bluuebunny/crossref_metadata_2025_split huggingface dataset:
Residual feed intake and the inclusion of crude glycerin in the diet of feedlot-finished Nellore cattle
Authors: Silva Gabriele Voltareli da , Batalha Camila Delveaux Araujo , Cyrillo Joslaine Noely dos Santos Gonçalves , Canesin Roberta Carrilho , Barducci Robson Sfaciotti , Bonilha Sarah Figueiredo Martins 
Published: December 2021

Context The beef market faces an increasing demand for an environmentally friendly production system with high-quality final products. The use of strategies that improve system efficiency without detriment on quality are desired for both producers and consumer. Aims This study aimed to evaluate the effects of residual feed intake (RFI) and dietary inclusion of crude glycerin on carcass and meat quality traits of feedlot-finished Nellore cattle. Methods Nellore bulls selected for growth and classified as high (n = 14) and low (n = 14) RFI, with average liveweight of 328 kg and age of 552 days were used. Bulls received a high-concentrate diet for 96 days before slaughter and were randomly allocated to two experimental diets in a 2 × 2 factorial arrangement: RFI class (low or high) and dietary inclusion (CG) or not (WCG) of crude glycerin (20% on dry-matter basis). Data were analysed with the SAS MIXED procedure considering RFI class and diet as fixed effects and selection line as a random effect. Key results There were no significant differences between RFI classes for dry-matter intake during finishing or production traits. Dry-matter intake tended to be reduced by 16% in CG bulls, without alterations in production. Dietary glycerin inclusion tended to increase the protein content in the Longissimus muscle and significantly reduced the fat content. In low-RFI bulls, shear force was higher in unaged beef, and shear force and myofibrillar fragmentation index tended to be higher in meat aged for 14 days. RFI class did not affect Longissimus muscle fatty acid profile, which was highly influenced by dietary glycerin inclusion. Bulls allocated to the CG treatment had a reduction in saturated fatty acids, an increase in odd-chain fatty acids, and a trend towards increased omega-3 fatty acids, which significantly increased the omega-3:omega-6 ratio. Conclusions The use of Nellore bulls classified as low-RFI and crude glycerin inclusion in finishing diets of Nellore cattle do not compromise production, carcass traits or beef properties. Implications This approach increases the efficiency and sustainability of the production process and improves the nutritional characteristics of beef for human consumption.
RNA-Seq analysis of resistant and susceptible soybean genotypes in response to stress from soybean cyst nematode (
Authors: Jiang Haipeng , Bu Fanshan , Yan Shixin , Li Yi , Wu Tong , Bai RuiYao , Xu Aitong , Zhao Xue , Han Yingpeng 
Published: December 2021

The soybean cyst nematode (SCN, Heterodera glycine Ichinohe) is a major disease affecting soybean (Glycine max (L.) Merr.) production and yield. Breeding of new SCN-resistant cultivars and understanding their resistance mechanisms are valuable for improving SCN resistance of soybean. However, we still know little about resistance mechanisms to SCN. The purpose of our analysis was to understand the different resistance mechanisms of resistant and susceptible lines to SCN by dissecting their transcriptional changes during infection by SCN HG type 1.2.3.5.7. In this study, 119 recombinant inbred lines derived from a cross of cv. Dongnong L-204 (SCN resistant) and cv. Heinong 37 (SCN susceptible) were identified for resistance status to SCN HG type 1.2.3.5.7. Roots of the lines identified as extremely resistant or susceptible (L5, L89) were sequenced by transcriptome, and we obtained 66.61 Gb of data. Compared with the untreated control, there were 8394 and 6899 differentially expressed genes in SCN-infected roots of L5 and L89, respectively. Genes of metabolic pathways, biosynthesis of secondary metabolites, plant hormone signal transduction, and plant–pathogen interaction pathway were significantly expressed in both resistant and susceptible genotypes. The expression of genes of phenylpropanoid biosynthesis, flavonoid biosynthesis, thiamine metabolism, cutin, suberin and wax biosynthesis, and endocytosis pathway was significantly higher in the resistant line than the susceptible line. Transcription factor analysis showed that 88 transcription factors from 18 transcription factor families responded to SCN stress. Nine genes were identified by reverse transcriptase qPCR to be associated with SCN resistance. This study helps us to understand better the mechanism of soybean resistance to SCN.
SARS-CoV-2 spreads through cell-to-cell transmission
Authors: Zeng Cong , Evans John P. , King Tiffany , Zheng Yi-Min , Oltz Eugene M. , Whelan Sean P. J. , Saif Linda J. , Peeples Mark E. , Liu Shan-Lu 
Published: December 2021

