bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a duplex qPCR assay with locked nucleic acid probes for A, B and E kappa-casein variants detection
Authors: Jiménez-Montenegro L. , Mendizabal J. A. , Alfonso L. , Azparren L. , Urrutia O. 
Published: September 2022

AbstractMilk proteins determine important milk technological characteristics. Among caseins, Ƙ-casein has been correlated with fat and protein content and cheese yield. Fourteen Ƙ-caseins variants have been described but the alleles A, B and E are the most important ones due to their frequency and/or influence on the technological aptitudes of milk. Therefore, in the present study two different duplex qPCR assays with locked nucleic acid probes (for positions 13104 and 13124 of the Ƙ-casein gene) were developed for the detection of A, B and E variants. Firstly, DNA isolation method from milk somatic cells and hair was optimised. The developed 13124-qPCR assay showed an increased sensitivity reaching up to 6.7 copies DNA copies/reaction at a 95% confidence level with A, B and E alleles reference samples. The 13104-qPCR assay reached up to 6.7 DNA copies/reaction for A allele reference sample and 67 DNA copies/reaction for B and E samples. Intra-assay variation results were below 6%. Applicability was determined using DNA samples from animals with known genotype for Ƙ-casein (AA, AB, BB, BE, AE, EE) and both assays were able to discriminate among the six genotypes with 100% accuracy. Thus, this qPCR method represents a sensitive and rapid option for the detection of Ƙ-casein alleles in both hair and milk samples.
Plant produced endotoxin binding recombinant proteins effectively remove endotoxins from protein samples
Authors: Khan Md Rezaul Islam , Thangarasu Muthamilselvan , Kang Hyangju , Hwang Inhwan 
Published: September 2022

AbstractLipopolysaccharides (LPS) are highly toxic compounds, even at a trace amount. When recombinant proteins are produced in E. coli, it is inevitable that LPS contaminates. However, LPS removal is still technically challenging and costly due to the high degree of solubility in a wide range of solvents. In this study, we explored the possibility of using the N-terminal region containing cysteine-rich, EGF-like, and sushi1–3 domains (CES3) of Factor C from the horseshoe crab Carcinoscorpius rotundicauda to develop a platform to remove LPS from recombinant proteins. We expressed CES3 as part of a recombinant protein, BiP:NT:CBM3:SUMO:CES3:His:HDEL, in Nicotiana benthamiana and found that purified or microcrystalline cellulose (MCC) bead-immobilised CES3 showed strong binding to LPS-containing E. coli. To produce CES3:CBM3 in an LPS-free environment, we generated Arabidopsis transgenic plants harbouring a recombinant gene, BiP:NT:SUMO:CES3:CBM3:HDEL, and found that transgenic plants mainly produce CES3:CBM3:His:HDEL, a truncated version of BiP:NT:SUMO:CES3:CBM3:HDEL via endogenous protease-mediated proteolytic processing in vivo. CES3:CBM3:HDEL purified from Arabidopsis plant extracts and immobilised onto MCC beads removed LPS contamination from protein samples. We propose that the CES3:CBM3 fusion protein produced in plants and immobilised on MCC beads can be a robust and easy platform for LPS removal from recombinant proteins.
Strata behaviour and stability control of the automatic roadway formation by roof cutting below a fault influenced longwall goaf
Authors: Gao Yubing , Gai Qiukai , Zhang Kedong , Fu Qiang , Zhang Xingxing 
Published: September 2022

AbstractAutomatic roadway formation by roof cutting (ARFRC) is a novel nonpillar mining method that has the potential to dramatically increase coal recovery while reducing the roadway excavation ratio. When this method is used below a fault influenced longwall goaf, large deformation and support failure occur in the roadway using conventional roadway formation techniques. In the study, the ARFRC method was tested in the Liliu mining area of China, which is characterized by goafs and faults. Field experiments and numerical modelling were used to evaluate the stability of the roadway by analysing the behaviour of overlying strata under the special geological condition. The results show that the surroundings of the formed roadway were greatly affected by the fault and the overlying coal pillar in the goaf. In the fault- and coal pillar-affected areas, the loads on the roadway roof increased by approximately 35% and 15%, respectively. According to the strata behaviour of the formed roadway surroundings, targeted support techniques for ARFRC were proposed, and the reliability of the support techniques were demonstrated by field practice.
Accurate and fast identification of minimally prepared bacteria phenotypes using Raman spectroscopy assisted by machine learning
Authors: Thomsen Benjamin Lundquist , Christensen Jesper B. , Rodenko Olga , Usenov Iskander , Grønnemose Rasmus Birkholm , Andersen Thomas Emil , Lassen Mikael 
Published: September 2022

