bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functionalization of a symmetric protein scaffold: Redundant folding nuclei and alternative oligomeric folding pathways
Authors: Tenorio Connie A. , Parker Joseph B. , Blaber Michael 
Published: April 2022

AbstractSuccessful de novo protein design ideally targets specific folding kinetics, stability thermodynamics, and biochemical functionality, and the simultaneous achievement of all these criteria in a single step design is challenging. Protein design is potentially simplified by separating the problem into two steps: (a) an initial design of a protein “scaffold” having appropriate folding kinetics and stability thermodynamics, followed by (b) appropriate functional mutation—possibly involving insertion of a peptide functional “cassette.” This stepwise approach can also separate the orthogonal effects of the “stability/function” and “foldability/function” tradeoffs commonly observed in protein design. If the scaffold is a protein architecture having an exact rotational symmetry, then there is the potential for redundant folding nuclei and multiple equivalent sites of functionalization; thereby enabling broader functional adaptation. We describe such a “scaffold” and functional “cassette” design strategy applied to a β‐trefoil threefold symmetric architecture and a heparin ligand functionality. The results support the availability of redundant folding nuclei within this symmetric architecture, and also identify a minimal peptide cassette conferring heparin affinity. The results also identify an energy barrier of destabilization that switches the protein folding pathway from monomeric to trimeric, thereby identifying another potential advantage of symmetric protein architecture in de novo design.
An enhancer sequence in the intrinsically disordered region of FtsZ promotes polymer‐guided substrate processing by ClpXP protease
Authors: Viola Marissa G. , Perdikari Theodora Myrto , Trebino Catherine E. , Rahmani Negar , Mathews Kaylee L. , Pena Carolina Mejia , Chua Xien Yu , Xuan Botai , LaBreck Christopher J. , Fawzi Nicolas L. , Camberg Jodi L. 
Published: April 2022

AbstractThe essential bacterial division protein in Escherichia coli, FtsZ, assembles into the FtsZ‐ring at midcell and recruits other proteins to the division site to promote septation. A region of the FtsZ amino acid sequence that links the conserved polymerization domain to a C‐terminal protein interaction site was predicted to be intrinsically disordered and has been implicated in modulating spacing and architectural arrangements of FtsZ filaments. While the majority of cell division proteins that directly bind to FtsZ engage either the polymerization domain or the C‐terminal interaction site, ClpX, the recognition and unfolding component of the bacterial ClpXP proteasome, has a secondary interaction with the predicted intrinsically disordered region (IDR) of FtsZ when FtsZ is polymerized. Here, we use NMR spectroscopy and reconstituted degradation reactions in vitro to demonstrate that this linker region is indeed disordered in solution and, further, that amino acids in the IDR of FtsZ enhance the degradation in polymer‐guided interactions.
Relative domain orientation of the L289K HIV‐1 reverse transcriptase monomer
Authors: Xi Zhaoyong , Ilina Tatiana V. , Guerrero Michel , Fan Lixin , Sluis‐Cremer Nicolas , Wang Yun‐Xing , Ishima Rieko 
Published: April 2022

AbstractHIV‐1 reverse transcriptase (RT) is a heterodimer comprised p66 and p51 subunits (p66/p51). Several single amino acid substitutions in RT, including L289K, decrease p66/p51 dimer affinity, and reduce enzymatic functioning. Here, small‐angle X‐ray scattering (SAXS) with proton paramagnetic relaxation enhancement (PRE), 19F site‐specific NMR, and size exclusion chromatography (SEC) were performed for the p66 monomer with the L289K mutation, p66L289K. NMR and SAXS experiments clearly elucidated that the thumb and RNH domains in the monomer do not rigidly interact with each other but are spatially close to the RNH domain. Based on this structural model of the monomer, p66L289K and p51 were predicted to form a heterodimer while p66 and p51L289K not. We tested this hypothesis by SEC analysis of p66 and p51 containing L289K in different combinations and clearly demonstrated that L289K substitution in the p51 subunit, but not in the p66 subunit, reduces p66/p51 formation. Based on the derived monomer model and the importance of the inter‐subunit RNH‐thumb domain interaction in p66/p51, validated by SEC, the mechanism of p66 homodimer formation was discussed.
Contemporary seminal vesicle invasion rates in NCCN high‐risk prostate cancer patients
Authors: Flammia Rocco S. , Hoeh Benedikt , Sorce Gabriele , Chierigo Francesco , Hohenhorst Lukas , Tian Zhen , Goyal Jordan A. , Leonardo Costantino , Briganti Alberto , Graefen Markus , Terrone Carlo , Saad Fred , Shariat Shahrokh F. , Montorsi Francesco , Chun Felix K. H. , Gallucci Michele , Karakiewicz Pierre I. 
Published: April 2022

