published: May 2019

AbstractThe transferred microbiota from mother to baby constitutes the initial infant gastrointestinal microbiota and has an important influence on the development and health of infants in human. However, the reproductive tract microbiota of avian species and its inheritance have rarely been studied. We aimed to characterize the microbial community in the chicken reproductive tract and determine the origin of the chicken embryo gut microbiota. Microbiota in four different portions of chicken oviduct were determined using 16S rRNA metagenomic approach with the IonTorrent platform. Additionally, we analyzed the mother hen’s magnum and cloaca, descendent egg, and embryo gut microbiota. The microbial composition and relative abundance of bacterial genera were stable throughout the entire chicken reproductive tract, without significant differences between the different parts of the oviduct. The chicken reproductive tract showed a relatively high abundance of Lactobacillus species. The number of bacterial species in the chicken reproductive tract significantly increased following sexual maturation. Core genera analysis detected 21 of common genera in the maternal magnum and cloaca, descendent egg shell, egg white, and embryo gut. Some elements of the maternal oviduct microbiota appear to be transferred to the embryo through the egg white and constitute most of the embryo gut bacterial population.
Contrasting endemism in pond-dwelling cyclic parthenogens: the Daphnia curvirostris species group (Crustacea: Cladocera)
Authors: Kotov Alexey A. , Taylor Derek J. 
Published: May 2019

AbstractPond-dwelling cyclic parthenogens are often proposed to be highly vagile. However, the Holarctic biogeography of parthenogens has been hampered by very limited sampling in the eastern Palearctic. Here we examine the geographic boundaries, diversity, and connectivity across the Palearctic for theDaphnia curvirostriscomplex (Cladocera: Daphniidae). Nuclear (HSP90) and mitochondrial (ND2) sequence data supported the existence of five main clades (most of which corresponded to presumptive species) with one eastern Palearctic clade being novel to this study (the average mitochondrial genetic divergence from known species was 19.2%).D.curvirostriss.s. was geographically widespread in the Palearctic, with a population genetic signature consistent with postglacial expansion. The Eastern Palearctic had local nine endemic species and/or subclades (other Holarctic regions lacked more than one endemic subclade). Even though several endemic species appeared to have survived Pleistocene glaciation in the eastern Palearctic, much of the Palearctic has been recolonized byD.curvirostriss.str. from a Western Palearctic refugium. A disjunct population in Mexico also shared its haplotypes withD.curvirostriss.str., consistent with a recent introduction. The only apparently endemic North American lineage was detected in a thermally disturbed pond system in northwestern Alaska. Our results for pond-dwelling cyclic parthenogens further support the hypothesis that the Eastern Palearctic is a diversity hotspot for freshwater invertebrates.
Reversal of established liver fibrosis by IC-2-engineered mesenchymal stem cell sheets
Authors: Itaba Noriko , Kono Yohei , Watanabe Kaori , Yokobata Tsuyoshi , Oka Hiroyuki , Osaki Mitsuhiko , Kakuta Hiroki , Morimoto Minoru , Shiota Goshi 
Published: May 2019

AbstractChronic hepatitis viral infection, alcoholic intoxication, and obesity cause liver fibrosis, which progresses to decompensated liver cirrhosis, a disease for which medical demands cannot be met. Since there are currently no approved anti-fibrotic therapies for established liver fibrosis, the development of novel modalities is required to improve patient prognosis. In this study, we clarified the anti-fibrotic effects of cell sheets produced from human bone marrow-derived mesenchymal stem cells (MSCs) incubated on a temperature-sensitive culture dish with the chemical compound IC-2. Orthotopic transplantation of IC-2-engineered MSC sheets (IC-2 sheets) remarkably reduced liver fibrosis induced by chronic CCl4 administration. Further, the marked production of fibrolytic enzymes such as matrix metalloproteinase (MMP)-1 and MMP-14, as well as thioredoxin, which suppresses hepatic stellate cell activation, was observed in IC-2 sheets. Moreover, the anti-fibrotic effect of IC-2 sheets was much better than that of MSC sheets. Finally, knockdown experiments revealed that MMP-14 was primarily responsible for the reduction of liver fibrosis. Here, we show that IC-2 sheets could be a promising therapeutic option for established liver fibrosis.