bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the binding properties of CASP14 targets and models
Authors: Egbert Megan , Ghani Usman , Ashizawa Ryota , Kotelnikov Sergei , Nguyen Thu , Desta Israel , Hashemi Nasser , Padhorny Dzmitry , Kozakov Dima , Vajda Sandor 
Published: August 2021

AbstractAn important question is how well the models submitted to CASP retain the properties of target structures. We investigate several properties related to binding. First we explore the binding of small molecules as probes, and count the number of interactions between each residue and such probes, resulting in a binding fingerprint. The similarity between two fingerprints, one for the X‐ray structure and the other for a model, is determined by calculating their correlation coefficient. The fingerprint similarity weakly correlates with global measures of accuracy, and GDT_TS higher than 80 is a necessary but not sufficient condition for the conservation of surface binding properties. The advantage of this approach is that it can be carried out without information on potential ligands and their binding sites. The latter information was available for a few targets, and we explored whether the CASP14 models can be used to predict binding sites and to dock small ligands. Finally, we tested the ability of models to reproduce protein–protein interactions by docking both the X‐ray structures and the models to their interaction partners in complexes. The analysis showed that in CASP14 the quality of individual domain models is approaching that offered by X‐ray crystallography, and hence such models can be successfully used for the identification of binding and regulatory sites, as well as for assembling obligatory protein–protein complexes. Success of ligand docking, however, often depends on fine details of the binding interface, and thus may require accounting for conformational changes by simulation methods.
Incorporating covariates information in adaptive clinical trials for precision medicine
Authors: Zhao Wanying , Ma Wei , Wang Fan , Hu Feifang 
Published: August 2021

AbstractPrecision medicine is the systematic use of information that pertains to an individual patient to select or optimize that patient's preventative and therapeutic care. Recent studies have classified biomarkers into predictive and prognostic biomarkers based on their roles in clinical studies. To design a clinical trial for precision medicine, predictive biomarkers and prognostic biomarkers should both be included. In statistical analysis, biomarkers are mathematically treated as covariates. We first classify covariates into predictive and prognostic covariates according to their roles. We then provide a brief review of recent advances in adaptive designs that incorporate covariates. However, the literature includes no designs that incorporate both prognostic covariates and predictive covariates simultaneously. In this paper, we propose a new family of covariate‐adjusted response‐adaptive (CARA) designs that incorporate both prognostic and predictive covariates and the responses. It is important to note that the predictive biomarkers and prognostic biomarkers play different roles in the new designs. The advantages of the proposed methods are demonstrated via numerical studies, and some further statistical issues are also discussed.
On reactivity of superatom Be8C with nucleophiles to produce hydrogen
Authors: Li Cui‐Mei , Wu Di , Chen Wei , Liu Jia‐Yuan , Yu Dan , Li Ying 
Published: August 2021

AbstractA new superatom, namely Be8C, has been characterized in terms of electronic structure, stability, and especially, chemical behavior. Intriguingly, both Be8C compounds and reactivity of Be8C with hydrochloric acid to release H2 are found to mimic zinc chemistry. On the other hand, the reaction of Be8C with water is also favorable both kinetically and thermodynamically, showing higher reactivity of Be8C compared with Zn. Both Langmuir‐Hinshelwood and Eley‐Rideal‐like mechanisms are possible for the studied reactions, and the latter mechanism is preferred over the former one as it involves one less reaction step and has a larger overall exothermcity and lower activation barrier for H2 formation. This comparative study unravels the similarities and differences between superatoms and atoms from a new perspective and suggests a promising research direction in superatom chemistry.
Robust estimation algorithm based on prior probability statistics
Authors: Wang Jing , Hao Gang 
Published: August 2021