AbstractThe worldwide increase of antimicrobial resistance (AMR) is a serious threat to human health. To avert the spread of AMR, fast reliable diagnostics tools that facilitate optimal antibiotic stewardship are an unmet need. In this regard, Raman spectroscopy promises rapid label- and culture-free identification and antimicrobial susceptibility testing (AST) in a single step. However, even though many Raman-based bacteria-identification and AST studies have demonstrated impressive results, some shortcomings must be addressed. To bridge the gap between proof-of-concept studies and clinical application, we have developed machine learning techniques in combination with a novel data-augmentation algorithm, for fast identification of minimally prepared bacteria phenotypes and the distinctions of methicillin-resistant (MR) from methicillin-susceptible (MS) bacteria. For this we have implemented a spectral transformer model for hyper-spectral Raman images of bacteria. We show that our model outperforms the standard convolutional neural network models on a multitude of classification problems, both in terms of accuracy and in terms of training time. We attain more than 96% classification accuracy on a dataset consisting of 15 different classes and 95.6% classification accuracy for six MR–MS bacteria species. More importantly, our results are obtained using only fast and easy-to-produce training and test data.
Quaternary structure of patient-homogenate amplified α-synuclein fibrils modulates seeding of endogenous α-synuclein
Authors: Frieg Benedikt , Geraets James A. , Strohäker Timo , Dienemann Christian , Mavroeidi Panagiota , Jung Byung Chul , Kim Woojin S. , Lee Seung-Jae , Xilouri Maria , Zweckstetter Markus , Schröder Gunnar F. 
Published: September 2022

AbstractParkinson’s disease (PD) and Multiple System Atrophy (MSA) are progressive and unremitting neurological diseases that are neuropathologically characterized by α-synuclein inclusions. Increasing evidence supports the aggregation of α-synuclein in specific brain areas early in the disease course, followed by the spreading of α-synuclein pathology to multiple brain regions. However, little is known about how the structure of α-synuclein fibrils influence its ability to seed endogenous α-synuclein in recipient cells. Here, we aggregated α-synuclein by seeding with homogenates of PD- and MSA-confirmed brain tissue, determined the resulting α-synuclein fibril structures by cryo-electron microscopy, and characterized their seeding potential in mouse primary oligodendroglial cultures. The combined analysis shows that the two patient material-amplified α-synuclein fibrils share a similar protofilament fold but differ in their inter-protofilament interface and their ability to recruit endogenous α-synuclein. Our study indicates that the quaternary structure of α-synuclein fibrils modulates the seeding of α-synuclein pathology inside recipient cells. It thus provides an important advance in the quest to understand the connection between the structure of α-synuclein fibrils, cellular seeding/spreading, and ultimately the clinical manifestations of different synucleinopathies.
Structural analysis of human CEACAM1 oligomerization
Authors: Gandhi Amit K. , Sun Zhen-Yu J. , Huang Yu-Hwa , Kim Walter M. , Yang Chao , Petsko Gregory A. , Beauchemin Nicole , Blumberg Richard S. 
Published: September 2022

AbstractThe human (h) CEACAM1 GFCC’ face serves as a binding site for homophilic and heterophilic interactions with various microbial and host ligands. hCEACAM1 has also been observed to form oligomers and micro-clusters on the cell surface which are thought to regulate hCEACAM1-mediated signaling. However, the structural basis for hCEACAM1 higher-order oligomerization is currently unknown. To understand this, we report a hCEACAM1 IgV oligomer crystal structure which shows how GFCC’ face-mediated homodimerization enables highly flexible ABED face interactions to arise. Structural modeling and nuclear magnetic resonance (NMR) studies predict that such oligomerization is not impeded by the presence of carbohydrate side-chain modifications. In addition, using UV spectroscopy and NMR studies, we show that oligomerization is further facilitated by the presence of a conserved metal ion (Zn++ or Ni++) binding site on the G strand of the FG loop. Together these studies provide biophysical insights on how GFCC’ and ABED face interactions together with metal ion binding may facilitate hCEACAM1 oligomerization beyond dimerization.
Characterising the AGB bump and its potential to constrain mixing processes in stellar interiors
Authors: Dréau G. , Lebreton Y. , Mosser B. , Bossini D. , Yu J. 
Published: September 2022

