bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microstructure and wear resistance of the laser-cladded Al0.8CrFeCoNiCu0.5Bx high-entropy alloy coating on aluminum
Authors: Li Yanzhou , Shi Yan 
Published: January 2020

Abstract
Coatings with excellent mechanical properties are difficult to prepare on the aluminum alloy surfaces by laser surface engineering because of the low melting point and active chemical properties of aluminum (Al). Based on the unique entropy effect of a high-entropy alloy, we suppress the cracks in the cladding layer caused by the dilution ratio of the substrate, obtaining coatings exhibiting excellent wear resistance. The Al0.8CrFeCoNiCu0.5Bx coating exhibited a BCC1 + BCC2 + FCC phase when the x ≤ 0.1. When x ≥ 0.2, boride was formed in the Al0.8CrFeCoNiCu0.5Bx coatings, and it became the main phase of the Al0.8CrFeCoNiCu0.5B0.3 and Al0.8CrFeCoNiCuB0.4 coatings; however, no Al-rich intermetallic compound with a complex phase structure was formed. When 0 ≤ x ≤ 0.3, the bonding strengths of the Al0.8CrFeCoNiCu0.5Bx coatings were 70.6–176.2 MPa. An increase in the boron content increased the hardness of all the coatings, except the Al0.8CrFeCoNiCu0.5B0.3 coating. The hardness was 479–705 HV (6–9 times that of the substrate). The wear rate of the coating ranged from 1.50 × 10−7 to 1.19 × 10−5 mm3/Nm, which was only 0.01%–5.43% that of the substrate. The Al0.8CrFeCoNiCu0.5B0.2 coating exhibited the highest resistance to wearing, and its wear mechanism was identified as abrasive wear.
Influence of exit velocity distribution on self-bending extrusion
Authors: Min Fanlei , Zhu Guangming , Yue Bowen , Wang Zongshen , Yang Zhenyu , Zhai Xiaoqing 
Published: January 2020

Abstract
We proposed a relationship model between the exit velocity distribution and the shape of the extrusion profile. To verify the model, we designed multiple-extrusion ram differential extrusion and used the Arbitrary Lagrangian-Eulerian (ALE) method to simulate the natural bending deformation of the sheet metal. The die experimental test used a self-bending extrusion die for sheet metal was designed via a spline curve with inclination as the contour of the deflector chamber. The results showed that the standard arc profile was extruded when the exit velocity was linear, and the relative error between the predicted radius of curvature and the ALE simulation result was controlled within 5%. The relative error between the predicted value and the actual experimental result was 9.9%. Thus, this study can provide a reference for the design of self-bending extrusion dies.
A prime analogue Erdős-Pomerance result for Drinfeld modules with arbitrary endomorphism rings
Authors: Kuo Wentang , Tweedle David 
Published: January 2020

Let

k

\mathbf {k}

be a global function field, and let

A

\mathbf {A}

be the elements of

k

\mathbf {k}

regular outside a fixed place

∞
\infty

.

Let

ϕ
:

A

→
K
{
τ
}

\phi :\mathbf {A}\to K\{\tau \}

be a Drinfeld module of generic characteristic and rank

n
n

. For a prime

℘
\wp

of

K
K

of good reduction, let

F

℘

\mathbb {F}_\wp

be the residue field at

℘
\wp

, and let

χ

A

(

ϕ
(

F

℘

)

)

\chi _\mathbf {A}\big (\phi (\mathbb {F}_\wp )\big )

be the Euler-Poincaré characteristic of

F

℘

\mathbb {F}_\wp

viewed as an

A

\mathbf {A}

-module.

We determine the normal order of the number of distinct prime ideals of

A

\mathbf {A}

dividing

χ

A

(

ϕ
(

F

℘

)

)

\chi _\mathbf {A}\big (\phi (\mathbb {F}_\wp )\big )

, denoted by

ω

A

(

χ

A

(

ϕ
(

F

℘

)

)

)

\omega _\mathbf {A}\Big (\chi _\mathbf {A}\big (\phi (\mathbb {F}_\wp )\big )\Big )

, as

℘
\wp

runs over primes of

K
K

of degree

x
x

with a specified splitting behaviour.