AbstractFor the nonlinear systems with uncertain system parameters, based on the recursive linear minimum variance estimation framework, the effect of the system parameters on the mean squared error (MSE) is analyzed, that is, the greater the system parameters deviation (whether they are positive or negative deviation) is, the greater the MSE is. Based on the analysis results and prior probability statistics (probability distributions or sampling distributions), an innovative robust estimation algorithm is proposed for nonlinear systems with uncertain system parameters. Three examples verify the effectiveness of the proposed algorithm.
Survival trees based on heterogeneity in time‐to‐event and censoring distributions using parameter instability test
Authors: Kundu Madan Gopal , Ghosh Samiran 
Published: August 2021

AbstractSurvival analysis of right‐censored data often arises in many areas of research including medical research. The effect of covariates (and their interactions) on survival distribution can be studied through existing methods that require pre‐specifying the functional form of the covariates including their interactions. Survival trees offer a relatively flexible approach when the form of covariates' effects is unknown. We have proposed the SurvCART algorithm to construct a survival tree. There are two features that distinguish the SurvCART algorithm from the rest. First, most of the currently available survival tree construction techniques are not based on a formal test of significance and, hence, prone to spurious findings. The proposed SurvCART algorithm utilizes the “conditional inference” framework that selects splitting variable via parameter instability test and subsequently finds the optimal split based on some maximally chosen statistic. We used likelihood score‐based parameter instability tests that converge to distribution with known distribution function so that thep‐value can be obtained easily without any approximation. Second, the SurvCART algorithm has the flexibility to extend the concept of heterogeneity to the censoring time distribution as well, a feature that can be useful when censoring distribution is influenced by baseline covariates. We evaluated the operating characteristics of the parameter instability test and compared the performance of the SurvCART algorithm with other survival tree algorithms via simulation. Finally, the SurvCART algorithm was applied to a real data setting. The proposed method is implemented in R package LongCART available on CRAN.
Salami-Tactics: when is it time for a major cut after multiple minor amputations?
Authors: Berli Martin C. , Rancic Zoran , Schöni Madlaina , Götschi Tobias , Schenk Pascal , Kabelitz Method , Böni Thomas , Waibel Felix W. A. 
Published: August 2021

Abstract
Introduction
Repetitive minor amputations carry the concomitant risks of multiple surgical procedures, major amputations have physical and economical major drawbacks. The aim of this study was to evaluate whether there is a distinct number of minor amputations predicting a major amputation in the same leg and to determine risk factors for major amputation in multiple minor amputations.

Materials and methods
A retrospective chart review including 429 patients with 534 index minor amputations between 07/1984 and 06/2019 was conducted. Patient demographics and clinical data including number and level of re-amputations were extracted from medical records and statistically analyzed.

Results
290 legs (54.3%) had one or multiple re-amputations after index minor amputation. 89 (16.7%) legs needed major amputation during follow up. Major amputation was performed at a mean of 32.5 (range 0 –
275.2) months after index minor amputation. No particular re-amputation demonstrated statistically significant elevated odds ratio (a.) to be a major amputation compared to the preceding amputation and (b.) to
lead to a major amputation at any point during follow up. Stepwise multivariate Cox regression analysis revealed minor re-amputation within 90 days (HR 3.8, 95% CI 2.0-7.3, p <0.001) as the only risk factor for
major amputation if at least one re-amputation had to be performed.

Conclusions
There is no distinct number of prior minor amputations in one leg that would justify a major amputation on its own. If a re-amputation has to be done, the timepoint needs to be considered as re-amputations within 90 days carry a fourfold risk for major amputation.

Level of evidence
Retrospective comparative study (Level III).
Aptitude and attitude: predictors of performance during and after basic laparoscopic skills training
Authors: Beattie Kirsty L. , Hill Andrew , Horswill Mark S. , Grove Philip M. , Stevenson Andrew R. L. 
Published: August 2021

Abstract
Background
Manual dexterity and visual-spatial ability are considered key to the development of superior laparoscopic skills. Nevertheless, these abilities do not reliably explain all the variance found in the technical performance of surgical trainees. Consequently, we must look beyond these abilities to improve our understanding of laparoscopic skills and to better identify/develop surgical potential earlier on.

