bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feasibility and performance of a novel probe panel to detect somatic DNA copy number alterations in clinical specimens for predicting prostate cancer progression
Authors: Liu Wennuan , Hou Jun , Petkewicz Jacqueline , Na Rong , Wang Chi‐Hsiung , Sun Jishan , Gallagher Johnie , Bogachkov Yedida Y. , Swenson Laura , Regner MaryAnn , Resurreccion W. Kyle , Isaacs William B. , Brendler Charles B. , Crawford Susan , Zheng S. Lilly , Helfand Brian T. , Xu Jianfeng 
Published: August 2020

AbstractBackgroundTo assess the feasibility of a novel DNA‐based probe panel to detect copy number alterations (CNAs) in prostate tumor DNA and its performance for predicting clinical progression.MethodsA probe panel was developed and optimized to measure CNAs in trace amounts of tumor DNA (2 ng) isolated from formalin‐fixed paraffin‐embedded tissues. Ten genes previously associated with aggressive disease were targeted. The panel's feasibility and performance were assessed in 175 prostate cancer (PCa) patients who underwent radical prostatectomy with a median 10‐year follow‐up, including 42 men who developed disease progression (either metastasis and/or PCa‐specific death). Association with disease progression was tested using univariable and multivariable analyses.ResultsThe probe panel detected CNAs in all 10 genes in tumor DNA isolated from either diagnostic biopsies or surgical specimens. A four‐gene model (PTEN/MYC/BRCA2/CDKN1B) had the strongest association with disease progression; 64.3% of progressors and 22.5% of non‐progressors had at least one CNA in these four genes, odds ratio (OR) (95% confidence interval) = 6.21 (2.77‐13.87),P = 8.48E−06. The association with disease progression remained significant after adjusting for known clinicopathological variables. Among the seven progressors of the 65 patients with clinically low‐risk disease, three (42.9%) had at least one CNA in these four genes.ConclusionsThe probe panel can detect CNAs in trace amounts of tumor DNA from biopsies or surgical tissues at the time of diagnosis or surgery. CNAs independently predict metastatic/lethal cancer, particularly among men with clinically low‐risk disease at diagnosis. If validated, this may improve current abilities to assess tumor aggressiveness.
Theoretical investigation on reverse intersystem crossing from upper triplet to lowest singlet: A “hot exciton” path for blue fluorescentOLEDs
Authors: Liu Yidan , Yuan Yizhong , Tian Xiaohui , Sun Jinyu 
Published: August 2020

AbstractNowadays, blue fluorescent organic light‐emitting diodes (FOLEDs) have attracted considerable attention from both academia and industry. According to spin statistics, electrical excitation results in the formation of ∼25% singlet excitons and ∼75% triplet excitons (signifying ~75% energy loss), which triggered wide‐ranging efforts to harvest as many triplet excitons as possible. The materials that can convert triplet excitons into singlet excitons from the high‐lying excited triplet states (referred as “hot exciton” channel) to realize high efficiency were reported, which can also efficaciously avoid the accumulation of triplet excitons in T1state. In this study, by means of density functional theory (DFT) and time‐dependent DFT, we have theoretically investigated the electronic and photophysical properties of 16 newly designed molecules with donor‐bridge‐acceptor framework to search for the blue FOLED materials exploiting the “hot exciton” path. Important properties, such as singlet‐triplet energy gaps, absorption and emission parameters, and reverse intersystem crossing rates (kRISC), of five target molecules were studied. The calculated results demonstrate that thiophene‐diphenylamine (kRISCup to 1.03 × 108 seconds−1) may have promising potential as blue FOLED materials by virtue of the “hot exciton” effect.
Microfluidic devices for detection of RNA viruses
Authors: Basiri Arefeh , Heidari Arash , Nadi Melina Farshbaf , Fallahy Mohammad Taha Pahlevan , Nezamabadi Sasan Salehi , Sedighi Mohammadreza , Saghazadeh Amene , Rezaei Nima 
Published: August 2020

