bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of AI‐based modeling on the accuracy of protein assembly prediction: Insights from CASP15
Authors: Ozden Burcu , Kryshtafovych Andriy , Karaca Ezgi 
Published: October 2023

AbstractIn CASP15, 87 predictors submitted around 11 000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact predictions, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind's AF2‐Multimer approach into custom‐built prediction pipelines. To evaluate the added value of participating methods, we compared the community models to the baseline AF2‐Multimer predictor. In over 1/3 of cases, the community models were superior to the baseline predictor. The main reasons for this improved performance were the use of custom‐built multiple sequence alignments, optimized AF2‐Multimer sampling, and the manual assembly of AF2‐Multimer‐built subcomplexes. The best three groups, in order, are Zheng, Venclovas, and Wallner. Zheng and Venclovas reached a 73.2% success rate over all (41) cases, while Wallner attained 69.4% success rate over 36 cases. Nonetheless, challenges remain in predicting structures with weak evolutionary signals, such as nanobody–antigen, antibody–antigen, and viral complexes. Expectedly, modeling large complexes also remains challenging due to their high memory compute demands. In addition to the assembly category, we assessed the accuracy of modeling interdomain interfaces in the tertiary structure prediction targets. Models on seven targets featuring 17 unique interfaces were analyzed. Best predictors achieved a 76.5% success rate, with the UM‐TBM group being the leader. In the interdomain category, we observed that the predictors faced challenges, as in the case of the assembly category, when the evolutionary signal for a given domain pair was weak or the structure was large. Overall, CASP15 witnessed unprecedented improvement in interface modeling, reflecting the AI revolution seen in CASP14.
Assessment of the assessment—All about complexes
Authors: Studer Gabriel , Tauriello Gerardo , Schwede Torsten 
Published: October 2023

AbstractPredicting model quality is a fundamental component of any modeling procedure, and blind assessment of these methods constitutes a crucial aspect of the Critical Assessment of Protein Structure Prediction (CASP) experiment. Historically, the main focus was on assessing methods that predict global and per‐residue accuracies in tertiary structure models. This focus shifted with the community's increased efforts in modeling complexes and assemblies. We asked the community to process the models from the CASP15 assembly category and provide estimates of the accuracy of the predicted quaternary structure, both globally and at the local interface level. Besides identifying remarkable accuracy of modeling groups in assessing their own predictions, we set up a benchmarking pipeline to highlight different aspects of quaternary structure models and introduced a simple consensus EMA method as baseline. While participating methods showed commendable performance, the baseline was difficult to surpass. It is important to point out that prediction performance varies for the individual CASP targets, highlighting potential areas of improvement and challenges ahead.
Towards the ‘rationality–emotion nexus’ for approaching international student mobility: An ethnography of African student migrants at a Chinese university
Authors: Wu Daisy Binfang , Hou Song 
Published: October 2023

AbstractThis paper examines how student motivations to study abroad are shaped by what might be called the ‘rationality–emotion nexus’. Drawing from 15 months of ethnographic engagement at a Chinese university, we show how rational factors (e.g., pursuit of financial resources) interact with emotional forces (e.g., love for family members) in dynamic and diverse ways to shape the pathways of African student migrants to higher education overseas. More specifically, we identify three distinct dynamics in the nexus: (i) rationality is entangled with emotions; (ii) rationality parallels emotions; and (iii) rationality and emotions transform each other. By foregrounding this nexus, the present study offers a critical intervention into international student mobility/migration studies as it develops ‘an integrative approach’ that transcends either a widely established rational framework of capital conversion or the emerging emotional geographies of transnational education migration.
Interaction of ancestry and agency: Challenges, constraints and options for second‐generation Albanian youth relocating from Greece
Authors: Michail Domna , King Russell 
Published: October 2023