AbstractBackgroundContemporary seminal vesicle invasion (SVI) rates in National Cancer Comprehensive Network (NCCN) high‐risk prostate cancer (PCa) patients are not well known but essential for treatment planning. We examined SVI rates according to individual patient characteristics for purpose of treatment planning.Materials and MethodsWithin Surveillance, Epidemiology, and End Results (SEER) database (2010–2015), 4975 NCCN high‐risk patients were identified. In the development cohort (SEER geographic region of residence: South, North‐East, Mid‐West, n = 2456), we fitted a multivariable logistic regression model predicting SVI. Its accuracy, calibration, and decision curve analyses (DCAs) were then tested versus previous models within the external validation cohort (SEER geographic region of residence: West, n = 2519).ResultsOut of 4975 patients, 28% had SVI. SVI rate ranged from 8% to 89% according to clinical T stage, prostate‐specific antigen (PSA), biopsy Gleason Grade Group and percentage of positive biopsy cores. In the development cohort, these variables were independent predictors of SVI. In the external validation cohort, the current model achieved 77.6% accuracy vs 73.7% for Memorial Sloan Kettering Cancer Centre (MSKCC) vs 68.6% for Gallina et al. Calibration was better than for the two alternatives: departures from ideal predictions were 6.0% for the current model vs 9.8% for MSKCC vs 38.5% for Gallina et al. In DCAs, the current model outperformed both alternatives. Finally, different nomogram cutoffs allowed to discriminate between low versus high SVI risk patients.ConclusionsMore than a quarter of NCCN high‐risk PCa patients harbored SVI. Since SVI positivity rate varies from 8% to 89%, the currently developed model offers a valuable approach to distinguish between low and high SVI risk patients.
Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors
Authors: T. Rajitha Rajeshwar , Smith Jeremy C. 
Published: April 2022

AbstractThe startling diversity in αβ T‐cell receptor (TCR) sequences and structures complicates molecular‐level analyses of the specificity and sensitivity determining T‐cell immunogenicity. A number of three‐dimensional (3D) structures are now available of ternary complexes between TCRs and peptides: major histocompatibility complexes (pMHC). Here, to glean molecular‐level insights we analyze structures of TCRs bound to human class I nonamer peptide–MHC complexes. Residues at peptide positions 4–8 are found to be particularly important for TCR binding. About 90% of the TCRs hydrogen bond with one or both of the peptide residues at positions 4 and 8 presented by MHC allele HLA‐A2, and this number is still ~79% for peptides presented by other MHC alleles. Residue 8, which lies outside the previously‐identified central peptide region, is crucial for TCR recognition of class I MHC‐presented nonamer peptides. The statistics of the interactions also sheds light on the MHC residues important for TCR binding. The present analysis will aid in the structural modeling of TCR:pMHC complexes and has implications for the rational design of peptide‐based vaccines and T‐cell‐based immunotherapies.
Mechanism design and force sensing of a novel cardiovascular interventional surgery robot
Authors: Wang Shuang , Liu Zheng , Shu Xiongpeng , Xie Le 
Published: April 2022

AbstractBackgroundRobotic‐assisted cardiovascular interventional surgery is an effective means to reduce the exposure of X‐ray radiation to surgeons. However, some of the existing design structures cannot meet the surgical requirements for the coordinated delivery of multiple instruments or lack force sensing function.MethodsThis article proposes a novel cardiovascular interventional surgery robot, which is in line with the operating habits of surgeons. Meanwhile, the force sensing function is integrated under the premise of satisfying the smaller size.ResultsExperimental results show that the proposed cardiovascular interventional surgery robot can quickly and accurately deliver multiple surgical instruments. Furthermore, it can accurately measure the force and torque experienced by the guidewire during the delivery process, which conforms to the derived dynamic model.ConclusionsThe results demonstrate the effectiveness of force sensing and indicate the promise of the presented master‐slave robotic system for cardiovascular interventional surgery.
Event‐triggered state estimation for recurrent neural networks with unknown time‐varying delays
Authors: Huong Dinh Cong , Trinh Hieu 
Published: April 2022