Significance
It is currently unknown if SARS-CoV-2 can spread through cell–cell contacts, and if so, the underlying mechanisms and implications. In this work, we show, by using lentiviral pseudotyped virus, that the spike protein of SARS-CoV-2 mediates the viral cell-to-cell transmission, with an efficiency higher than that of SARS-CoV. We also find that cell–cell fusion contributes to cell-to-cell transmission, yet ACE2 is not absolutely required. While the authentic variants of concern (VOCs) B.1.1.7 (alpha) and B.1.351 (beta) differ in cell-free infectivity from wild type and from each other, these VOCs have similar cell-to-cell transmission capability and exhibit differential sensitivity to neutralization by vaccinee sera. Results from our study will contribute to a better understanding of SARS-CoV-2 spread and pathogenesis.
Minimally-modeled search of higher multipole gravitational-wave radiation in compact binary coalescences
Authors: Vedovato G , Milotti E , Prodi G A , Bini S , Drago M , Gayathri V , Halim O , Lazzaro C , Lopez D , Miani A , O’Brien B , Salemi F , Szczepanczyk M , Tiwari S , Virtuoso A , Klimenko S 
Published: December 2021

Abstract
As the Advanced LIGO and Advanced Virgo interferometers, soon to be joined by the KAGRA interferometer, increase their sensitivity, they detect an ever-larger number of gravitational waves with a significant presence of higher multipoles (HMs) in addition to the dominant (2, 2) multipole. These HMs can be detected with different approaches, such as the minimally-modeled burst search methods, and here we discuss one such approach based on the coherent WaveBurst (cWB) pipeline. During the inspiral phase the HMs produce chirps whose instantaneous frequency is a multiple of the dominant (2, 2) multipole, and here we describe how cWB can be used to detect these spectral features. The search is performed within suitable regions of the time-frequency representation; their shape is determined by optimizing the receiver operating characteristics. This novel method has already been used in the GW190814 discovery paper (Abbott et al 2020 Astrophys. J. Lett.
896 L44) and is very fast and flexible. Here we describe in full detail the procedure used to detect the (3, 3) multipole in GW190814 as well as searches for other HMs during the inspiral phase, and apply it to another event that displays HMs, GW190412, replicating the results obtained with different methods. The procedure described here can be used for the fast analysis of HMs and to support the findings obtained with the model-based Bayesian parameter estimates.
Effect of the electric field profile on the accuracy of E-FISH measurements in ionization waves
Authors: Chng Tat Loon , Pai David Z , Guaitella Olivier , Starikovskaia Svetlana M , Bourdon Anne 
Published: December 2021

Abstract
Electric field induced second harmonic (E-FISH) generation has emerged as a versatile tool for measuring absolute electric field strengths in time-varying, non-equilibrium plasmas and gas discharges. Yet recent work has demonstrated that the E-FISH signal, when produced with tightly focused laser beams, exhibits a strong dependence on both the length and shape of the applied electric field profile (along the axis of laser beam propagation). In this paper, we examine the effect of this dependence more meaningfully, by predicting what an E-FISH experiment would measure in a plasma, using 2D axisymmetric numerical fluid simulations as the true value. A pin-plane nanosecond discharge at atmospheric pressure is adopted as the test configuration, and the electric field evolution during the propagation of the ionization wave (IW) is specifically analysed. We find that the various phases of this evolution (before and up to the front arrival, immediately behind the front and after the connection to the grounded plane) are quite accurately described by three unique electric field profile shapes, each of which produces a different response in the E-FISH signal. As a result, the accuracy of an E-FISH measurement is generally predicted to be comparable in the first and third phases of the IW evolution, and significantly poorer in the second (intermediate) phase. Fortunately, even though the absolute error in the field strength at certain time instants could be large, the overall shape of the field evolution curve is relatively well captured by E-FISH. Guided by the simulation results, we propose a procedure for estimating the error in the initial phase of the IW development, based on the presumption that the starting field profile mirrors that of its corresponding Laplacian conditions before evolving further. We expect that this approach may be readily generalized and applicable to other IW problems or phenomena, thus extending the utility of the E-FISH diagnostic.
Characterization of FBK 3D pixel sensor modules based on RD53A readout chip for the ATLAS ITk
Authors: Samy Md.A.A. , Lapertosa A. , Vannoli L. , Gemme C. , Dalla Betta G.-F. 
Published: December 2021