AbstractThe Greek economic crisis resulted in tens of thousands of Albanian migrants returning to their home country. Amongst the returnees were many second‐generation children of the immigrants, who either returned with their families or relocated as individuals, leaving family members in Greece. Since the second generation were brought up in Greece they are not true returnees; we call their movement ‘relocation’ rather than return. Based on in‐depth interviews with 158 second‐generation ‘relocatees’ aged 18–35, we ask: How are the second generation's future aspirations in the ancestral homeland shaped by family bonds, sociocultural factors and employment and business options there? Among the themes that emerge from our analysis are issues of agency, youth mobility, economic survival, hybrid and dual identities, and feelings of belonging. In their (re)integration, relocatees face both economic and emotional challenges. Our key finding is that, despite the need to escape unemployment and loss of livelihood in Greece, the young‐adult second generation struggles to settle in Albania, above all due to what they see as the challenging sociocultural and infrastructural environment. Women, especially, bemoan the loss of freedom that they enjoyed in Greece. Most relocatees want to go back to Greece when the economic situation there improves.
A multistate platform model for time‐to‐event endpoints in oncology clinical trials
Authors: Lin Chih‐Wei , Nagase Mario , Doshi Sameer , Dutta Sandeep 
Published: October 2023

AbstractA multistate platform model was developed to describe time‐to‐event (TTE) endpoints in an oncology trial through the following states: initial, tumor response (TR), progressive disease (PD), overall survival (OS) event (death), censor to the last evaluable tumor assessment (progression‐free survival [PFS] censor), and censor to study end (OS censor), using an ordinary differential equation framework. Two types of piecewise functions were used to describe the hazards for different events. Piecewise surge functions were used for events that require tumor assessments at the scheduled study visit times (TR, PD, and PFS censor). Piecewise constant functions were used to describe hazards for events that occur evenly throughout the study (OS event and OS censor). The multistate TTE model was applied to describe TTE endpoints from a published phase III study. The piecewise surge functions well‐described the observed surges of hazards/events for TR, PD, PFS, and OS occurring near scheduled tumor assessments and showed good agreement with all Kaplan‐Meier curves. With the flexibility of piecewise hazard functions, the model was able to evaluate covariate effects in a time‐variant fashion to better understand the temporal patterns of disease prognosis through different disease states. This model can be applied to advance the field of oncology trial design and optimization by: (1) enabling robust estimations of baseline hazards and covariate effects for multiple TTE endpoints, (2) providing a platform model for understanding the composition and correlations between different TTE endpoints, and (3) facilitating oncology trial design optimization through clinical trial simulations.
Cool semi‐arid cropping treatments alter Avena fatua's performance and competitive intensity
Authors: Larson Christian D. , Wong Mei Ling , Carr Patrick M. , Seipel Timothy 
Published: October 2023

AbstractIntroductionMultiple herbicide‐resistant Avena fatua L. is common in the Northern Great Plains, USA. This prevalence and the ecological impacts of tillage in this semi‐arid agricultural region have created a need for integrated weed management, with a specific knowledge gap in using annual forage crops and targeted grazing for A. fatua suppression.Materials and MethodsA 2‐year study in central Montana, USA, assessed A. fatua performance (aboveground biomass, stem density and seed production) in response to seven cropping treatments: (1–4) tall and short spring wheat cultivars crossed with high and low seeding rates, (5–6) annual forage mixture terminated using sheep grazing and simulated haying and (7) tilled fallow. Avena fatua's competitive intensity in wheat and the annual forage mixture was determined using a relative competition intensity index.ResultsAvena fatua performance was lowest in tilled fallow, although stem density and seed production did not differ from the grazed annual forage treatment. Response variables were lower in the forage treatments compared with the wheat treatments, and there were no differences among the four fully crossed wheat treatments. Separate analysis of the wheat treatments indicated lower A. fatua biomass and stem density when wheat was sown at a higher rate with no impact of wheat height. Avena fatua competition impacted wheat and forage crops but was more intense for wheat.ConclusionTillage was the most effective treatment at reducing A. fatua performance, but annual forage mixtures can be used to resist A. fatua invasion (reduced A. fatua competitive intensity) and limit its performance after invasion. We conclude that crop sequences that combine higher cash crop (wheat) seeding rates and competitive annual forage mixtures may be utilized to manage A. fatua invaded systems, thereby reducing heavy reliance on tillage in the US Northern Great Plains and similar semi‐arid regions.
Capacity Retention Through a Separator Coated with Bifunctional Ferroelectric Nanoparticles and Modified Cathodes for Li−S Batteries
Authors: Katiyar Rajesh K. , Zuluaga Gomez Claudia C. , Katiyar Swati , Tripathi Balram , Morell Gerardo , Weiner Brad R. , Katiyar Ram S. 
Published: October 2023