SummaryThere is a long way to go before the coronavirus disease 2019 (Covid‐19) outbreak comes under control. qRT‐PCR is currently used for the detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the causative agent of Covid‐19, but it is expensive, time‐consuming, and not as sensitive as it should be. Finding a rapid, easy‐to‐use, and cheap diagnostic method is necessary to help control the current outbreak. Microfluidic systems provide a platform for many diagnostic tests, including RT‐PCR, RT‐LAMP, nested‐PCR, nucleic acid hybridization, ELISA, fluorescence‐Based Assays, rolling circle amplification, aptamers, sample preparation multiplexer (SPM), Porous Silicon Nanowire Forest, silica sol‐gel coating/bonding, and CRISPR. They promise faster, cheaper, and easy‐to‐use methods with higher sensitivity, so microfluidic devices have a high potential to be an alternative method for the detection of viral RNA. These devices have previously been used to detect RNA viruses such as H1N1, Zika, HAV, HIV, and norovirus, with acceptable results. This paper provides an overview of microfluidic systems as diagnostic methods for RNA viruses with a focus on SARS‐CoV‐2.
Alpha‐1‐antitrypsin: A possible host protective factor against Covid‐19
Authors: de Loyola Mariana Braccialli , dos Reis Thaís Tereza Aguiar , de Oliveira Guilherme Xavier Lyra Malcher , da Fonseca Palmeira Julys , Argañaraz Gustavo A. , Argañaraz Enrique R. 
Published: August 2020

SummaryUnderstanding Covid‐19 pathophysiology is crucial for a better understanding of the disease and development of more effective treatments. Alpha‐1‐antitrypsin (A1AT) is a constitutive tissue protector with antiviral and anti‐inflammatory properties. A1AT inhibits SARS‐CoV‐2 infection and two of the most important proteases in the pathophysiology of Covid‐19: the transmembrane serine protease 2 (TMPRSS2) and the disintegrin and metalloproteinase 17 (ADAM17). It also inhibits the activity of inflammatory molecules, such as IL‐8, TNF‐α, and neutrophil elastase (NE). TMPRSS2 is essential for SARS‐CoV‐2‐S protein priming and viral infection. ADAM17 mediates ACE2, IL‐6R, and TNF‐α shedding. ACE2 is the SARS‐CoV‐2 entry receptor and a key component for the balance of the renin‐angiotensin system, inflammation, vascular permeability, and pulmonary homeostasis. In addition, clinical findings indicate that A1AT levels might be important in defining Covid‐19 outcomes, potentially partially explaining associations with air pollution and with diabetes. In this review, we focused on the interplay between A1AT with TMPRSS2, ADAM17 and immune molecules, and the role of A1AT in the pathophysiology of Covid‐19, opening new avenues for investigating effective treatments.
Succinylated Starches for Dye Removal
Authors: Soto Diana , León Orietta , Muñoz‐Bonilla Alexandra , Fernandez‐García Marta 
Published: August 2020

AbstractSuccinylated bitter cassava starches are evaluated for the removal of cationic, methylene blue (MB) and anionic, methyl orange (MO) dyes present in water. The native starch (NS) extracted from bitter cassava by the dry method, is modified using succinic anhydride (SA) as esterifying agent and sodium hydroxide, sodium carbonate, sodium sulfate, and sodium chloride as non‐toxic and environmentally friendly catalysts. The effect of the type and concentration of catalyst on the modification is evaluated. Starch replacement with SA is confirmed by Fourier transform infrared spectroscopy, wide‐angle X‐ray diffraction, thermogravimetric analysis, and scanning electron microscopy. The degree of substitution in the resulting succinylated starches is determined by volumetric analysis, presenting high values (0.5–0.9). These materials act as superabsorbent gels, sensitive to changes in pH and ionic strength, and mostly with anti‐polyelectrolytic behavior. MB dye has a higher affinity for succinylated starches than the MO dye. The removal capacity of MB is also influenced by the pH and the ionic strength of the solution. The kinetics and adsorption isotherms are satisfactorily adjusted to the pseudo‐second order and Freundlich models, respectively. The esters functionalities of the starch prove to be reusable adsorbents, completing successfully five cycles of adsorption‐desorption.
Groundwater Upwelling Regulates Thermal Hydrodynamics and Salmonid Movements during High‐Temperature Events at a Montane Tributary Confluence
Authors: Ritter Thomas David , Zale Alexander V. , Grisak Grant , Lance Michael J. 
Published: August 2020