Abstract
CERN is planning to upgrade its Large Hadron Collider to the High Luminosity phase (HL-LHC), pushing detector technologies to cope with unprecedently demanding performance in terms of particle rate and radiation hardness. The ATLAS experiment decided to equip the innermost layer (L0) of its Inner Tracker (ITk) with small-pitch 3D pixels of two different geometries, i.e., 25 µm × 100 µm for the central barrel and 50 µm × 50 µm for the lateral rings. A new generation of 3D pixels featuring these small-pitch dimensions and reduced active thickness (∼150 µm) has been developed to this purpose within a collaboration of INFN and FBK since 2014. Recently, the R&D activities have been focused on the characterization of modules based on sensors compatible with the RD53A readout chip, which were tested in laboratory and at beam lines. In this paper, we report on the characterization of modules irradiated with protons up to a fluence of 1 × 1016 neq/cm2, including threshold tuning and noise measurements, and results from beam tests performed at DESY. Moreover, we will discuss about the electrical characteristics at wafer level and at module level before and after irradiation.
Helium isotope separation by bi-layer membranes of g-C3N4
Authors: Poteryaeva Valentina A , Bubenchikov Alexey M , Bubenchikov Michael A , Lun-Fu Alexandr V , Jambaa Soninbayar 
Published: December 2021

Abstract
The problem of helium isotope separation via bi-layer membranes of graphitic carbon nitride g-C3N4 has been studied. The probability of passing isotopes through the membrane is derived from solving the Schrödinger integral equation using Hermite polynomials. The potential energy of the membrane is calculated based on modified Lennard-Johnes potential. The separation degree of the 3He/4He reaches the value of 1045 due to the resonant effect.
Dual-function of the ZnO nano-sheets as light absorber scaffold and electron transport material in perovskite solar cells
Authors: Bui Cong-Dan , Cao Van-Phuoc , Nguyen Van-Quy , Bui Thi-Hang , Tran Van-Dang 
Published: December 2021

Abstract
Recent advances in the development of perovskite solar cells using CH3NH3PbI3 as the absorber material have reached over 18.7% in power conversion efficiency. The best performance perovskite-based cells required support of a mesoporous charge collector. In this work we present a new process for preparing perovskite solar cells with the structure of AZO/Au/AZO(AAA)/ZnO-sheets/CH3NH3PbI3/HTM/Au. Herein, ZnO nanosheets layer was prepared by electrochemical deposition method using zinc nitrate hexahydrate as nutrient solution, then annealed at 150 °C in ambient air. The results show that high crystal ZnO sheets assembled simply from AZO top layer could act as electron transporter and scaffold for perovskite layer. The presentation of ZnO scaffold was exploited to improve 19% in power conversion efficiency, offering great promise for further improvement of the low-temperature, low-cost processing solar technology.
Biological synthesis, physico-chemical characterization of undoped and Co doped α-Fe2O3 nanoparticles using Tribulus terrestris leaf extract and its antidiabetic, antimicrobial applications
Authors: Sakthi Athithan A S , Jeyasundari J , Jacob Y B A 
Published: December 2021

Abstract
Hematite (α-Fe2O3) nanoparticles (NPs) were chemically and thermodynamically more stable among iron oxide nanoparticles. Doping of Co2+ metal ion in α-Fe2O3 can modify the structural, optical and magnetic properties of NPs and also enhances the potential of the biomedical applications. In the current study, undoped and Co doped hematite nanoparticles were synthesised by co-precipitation method using Tribulus terrestris L. leaf extract as bio-reductant. The magnetic, optical and structural investigations were studied with the help of Ultraviolet-visible (UV-Vis), Fourier Transform Infrared (FTIR), Scanning Electron Microscopy equipped with Energy Dispersive X-ray (SEM-EDX) Spectroscopy, Vibrating Sample Magnetometer (VSM) and X-ray Diffraction (XRD) Spectroscopy. XRD analysis shows that synthesized nanoparticles were in hematite phase, rhombohedral in structure. XRD spectral pattern clearly evidenced that prepared α-Fe2O3 and Co-Fe2O3 NPs were highly crystalline with no impurity peaks. Using VSM spectra, the M-H curve indicates that saturation magnetisation (Ms) value increases for Co-Fe2O3 NPs than undoped α-Fe2O3 NPs, it can be clearly seen that doping largely affects the magnetic nature of nanoparticles. In the UV-Vis spectra, absorption maxima increases and band gap value decreases for cobalt doped hematite nanoparticles indicating the substitution of Fe2+ ions by Co2+ ions in α-Fe2O3 lattice sites. Antidiabetic and antimicrobial activity of the synthesized undoped and Co doped hematite NPs were tested by alpha-amylase inhibitory and disc diffusion method. The Co-Fe2O3 NPs have greatly inhibited the digestive enzyme and microbial strains as compared to undoped α-Fe2O3 NPs.
The investigation of the effect of nano particles on dry sliding wear and corrosion behavior of Al-Mg/Al2O3 composites
Authors: A Chandrashekar , Mohanavel V , Kaladgi Abdul Razak , R Vinod Kumar , Ravichandran M , Arunkumar G L , Basheer Dadapeer 
Published: December 2021

