bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutation Spectrum of Tuberous Sclerosis Complex Patients in Indian Population
Authors: Sudarshan Shruthi , Kumar Atin , Gupta Arun , Bhari Neetu , Sethuraman Gomathy , Kaushal Tanuja , Pradhan Ankita , Sapra Savita , Gupta Neerja , Kaur Punit , Gulati Sheffali , Chakrawarty Biswaroop , Danda Sumita , Bhatt Meenakshi , Kapoor Seema , Girisha Katta M. , Sankhyan Naveen , Kabra Madhulika , Chowdhury Madhumita Roy 
Published: September 2020

AbstractTuberous sclerosis complex (TSC) is a multiorgan disorder characterized by formation of hamartomas and broad phenotypic spectrum including seizures, mental retardation, renal dysfunction, skin manifestations and brain tubers. It is inherited in an autosomal dominant pattern, caused due to mutation in either TSC1 or TSC2 genes. Seizures are one of the major presenting symptoms of TSC that helps in early diagnosis. The present study describes the mutation spectrum in TSC1 and TSC2 genes in TSC patients and their association with neurocognitive-behavioral phenotypes. Ninety-eight TSC patients were enrolled for TSC genetic testing after detailed clinical and neurobehavioral assessment. Large genomic rearrangement testing was performed by multiplex ligation-dependent probe amplification (MLPA) technique for all cases and Sanger sequencing was performed for MLPA negative cases. Large rearrangements were identified in approximately 1% in TSC1 and 14.3% in TSC2 genes. The present study observed the presence of duplications in two (2%) cases, both involving TSC2/PKD1 contiguous genes which to the best of our knowledge is reported for the first time. 8.1% of small variants were identified in the TSC1 gene and 85.7% in TSC2 gene, out of which 23 were novel variations and no variants were found in six (6.1%) cases. This study provides a representative picture of the distribution of variants in the TSC1 and TSC2 genes in Indian population along with the detailed assessment of neurological symptoms. This is the largest cohort study from India providing an overview of comprehensive clinical and molecular spectrum.
Mapping the community: use of research evidence in policy and practice
Authors: Farley-Ripple Elizabeth N. , Oliver Kathryn , Boaz Annette 
Published: September 2020

AbstractThe use of research evidence (URE) in policy and practice is relevant to many academic disciplines, as well as policy and practice domains. Although there has been increased attention to how such evidence is used, those engaged in scholarship and practice in this area face challenges in advancing the field. This paper attempts to “map the field” with the objective of provoking conversation about where we are and what we need to move forward. Utilizing survey data from scholars, practitioners, and funders connected to the study of the use of research evidence, we explore the extent to which URE work span traditional boundaries of research, practice, and policy, of different practice/policy fields, and of different disciplines. Descriptive and network analyses point to the boundary spanning and multidisciplinarity of this community, but also suggest exclusivity, as well as fragmentation among disciplines and literatures on which this work builds. We conclude with opportunities for to improve the connectedness, inclusiveness, relationship to policy and practice, and sustainability of URE scholarship.
Advanced LIGO squeezer platform for backscattered light and optical loss reduction
Authors: Fernández-Galiana Álvaro , McCuller Lee , Kissel Jeff , Barsotti Lisa , Miller John , Tse Maggie , Evans Matthew , Aston Stuart M , Abbott Richard , Shaffer Thomas J , Pele Arnaud , Romie Janeen H , Weaver Betsy , Fritschel Peter , Mavalvala Nergis , Matichard Fabrice 
Published: September 2020