Furthermore, let

a
∈
K

a\in K

be non-torsion for

ϕ
\phi

, and let

f
a

(
℘
)

f_a(\wp )

be the Euler-Poincaré characteristic of the submodule of

ϕ
(

F

℘

)

\phi (\mathbb {F}_\wp )

generated by

a
a

modulo

℘
\wp

. We also consider the problem of determining the distribution of

ω

A

(

f
a

(
℘
)

)

\omega _\mathbf {A}\big (f_a(\wp ) \big )

as

℘
\wp

runs over primes of

K
K

of degree

x
x

with a specified splitting behaviour.

Note that we do not make restrictions on

A

\mathbf {A}

,

ϕ
\phi

, or its endomorphism ring

E
n
d

K

{sep}

(
ϕ
)

\rm {End}_{K^\textrm {{sep}}}(\phi )

.
Biological applications of knowledge graph embedding models
Authors: Mohamed Sameh K , Nounu Aayah , Nováček Vít 
Published: January 2020

AbstractComplex biological systems are traditionally modelled as graphs of interconnected biological entities. These graphs, i.e. biological knowledge graphs, are then processed using graph exploratory approaches to perform different types of analytical and predictive tasks. Despite the high predictive accuracy of these approaches, they have limited scalability due to their dependency on time-consuming path exploratory procedures. In recent years, owing to the rapid advances of computational technologies, new approaches for modelling graphs and mining them with high accuracy and scalability have emerged. These approaches, i.e. knowledge graph embedding (KGE) models, operate by learning low-rank vector representations of graph nodes and edges that preserve the graph’s inherent structure. These approaches were used to analyse knowledge graphs from different domains where they showed superior performance and accuracy compared to previous graph exploratory approaches. In this work, we study this class of models in the context of biological knowledge graphs and their different applications. We then show how KGE models can be a natural fit for representing complex biological knowledge modelled as graphs. We also discuss their predictive and analytical capabilities in different biology applications. In this regard, we present two example case studies that demonstrate the capabilities of KGE models: prediction of drug–target interactions and polypharmacy side effects. Finally, we analyse different practical considerations for KGEs, and we discuss possible opportunities and challenges related to adopting them for modelling biological systems.
DeepHIT: a deep learning framework for prediction of hERG-induced cardiotoxicity
Authors: Ryu Jae Yong , Lee Mi Young , Lee Jeong Hyun , Lee Byung Ho , Oh Kwang-Seok 
Published: January 2020

Abstract

Motivation
Blockade of the human ether-à-go-go-related gene (hERG) channel by small compounds causes a prolonged QT interval that can lead to severe cardiotoxicity and is a major cause of the many failures in drug development. Thus, evaluating the hERG-blocking activity of small compounds is important for successful drug development. To this end, various computational prediction tools have been developed, but their prediction performances in terms of sensitivity and negative predictive value (NPV) need to be improved to reduce false negative predictions.

Results
We propose a computational framework, DeepHIT, which predicts hERG blockers and non-blockers for input compounds. For the development of DeepHIT, we generated a large-scale gold-standard dataset, which includes 6632 hERG blockers and 7808 hERG non-blockers. DeepHIT is designed to contain three deep learning models to improve sensitivity and NPV, which, in turn, produce fewer false negative predictions. DeepHIT outperforms currently available tools in terms of accuracy (0.773), MCC (0.476), sensitivity (0.833) and NPV (0.643) on an external test dataset. We also developed an in silico chemical transformation module that generates virtual compounds from a seed compound, based on the known chemical transformation patterns. As a proof-of-concept study, we identified novel urotensin II receptor (UT) antagonists without hERG-blocking activity derived from a seed compound of a previously reported UT antagonist (KR-36676) with a strong hERG-blocking activity. In summary, DeepHIT will serve as a useful tool to predict hERG-induced cardiotoxicity of small compounds in the early stages of drug discovery and development.

Availability and implementation
https://bitbucket.org/krictai/deephit and https://bitbucket.org/krictai/chemtrans

Supplementary information
Supplementary data are available at Bioinformatics online.
Census of halide-binding sites in protein structures
Authors: Skitchenko Rostislav K , Usoltsev Dmitrii , Uspenskaya Mayya , Kajava Andrey V , Guskov Albert 
Published: January 2020

Abstract

Motivation
Halides are negatively charged ions of halogens, forming fluorides (F−), chlorides (Cl−), bromides (Br−) and iodides (I−). These anions are quite reactive and interact both specifically and non-specifically with proteins. Despite their ubiquitous presence and important roles in protein function, little is known about the preferences of halides binding to proteins. To address this problem, we performed the analysis of halide–protein interactions, based on the entries in the Protein Data Bank.