AbstractWe consider the problem of event‐triggered state estimation for recurrent neural networks subject to unknown time‐varying delays by proposing a robust dynamic event‐triggered state observer. A method based on a novel state observer and a dynamic event‐triggered mechanism (ETM) is proposed to provide robust state estimation of the delayed recurrent neural networks. The significance of the new dynamic ETM is that it helps to reduce unnecessary transmissions from the sensors to the observer. A sufficient condition for the existence of the dynamic event‐triggered state observer in terms of a convex optimization problem is proposed based on Lyapunov theory combined with free‐weighting matrix technique and some useful inequalities such as Wirtinger‐based integral inequality, Cauchy matrix inequality and reciprocally convex combination inequality. The effectiveness of the proposed estimation method is demonstrated by two numerical examples and simulation results. In contrast to the event‐triggered state estimation methods currently available in the literature, which require that the time delays are constant or unknown time‐varying but must be differentiable and event‐triggered conditions depend on continuous supervisions, the one in this article only requires the information of upper and lower bounds of the unknown time‐varying delays and the event‐triggered conditions depend on discrete supervisions, which provides more practicality and potential saving in network bandwidth.
A distribution‐free procedure for testing versatile alternative in medical multisample comparison studies
Authors: Mukherjee Amitava , Kössler Wolfgang , Marozzi Marco 
Published: April 2022

AbstractWe propose a test for multisample comparison studies that can be applied without strict assumptions, especially when the underlying population distributions are far from normal. The new test can detect differences not only in location or scale but also in shape parameters among parent population distributions. We are motivated by numerous medical studies, where the variables are not normally distributed and may present in the various groups more complex differences than simple differences in a particular aspect of underlying distributions, such as location or scale. In these situations, traditional ANOVA and Kruskal‐Wallis tests are unreliable since the underlying assumptions are not valid. The proposed procedure also allows the researcher to determine which aspects are more responsible for a significant result. This is an important practical advantage over procedures that test for general differences among the distribution functions but cannot identify which aspects lead to significant results. The asymptotic distribution of the test statistic is analyzed along with its small sample behavior against several competing tests. The practical advantages of the proposed procedure are illustrated with a multisample comparison study of a biomarker for liver damage in patients with hepatitis C.
The Corrected Values of ΔrHo(CaHbOd, a≤16) of Atomization of the Aromatic Compounds and Their Uncertainties Determined Using Several Quantum Mechanical Approaches
Authors: Poskrebyshev Gregory A. 
Published: April 2022

AbstractThe empirical linear scaling dependencies between the literature (ΔrHo(Xn,TAB)) and the calculated (ΔrHo((Xn)i,CALC)) values of atomization of 31 reference aromatic and related compounds (T=298.15 K), as well as their standard errors ((SE4)i≅(σ4)i, Stand.Dev.), are determined for the different quantum mechanical (QMi) approaches. These dependencies are compared and used for the determination of the values of ΔrHo((Xn)i,CORRE)±3(SE4)i of atomization reactions of considered not reference aromatic compounds, as well as for the determination of their values of ΔfHo((Xn)i,CORRE)±3(SE4)i. The values of ΔfHo((Xn)i,CORRE)MEAN±3SEYE (≥99.4 % confidence interval), determined using the intersections of the 3(SE4)i intervals, are consistent with all QMi approaches and their literature values. The M06‐2X/6–311++G(d,p), M08HX/6–311++G(d,p) and wB97XD/6–311++G(d,p) approaches are recommended for the achievement of accuracy (SEYE)≤3.8 kJ/mol of the calculated values of ΔfHo((Xn)i,CORRE)MEAN. The effects of the number of O−H groups, size and multiplicity of compounds on values of error, also studied in this work, demonstrate the limitations of using of several scaled dependencies.
Improved Pyrolysis Performance of a Cyclic Phosphate‐Melamine Intumescent Fire‐Retardant Coating System Using Ceria as an Additive
Authors: Wang Linyuan , Zhu Jiajie , Deng Hongbo , Lyu Ruiqi , Wei Yue , Lan Xubin 
Published: April 2022

