bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of protein–ligand complexes in CASP15
Authors: Robin Xavier , Studer Gabriel , Durairaj Janani , Eberhardt Jerome , Schwede Torsten , Walters W. Patrick 
Published: October 2023

AbstractCASP15 introduced a new category, ligand prediction, where participants were provided with a protein or nucleic acid sequence, SMILES line notation, and stoichiometry for ligands and tasked with generating computational models for the three‐dimensional structure of the corresponding protein–ligand complex. These models were subsequently compared with experimental structures determined by x‐ray crystallography or cryoEM. To assess these predictions, two novel scores were developed. The Binding‐Site Superposed, Symmetry‐Corrected Pose Root Mean Square Deviation (BiSyRMSD) evaluated the absolute deviations of the models from the experimental structures. At the same time, the Local Distance Difference Test for Protein–Ligand Interactions (lDDT‐PLI) assessed the ability of models to reproduce the protein–ligand interactions in the experimental structures. The ligands evaluated in this challenge range from single‐atom ions to large flexible organic molecules. More than 1800 submissions were evaluated for their ability to predict 23 different protein–ligand complexes. Overall, the best models could faithfully reproduce the geometries of more than half of the prediction targets. The ligands' size and flexibility were the primary factors influencing the predictions' quality. Small ions and organic molecules with limited flexibility were predicted with high fidelity, while reproducing the binding poses of larger, flexible ligands proved more challenging.
Case–control matching‐guided exposure‐efficacy relationship for avelumab in patients with urothelial carcinoma
Authors: Soltantabar Pooneh , Alhadab Ali , Hibma Jennifer , Roychoudhury Satrajit , Wang Diane D. , Bello Carlo , Elmeliegy Mohamed 
Published: October 2023

AbstractExposure‐response (E‐R) analyses are an integral component of understanding the benefit/risk profile of novel oncology therapeutics. These analyses are typically conducted using data from the treatment arm to characterize the relationship between drug exposure (low vs. high) and efficacy or safety outcomes. For example, outcomes of patients with lower exposure in the treatment arm (e.g., Q1) might be compared to outcomes of those with higher drug exposure (Q2, Q3, and Q4). Outcomes from the lowest exposure quartile may be also compared to the control arm to evaluate whether the Q1 subgroup derived clinical benefit. However, the sample size and the distribution of patient baseline characteristics and disease risk factors are not balanced in such a comparison (Q1 vs. control), which may bias the analysis and causal interpretation of clinical benefit in the Q1 subgroup. Herein, we report the use of case–control matching to account for this bias and better understand the E‐R relationship for avelumab in urothelial carcinoma, a PD‐L1 inhibitor approved for the treatment of several cancers. Data from JAVELIN‐100 was utilized which is a phase III study of avelumab in first‐line maintenance treatment in patients with urothelial carcinoma; this clinical study demonstrated superiority of avelumab versus best‐supportive care leading to approval in the United States, Europe, and other countries. A post hoc case‐control matching method was implemented to compare the efficacy outcome between Q1 avelumab subgroup and matched patients extracted from the control arm with similar baseline characteristics, which showed a clinically relevant difference in overall survival in favor of the Q1 avelumab subgroup. This analysis demonstrates the importance of accounting for imbalance in important baseline covariates when comparing efficacy outcomes between subgroups within the treatment arm versus the control arm.
Analog Quantum Bit Based on Pancharatnam‐Berry Phase Metasurfaces
Authors: Chen Long , You Jian Wei , Gu Ze , Ma Qian , Cui Tie Jun 
Published: October 2023

AbstractThe emergence of information metamaterials has spurred significant advances in the field of information sciences. However, the current studies are predominantly focused on classical bits as the fundamental information units, and the classical bit can only be located at two poles of Bloch sphere, resulting in limited information capacity. To break such limit, quantum bits (qubits) offer a promising solution since they have superposition states anywhere on the Bloch sphere. Here, a Pancharatnam‐Berry (PB) phase metasurface is used to emulate the qubits. Firstly, it proposes a theoretical concept of analog quantum bit and develops its mathematical and geometrical representations. Subsequently, a meta‐atom is designed as a physical platform to implement the concept of analog qubits. By manipulating the geometric configuration of the proposed meta‐atom, it achieves arbitrary superpositions of polarization states. A PB phase metasurface is experimentally fabricated to validate that the proposed analog qubit can be used to emulate the quantum bit in terms of both mathematical and geometrical representations. This work not only provides a theoretical foundation to go beyond the information limit of classical bits but also develops a feasible physics platform to investigate quantum information metasurfaces, which would complement and revolutionize classical information science.
Prominin‐1 expression in the testis/epididymis and fertility
Authors: Fargeas Christine A. , Jászai József , Corbeil Denis 
Published: October 2023