Results
We have compiled a pipeline for the quick analysis of halide-binding sites in proteins using the available software. Our analysis revealed that all of halides are strongly attracted by the guanidinium moiety of arginine side chains, however, there are also certain preferences among halides for other partners. Furthermore, there is a certain preference for coordination numbers in the binding sites, with a correlation between coordination numbers and amino acid composition. This pipeline can be used as a tool for the analysis of specific halide–protein interactions and assist phasing experiments relying on halides as anomalous scatters.

Availability and implementation
All data described in this article can be reproduced via complied pipeline published at https://github.com/rostkick/Halide_sites/blob/master/README.md.

Supplementary information
Supplementary data are available at Bioinformatics online.
Estimating the power of sequence covariation for detecting conserved RNA structure
Authors: Rivas Elena , Clements Jody , Eddy Sean R 
Published: January 2020

Abstract

Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long non-coding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against their proposed conserved structures.

Availability and implementation
The R-scape web server is at eddylab.org/R-scape, with a link to download the source code.

Supplementary information
Supplementary data are available at Bioinformatics online.
Novel localizations and interactions of intercellular bridge proteins revealed by proteomic profiling†
Authors: Iwamori Tokuko , Iwamori Naoki , Matsumoto Masaki , Imai Hiroyuki , Ono Etsuro 
Published: January 2020

Abstract
Intercellular bridges (ICBs) connecting germ cells are essential for spermatogenesis, and their deletion causes male infertility. However, the functions and component factors of ICBs are still unknown. We previously identified novel ICB-associated proteins by proteomics analysis using ICB enrichment. Here, we performed immunoprecipitation–proteomics analyses using antibodies specific to known ICB proteins MKLP1, RBM44, and ectoplasmic specialization-associated protein KIAA1210 and predicted protein complexes in the ICB cores. KIAA1210, its binding protein topoisomerase2B (TOP2B), and tight junction protein ZO1 were identified as novel ICB proteins. On the other hand, as well as KIAA1210 and TOP2B, MKLP1 and RBM44, but not TEX14, were localized at the XY body of spermatocytes, suggesting that there is a relationship between ICB proteins and meiotic chromosomes. Moreover, small RNAs interacted with an ICB protein complex that included KIAA1210, RBM44, and MKLP1. These results indicate dynamic movements of ICB proteins and suggest that ICB proteins could be involved not only in the communication between germ cells but also in their epigenetic regulation. Our results provide a novel perspective on the function of ICBs and could be helpful in revealing the biological function of the ICB.
Glacier Retreat and Pacific Salmon
Authors: Pitman Kara J , Moore Jonathan W , Sloat Matthew R , Beaudreau Anne H , Bidlack Allison L , Brenner Richard E , Hood Eran W , Pess George R , Mantua Nathan J , Milner Alexander M , Radić Valentina , Reeves Gordon H , Schindler Daniel E , Whited Diane C 
Published: January 2020

AbstractGlaciers have shaped past and present habitats for Pacific salmon (Oncorhynchus spp.) in North America. During the last glacial maximum, approximately 45% of the current North American range of Pacific salmon was covered in ice. Currently, most salmon habitat occurs in watersheds in which glacier ice is present and retreating. This synthesis examines the multiple ways that glacier retreat can influence aquatic ecosystems through the lens of Pacific salmon life cycles. We predict that the coming decades will result in areas in which salmon populations will be challenged by diminished water flows and elevated water temperatures, areas in which salmon productivity will be enhanced as downstream habitat suitability increases, and areas in which new river and lake habitat will be formed that can be colonized by anadromous salmon. Effective conservation and management of salmon habitat and populations should consider the impacts of glacier retreat and other sources of ecosystem change.
p130Cas induces bone invasion by oral squamous cell carcinoma by regulating tumor epithelial–mesenchymal transition and cell proliferation
Authors: Yaginuma Tatsuki , Gao Jing , Nagata Kengo , Muroya Ryusuke , Fei Huang , Nagano Haruki , Chishaki Sakura , Matsubara Takuma , Kokabu Shoichiro , Matsuo Kou , Kiyoshima Tamotsu , Yoshioka Izumi , Jimi Eijiro 
Published: January 2020