Abstract
The Advanced LIGO gravitational-wave detectors are limited by optical quantum noise in most of their detection band. To overcome this limit, squeezed vacuum states have been injected into the Advanced LIGO detectors during the third observing run (O3), leading to an increase of their detection rate by about 40% to 50%. Here we present a key element of LIGO’s squeezed vacuum source: the seismic isolation platform that houses core components placed in ultra-high vacuum. This paper describes the architecture of the isolation platform as well as the active control system, tuned to minimize backscattered light that otherwise deteriorates the sensitivity of the detectors. This architecture permits fewer optical Faraday isolators in the optical path of the squeezing system, minimizing optical losses to maximize the quantum noise improvement. The system reliably operated throughout LIGO’s O3 with no evidence of noise from backscattered light. The innovative architecture of this platform makes it ideal for straightforward reshaping and adaptation to other gravitational-wave detector subsystems and low-noise optical instrumentation.
Hölder-logarithmic stability in Fourier synthesis
Authors: Isaev Mikhail , Novikov Roman G 
Published: September 2020

Abstract
We prove a Hölder-logarithmic stability estimate for the problem of finding a sufficiently regular compactly supported function v on

R

d

from its Fourier transform

F
v

given on [−r, r]
d
. This estimate relies on a Hölder stable continuation of

F
v

from [−r, r]
d
to a larger domain. The related reconstruction procedures are based on truncated series of Chebyshev polynomials. We also give an explicit example showing optimality of our stability estimates.
A novel baseline-free defect detection and localization method of welded steel plate based on reciprocity loss
Authors: He Tianhao , Xing Gailan , Li Yong , Li Qinfei , Zhou Shaoping 
Published: September 2020

Abstract
In recent years, ultrasonic Lamb waves have been widely applied to the field of non-destructive testing of plate-like structures as they have outstanding advantages, such as low attenuation, high sensitivity, and wide detection range. Current studies about defect-detection of plate-like structures using Lamb waves mostly focus on non-weld plate-like structures, and defect-detection methods are based on baseline data. This paper proposes a novel baseline-free damage inspection method of welded plate-like structures, which is based on the principle of reciprocity loss and combines the OPTICS and K-means intelligent clustering algorithms to achieve accurate defect localization. In order to verify the location accuracy of the clustering defect localization algorithm, this paper performs comparative experiments between the ellipse imaging algorithm and the clustering algorithm, which use baseline data as health signals. The comparative experimental results show that the single-defect location accuracy of the clustering algorithm is greatly improved compared with the traditional ellipse algorithm. Moreover, in order to verify the validity and feasibility of the baseline-free method, this paper applies this method to obtain characteristic signals and combines the clustering algorithm to locate both single-defect and double-defects. The experimental result of baseline-free method shows that this method can successfully detect and locate multiple defects, which gets rid of the dependence of baseline data.
Apparent differences between single layer molybdenum disulphide fabricated via chemical vapour deposition and exfoliation
Authors: Pollmann Erik , Madauß Lukas , Schumacher Simon , Kumar Uttam , Heuvel Flemming , vom Ende Christina , Yilmaz Sümeyra , Güngörmüs Sümeyra , Schleberger Marika 
Published: September 2020

Abstract
Innovative applications based on two-dimensional solids require cost-effective fabrication processes resulting in large areas of high quality materials. Chemical vapour deposition is among the most promising methods to fulfill these requirements. However, for 2D materials prepared in this way it is generally assumed that they are of inferior quality in comparison to the exfoliated 2D materials commonly used in basic research. In this work we challenge this assumption and aim to quantify the differences in quality for the prototypical transition metal dichalcogenide MoS2. To this end single layers of MoS2 prepared by different techniques (exfoliation, grown by different chemical vapour deposition methods, transfer techniques and as vertical heterostructure with graphene) are studied by Raman and photoluminescence spectroscopy, complemented by atomic force microscopy. We demonstrate that as-prepared MoS2, directly grown on SiO2, differs from exfoliated MoS2 in terms of higher photoluminescence, lower electron concentration and increased strain. As soon as a water film is intercalated (e.g. by transfer) underneath the grown MoS2, in particular the (opto)electronic properties become practically identical to those of exfoliated MoS2. A comparison of the two most common precursors shows that the growth with MoO3 causes greater strain and/or defect density deviations than growth with ammonium heptamolybdate. As part of a heterostructure directly grown MoS2 interacts much stronger with the substrate and in this case an intercalated water film does not lead to the complete decoupling, which is typical for exfoliation or transfer. Our work shows that the supposedly poorer quality of grown 2D transition metal dichalcogenides is indeed a misconception.
Coupling between structural properties and charge transport in nano-crystalline and amorphous graphitic carbon films, deposited by electron-beam evaporation
Authors: Brus V V , Ilashchuk M I , Orletskyi I G , Solovan M M , Parkhomenko G P , Babichuk I S , Schopp N , Andrushchak G O , Mostovyi A I , Maryanchuk P D 
Published: September 2020