Context. In the 1990s, theoretical studies motivated the use of the asymptotic giant branch bump (AGBb) as a standard candle given the weak dependence between its luminosity and stellar metallicity. Because of the small size of observed asymptotic giant branch (AGB) samples, detecting the AGBb is not an easy task. However, this has now been made possible thanks to the wealth of data collected by the CoRoT, Kepler, and TESS space-borne missions.
Aims. It is well-known that the AGB bump provides valuable information on the internal structure of low-mass stars, particularly on mixing processes such as core overshooting during the core He-burning phase. Here, we investigate the dependence of the AGBb position on stellar parameters such as the stellar mass and metallicity based on the calibration of stellar models to observations.
Methods. In this context, we analysed ∼4000 evolved giants observed by Kepler and TESS, including red giant branch (RGB) stars and AGB stars, for which asteroseismic and spectrometric data are available. By using statistical mixture models, we detected the AGBb both in frequency at maximum oscillation power, νmax, and in effective temperature, Teff. Then, we used the Modules for Experiments in Stellar Astrophysics (MESA) stellar evolution code to model AGB stars and match the AGBb occurrence with observations.
Results. From the observations, we were able to derive the AGBb location in 15 bins of mass and metallicity. We noted that the higher the mass, the later the AGBb occurs in the evolutionary track, which agrees with theoretical works. Moreover, we found a slight increase in the luminosity at the AGBb when the metallicity increases. By fitting those observations with stellar models, we noticed that low-mass stars (M ≤ 1.0 M⊙) require a small core overshooting region during the core He-burning phase. This core overshooting extent increases toward high mass; however, above M ≥ 1.5 M⊙, we found that the AGBb location cannot be reproduced with a realistic He-core overshooting alone. Thus, additional mixing processes have to be invoked instead.
Conclusions. The observed dependence on metallicity complicates the application of the AGBb as a standard candle. Moreover, different mixing processes may occur according to stellar mass. At low mass (M ≤ 1.5 M⊙), the AGBb location can be used to constrain the He-core overshooting. At high mass (M ≥ 1.5 M⊙), an additional mixing induced, for instance, by rotation is needed to reproduce what is seen in observations.
Tilting Uranus via the migration of an ancient satellite
Authors: Saillenfest Melaine , Rogoszinski Zeeve , Lari Giacomo , Baillié Kevin , Boué Gwenaël , Crida Aurélien , Lainey Valéry 
Published: September 2022

Context. The 98° obliquity of Uranus is commonly attributed to giant impacts that occurred at the end of the planetary formation. This picture, however, is not devoid of weaknesses.
Aims. On a billion-year timescale, the tidal migration of the satellites of Jupiter and Saturn has been shown to strongly affect their spin-axis dynamics. We aim to revisit the scenario of tilting Uranus in light of this mechanism.
Methods. We analyse the precession spectrum of Uranus and identify the candidate secular spin-orbit resonances that could be responsible for the tilting. We determine the properties of the hypothetical ancient satellite required for a capture and explore the dynamics numerically.
Results. If it migrates over 10 Uranus’s radii, a single satellite with minimum mass 4 × 10−4 Uranus’s mass is able to tilt Uranus from a small obliquity and make it converge towards 90°. In order to achieve the tilting in less than the age of the Solar System, the mean drift rate of the satellite must be comparable to the Moon’s current orbital expansion. Under these conditions, simulations show that Uranus is readily tilted over 80°. Beyond this point, the satellite is strongly destabilised and triggers a phase of chaotic motion for the planet’s spin axis. The chaotic phase ends when the satellite collides into the planet, ultimately freezing the planet’s obliquity in either a prograde or a plainly retrograde state (as Uranus today). Spin states resembling that of Uranus can be obtained with probabilities as large as 80%, but a bigger satellite is favoured, with mass 1.7 × 10−3 Uranus’s mass or more. Yet, a smaller ancient satellite is not categorically ruled out, and we discuss several ways to improve this basic scenario in future studies. Interactions among several pre-existing satellites are a promising possibility.
Conclusions. The conditions required for the tilting seem broadly realistic, but it remains to be determined whether Uranus could have hosted a big primordial satellite subject to substantial tidal migration. The efficiency of tidal energy dissipation within Uranus is required to be much higher than traditionally assumed, more in line with that measured for the migration of Titan. Hints about these issues would be given by a measure of the expansion rate of Uranus’s main satellites.
Forensic Investigation Concerning Inspection and Diagnosis of Condition of Water Storage Systems in the Gulf
Authors: Grantham Michael , Polder Rob 
Published: September 2022