AbstractGadolinium (Gd) and Nickel (Ni) doped bismuth ferrite (BiFeO3) nanoparticles Bi0.925Gd.075Fe0.95Ni0.05O3 (BGFNO) with spontaneous polarization (2.5 μC/cm2) were mechano‐chemically synthesized and used to achieve high capacity retention in lithium sulfur (Li−S) batteries. The BGFNO particles were coupled with single walled carbon nanotubes (SWCNT)/sulfur (S) composite cathodes as well as coated on separator. The X‐ray diffraction of BGFNO@S/SWCNT cathodes show an orthorhombic structure with particle size distribution of 20–26 nm, while Raman spectra substantiate efficient coupling of BGFNO with S/SWCNT cathodes, in agreement with SEM images, showing the interconnected network of composites. The specific discharge capacity of S60BGFNO30SWCNT10 composite cathode @ 200 mA/g together with BGFNO coated separator gains maximum capacity up to 1611 mAh/g and retains up to 1294 mAh/g after 50th cycle with improved capacity retention of 80 % showing suppression of polysulfides formation. The coated separator controls transport of carrier ions and side reactions, however modified cathodes with BGFNO particles acts as trapping center for polysulfides to enhance the electrochemical performance of the cells. The Coulombic efficiency(CE) for BGFNO/S/SWCNT composites @ 100 mA/g attained >98 % and CE @ 200 mA/g it is attained > 80 to 90 % compared to S/SWCNT composites in terms of improved cycle stability and reaction kinetics.
Facile Synthesis of Graphitic Fungal Carbon Dots for Sensing of Food Adulterants and “Bio‐Imaging” of Human Kidney Cell Line
Authors: Kumari Puja , Pratap Ravi , Gautam Veer S. , Das Megha , Hassan Nurul , Lahiri Jayeeta , Mishra Archana , Yadav Sanjeev K. , Kharwar Ravindra N. , Parmar Avanish S. 
Published: October 2023

AbstractIn the current study, a simple and environmentally friendly hydrothermal treatment of fungal biomass for the preparation of carbon nanodots (CND) has been reported. The optical and structural characteristics of the CND have been thoroughly investigated using X‐ray Diffraction (XRD), Transmission Electron Microscopy (TEM), UV‐Visible, and fluorescence spectroscopy methods. Elemental analyses and Fourier Transform Infrared spectroscopy (FTIR) have been used to highlight the surface functionality and composition of the CND.CND have been employed as a fluorescence probe for sensitive and selective detection of rhodamine B (Rh−B) and malachite green (MG) because the presence of food adulterants quenches the fluorescence of the CND. Finally, human embryonic kidney 293 (HEK 293) cell lines have been used to assess the biocompatibility and bio‐imaging features of CND. Fluorescence microscopy has been used for qualitative examination of the cellular uptake of CND, while the MTT test has been used for quantitative analysis of the cell‐type‐dependent uptake of CND. The article further investigates the sensing of food adulterants. Therefore, we have validated the practicality of CND obtained from the new carbon source for versatile applications.
Green Synthesis and Theoretical Study of New Imidazopyrimidine Derivatives via One‐Pot Multicomponent Reactions
Authors: Ezzatzadeh Elham , Mohammadi Marziyeh , Hossaini Zinatossadat , Khandan Samira 
Published: October 2023

AbstractAg/Fe3O4/SiO2@MWCNTs MNCs magnetic nanocomposites as an effective catalyst was employed for generating of imidazopyrimidine derivatives in high yields. The structure of synthesized nanoatalyst was confirmed by SEM, XRD, TEM, VSM, EDX and XPS analysis. These new compounds were synthesized by using multicomponent reaction of cyclic guanidine derivatives, electron deficient acetylenic compounds, tert‐butyl isocyanide, ethyl bromopyruvate and synthesized nanocatalyst in aqueous media at room temperature. It should be mentioned that the high performance of nanocatalyat was synthesized by using water extract of Petasits hybridus leaves, which was utilized in these reactions for many times to confirm the reusability of nanocatalyst. The antioxidant property of new synthesized imidazopyrimidine was evaluated by two procedures and compound 5 b have the high property relative to other compounds. Also, the antimicrobial activity of new generated imidazopyrimidine was evaluated by disk distribution process utilizing two kinds of Gram‐negative bacteria and Gram‐positive bacteria; proving bacterial growth was stopped by using of these compounds. Also, to better understanding reaction mechanism density functional theory (DFT) based quantum chemical methods have been applied. Applied to the preparation of imidazopyrimidine derivatives, this method has short reaction times, high product yields, and the ability to separate catalyst and product using simple procedures.
Recent Advances on the Utilization of TiO2‐Based Catalysts in the Photocatalytic Reduction of CO2 to Methane
Authors: Mutiara Siska , Saputera Wibawa Hendra , Devianto Hary , Sasongko Dwiwahju 
Published: October 2023