AbstractIn this study, cyclic phosphate ester (PEA)‐melamine (MEL) epoxy fire‐retardant coatings were prepared using ceria (CeO2) as an additive. In addition, the effect of ceria on the fireproof performance of the fire‐retardant coatings was analyzed. PEA was prepared and characterized as a flame retardant and a hardener in the system. PEA was mixed with epoxy resin and ceria to produce the coatings, which were then characterized in terms of thermal stability, flame‐retardant performance, and smoke suppression property. Results showed that ceria can significantly improve the fire resistance of the coatings. Compared with the coating without ceria, the coating with 6 % ceria had 56 % lower peak of heat release rate and 61 % lower peak smoke production rate. Thermogravimetric analysis revealed that the addition of ceria improved the thermal stability of the coatings and increased the weight of the residual char to 43.5 %. The internal condition of the foam structure of the expanded residual char was studied using scanning electron microscope. The infrared spectrum of the residual char indicated that the introduction of ceria effectively promoted the formation of cross‐linked structures.
Preparation of β‐hydroxy Ketones via High Efficient Aldol Reaction over Nickel Oxide Nanoparticles as a Powerful and Reusable Heterogeneous Catalyst: Central Composite Design
Authors: Hashemzadeh Elma , Tadayon Fariba , Alahyari Mozhgan 
Published: April 2022

AbstractNickel oxide nanoparticles (NiO NPs) as a new catalyst were fabricated via the sol‐gel method. The characterization of the synthesized nanocatalyst was assessed by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X‐ray diffraction (XRD), and Fourier‐transform infrared (FT‐IR) spectroscopy. Its catalytic efficiency was evaluated in the aldol condensation reaction using an environmentally‐friendly procedure. Among various solvents, including dimethyl sulfoxide (DMSO), dimethylformamide (DMF), tetrahydrofuran (THF), dichloromethane (CH2Cl2), and water, the highest yield (82 %) was related to the water with room temperature, the reaction time of 5 h, and amount catalyst of 30 mmol. Response surface methodology (RSM) based on the central composite design (CCD) was applied to optimize the experimental factors of aldol reaction, as well as the investigation of interaction between the parameters. The results revealed that the temperature of 25 °C and a catalyst amount of 30 mmol had high performance (73.93 %). The preparation of catalyst was accomplished using inexpensive and easily available materials. The synthesized NPs were found to be an efficient and reusable catalyst for the aldol reaction.
The Factors Dictating Properties of Atomically Precise Metal Nanocluster Electrocatalysts
Authors: Yan Hao , Xiang Huixin , Liu Jiaohu , Cheng Ranran , Ye Yongqi , Han Yunhu , Yao Chuanhao 
Published: April 2022

AbstractMetal nanoparticles occupy an important position in electrocatalysis. Unfortunately, by using conventional synthetic methodology, it is a great challenge to realize the monodisperse composition/structure of metal nanoparticles at the atomic level, and to establish correlations between the catalytic properties and the structure of individual catalyst particles. For the study of well‐defined nanocatalysts, great advances have been made for the successful synthesis of nanoparticles with atomic precision, notably ligand‐passivated metal nanoclusters. Such well‐defined metal nanoclusters have become a type of model catalyst and have shown great potential in catalysis research. In this review, the authors summarize the advances in the utilization of atomically precise metal nanoclusters for electrocatalysis. In particular, the factors (e.g., size, metal doping/alloying, ligand engineering, support materials as well as charge state of clusters) affecting selectivity and activity of catalysts are highlighted. The authors aim to provide insightful guidelines for the rational design of electrocatalysts with high performance and perspectives on potential challenges and opportunities in this emerging field.
Google Translate and Biliterate Composing: Second‐Graders' Use of Digital Translation Tools to Support Bilingual Writing
Authors: Rowe Lindsey W. 
Published: April 2022