Sandberg were asked to visit and comment on a sizeable project in the Gulf involving water storage towers, ground reservoirs and ancillary buildings in contemplation of legal proceedings. The structures had been built by a contractor but some problems had occurred in construction due to the high temperatures and issues with the concrete placement. The main issue that needed to be resolved was whether the problems that occurred were within acceptable limits for that type of construction and what repair recommendations were appropriate.
The Client for the project had rejected the structures and was aiming for demolition and reconstruction which was a draconian step, given the level of problems – all of which were easily repairable. A significant amount of misdiagnosis had occurred with dark flecks on the surface of reservoirs being attributed to corrosion of reinforcement, for example, when in fact they were due to mould growth on the surface of the concrete and were literally surface deep only. There were also significant questions to be answered as to what constituted an acceptable level of leakage from water storage towers. An issue was also present with very severe corrosion to some reinforcing bars close to ground level in several ground reservoirs, despite the reinforcement being epoxy coated. It was considered highly likely that this damage was in fact due to stray current corrosion from current leakage from the cathodically protected water pipelines that delivered water to the facilities in question.This paper will discuss the inspection and diagnosis of the problems and the feasibility and need for appropriate repairs.
Alkenylboronic Ester Activation to Nucleophilic Addition and Electrophilic Trapping with Carbonyl Groups
Authors: Fernández Elena , González Sara 
Published: September 2022

AbstractCarbolithiation of (1-phenylvinyl)boronic acid pinacol ester with tert-butyllithium was used to generate α-phenylboryl carbanions that reacted in a straightforward manner with carbonyl groups through a boron–Wittig sequence. When unhindered α,β-unsaturated carbonyl compounds were used, 1,4-addition of the α-phenylboryl carbanions was observed over the boron–Wittig sequence.
A Brønsted Acid Catalyzed Easy Access to Conjugated Diene-­Diones from Tertiary Propargyl Alcohols and 1,3-Dicarbonyl ­Compounds
Authors: Chatterjee Paresh Nath , Kalita Gitumoni , Khatua Snehadrinarayan 
Published: September 2022

AbstractA simple protocol catalyzed by a Brønsted acid, trifluoromethanesulfonic acid (CF3SO3H), to synthesize conjugated diene-diones from easily accessible tertiary propargyl alcohols and 1,3-dicarbonyl compounds is described. Reactions are performed in an air atmosphere by using undried solvents with water being the environmentally benign side product of the process. Preliminary synthetic applications of the conjugated diene-diones in the formation of conjugated dieneones and furans are also reported herein.
Impact of Asymptomatic Superior Mesenteric Vein Thrombosis on the Outcomes of Patients with Liver Cirrhosis
Authors: Wang Le , Guo Xiaozhong , Bai Zhaohui , Yin Yue , Xu Shixue , Pan Jiahui , Mancuso Andrea , Noronha Ferreira Carlos , Qi Xingshun 
Published: September 2022