AbstractAddressing the escalating concerns over increasing carbon dioxide (CO2) emissions and their detrimental effect on the environment has become global attention. One promising alternative to tackle this issue involves utilizing photocatalytic technology to convert CO2 into more valuable chemicals, with methane (CH4) being a notable targeted product. This article presents a comprehensive review of the exploration of TiO2‐based photocatalysts by researchers worldwide for such applications. The initial discussion revolves around fundamental aspects, including the basic principles, thermodynamics, kinetics, and reaction mechanisms involved in the process. Additionally, to enhance the efficiency of these aspects, support from other factors is necessary, including the physicochemical properties of the photocatalyst through various catalyst synthesis methods (such as sol‐gel, precipitation, hydrothermal, and solvothermal) as well as employing catalyst modification techniques (such as doping, heterojunction, and surface modifications). Furthermore, the review delves into an examination of parameters that influence the photocatalytic CO2 reduction to methane process, as they directly impact the yield and selectivity of the desired product. Ultimately, the existing challenges and potential research opportunities that could provide comprehensive solutions for the applications of photocatalytic technology for converting CO2 to CH4 as a whole are elaborated in this review.
Molecular Diversity of Base Promoted Annulation of MBH Carbonates of Isatins and Dialkyl But‐2‐ynedioates
Authors: Tang Ting , Liu Xue‐Yan , Sun Jing , Yan Chao‐Guo 
Published: October 2023

AbstractDABCO promoted one‐pot three‐component reaction of aromatic amines, dialkyl but‐2‐ynedioates and MBH nitriles of isatins selectively afforded two diastereomeric spiro[indoline‐3,4′‐pyridines] in comparable yields. On the other hand, DABCO promoted cyclization of dialkyl but‐2‐ynedioates and MBH carbonates of isatins in DCM at room temperature gave spiro[cyclopentane‐1,3′‐indoline] derivatives, while the reaction of dialkyl but‐2‐ynedioates and MBH nitriles of isatins in chloroform at 70 °C resulted in unique cyclopenta[c]quinolone derivatives with ring‐opening of isatin moiety. A plausible reaction mechanism was rationally proposed to explain formation of the different products.
In Situ Constructing of Rigid‐Soft Coupling Solid–Electrolyte Interphase on Silicon Electrode toward High‐Performance Lithium Ion Batteries
Authors: Li Zhenxiao , Hu Tingjie , Yang Juan , Yu Xia , Su Fanyun , Bai Qixian , Ma Yayun , Song Yanchun , Jia Ming , Zhou Xiangyang , Tang Jingjing 
Published: October 2023

AbstractThe application of Si anodes is hindered by some critical issues such as large volume changes of bare Si and fragile solid–electrolyte interface (SEI), resulting in low coulombic efficiency and rapid capacity decay. Herein, a multifunctional SEI film with high content of LiF is in situ constructed via the surface grafting of carbon–fluorine functionalized groups on silicon nanoparticles (SiNPs) during cycling. Mechanical study demonstrates that the incorporation of LiF with high modulus and unbroken carbon–fluorine groups with highly elastic guarantee the rigid‐soft coupling SEI film on Si electrode. Furthermore, it is demonstrated that the rigid‐soft coupling SEI film can effectively accommodate the volume expansion of Si nanoparticles during lithiation process, with the electrode expanding rate of only 114.16% after 100 cycles (263.87% for bare Si without surface modification). Afterward, with the aid of well‐designed rigid‐soft coupling SEI, the initial Coulomb efficiency of 89.8% is achieved, showing a reversible capacity of 1477 mAh g−1 after 200 cycles at 1.2 A g−1. This work provides a simple and efficient solution that can potentially facilitate the practical application of Si anodes.
Ubiquitin‐specific peptidase 10 attenuates the ferroptosis to promote thyroid cancer malignancy by facilitating GPX4 via elevating SIRT6
Authors: Lian Feng , Dong Dandan , Pu Jiaxi , Yang Guanghua , Yang Jing , Yang Shaofei , Wang Yijie , Zhao Bin , Lu Minhao 
Published: October 2023