Abstract
Aluminum matrix composites were extensively used as structural material as it possesses good surface properties such as wear and corrosion resistance. The practical importance of nano particles in composite materials has triggered widespread attention towards the enhancement of its properties. In this study, Al-Mg/Al2O3 (0–8 wt%) metal matrix nano composites fabricated by two step stir casting route was investigated to comprehend its wear and corrosion behaviour. The Pin-on-Disc dry sliding wear test was performed on Al-Mg/Al2O3 (0–8 wt%) by adopting Design of Experiments under the action of different contact loads and sliding distance following the ASTM G99 Standard. The experimental results conveyed that specific wear rate decreases with increase in sliding distance. Statistical analysis was performed by Taguchi’s Technique and Analysis of Variance (ANOVA) to determine the most dominating factor that influences specific wear rate for the optimum weight percentage of reinforcement. Analysis revealed adequacy with the constructed model in predicting the wear behavior of composite and unreinforced Al-Mg alloy. The corrosion behaviour of the base alloy and composites was analysed by static immersion and electrochemical assessments, by immersing prepared specimens in aqueous sodium chloride (3.5%) solution. The dependance of corrosion rate of the composites with the weight percentage of Al2O3, exposure duration and temperature of the corrosive medium was studied in detail. Corrosion test results exhibit that corrosion rate decreases with increase in weight percentage of Al2O3 particles and exposure duration, whereas it follows reverse trend with increase in corrosion medium temperature.
Effect of electrochemical modification of titanium hydride fraction on oxygen content in surface and deep layers
Authors: Yastrebinsky R N , Pavlenko V I , Gorodov A I , Karnauhov A A , Cherkashina N I , Yastrebinskay A V 
Published: December 2021

Abstract
The paper presents a study of the microstructure and oxygen concentration in the surface and deep layers of fractions of unmodified titanium hydride and titanium hydride modified by electrodeposited layers of Ti and Cu at temperatures of 300 °C–900 °C. The composition of the oxide layer and the concentration of titanium and oxygen atoms are estimated. It is shown that an increase in the thickness and compaction of the oxide layer with increasing temperature prevents the penetration of oxygen into the deep layers of the unmodified fraction of titanium hydride. Modification of titanium hydride by electrochemical deposition of metallic titanium at a temperature of 700 °C reduces the oxygen concentration in titanium hydride at a layer depth of 50 μm from 35 wt% to 12.5 wt%. Electrodeposition of coatings based on titanium and copper at 700 °C reduces the oxygen concentration to 9.2 wt%, which may be due to the protective mechanism of the formed copper titanate layer. At 900 °C, in the modification layer based on titanium and copper, due to the eutectoid transformation of the β-phase of titanium, the process of contact melting occurs and a multiphase zone is formed. The oxygen concentration at a layer depth of 50 μm is no more than 12.4 wt%.
Uncovering the phylogeography of Schinus terebinthifolia in South Africa to guide biological control
Authors: Canavan Kim , Magengelele Nwabisa L , Paterson Iain D , Williams Dean A , Martin Grant D 
Published: December 2021