Background The impact of asymptomatic superior mesenteric vein (SMV) thrombosis on the outcomes of cirrhotic patients remains uncertain.
Methods Nonmalignant cirrhotic patients who were consecutively admitted between December 2014 and September 2021 and underwent contrast-enhanced computed tomography/magnetic resonance imaging scans were screened. Portal venous system thrombosis (PVST) was identified. Death and hepatic decompensation were the outcomes of interest. Nelson–Aalen cumulative risk curve analysis and competing risk regression analysis were performed to evaluate the impact of asymptomatic SMV thrombosis and portal vein thrombosis (PVT) on the outcomes.
Results Overall, 475 patients were included, of whom 67 (14.1%) had asymptomatic SMV thrombosis, 95 (20%) had PVT, and 344 (72.4%) did not have any PVST. Nelson–Aalen cumulative risk curve analyses showed that the cumulative incidences of death (p = 0.653) and hepatic decompensation (p = 0.630) were not significantly different between patients with asymptomatic SMV thrombosis and those without PVST, but the cumulative incidences of death (p = 0.021) and hepatic decompensation (p = 0.004) were significantly higher in patients with PVT than those without PVST. Competing risk regression analyses demonstrated that asymptomatic SMV thrombosis was not a significant risk factor for death (subdistribution hazard ratio [sHR] = 0.89, p = 0.65) or hepatic decompensation (sHR = 1.09, p = 0.63), but PVT was a significant risk factor for death (sHR = 1.56, p = 0.02) and hepatic decompensation (sHR = 1.50, p = 0.006). These statistical results remained in competing risk regression analyses after adjusting for age, sex, and Child–Pugh score.
Conclusion Asymptomatic SMV thrombosis may not influence the outcomes of cirrhotic patients. The timing of intervention for asymptomatic SMV thrombosis in liver cirrhosis should be further explored.
Modelling of solidification structure and macro-segregation in an industrial DC cast slab
Authors: Chen Q P , Shi H , Shen H F 
Published: September 2022

Abstract
A cellular automaton (CA)-finite element (FE) model was implemented for multi-scale modelling of micro-segregation, mesoscopic grain structure and macroscopic segregation during direct chill (DC) casting of industrial billets or slabs. The macroscopic transport of mass, momentum, energy and solutes was solved on an FE grid, while the mesoscopic grain structure governed by nucleation, growth kinetics and grain evolution was calculated on a CA grid. The solidification path was determined using a modified micro-segregation model for multi-component aluminium alloys. An Euler representation was used for pre-processing and post-processing, and a Lagrangian representation was used for expanding the calculation domain and for resolving the CAFE model. By simulating a DC casting experiment of the 2024 aluminium alloy, a typical grain structure was reproduced, and the composition map showed a reasonable deviation. This model was applied to an industrial-scale DC cast slab of an Al-3.5Cu-1.5 Mg (wt. %) alloy, and three simulations with different nucleation undercoolings were performed for a grain-unrefined slab, a grain-refined slab and an equilibrium solidified slab, respectively. The slabs tended to solidify at equilibrium with the decreasing nucleation undercooling. The earlier release of latent heat yielded a smaller liquid undercooling region ahead of the solidification front, and a finer grain structure. A typical grain structure with coarse equiaxial grains at the centre and fine columnar grains near the bottom surface as well as sidewall was observed for the grain-unrefined slab. By contrast, the grain structure of the grain-refined slab was fully equiaxial. Furthermore, the grain structure, temperature field, melt flow and macro-segregation were quantitatively investigated.
Pulse-echo speed-of-sound imaging using convex probes
Authors: Jaeger Michael , Stähli Patrick , Martiartu Naiara Korta , Yolgunlu Parisa Salemi , Frappart Thomas , Fraschini Christophe , Frenz Martin 
Published: September 2022

Abstract
Computed ultrasound tomography in echo mode (CUTE) is a new ultrasound (US)-based medical imaging modality with promise for diagnosing various types of disease based on the tissue’s speed of sound (SoS). It is developed for conventional pulse-echo US using handheld probes and can thus be implemented in state-of-the-art medical US systems. One promising application is the quantification of the liver fat fraction in fatty liver disease. So far, CUTE was using linear array probes where the imaging depth is comparable to the aperture size. For liver imaging, however, convex probes are preferred since they provide a larger penetration depth and a wider view angle allowing to capture a large area of the liver. With the goal of liver imaging in mind, we adapt CUTE to convex probes, with a special focus on discussing strategies that make use of the convex geometry in order to make our implementation computationally efficient. We then demonstrate in an abdominal imaging phantom that accurate quantitative SoS using convex probes is feasible, in spite of the smaller aperture size in relation to the image area compared to linear arrays. A preliminary in vivo result of liver imaging confirms this outcome, but also indicates that deep quantitative imaging in the real liver can be more challenging, probably due to the increased complexity of the tissue compared to phantoms.