AbstractResearch is needed exploring how teachers and students in English‐medium schools transform classrooms to welcome and value bilingualism and biliteracy. This article draws on social literacies and placed resources perspectives to explore how one classroom of second‐grade students used Google Translate as a tool to support their biliterate composing. Constant comparative analyses revealed three patterns related to students' use of this tool. Students used Google Translate to support their inclusion of bilingual text and to interact with peers. They also negotiated limitations around the use of Google Translate. Examples of each pattern are used to illustrate how students interactionally engaged with this tool, using it to position themselves as bilingual authors and language learners, and grappling with material and ideological baggage (e.g., standardized language ideologies) the tool brought to the classroom. Implications for educators working in similar contexts are discussed, including how the use of digital translation tools can foster students' bilingual writing by offering in‐the‐moment spelling and vocabulary support. Further discussion includes how the use of Google Translate might contribute to shifting monoglossic classroom ideologies towards ones that value multilingualism.
Sesamol protects against aluminum oxide nanoparticles‐induced hepatorenal toxicity in rats via modulation of oxidative stress, inflammation, apoptosis, and DNA damage
Authors: El‐Borai Nermeen B. , Elkhadrawey Basma A. , AbuBakr Huda O. , Anis Anis , El‐Bialy Badr E. , Elsabbagh Hesham S. , Abou‐Zeid Shimaa M. 
Published: April 2022

AbstractAluminum oxide nanoparticles (Al2O3‐NPs) are exceedingly used in various industrial and commercial applications, providing growing concerns about their potential adverse impacts on animals and human health. Therefore, the present study was conducted to evaluate the potential protective effect of sesamol (SML) against the induced hepatorenal toxicity of Al2O3‐NPs. Forty male rats were randomly assigned into four groups and treated orally for 28 consecutive days. Control group received distilled water. SML group received SML (100 mg/kg bw). Al2O3‐NPs group received Al2O3‐NPs (100 mg/kg bw). SML + Al2O3‐NPs group received SML 2 h prior to Al2O3‐NPs. The results revealed that Al2O3‐NPs significantly increased serum alanine aminotransferase and aspartate aminotransferase activities and serum urea and creatinine levels. Moreover, Al2O3‐NPs induced a significant elevation in malondialdehyde level with significant reduction in reduced glutathione content and catalase and superoxide dismutase activities, together with a marked increase of 8‐hydroxy‐2‐desoxyguanosine level in the hepatic and renal tissues. Also, up‐regulations of glutathione‐S‐transferase, tumor necrosis factor‐alpha, and caspase‐3 mRNA gene expressions were recorded in the liver and kidneys. Additionally, Al2O3‐NPs induced multifocal areas of necrosis in hepatic parenchyma with glomerular mesangial cell proliferation and glomerular sclerosis in kidney tissues. Conversely, concomitant treatment with sesamol mitigated Al2O3‐induced hepatorenal toxicity evidenced by improvement of liver and kidney functions that correlated with regulation of oxidant/antioxidant status, inflammatory, and apoptotic biomarkers and reduction of DNA and tissues damages. In conclusion, sesamol could exert a promising protective role against hepatorenal toxicity of Al2O3‐NPs, possibly via its antioxidant, anti‐inflammatory and anti‐apoptotic properties.
Molecular Precursors to Group IV Dichalcogenides MS2 (M=Ti, Zr, Hf)
Authors: Brune Veronika , Hegemann Corinna , Wilhelm Michael , Ates Nursima , Mathur Sanjay 
Published: April 2022

AbstractNew chemical routes to synthesize layered 2D transition metal dichalcogenides (TMDCs) are highly desired. We report here a new class of molecular precursors of general formula [MIV(SC2H4N(Me)C2H4S)2] (MIV=Ti, Zr, Hf) that offers a reliable synthetic access to 2D TMDC materials as demonstrated in the representative case of TiS2 synthesis. The complexation of the TM centers by the chelating tridentate ligand (HSC2H4)2NMe produced stable monomeric complexes, [Ti(SC2H4N(Me)C2H4S)2], [Zr(SC2H4N(Me)C2H4S)2] and [Hf(SC2H4N(Me)C2H4S)2], displaying a distorted octahedral environment around metal centers formed by four S and two N donor atoms of the ligand moiety. The characterization of molecular precursors by NMR, single‐crystal diffraction analysis, IR spectroscopy and elemental analysis confirmed the presence of metal‐sulfur bonds that are crucial in facilitating the formation of MS2 phases. Thermal decomposition behaviour of the three molecular compounds was investigated by TG‐DCS measurements that confirmed their decomposition into solid phases. Interestingly, the preorganized M−S bonds in the precursor molecules also influenced the formation of titanium disulfide thin films by chemical vapor phase deposition. The solid thin films of TiS2 were characterized by X‐ray spectroscopy analysis and atomic scale imaging. The complexes presented in this work represent a promising chemistry driven approach towards reproducible and scalable synthesis of van der Waals 2D heterostructures.