AbstractThe Smith River is a popular recreational sport fishery in western Montana, but salmonid abundances there are thought to be artificially limited by riparian land‐use alterations, irrigation water withdrawals, and high summer water temperatures. We used integrated networks of temperature loggers, PIT tag antenna stations, and in situ temperature mapping to investigate the thermal hydrodynamics and associated movements of PIT‐tagged salmonids at the confluence of Tenderfoot Creek, a major, unaltered coldwater tributary of the Smith River. Contrary to expectations, Tenderfoot Creek itself was not used as a thermal refuge by salmonids during periods of high water temperatures in Smith River; rather, its cool outflow plume into the main stem was used instead. Mean daily outflow water temperatures averaged 2.9°C lower than those of the Smith River during summer and ranged from 0.5°C to 6.1°C lower. Moreover, measured and estimated temperatures in the outflow were cooler (by up to 2.8°C) than in Tenderfoot Creek itself at times as a result of groundwater upwelling at the confluence. Detections of PIT‐tagged fish in the thermal plume increased, especially at night, when daily mean water temperatures exceeded 20°C in the main‐stem Smith River; more than four times as many PIT‐tagged fish were detected in the plume (N = 52) than along the opposite bank (N = 12), which ostensibly afforded better cover. Coldwater tributary confluences may provide superior thermal refuges for salmonids—cooler than the tributaries themselves—when water temperatures in river main stems are stressful.
The challenge of predicting distal active site mutations in computational enzyme design
Authors: Osuna Sílvia 
Published: August 2020

AbstractMany computational enzyme design approaches have been developed in recent years that focus on a reduced set of key enzymatic features. Initial protocols mostly focused on the chemical steps(s) through transition state stabilization, whereas most recent approaches exploit the enzyme conformational dynamics often crucial for substrate binding, product release, and allosteric regulation. The detailed evaluation of the conformational landscape of many laboratory‐evolved enzymes has revealed dramatic changes on the relative stabilities of the conformational states after mutation, favoring those conformational states key for the novel functionality. Of note is that these mutations are often located all around the enzyme structure, which contrasts with most of the computational design strategies that reduce the problem into active site alterations. Recent computational strategies have been developed that consider enzyme design as a population shift problem, that is, redistribution of the relative stabilities of the conformational states induced by mutations. These strategies focus on reconstructing the conformational landscape of the enzyme, applying correlation‐based tools to elucidate the underlying allosteric network of interactions and identify potential mutation hotspots located at the active site, but most importantly at distal positions for the first time.This article is categorized under:
Structure and Mechanism > Computational Biochemistry and Biophysics
Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods
Software > Molecular Modeling
A review of h‐likelihood and hierarchical generalized linear model
Authors: Jin Shaobo , Lee Youngjo 
Published: August 2020

AbstractFisher's classical likelihood has become the standard procedure to make inference for fixed unknown parameters. Recently, inferences of unobservable random variables, such as random effects, factors, missing values, etc., have become important in statistical analysis. Because Fisher's likelihood cannot have such unobservable random variables, the full Bayesian method is only available for inference. An alternative likelihood approach is proposed by Lee and Nelder. In the context of Fisher likelihood, the likelihood principle means that the likelihood function carries all relevant information regarding the fixed unknown parameters. Bjørnstad extended the likelihood principle to extended likelihood principle; all information in the observed data for fixed unknown parameters and unobservables are in the extended likelihood, such as the h‐likelihood. However, it turns out that the use of extended likelihood for inferences is not as straightforward as the Fisher likelihood. In this paper, we describe how to extract information of the data from the h‐likelihood. This provides a new way of statistical inferences in entire fields of statistical science.This article is categorized under:
Statistical Models > Generalized Linear Models
Algorithms and Computational Methods > Maximum Likelihood Methods
Gravitational phase transition mediated by thermalon in Einstein-Gauss-Bonnet-Maxwell-Kalb-Ramond gravity
Authors: Samart Daris , Channuie Phongpichit 
Published: August 2020