Abstract
Nano-crystalline and amorphous films of graphitized carbon were deposited by electron-beam evaporation of bulk graphite. Structural properties and the size of graphite nanoclusters (L ≈ 1.2–5 nm) in the films were determined from the analysis of their Raman spectra. Electrical properties of the bulk nano-crystalline graphite reference sample and the deposited graphitic carbon films were measured by means of the Hall effect technique within the temperature range from 290 to 420 K. The electrical conductivity σ and Hall mobility μH
of all samples exhibited exponential temperature dependences, indicating on the non-metallic behavior. Electrical properties of the amorphous graphitic carbon thin films, deposited at low substrate temperatures (620 and 750 K) were analyzed in the scope of the hopping charge transport mechanism via localized states. We have shown that the charge transport in the bulk and thin film (920 K) nano-crystalline graphite samples is carried out via the tunneling and thermionic emission over potential barriers at the grain boundaries.This paper contributes towards better understanding of coupling between structural and electrical properties of graphitic carbon thin films.
Excitation of electrostatic solitary waves during neutralization of ion beam pulse by plasma
Authors: Lan C , Dong P , Li J 
Published: September 2020

Abstract
The possibility of exciting electrostatic solitary waves (ESWs) during the neutralization of ion beam pulses by plasmas is investigated using a two-dimensional (2D) electrostatic particle-in-cell (PIC) code. The simulation results show that if an axial magnetic field is applied, an ESW can be excited when the ion beam enters the plasma. The ESW is caused by the phase space vortex motion of electrons in the potential well formed by the plasma and the ion beam. The ESW is very stable and has a very long lifetime when it propagates in the plasma and the ion beam. The ESW has a 2D space structure, with about 3 cm length and more than twice the width of the ion beam. The splitting of the ESW is observed when it encounters a potential drop. The excitation conditions of the ESW are also discussed.
Entropy production at criticality in a nonequilibrium Potts model
Authors: Martynec Thomas , Klapp Sabine H L , Loos Sarah A M 
Published: September 2020

Abstract
Understanding nonequilibrium systems and the consequences of irreversibility for the system’s behavior as compared to the equilibrium case, is a fundamental question in statistical physics. Here, we investigate two types of nonequilibrium phase transitions, a second-order and an infinite-order phase transition, in a prototypical q-state vector Potts model which is driven out of equilibrium by coupling the spins to heat baths at two different temperatures. We discuss the behavior of the quantities that are typically considered in the vicinity of (equilibrium) phase transitions, like the specific heat, and moreover investigate the behavior of the entropy production (EP), which directly quantifies the irreversibility of the process. For the second-order phase transition, we show that the universality class remains the same as in equilibrium. Further, the derivative of the EP rate with respect to the temperature diverges with a power-law at the critical point, but displays a non-universal critical exponent, which depends on the temperature difference, i.e., the strength of the driving. For the infinite-order transition, the derivative of the EP exhibits a maximum in the disordered phase, similar to the specific heat. However, in contrast to the specific heat, whose maximum is independent of the strength of the driving, the maximum of the derivative of the EP grows with increasing temperature difference. We also consider entropy fluctuations and find that their skewness increases with the driving strength, in both cases, in the vicinity of the second-order transition, as well as around the infinite-order transition.
Communication tasks in operational theories
Authors: Heinosaari Teiko , Kerppo Oskari , Leppäjärvi Leevi 
Published: September 2020