Purpose
To assess the individual and collective impact of physical, cognitive, visual, and psychological variables on performance during and after basic simulation-based laparoscopic skills training.

Method
Thirty-four medical students (laparoscopic novices) completed a proficiency-based laparoscopic skills training program (using either a 2D or 3D viewing mode). This was followed by one testing session, a follow-up testing session with new (yet similar) tasks, and a series of physical, cognitive, visual, and psychological measures.

Results
The statistical models that best predicted variance in training performance metrics included four variables: viewingmode (2D vs 3D), psychologicalflexibility, perceivedtaskdemands, and manualdexterity (bimanual). In subsequent testing, a model that included viewingmode and manualdexterity (assembly) best predicted performance on the pre-practiced tasks. However, for a highly novel, spatially complex laparoscopic task, performance was best predicted by a model that comprised viewingmode, visual-spatialability, and perceivedtaskdemands. At follow-up, manualdexterity (assembly) alone was the best predictor of performance on new (yet similar) tasks.

Conclusion
By focussing exclusively on physical/cognitive abilities, we may overlook other important predictors of surgical performance (e.g. psychological variables). The present findings suggest that laparoscopic performance may be more accurately explained through the combined effects of physical, cognitive, visual, and psychological variables. Further, the results suggest that the predictors may change with both task demands and the development of the trainee. This study highlights the key role of psychological skills in overcoming initial training challenges, with far-reaching implications for practice.
Water Insecurity is Associated with Lack of Viral Suppression and Greater Odds of AIDS-Defining Illnesses Among Adults with HIV in Western Kenya
Authors: Nagata Jason M. , Miller Joshua D. , Cohen Craig R. , Frongillo Edward A. , Weke Elly , Burger Rachel , Wekesa Pauline , Sheira Lila A. , Mocello A. Rain , Otieno Phelgona , Butler Lisa M. , Bukusi Elizabeth A. , Weiser Sheri D. , Young Sera L. 
Published: August 2021

AbstractReliable access to safe and acceptable water in sufficient quantities (i.e., water security) is important for medication adherence and limiting pathogen exposure, yet prior studies have only considered the role of food security as a social determinant of HIV-related health. Therefore, the objective of this analysis was to assess the relationships between household water insecurity and HIV-related outcomes among adults living with HIV in western Kenya (N = 716). We conducted a cross-sectional analysis of baseline data fromShamba Maisha(NCT02815579), a cluster randomized controlled trial of a multisectoral agricultural and asset loan intervention. Baseline data were collected from June 2016 to December 2017. We assessed associations between water insecurity and HIV-related outcomes, adjusting for clinical and behavioral confounders, including food insecurity. Each five-unit higher household water insecurity score (range: 0–51) was associated with 1.21 higher odds of having a viral load ≥ 1000 copies/mL (95% CI 1.07, 1.36) and 1.26 higher odds of AIDS-defining illness (95% CI 1.11, 1.42). Household water insecurity was not associated with CD4 cell count (B: 0.27; 95% CI −3.59, 13.05). HIV treatment and support programs should consider assessing and addressing water insecurity in addition to food insecurity to optimize HIV outcomes.
Metainferential Reasoning on Strong Kleene Models
Authors: Fjellstad Andreas 
Published: August 2021