Abstract
Bone invasion is a critical factor in determining the prognosis of oral squamous cell carcinoma (OSCC) patients. Transforming growth factor β (TGF-β) is abundantly expressed in the bone matrix and is involved in the acquisition of aggressiveness by tumors. TGF-β is also important to cytoskeletal changes during tumor progression. In this study, we examined the relationship between TGF-β signaling and cytoskeletal changes during bone invasion by OSCC. Immunohistochemical staining of OSCC samples from five patients showed the expression of p130Cas (Crk-associated substrate) in the cytoplasm and phosphorylated Smad3 expression in the nucleus in OSCC cells. TGF-β1 induced the phosphorylation of Smad3 and p130Cas, as well as epithelial–mesenchymal transition (EMT) accompanied by the downregulation of the expression of E-cadherin, a marker of epithelial cells, and the upregulation of the expression of N-cadherin, or Snail, a marker of mesenchymal cells, in human HSC-2 cells and mouse squamous cell carcinome VII (SCCVII) cells. SB431542, a specific inhibitor of Smad2/3 signaling, abrogated the TGF-β1-induced phosphorylation of p130Cas and morphological changes. Silencing p130Cas using an short hairpin RNA (shRNA) or small interfering RNA in SCCVII cells suppressed TGF-β1-induced cell migration, invasion, EMT and matrix metalloproteinase-9 (MMP-9) production. Compared with control SCCVII cells, SCCVII cells with silenced p130Cas strongly suppressed zygomatic and mandibular destruction in vivo by reducing the number of osteoclasts, cell proliferation and MMP-9 production. Taken together, these results showed that the expression of TGF-β/p130Cas might be a new target for the treatment of OSCC bone invasion.
Spatiotemporal Differences in the Regional Cortical Plate and Subplate Volume Growth during Fetal Development
Authors: Vasung Lana , Rollins Caitlin K , Velasco-Annis Clemente , Yun Hyuk Jin , Zhang Jennings , Warfield Simon K , Feldman Henry A , Gholipour Ali , Grant P Ellen 
Published: January 2020

AbstractThe regional specification of the cerebral cortex can be described by protomap and protocortex hypotheses. The protomap hypothesis suggests that the regional destiny of cortical neurons and the relative size of the cortical area are genetically determined early during embryonic development. The protocortex hypothesis suggests that the regional growth rate is predominantly shaped by external influences. In order to determine regional volumes of cortical compartments (cortical plate (CP) or subplate (SP)) and estimate their growth rates, we acquired T2-weighted in utero MRIs of 40 healthy fetuses and grouped them into early (&lt;25.5 GW), mid- (25.5–31.6 GW), and late (&gt;31.6 GW) prenatal periods. MRIs were segmented into CP and SP and further parcellated into 22 gyral regions. No significant difference was found between periods in regional volume fractions of the CP or SP. However, during the early and mid-prenatal periods, we found significant differences in relative growth rates (% increase per GW) between regions of cortical compartments. Thus, the relative size of these regions are most likely conserved and determined early during development whereas more subtle growth differences between regions are fine-tuned later, during periods of peak thalamocortical growth. This is in agreement with both the protomap and protocortex hypothesis.
Segregated Expression of ENaC Subunits in Taste Cells
Authors: Lossow Kristina , Hermans-Borgmeyer Irm , Meyerhof Wolfgang , Behrens Maik 
Published: January 2020

AbstractSalt taste is one of the 5 basic taste qualities. Depending on the concentration, table salt is perceived either as appetitive or aversive, suggesting the contribution of several mechanisms to salt taste, distinguishable by their sensitivity to the epithelial sodium channel (ENaC) blocker amiloride. A taste-specific knockout of the α-subunit of the ENaC revealed the relevance of this polypeptide for low-salt transduction, whereas the response to other taste qualities remained normal. The fully functional ENaC is composed of α-, β-, and γ-subunits. In taste tissue, however, the precise constitution of the channel and the cell population responsible for detecting table salt remain uncertain. In order to examine the cells and subunits building the ENaC, we generated mice carrying modified alleles allowing the synthesis of green and red fluorescent proteins in cells expressing the α- and β-subunit, respectively. Fluorescence signals were detected in all types of taste papillae and in taste buds of the soft palate and naso-incisor duct. However, the lingual expression patterns of the reporters differed depending on tongue topography. Additionally, immunohistochemistry for the γ-subunit of the ENaC revealed a lack of overlap between all potential subunits. The data suggest that amiloride-sensitive recognition of table salt is unlikely to depend on the classical ENaCs formed by α-, β-, and γ-subunits and ask for a careful investigation of the channel composition.
Can China Change the International System? The Role of Moral Leadership
Authors: Larson Deborah Welch 
Published: January 2020