Abstract
We investigate the question which communication tasks can be accomplished within a given operational theory. The concrete task is to find out which communication matrices have a prepare-and-measure implementation with multiple states and a single measurement from a given theory, without using shared randomness. To set a general framework for this question we develop the ultraweak matrix majorization in the set of communication matrices. This preorder gives us means to determine when one communication task is more difficult than another. Furthermore, we introduce several monotones which can be used to compare and characterize the communication matrices. We observe that not only do the monotones allow us to compare communication matrices, but also their maximal values in a given theory are seen to relate to some physical properties of the theory. The maximal values can then be thought as ‘dimensions’, allowing us to compare different theories to each other. We analyse the introduced monotones one by one and demonstrate how the set of implementable communication matrices is different in several theories with the focus being mainly on the difference between classical and quantum theories of a given dimension.
Integrals whose saddle-point expansions terminate
Authors: Berry M V 
Published: September 2020

Abstract
The saddle-point expansion for integrals with integrand exp(−kf(x)) is a series in powers of 1/k. Usually this series diverges, but there is a family of exponent functions f(x), defining a family of canonical integrals, for which the series terminates and the saddle-point expansion is exact. For this family, the transformation x → X such that f(x) = X
2 possesses a Jacobian that is a polynomial in X, whose coefficients parameterise the canonical integrals.
Evaluation of surface properties and shear bond strength of zirconia substructure after sandblasting and acid etching
Authors: Zhang Qingqing , Yao Chun , Yuan Chunping , Zhang Hao , Liu Lin , Zhang Yue , Bai Jing , Tang Chunbo 
Published: September 2020

Abstract
To compare the effects of different surface treatment methods on the surface characteristics of yttria-stabilized tetragonal zirconia (Y-TZP) and relevant shear bond strength (SBS) between zirconia and composite resin. Forty-eight Y-TZP ceramics were randomly divided into four groups based on the specific surface treatments: Group C (blank treatment), Group Sand (sandblasting with 80 μm Al2O3 particles), Group HF (etched with 40% hydrofluoric acid for 10 min), and Group H2SO4 (etched with hot sulfuric acid for 10 min). Surface characteristics of the treated specimens, including morphology, roughness, wettability, chemical composition and crystalline structure were analyzed. SBS was tested by bonding ceramics to resin cement in the same group. Kruskal-Wallis test followed by pair wise comparison was conducted for statistical processing. A significance level of α = 0.05 was set. Three kinds of surface structures with different widths and heights in roughness were obtained, including micron-scale pit/peak size by sandblasting, nano-scale pit/peak size by hydrofluoric acid etching and middle submicron-scale pit/peak size by hot sulfuric acid etching. By comparison, the specimens of Group HF showed the most favorable wettability, the highest SBS and the lowest phase transformation than those of other groups. Therefore, HF etching was considered as a promising surface treatment to promote resin–zirconia bonding without excessive surface damage. The height, width, frequency and regularity of roughness altogether affected the shear strength.
Improvement the efficacy of Al/CuPc/n-Si/Al Schottky diode based on strong light absorption and high photocarriers response
Authors: Elgazzar Elsayed 
Published: September 2020

Abstract
Copper phthalocyanine has been prepared by simple chemical approach and its structural and optical properties were investigated. X-ray diffraction pattern exhibits a notable peak at

2
θ
=
6.75
°

assigned to the

α
−

phase of CuPc. SEM images show the particles distributed in nanospheres with average size at about 50 nm. The linear optical constants like optical band gap

(

E

g

)

and dielectric constants (

ε
′
,
ε
″

) were estimated from transmittance and reflectance spectra in the wavelength range from 250 to 900 nm. The energy gap was found to be 1.62 and 2.90 eV dependent on the incident photon energy. Al/CuPc/n-Si/Al Schottky diode has been fabricated using thermal evaporation technique. The electronic parameters such as the ideality factor