AbstractBarrio et al. (Journal of Philosophical Logic, 49(1), 93–120, 2020) and Pailos (Review of Symbolic Logic, 2020(2), 249–268, 2020) develop an approach to define various metainferential hierarchies on strong Kleene models by transferring the idea of distinct standards for premises and conclusions from inferences to metainferences. In particular, they focus on a hierarchy named the $\mathbb {S}\mathbb {T}$
S
T
-hierarchy where the inferential logic at the bottom of the hierarchy is the non-transitive logic ST but where each subsequent metainferential logic ‘says’ about the former logic that it is transitive. While Barrio et al. (2020) suggests that this hierarchy is such that each subsequent level ‘in some intuitive sense, more classical than’ the previous level, Pailos (2020) proposes an extension of the hierarchy through which a ‘fully classical’ metainferential logic can be defined. Both Barrio et al. (2020) and Pailos (2020) explore the hierarchy in terms of semantic definitions and every proof proceeds by a rather cumbersome reasoning about those semantic definitions. The aim of this paper is to present and illustrate the virtues of a proof-theoretic tool for reasoning about the $\mathbb {S}\mathbb {T}$
S
T
-hierarchy and the other metainferential hierarchies definable on strong Kleene models. Using the tool, this paper argues that each level in the $\mathbb {S}\mathbb {T}$
S
T
-hierarchy is non-classical to an equal extent and that the ‘fully classical’ metainferential logic is actually just the original non-transitive logic ST ‘in disguise’. The paper concludes with some remarks about how the various results about the $\mathbb {S}\mathbb {T}$
S
T
-hierarchy could be seen as a guide to help us imagine what a non-transitive metalogic for ST would tell us about ST. In particular, it teaches us that ST is from the perspective of ST as metatheory not only non-transitive but also transitive.
Asymmetry cannot solve the circularity/regress problem of property structuralism
Authors: Busse Ralf 
Published: August 2021

AbstractStrong dispositional monism (SDM), the position that all fundamental physical properties consist in dispositional relations to other properties, is naturally construed as property structuralism. J. Lowe’s circularity/regress objection (CRO) constitutes a serious challenge to SDM that questions the possibility of a purely relational determination of all property essences. The supervenience thesis of A. Bird’s graph-theoretic asymmetry reply to CRO can be rigorously proved. Yet the reply fails metaphysically, because it reveals neither a metaphysical determination of identities on a purely relational basis nor a determination specifically of identities in the sense of essences. Asymmetry is thus not by itself sufficient for a solution to CRO. But it cannot even help to answer CRO when a model for the determination of essences is taken as a basis. Nor is asymmetry necessary for a reply, as property structures may well be symmetric. A metaphysics of dispositional properties as grounded in a purely relational structure faces serious obstacles, and the properties would not be fundamental. Since essence and grounding are notions of metaphysical priority, there can be no essentially dispositional metaphysically fundamental properties, and the prospects of a “coherentist” metaphysics of basic properties are dim. A modal retreat that refrains from a post-modal conception of essence and simply claims that fundamental properties play dispositional roles by metaphysical necessity is unsatisfactory.
Comparison of metal burden in different muscle tissues of Great cormorant (Phalacrocorax carbo)
Authors: Lehel József , Grúz Adrienn , Bartha András , Pintér Imre , Lénárt Zoltán , Major László , Menyhárt László , Szabó Rita , Budai Péter 
Published: August 2021

AbstractConcentrations of 12 metals (As, Ba, Cd, Co, Cr, Cu, Hg, Mn, Mo, Ni, Pb and Zn) were examined in the pectoral and thigh muscle of great cormorants (Phalacrocorax carbo). The samples were collected from Central Tisza-Jászság Nature Conservation Area in Hungary. The tissue samples were analysed by inductively coupled plasma optical emission spectroscopy (ICP-OES). The aim of the study was to examine the impacts of heavy metal pollution on the water birds, determine the concentrations of the abovementioned metals in the different muscle tissues of these wetland birds, and provide the basic materials for monitoring the environmental pollution. Among the investigated elements/metals, the detected concentrations of As, Ba, Cd, Co, Cr, Mo and Ni were below the detection limit. Higher concentration of Cu, Hg, Mn and Pb was measured in the pectoral muscle compared to the thigh muscle, but only in the case of Cu and Mn were found significant differences between the tissues. In the case of the Zn concentration, the higher value was detected in the thigh muscle. There were no statistical differences between males and females in either metal concentrations.
Has sustainability science turned left?
Authors: Bodin Örjan 
Published: August 2021