AbstractThe contribution of Prominin‐1 (aka CD133) to male fertility has recently been (re)investigated, with contradictory results. Early findings, essential for deciphering its role, have unfortunately been neglected. Here, the authors present what is currently known about its expression in the male reproductive system of rodents and men so that its involvement in male fertility can be re‐examined and discussed in the light of these elements.
In situ skid estimation for mobile robots in outdoor environments
Authors: Nourizadeh Payam , McFadden Fiona J. Stevens , Browne Will N. 
Published: October 2023

AbstractSkidding is a surface hazard for mobile robots' navigation and traction control systems when operating in outdoor environments and uneven terrains due to the wheel–terrain interaction. It could lead to large trajectory tracking errors, losing the robot's controllability, and mission failure occurring. Despite research in this field, the development of a real‐world feasible in situ skid estimation system with the capability of operating in harsh and unforeseen environments using low‐cost/power and ease of integrating sensors is still an open problem in terramechanics. This paper presents a novel velocity‐based definition for skidding that enables a real‐world feasible estimation for the mobile robot's undesired skidding at the vehicle‐level in outdoor environments. The proposed technique estimates the undesired skidding using a combination of two proprioceptive sensors (e.g., inertial measurement unit and wheel encoder) and deep learning. The practicality of a velocity‐based definition and the performance of the proposed undesired skid estimation technique are evaluated experimentally in various outdoor terrains. The results show that the proposed technique performs with less than 11.79 mm/s mean absolute error and estimates the direction of undesired skidding with approximately 98% accuracy.
Temperature‐Sensitive Properties and Mechanism of Smart Magnetic Fluids Modified with Cellulose Derivatives
Authors: Yang Shuying , Jiang Hui , Duan Le , Zuo Kaixuan , Urujeni Gisèle Ineza , Li DuoDuo , Yao Yuyang , Xiao Deli 
Published: October 2023

AbstractCombining magnetic materials with environmentally sensitive polymers to develop intelligent magnetic fluids that respond to external stimuli has become a new research hotspot. At present, the bottlenecks in the development of temperature‐sensitive materials are the complex composition, and its properties in different laboratories vary greatly. Moreover, despite extensive research on magnetic fluids, there remains a dearth of systematic investigation into temperature‐sensitive intelligent magnetic fluids. In this study, we utilized a UV‐visible spectrophotometer to measure the change in transmittance of different magnetic fluid solutions with temperature variation. We systematically investigated the effects of the magnetic fluid dispersion medium, size and concentration of magnetic nanoparticles, type and viscosity of cellulose on the temperature sensitivity of the magnetic fluid. We found that compared with Hydroxypropyl Methyl Cellulose (HPMC) (type I), HPMC (type II) modified magnetic fluid has better stability and a higher phase transition temperature. Moreover, with the increase of the concentration of magnetic fluid, the phase transition temperature is higher. In addition, the lower the viscosity of HPMC‐modified magnetic fluid, the better the stability and the higher the phase transition temperature. We also studied the mechanism of temperature sensitivity, and the results showed that hydrogen bond interactions play an important role. This research will facilitate the use of temperature‐sensitive smart magnetic fluids for biomedical application.
Synergistic Effect of Selenium Dioxide for Better Photocatalytic Performance of Conventional Semiconductors Distributed into Mesoporous SBA‐15
Authors: Ranjbar‐Niavol Neda , Zanjanchi Mohammad Ali , Farjood Mehrdad 
Published: October 2023

AbstractThe mesoporous SBA‐15 was synthesized in acidic conditions by hydrothermal method using Pluronic surfactant P123. A combination of SeO2, TiO2, and CuO was loaded in SBA‐15 in pairs or singly. Synthesized SBA‐15 and some loaded mesoporous materials were characterized using several standard techniques. The efficiency of the synthesized photocatalysts was verified for the decomposition of two different dyes (methylene blue (MB) and methyl green (MG)) under ultraviolet and visible light radiation. The results show that the synthesized photocatalyst based on SBA‐15 with 5 % by weight of TiO2 and 5 % by weight of SeO2 has better performance (about 98 % of MB or MG were degraded within 120 min under UV radiation). Also, the photocatalyst with 5 % by weight of SeO2 and 5 % by weight of CuO shows a good performance for the degradation of the dyes under visible irradiation in the presence of H2O2 (complete elimination of MB and MG within 150 and 75 min, respectively). The scavenging test shows that superoxide has a governing role for the degradation of the dyes. The photocatalysts are reusable and they could preserve more than 74 % of the efficiency following 4 times of consecutive use for the degradation of the dyes.
Graphene‐Based Nano Materials: Biomedical Applications
Authors: Jakhar Ajay , Sharma Jyoti , Sharma Sharad , Krishan Sharma Lavanya 
Published: October 2023