(
n
)
,

series resistance

(

R

s

)

,

and barrier height (

ϕ

b

) were evaluated in dark by applying the (I–V), Cheung-Chung, and Norde models. At various illumination intensities, the photocurrent sensitivity was studied based on the response of trapped charge carriers. At 1 Mhz, the built-in voltage

(

V

b
i

)

and donor concentration

(

N

d

)

were calculated from (C–V) measurements. The findings revealed that CuPc/n-type Si can be used as photodiode in optoelectronic applications.
Graph convolutional networks for epigenetic state prediction using both sequence and 3D genome data
Authors: Lanchantin Jack , Qi Yanjun 
Published: September 2020

Abstract

Motivation
Predictive models of DNA chromatin profile (i.e. epigenetic state), such as transcription factor binding, are essential for understanding regulatory processes and developing gene therapies. It is known that the 3D genome, or spatial structure of DNA, is highly influential in the chromatin profile. Deep neural networks have achieved state of the art performance on chromatin profile prediction by using short windows of DNA sequences independently. These methods, however, ignore the long-range dependencies when predicting the chromatin profiles because modeling the 3D genome is challenging.

Results
In this work, we introduce ChromeGCN, a graph convolutional network for chromatin profile prediction by fusing both local sequence and long-range 3D genome information. By incorporating the 3D genome, we relax the independent and identically distributed assumption of local windows for a better representation of DNA. ChromeGCN explicitly incorporates known long-range interactions into the modeling, allowing us to identify and interpret those important long-range dependencies in influencing chromatin profiles. We show experimentally that by fusing sequential and 3D genome data using ChromeGCN, we get a significant improvement over the state-of-the-art deep learning methods as indicated by three metrics. Importantly, we show that ChromeGCN is particularly useful for identifying epigenetic effects in those DNA windows that have a high degree of interactions with other DNA windows.

Availability and implementation
https://github.com/QData/ChromeGCN.

Supplementary information
Supplementary data are available at Bioinformatics online.
An efficient framework to identify key miRNA–mRNA regulatory modules in cancer
Authors: Mokhtaridoost Milad , Gönen Mehmet 
Published: September 2020

Abstract

Motivation
Micro-RNAs (miRNAs) are known as the important components of RNA silencing and post-transcriptional gene regulation, and they interact with messenger RNAs (mRNAs) either by degradation or by translational repression. miRNA alterations have a significant impact on the formation and progression of human cancers. Accordingly, it is important to establish computational methods with high predictive performance to identify cancer-specific miRNA–mRNA regulatory modules.

Results
We presented a two-step framework to model miRNA–mRNA relationships and identify cancer-specific modules between miRNAs and mRNAs from their matched expression profiles of more than 9000 primary tumors. We first estimated the regulatory matrix between miRNA and mRNA expression profiles by solving multiple linear programming problems. We then formulated a unified regularized factor regression (RFR) model that simultaneously estimates the effective number of modules (i.e. latent factors) and extracts modules by decomposing regulatory matrix into two low-rank matrices. Our RFR model groups correlated miRNAs together and correlated mRNAs together, and also controls sparsity levels of both matrices. These attributes lead to interpretable results with high predictive performance. We applied our method on a very comprehensive data collection by including 32 TCGA cancer types. To find the biological relevance of our approach, we performed functional gene set enrichment and survival analyses. A large portion of the identified modules are significantly enriched in Hallmark, PID and KEGG pathways/gene sets. To validate the identified modules, we also performed literature validation as well as validation using experimentally supported miRTarBase database.

Availability and implementation
Our implementation of proposed two-step RFR algorithm in R is available at https://github.com/MiladMokhtaridoost/2sRFR together with the scripts that replicate the reported experiments.

Supplementary information
Supplementary data are available at Bioinformatics online.