AbstractAs the urgent need for societies to steer towards sustainability is becoming increasingly apparent, sustainability science as a research community is facing difficult challenges successfully navigating the intensifying and often harsh political debates. An important line of conflict is (still) between the political left and right, although other conflicts are gaining increasing attention. As private corporations are stepping up their conservation agendas and non-governmental organizations are increasingly embracing market mechanisms to achieve healthier ecosystems, the scholarly community of sustainability science appears to be turning more to the political left. To navigate these entangled scientific and political landscapes, accomplishing constructive debates emphasizing the value of nurturing a broad spectra of viewpoints should be given higher priority in all forums where issues of sustainability are discussed.
Assessment in ‘survival mode’: student and faculty perceptions of online assessment practices in HE during Covid-19 pandemic
Authors: Meccawy Zilal , Meccawy Maram , Alsobhi Aisha 
Published: August 2021

AbstractThis paper presents a cross-sectional study that demonstrates how King Abdulaziz University has responded to the lockdown imposed by the Ministry of Education in Saudi Arabia due to the Covid-19 pandemic. The purpose of this study was to examine the perceptions of students and faculty towards assessment that had to take place online due to physical or social distancing rules and lockdowns. A descriptive mixed-method study was conducted with two different self-administered questionnaires that were developed for students and faculty, respectively. A total of 547 responses were received from undergraduate students and 213 from faculty. The main finding suggests the need for a multilevel approach to the problems of cheating and plagiarism, including raising student awareness and ethics, training teachers to detect cheating methods, and institutions activating their code of practice and applying severe sanctions on those who engage in such practices.
Infodemic in Germany and Brazil
Authors: Leschzyk Dinah K. 
Published: August 2021

AbstractEven though the topic of infodemic – a blending of the words information and pandemic – emerged just in 2020 it addresses a question that has been crucial ever since in communication: How to establish – or undermine – credibility? This article deals with rhetorical techniques applied by Brazilian President Jair Messias Bolsonaro (2019–) and high-ranking politicians of the German party AfD (Alternative für Deutschland) during the COVID-19-pandemic. The analysis is based on tweets published through their official accounts during the first year of the pandemic (@jairbolsonaro, @AfD). Meanwhile Bolsonaro, who was in charge during the crisis, attacks the media claiming they would spread panic and false information, AfD, an opposition party, concentrates its criticism on the federal and state governments. The key concept credibility‹ as discussed by Ortwin Renn (2019) and basic claims that appear in Aristotle’s »Rhetoric«, dating from the 4th century BC, build the theoretical basis of this study. Methodologically, the analysis is based on the Discourse-Historical Approach (Reisigl/Wodak 2001), focusing on discursive strategies of negative other representation, and a framework for studies on the language of legitimation and delegitimation developed by Theo van Leeuwen (1996).
Balancing Technology, Pedagogy and the New Normal: Post-pandemic Challenges for Higher Education
Authors: Rapanta Chrysi , Botturi Luca , Goodyear Peter , Guàrdia Lourdes , Koole Marguerite 
Published: August 2021

AbstractThe Covid-19 pandemic has presented an opportunity for rethinking assumptions about education in general and higher education in particular. In the light of the general crisis the pandemic caused, especially when it comes to the so-called emergency remote teaching (ERT), educators from all grades and contexts experienced the necessity of rethinking their roles, the ways of supporting the students’ learning tasks and the image of students as self-organising learners, active citizens and autonomous social agents. In our first Postdigital Science and Education paper, we sought to distil and share some expert advice for campus-based university teachers to adapt to online teaching and learning. In this sequel paper, we ask ourselves: Now that campus-based university teachers have experienced the unplanned and forced version of Online Learning and Teaching (OLT), how can this experience help bridge the gap between online and in-person teaching in the following years? The four experts, also co-authors of this paper, interviewed aligning towards an emphasis on pedagogisation rather than digitalisation of higher education, with strategic decision-making being in the heart of post-pandemic practices. Our literature review of papers published in the last year and analysis of the expert answers reveal that the ‘forced’ experience of teaching with digital technologies as part of ERT can gradually give place to a harmonious integration of physical and digital tools and methods for the sake of more active, flexible and meaningful learning.