AbstractGraphene is a single layered two‐dimensional structure of graphite and it has been a flaming topic of research due to its remarkable properties. The efficiency of graphene‐based materials is exploited in many spheres of life ranging from biosensing, targeted drug delivery, bio‐imaging, quantum physics, transportation, energy storage devices, faster electronics, and many more. Graphene is made of a monolayer of sp2carbon atoms organized in a hexagonal pattern with a C−C bond length of 1.42 A. Graphene has attracted interest in the development of electrochemical sensors and biosensors due to its excellent electrical conductivity, significant surface area, and high electron transfer potential. Because of these exclusive characteristics, it has also become a suitable contender for extensive biomedical uses that favors the differentiation of human mesenchymal stem cells (MSC) into bone cells and inhibit proliferation of cells, fluorescence quenching, drug/gene delivery, tissue engineering and antitumor treatments. In last ten years, notable research has been conducted to explore its biomedical applications. Encouraged by its numerous successful integrations into the biomedical fields, the up‐to‐date developments of graphene applications in various dimensions of biomedical field such as biosensors, gene and drug delivery, photo‐thermal therapy, bio‐imaging and tissue engineering are summarized here.
“Why am I here?”: A phenomenological exploration of first‐generation college student experiences in STEM majors within a predominantly white institution
Authors: Marco‐Bujosa Lisa M. , Baker Lauren , Malott Krista M. 
Published: October 2023

AbstractFirst‐generation college students (FGCSs) are a growing population in undergraduate education. Research on FGCS primarily focuses on the challenges and barriers they encounter in college. While important, this literature offers a limited view of FGCS as learners. Moreover, minimal literature has examined these students' lived experiences within sciences, technology, engineering, and mathematics (STEM). This study explores the learning experiences of FGCS (N = 17) in undergraduate STEM programs at a mid‐sized, private, predominantly white institution. Guided by the frameworks of intersectionality and social cognitive career theory, the researchers utilized a qualitative, phenomenological research methodology to hear the perspectives of FGCS to and to identify problematic higher educational structures in STEM. Findings point to an elitist stance underlying STEM programs based in general disciplinary norms that restricted FGCS access to STEM majors and careers across social, academic, and professional elements of the academic experience. FGCS who were multiply minoritized based upon race, gender, and social class experienced the compounding of marginalization, and academic success and persistence came at a personal cost. Students also reported relying predominantly on personal strengths and motivations to overcome elitism in STEM rather than on institutional supports. Findings also highlight the variation in the first‐generation experience and identify the unique barriers FGCS encounter within STEM fields. Implications for dismantling inequitable structures for higher education in STEM attending to the social, academic, and professional inclusion of FGCS.
An efficient acoustic classifier for high‐priority avian species in the southern Great Plains using convolutional neural networks
Authors: Wolfe Brandon , Proctor Mike D. , Nolan Victoria , Webb Stephen L. 
Published: October 2023

AbstractPassive acoustic monitoring is a valuable ecological and conservation tool that allows researchers to collect data from vocal species across large geographic areas and temporal spans. Grassland bird populations, many of which are indicators of ecosystem health, have experienced precipitous declines over the past several decades. Acoustic monitoring of grassland bird populations provides opportunities to monitor declines and focus conservation practices, yet the ability to identify species efficiently and accurately from acoustic data is challenging. Therefore, development of automated classifiers such as convolutional neural networks (CNNs) are at the forefront of streamlining detection and identification of individual species. Here, we present a CNN classifier for 5 key grassland bird species across southcentral Oklahoma, a part of the southern Great Plains: northern bobwhite (Colinus virginianus), painted bunting (Passerina ciris), dickcissel (Spiza americana), eastern meadowlark (Sturnella magna), and Bell's vireo (Vireo bellii). We compiled a high‐quality training dataset consisting of 6,933 calls, built semiautonomously using template matching that can be expanded easily to any bird species of interest. Our trained multilabel CNN achieved a high level of classification accuracy (≥98%) for the 5 species using the library of test calls and field recordings played using a programmable game caller. The ability to conduct acoustic wildlife surveys across large spatial extents will allow for more efficient monitoring of wildlife to determine key population parameters and trends and effects of biotic and abiotic factors (e.g., vegetation, disturbance, weather) on these key species.
Double Kerr-Schild spacetimes and the Newman-Penrose map
Authors: Farnsworth Kara , Graesser Michael L. , Herczeg Gabriel 
Published: October 2023

Abstract
The Newman-Penrose map, which is closely related to the classical double copy, associates certain exact solutions of Einstein’s equations with self-dual solutions of the vacuum Maxwell equations. Here we initiate an extension of the Newman-Penrose map to a broader class of spacetimes. As an example, we apply principles from the Newman-Penrose map to associate a self-dual gauge field to the Kerr-Taub-NUT-(A)dS spacetime and we show that the result agrees with previously studied examples of classical double copies. The corresponding field strength exhibits a discrete electric-magnetic duality that is distinct from its (Hodge star) self-dual property.
On s-confining SUSY-QCD with anomaly mediation
Authors: de Lima Carlos Henrique , Stolarski Daniel 
Published: October 2023