Abstract
In this work, we study the possible existence of gravitational phase transition from AdS to dS asymptotic geometries in Einstein-Gauss-Bonnet gravity by adding the Maxwell one-form field (Aμ) and the Kalb-Ramond two-form field (Bμν) as impurity substitutions. The phase transitions proceed via the bubble nucleation of spherical thin-shells described by different branches of the solutions which host a dS black hole in the interior and asymptotic thermal AdS state in the exterior. We analyze the phase diagrams of the free energy and temperature to demonstrate the existence of the phase transitions in the grand canonical ensemble (fixed electrical potential). The phase transitions of having the one-form and two-form charges are possible in which the critical temperature is lower than that of the neutral case. Comparing results with existing literature, more importantly, our analyses show that the critical temperature and the Gauss-Bonnet coupling λ of the phase transitions get decreased by adding more types of the charges.
Consequences of vector-like quarks of Nelson-Barr type
Authors: Cherchiglia A.L. , Nishi C.C. 
Published: August 2020

AbstractThe Nelson-Barr mechanism to solve the strong CP problem requires vector- like quarks (VLQs) to transmit the spontaneous CP breaking to the SM. We study the scenario where only these VLQs are within reach at the TeV scale while the spontaneous CP breaking sector is inaccessible. We investigate how these VLQs of Nelson-Barr type differ from generic VLQs and find from parameter counting that one less parameter is needed. In particular, for one VLQ of Nelson-Barr type, there is only one CP odd quantity that is responsible for all CP violation. In this case, we solve the technical problem of parametrizing only the new physics parameters while keeping the SM parameters as independent inputs. For one down-type VLQ, the model is largely flavor safe because the VLQ couplings to the SM up quarks and theWare hierarchically smaller for lighter quarks.
Causality and stability conditions of a conformal charged fluid
Authors: Taghinavaz Farid 
Published: August 2020

Abstract
In this paper, I study the conditions imposed on a normal charged fluid so that the causality and stability criteria hold for this fluid. I adopt the newly developed General Frame (GF) notion in the relativistic hydrodynamics framework which states that hydrodynamic frames have to be fixed after applying the stability and causality conditions. To do this, I take a charged conformal matter in the flat and 3 + 1 dimension to analyze better these conditions. The causality condition is applied by looking to the asymptotic velocity of sound hydro modes at the large wave number limit and stability conditions are imposed by looking to the imaginary parts of hydro modes as well as the Routh-Hurwitz criteria. By fixing some of the transports, the suitable spaces for other ones are derived. I observe that in a dense medium having a finite U(1) charge with chemical potential μ0, negative values for transports appear and the second law of thermodynamics has not ruled out the existence of such values. Sign of scalar transports are not limited by any constraints and just a combination of vector transports is limited by the second law of thermodynamic. Also numerically it is proved that the most favorable region for transports $$ {\tilde{\upgamma}}_{1,2}, $$

γ
˜

1
,
2

,
coefficients of the dissipative terms of the current, is of negative values.
Notes on the 11D pure spinor wordline vertex operators
Authors: Guillen Max 
Published: August 2020

Abstract
The construction of the ghost number zero and one vertex operators for the 11D pure spinor superparticle will be revisited. In this sense, an alternative way of defining the ghost number one vertex operator will be given after introducing a ghost number -2 operator made out of physical operators defined on the 11D non-minimal pure spinor superspace. This procedure will make explicit and transparent the relation between the ghost number three and one vertex operators. In addition, using a non-Lorentz covariant b-ghost, ghost number zero and two vertex operators satisfying standard descent equations will be presented in full form.
The SO(10)-inspired leptogenesis timely opportunity
Authors: Di Bari Pasquale , Samanta Rome 
Published: August 2020

