bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measuring homoplasy I: comprehensive measures of maximum and minimum cost under parsimony across discrete cost matrix character types
Authors: Hoyal Cuthill Jennifer F. , Lloyd Graeme T. 
Published: June 2024

AbstractHere, we propose, prove mathematically and discuss maximum and minimum measures of maximum parsimony evolution across 12 discrete phylogenetic character types, classified across 4467 morphological and molecular datasets. Covered character types are: constant, binary symmetric, multistate unordered (non‐additive) symmetric, multistate linear ordered symmetric, multistate non‐linear ordered symmetric, binary irreversible, multistate irreversible, binary Dollo, multistate Dollo, multistate custom symmetric, binary custom asymmetric and multistate custom asymmetric characters. We summarize published solutions and provide and prove a range of new formulae for the algebraic calculation of minimum (m), maximum (g) and maximum possible (gmax) character cost for applicable character types. Algorithms for exhaustive calculation of m, g and gmax applicable to all classified character types (within computational limits on the numbers of taxa and states) are also provided. The general algorithmic solution for minimum steps (m) is identical to a minimum spanning tree on the state graph or minimum weight spanning arborescence on the state digraph. Algorithmic solutions for character g and gmax are based on matrix mathematics equivalent to optimization on the star tree, respectively for given state frequencies and all possible state frequencies meeting specified numbers of taxa and states. We show that maximizing possible cost (gmax) with given transition costs can be equivalent to maximizing, across all possible state frequency combinations, the lowest implied cost of state transitions if any one state is ancestral on the star tree, via the solution of systems of linear equations. The methods we present, implemented in the Claddis R package, extend to a comprehensive range, the fundamental character types for which homoplasy may be measured under parsimony using m, g and gmax, including extra cost (h), consistency index (ci), retention index (ri) or indices based thereon.
Policy mobilities, ‘informational infrastructures’ and the ‘digital turn’: Towards a research agenda
Authors: Ward Kevin 
Published: June 2024

AbstractThis paper draws together elements of the academic literature on policy mobilities on the one hand, and on the ‘digital turn’ on the other. It argues that COVID‐19 accelerated the digitalization of everyday life asking we think through how those already existing informational infrastructures supporting the mobility of policies are continuing to evolve, as are the methods available for researching them. This has potential consequences for how cities practice policy comparison exchange, and learning and how these processes are studied. This paper sets out a three‐pronged schema to take seriously the intersection of policy mobilities and the digital. They are policy mobilities through the digital, policy mobilities produced by the digital and policy mobilities of the digital. It concludes by outlining fruitful areas for a future research agenda.
The role of electrochemotherapy in the treatment of locally advanced or recurrent eyelid‐periocular basal cell carcinoma: long‐term results
Authors: Vass Attila , Polgár Nóra , Sándor Szilvia Alexa , Ágoston Dóra , Rózsa Petra , Csányi Ildikó , Ócsai Henriette , Baltás Eszter , Oláh Judit , Kis Erika Gabriella , Tóth‐Molnár Edit 
Published: June 2024

AbstractBackgroundWhile electrochemotherapy (ECT) is increasingly utilized as a highly effective method in the treatment of tumors in the head and neck region, there is significantly less data available for eyelid‐periocular skin tumors. Our group reported the first extensive case series of eyelid‐periocular basal cell carcinoma (BCC) patients with short‐term follow‐up treatment with ECT. The present study aims to report our long‐term results of eyelid‐periocular BCC cases treated with ECT.MethodsThe treatments were performed according to the ESOPE (European Standard Operating Procedures on Electrochemotherapy) guidelines using the Cliniporator™ device. All patients received bleomycin‐based ECT, administered intratumorally or intravenously. Tumor response was evaluated using the RECIST 1.1 criteria.ResultsThe results of 19 patients treated with ECT are presented. Four patients had locally advanced primary tumors, while 15 patients had recurrent tumors. Bleomycin was administered intratumorally in four patients and intravenously in 15 patients. The overall response was 100%, while the complete response rate proved to be 95%. In three cases (15.8%), recurrence was observed during the mean follow‐up period of 78.9 months.ConclusionsECT can effectively treat locally advanced or recurrent BCC in the eyelid‐periocular skin region. Excellent tumor control can be achieved with good functional and cosmetic results without systemic adverse events with long interval follow‐up.
Exploring the impact of harvest year on the mineral composition of Mimosa scabrella Bentham honeydew honey from Santa Catarina (Brazil) using ICP‐MS and chemometric tools
Authors: Silva Bibiana , Gonzaga Luciano Valdemiro , Maltez Heloísa França , Samochvalov Kátia Bennett , Fett Roseane , Costa Ana Carolina Oliveira 
Published: June 2024