Abstract
Schinus terebinthifolia is a problematic invasive alien plant (IAP) in South Africa that is a high priority target for biological control. Biological control has been implemented in the states of Florida and Hawaii (USA), where S. terebinthifolia is also an IAP. Phylogeographic work determined that there have been multiple introductions of two lineages (haplotype A and B) into the USA. Haplotype A was introduced to western Florida and Hawaii, while haplotype B was introduced to eastern Florida. Haplotypes A and B have subsequently hybridized in Florida, resulting in novel plant genotypes. Biological control agents in the USA are known to vary in efficacies on the two different haplotypes and hybrids. This study used molecular techniques to uncover the source populations of S. terebinthifolia in South Africa using chloroplast DNA and microsatellites. Populations from the introduced ranges in Florida (east, west and hybrids) and Hawaii were included (n = 95). All South Africa populations (n = 51) were found to be haplotype A. Microsatellite analysis determined shared alleles with western Florida and Hawaiian populations. The likely source of South African S. terebinthifolia was determined to be western Florida through the horticultural trade. These results will help guide a biological control programme to source agents that perform well on these populations in the USA. Furthermore, the presence of only one haplotype in South Africa highlights the need to ensure no further introductions of other haplotypes of the plant are made, in order to avoid similar hybridization events like those recorded in Florida.
In vitro transcytosis of Helicobacter pylori histidine-rich protein through gastric epithelial-like cells and the blood–brain barrier
Authors: Iwasaki Takashi , Maruyama Aiki , Inui Yurika , Sakurai Toshihiko , Kawano Tsuyoshi 
Published: December 2021

ABSTRACT
Recent epidemiological studies have supported the correlation between Helicobacter pylori infection and the development of Alzheimer’s disease. HpHpn, a histidine-rich H. pylori protein, forms amyloid-like oligomers; it may be a pathogenic factor for Alzheimer’s disease progression. HpHpn may also be transported from the gastric epithelium to the brain. However, HpHpn is secreted from H. pylori on the outer surface of gastric epithelia; therefore, the hypothesized movement of HpHpn across the gastric epithelium to the blood remains controversial. Here, we found the HpHpn showed acidic pH-dependent cellular uptake and subsequent secretion in human gastric epithelial-like carcinoma cells. Furthermore, HpHpn exhibited in vitro permeability across the blood–brain barrier. Although further in vivo experiments are required, our findings suggest that in vitro transcytosis of HpHpn in gastric epithelial cells and the blood–brain barrier may provide new insights into the correlation between H. pylori infections and Alzheimer’s disease progression.
LYRUS: a machine learning model for predicting the pathogenicity of missense variants
Authors: Lai Jiaying , Yang Jordan , Gamsiz Uzun Ece D , Rubenstein Brenda M , Sarkar Indra Neil 
Published: December 2021

Abstract

Summary
Single amino acid variations (SAVs) are a primary contributor to variations in the human genome. Identifying pathogenic SAVs can provide insights to the genetic architecture of complex diseases. Most approaches for predicting the functional effects or pathogenicity of SAVs rely on either sequence or structural information. This study presents 〈Lai Yang Rubenstein Uzun Sarkar〉 (LYRUS), a machine learning method that uses an XGBoost classifier to predict the pathogenicity of SAVs. LYRUS incorporates five sequence-based, six structure-based and four dynamics-based features. Uniquely, LYRUS includes a newly proposed sequence co-evolution feature called the variation number. LYRUS was trained using a dataset that contains 4363 protein structures corresponding to 22 639 SAVs from the ClinVar database, and tested using the VariBench testing dataset. Performance analysis showed that LYRUS achieved comparable performance to current variant effect predictors. LYRUS’s performance was also benchmarked against six Deep Mutational Scanning datasets for PTEN and TP53.

Availability and implementation
LYRUS is freely available and the source code can be found at https://github.com/jiaying2508/LYRUS.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
RAxML Grove: an empirical phylogenetic tree database
Authors: Höhler Dimitri , Pfeiffer Wayne , Ioannidis Vassilios , Stockinger Heinz , Stamatakis Alexandros 
Published: December 2021

Abstract

Summary
The assessment of novel phylogenetic models and inference methods is routinely being conducted via experiments on simulated as well as empirical data. When generating synthetic data it is often unclear how to set simulation parameters for the models and generate trees that appropriately reflect empirical model parameter distributions and tree shapes. As a solution, we present and make available a new database called ‘RAxML Grove’ currently comprising more than 60 000 inferred trees and respective model parameter estimates from fully anonymized empirical datasets that were analyzed using RAxML and RAxML-NG on two web servers. We also describe and make available two simple applications of RAxML Grove to exemplify its usage and highlight its utility for designing realistic simulation studies and analyzing empirical model parameter and tree shape distributions.

Availability and implementation
RAxML Grove is freely available at https://github.com/angtft/RAxMLGrove.

Supplementary information
Supplementary data are available at Bioinformatics online.