Abstract
In this work, we present a comprehensive study of the phase diagram of supersymmetric QCD with Nf = Nc + 1 flavors perturbed by Anomaly Mediated Supersymmetry Breaking (AMSB). We extend the previous analyses on s-confining ASQCD theories in three different directions. We show that the existence of the QCD-like vacuum is independent of the size of the SUSY breaking parameter. We further expand the analysis of these models by including two and three-loop contributions to investigate the robustness and limitations of the results. Finally, we include the leading effect of higher-order Kähler terms to investigate the stability of the phase diagram as we approach the confining energy scale. The analysis with higher order Kähler terms is also extended for Nc = 2 for which AMSB alone gives inconclusive results.
2-index chiral gauge theories
Authors: Anber Mohamed M. , Chan Samson Y. L. 
Published: October 2023

Abstract
We undertake a systematic study of the 4-dimensional SU(N) 2-index chiral gauge theories and investigate their faithful global symmetries and dynamics. These are a finite set of theories with fermions in the 2-index symmetric and anti-symmetric representations, with no fundamentals, and they do not admit a large-N limit. We employ a combination of perturbative and nonperturbative methods, enabling us to constrain their infrared (IR) phases. Specifically, we leverage the ’t Hooft anomalies associated with continuous and discrete groups to eliminate a few scenarios. In some cases, the anomalies rule out the possibility of fermion composites. In other cases, the interplay between the continuous and discrete anomalies leads to multiple higher-order condensates, which inevitably form to match the anomalies. Further, we pinpoint the most probable symmetry-breaking patterns by searching for condensates that match the full set of anomalies resulting in the smallest number of IR degrees of freedom. Higher-loop β-function analysis suggests that a few theories may flow to a conformal fixed point.
JASON in Europe: Contestation and the Physicists’ Dilemma about the Vietnam War
Authors: Ienna Gerardo , Turchetti Simone 
Published: October 2023

AbstractThis article examines the contestation that in the summer of 1972 disrupted workshops in Western Europe featuring renowned physicists affiliated to the top-secret JASON advisory group. Set up by the US Department of Defense research division, JASON was responsible for outlining new bombing strategies in the context of the Vietnam War. Some of the physicists involved in the protest had contributed instead to the International War Crimes (Russell) Tribunal, gathering evidence in Indochina on the allegedly genocidal character of the US bombing. In reconstructing the history of the contestation, this article contends that the conflict was an opportunity for advertising diverging political stances in the rebellious atmosphere of early 1970s, as much as to convey competing views about the physicists’ influence on global affairs. In particular, while JASON members boasted that their advisory roles stifled bellicose approaches, the protesters recalled the merits of independent inquiry and advocacy “from below” the elitist sphere of government advice, describing these as a better way to advance principles of global social justice.
Evaluation of chemical constituents of Rooibos (Aspalathus linearis) and Honeybush (Cyclopia intermedia) as adenosine A1/A2A receptor ligands
Authors: Gouws Liezel , Janse van Rensburg Helena D. , Terre’Blanche Gisella , Van der Walt Mietha M. 
Published: October 2023

AbstractRooibos (Aspalathus linearis) and Honeybush (Cyclopia intermedia) are popular tisanes in South Africa and are of growing interest due to the wide variety of flavonoids and other phytochemicals they contain. Despite their history as herbal teas and traditional medicines, the chemical constituents of these tisanes have yet to be studied for their effects on adenosine receptors. A series of 30 commercially available chemical constituents of Rooibos and Honeybush were investigated via radioligand binding studies to determine their adenosine A1 and A2A receptor affinity at both rat and human subtypes in order to establish structure-activity relationships and identify novel adenosine receptor ligands. In addition, in silico evaluations of the 30 test compounds were also performed to predict their physiochemical and pharmacokinetic properties. The most promising chemical constituent was kaempferol (28) which showed sub-micromolar affinity towards the rat A1 subtype (rA1Ki = 0.7287 μM; hA1Ki = 9.88 µM) and acted as an antagonist toward adenosine rA1 receptors. Additionally, quercetin (2), chrysoeriol (8), luteolin (9), eriodyctiol (12), and naringenin (27) also showed adenosine A1 and/or A2A receptor affinity. It was observed that a flavonol scaffold is preferred to flavone and flavanone scaffolds, and within the flavonols, C4’-OH substitution on ring B is preferred to C3’,4’-diOH substitution. These phytochemicals, specifically kaempferol (28), may be considered lead-like and valuable in designing novel ligands, based on in vitro and in silico evaluation.