Abstract
Yan Xuetong’s Leadership and the Rise of Great Powers argues that China should follow moral values in its foreign policy in order to attain international leadership. Drawing on ancient Chinese thought, Yan makes the case that China should strive for humane authority, influencing other states by leading through moral example and attracting supporters through providing benefits rather than using coercion. This essay evaluates the feasibility of China’s attainment of humane authority, which is related to status. Humane authority follows norms consistently toward rivals as well as friendly states whereas a hegemon uses a double standard. But double standards may not be so easily avoided because they derive from inherent psychological bias. The option of acquiring followers by providing them with security guarantees is not available to China in East Asia because of the prior existence of the US alliance system. Yan predicts that China’s growth will lead to a bipolar structure but points out that the conditions for a Cold War are absent. Nevertheless, technological competition between the US and China could lead to a ‘new Cold War’, which would hamper China’s efforts to widen its circle of followers. To be a humane authority, China should also avoid a war with the USA. There is a risk that naval competition could lead to local conflicts as a result of security dilemma dynamics. The two states should control status rivalry through a division of labour, by accepting the other’s pre-eminence in different areas through social cooperation.
Diagnostic Test Accuracy of Commercial Tests for Detection of Shiga Toxin–Producing Escherichia coli: A Systematic Review and Meta-Analysis
Authors: Tarr Gillian A M , Lin Chu Yang , Vandermeer Ben , Lorenzetti Diane L , Tarr Phillip I , Chui Linda , Hartling Lisa , Freedman Stephen B 
Published: January 2020

Abstract

Background
Rapid detection of Shiga toxin–producing Escherichia coli (STEC) enables appropriate monitoring and treatment. We synthesized available evidence to compare the performance of enzyme immunoassay (EIA) and PCR tests for the detection of STEC.

Methods
We searched published and gray literature for studies of STEC EIA and/or PCR diagnostic test accuracy relative to reference standards including at least one nucleic acid amplification test. Two reviewers independently screened studies, extracted data, and assessed quality with the second version of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Bivariate random effects models were used to meta-analyze the clinical sensitivity and specificity of commercial EIA and PCR STEC diagnostic tests, and summary receiver operator characteristic curves were constructed. We evaluated the certainty of evidence with the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach.

Results
We identified 43 articles reflecting 25 260 specimens. Meta-analysis of EIA and PCR accuracy included 25 and 22 articles, respectively. STEC EIA pooled sensitivity and specificity were 0.681 (95% CI, 0.571–0.773; very low certainty of evidence) and 1.00 (95% CI, 0.998–1.00; moderate certainty of evidence), respectively. STEC PCR pooled sensitivity and specificity were 1.00 (95% CI, 0.904–1.00; low certainty of evidence) and 0.999 (95% CI, 0.997–0.999; low certainty of evidence), respectively. Certainty of evidence was downgraded because of high risk of bias.

Conclusions
PCR tests to identify the presence of STEC are more sensitive than EIA tests, with no meaningful loss of specificity. However, given the low certainty of evidence, our results may overestimate the difference in performance.
Cochlear Implant Nonuse: Insight from Deaf Adults
Authors: Salehomoum Maryam 
Published: January 2020

Abstract
Research examining the outcome of pediatric cochlear implantation consists of certain limitations, including the use of assessments that are often restricted to auditory-spoken skills, biased recruitment practices, and lack of consideration for identity development. To better understand the long-term outcome of implantation, it is vital to seek out individuals who decide to stop using their device and elicit feedback related to their decision. Thus, 11 adults, who were past cochlear implant (CI) users, were interviewed to gain insight into factors that had led to their decision regarding cochlear implant nonuse. Results indicated several variables to have played a role, but the most prominent factors were limitations in postimplant auditory perceptual development and development of a d/Deaf identity. Although cochlear implant practices and technology have improved over the past few decades, we need to recognize the continued variability in outcome to ensure the provision of the most accurate information and appropriate services.