Abstract
We study the connection between absolute neutrino mass and neutrino mixing parameters within SO(10)-inspired leptogenesis. We show that current favoured values of the unknown neutrino mixing parameters point toward values of the absolute neutrino mass scale that will be fully tested by cosmological observations and neutrinoless double beta decay experiments during next years. In particular, for mD2/mcharm≤ 5, where mD2 is the intermediate Dirac neutrino mass, and for current best fit values of the Dirac phase δ and the atmospheric mixing angle θ23, we derive a lower bound on the neutrinoless double beta decay effective neutrino mass mee ≳ 31 meV and on the sum of the neutrino masses Σimi ≳ 125 meV. These lower bounds hold for normally ordered neutrino masses, as currently favoured by global analyses, and approximately for δ ∈ [155°, 240°] and θ23 in the second octant. If values in this region will be confirmed by future planned long baseline experiments, then a signal at next generation neutrinoless double beta decay experiments is expected, despite neutrino masses being normally ordered. Outside the region, the lower bounds strongly relax but a great fraction of the allowed range of values still allows a measurement of the lightest neutrino mass. Therefore, in the next years low energy neutrino experiments will provide a stringent test of SO(10)-inspired leptogenesis, that might result either in severe constraints or in a strong evidence.
Multi-boundary correlators in JT gravity
Authors: Okuyama Kazumi , Sakai Kazuhiro 
Published: August 2020

AbstractWe continue the systematic study of the thermal partition function of Jackiw-Teitelboim (JT) gravity started in [arXiv:1911.01659]. We generalize our analysis to the case of multi-boundary correlators with the help of the boundary creation operator. We clarify how the Korteweg-de Vries constraints arise in the presence of multiple boundaries, deriving differential equations obeyed by the correlators. The differential equations allow us to compute the genus expansion of the correlators up to any order without ambiguity. We also formulate a systematic method of calculating the WKB expansion of the Baker-Akhiezer function and the ’t Hooft expansion of the multi-boundary correlators. This new formalism is much more efficient than our previous method based on the topological recursion. We further investigate the low temperature expansion of the two-boundary correlator. We formulate a method of computing it up to any order and also find a universal form of the two-boundary correlator in terms of the error function. Using this result we are able to write down the analytic form of the spectral form factor in JT gravity and show how the ramp and plateau behavior comes about. We also study the Hartle-Hawking state in the free boson/fermion representation of the tau-function and discuss how it should be related to the multi-boundary correlators.
Weyl anomaly induced Fermi condensation and holography
Authors: Chu Chong-Sun , Miao Rong-Xin 
Published: August 2020

Abstract
Recently it is found that, due to Weyl anomaly, a background scalar field induces a non-trivial Fermi condensation for theories with Yukawa couplings. For simplicity, the paper consider only scalar type Yukawa coupling and, in the BCFT case, only for a specific boundary condition. In these cases, the Weyl anomaly takes on a simple special form. In this paper, we generalize the results to more general situations. First, we obtain general expressions of Weyl anomaly due to a background scalar and pseudo scalar field in general 4d BCFTs. Then, we derive the general form of Fermi condensation from the Weyl anomaly. It is remarkable that, in general, Fermi condensation is non-zero even if there was not a non-vanishing scalar field background. Finally, we verify our results with free BCFT with Yukawa coupling to scalar and pseudo-scalar background potential with general chiral bag boundary condition and with holographic BCFT. In particular, we obtain the shape and curvature dependence of the Fermi condensate from the holographic one point function.
Resonating AdS soliton
Authors: Garbiso Markus , Ishii Takaaki , Murata Keiju 
Published: August 2020

Abstract
The AdS soliton is a nonsingular spacetime that has a flat conformal boundary with a compact S1 direction. We find a horizonless cohomogeneity-1 metric that describes nonlinear gravitational oscillations of the AdS soliton in five dimensions. We call this spacetime the resonating AdS soliton. This solution is obtained as the nonlinear extension of normal modes of the AdS soliton dual to spin-2 glueball excitations. The boundary energy momentum tensor of the resonating AdS soliton has time periodic components, and it is interpreted as a coherently excited state in the dual field theory. Physical quantities of the resonating AdS soliton are multivalued at a fixed energy, suggesting a transition between different frequency solutions. The energy of the resonating AdS soliton is higher than that of the undeformed AdS soliton, in accordance with the positive energy conjecture proposed by Horowitz and Myers.