AbstractPurposeUbiquitin‐specific peptidase 10 (USP10) has been found to have oncogenic activity in several human tumors. This study first revealed the exact function of USP10 on the progression of thyroid cancer (THCA) by researching its effect on the ferroptosis.MethodsUSP10 expression in THCA patients was analyzed by online data analysis and in 75 THCA cases was scrutinized by real‐time quantitative reverse transcription‐polymerase chain reaction and Western blot. Influence of USP10 on the viability, colony formation, migration and invasion of THCA cells was demonstrated by cell counting kit‐8, colony formation, wound healing and Transwell invasion assays. Effect of USP10 on the Erastin‐induced ferroptosis in THCA cells was evaluated by detecting the ferroptosis‐related indicators. Intrinsic mechanism of USP10, glutathione peroxidase 4 (GPX4) and sirtuin 6 (SIRT6) in regulating THCA progression was identified. In vivo xenograft experiment was implemented.ResultsUSP10 was abundantly expressed in THCA patients, linking to poor outcome. USP10 overexpression enhanced the viability, colony formation, migration and invasion of THCA cells. USP10 mitigated the Erastin‐induced ferroptosis in THCA cells, decreased the levels of iron, Fe2+, malondialdehyde, lipid reactive oxygen species, reduced mitochondrial superoxide level, and increased mitochondrial membrane potential. USP10 facilitated the expression of ferroptosis suppressor GPX4 by elevating SIRT6. Loss of USP10 repressed the in vivo growth of THCA cells.ConclusionUSP10 might attenuate the ferroptosis to promote thyroid cancer malignancy by facilitating GPX4 via elevating SIRT6. It might be novel target for the treatment of THCA.
Nano‐selenium alleviates cadmium‐induced neurotoxicity in cerebrum via inhibiting gap junction protein connexin 43 phosphorylation
Authors: Xu Ya‐Ru , Talukder Milton , Li Chen‐Xi , Zhao Ying‐Xin , Zhang Cong , Ge Jing , Li Jin‐Long 
Published: October 2023

AbstractCadmium (Cd) as a ubiquitous toxic heavy metal is reported to affect the nervous system. Selenium (Se) has been shown to have antagonistic effects against heavy metal toxicity. In addition, it shows potential antioxidant and anti‐inflammatory properties. Thus, the purpose of this study was to determine the possible mechanism of brain injury after high Cd exposure and the mitigation of Nano‐selenium (Nano‐Se) against Cd‐induced brain injury. In this study, the Cd‐treated group showed a decrease in the number of neurons in brain tissue, swelling of the endoplasmic reticulum and mitochondria, and the formation of autophagosomes. Nano‐Se intervention restored Cd‐caused alterations in neuronal morphology, endoplasmic reticulum, and mitochondrial structure, thereby reducing neuronal damage. Furthermore, we found that some differentially expressed genes were involved in cell junction and molecular functions. Subsequently, we selected eleven (11) related differentially expressed genes for verification. The qRT‐PCR results revealed the same trend of results as determined by RNA‐Seq. Our findings also showed that Nano‐Se supplementation alleviated Cx43 phosphorylation induced by Cd exposure. Based on immunofluorescence colocalization it was demonstrated that higher expression of GFAP and lower expressions of Cx43 were restored by Nano‐Se supplementation. In conclusion, the data presented in this study establish a direct association between the phosphorylation of Cx43 and the occurrence of autophagy and neuroinflammation. However, it is noteworthy that the introduction of Nano‐Se supplementation has been observed to mitigate these alterations. These results elucidate the relieving effect of Nano‐Se on Cd exposure‐induced brain injury.