SummaryThis study investigated the variation in mineral elements in bracatinga (Mimosa scabrella Bentham) honeydew honeys produced biannually over three consecutive harvest years. The aim was to assess the relationship between the year of production and the concentration of fourteen rare earth elements and six trace elements analysed using ICP‐MS. The concentrations of the twenty elements varied (P < 0.001) among all the honey samples. The dominant rare earth elements were Eu, followed by Nd and La, while Pd and Au were the major trace elements. Cluster analysis (CA) and linear discriminant analysis (LDA) were performed using all the elements identified. The LDA categorised (83.3% accuracy) the bracatinga honeydew honey samples according to their harvest year. Discriminant functions, influenced by Ce, Tb, and Th, show distinct elemental patterns in bracatinga honeydew honeys, varying with harvest year. This reflects fluctuations in yearly climatic conditions and is important to guarantee accurate characterisation.
Genetic relationships between and within some Malawian cichlid genera
Authors: Hashem Shaharior , Kawai Koichiro , Kushida Tetsuyasu , Hamaoka Erika , Kofi Fatsi Patrick Senam , Saito Hidetoshi 
Published: June 2024

AbstractGenetic relationships were examined for a total of 90 individuals of 90 species or species var. from 13 genera of Malawian cichlids based on the sequences of an amplified 991‐bp fragment of the mtDNA control region (mtDNA‐CR). In the network analysis, no exclusive clades were made by all the members of any genera in this study. However, congeneric clades were observed by genera Buccochromis, Copadichromis, Protomelas, and Sciaenochromis, whereas no congeneric clades were observed by genera Mylochromis, Nimbochromis, and Otopharynx. In non‐mbuna, an Aulonocara–Lethrinops group was divided into two groups, and the mean genetic distance of the larger group was much lower from mbuna than from other non‐mbuna. Overall mean genetic distance within a genus was generally low in mbuna, whereas it was relatively high in non‐mbuna. In the genetic tree of each genus, two or more large clades were observed, and some clades, such as those of Aulonocara hansbaenschi and Aulonocara nyassae in genus Aulonocara, Lethrinops micrentodon and Lethrinops sp. “gold harbor” in Lethrinops, and Otopharynx ovatus and Otopharynx brooksi in Otopharynx, were very deeply differentiated. Besides, a mbuna species, Pseudotropheus crabro, was extremely deeply differentiated from other members of this genus. These results suggest a widespread morphological convergence across the taxa in parallel with deep genetic differentiation in the long evolutionary story and some possibility of generation of the species of Aulonocara–Lethrinops group by hybridization of small non‐mbuna and mbuna species. Furthermore, taxonomical reexamination is necessary based on a strong support by genetic connection.
Risk factors for noncarious cervical lesions: A case–control study
Authors: Kong Weiyang , Ma Haoran , Qiao Feng , Xiao Mo , Wang Li , Zhou Liwen , Chen Yuxin , Liu Juan , Wang Yuanyuan , Wu Ligeng 
Published: June 2024

AbstractObjectivesNoncarious cervical lesions (NCCLs) are multifactorial and can be caused by the anatomical structure of the teeth, erosion, abrasion and abnormal occlusion. The aim of this case–control study was to explore the risk factors for NCCLs.MethodsCone‐beam computed tomography was used to determine whether a wedge‐shaped defect existed at the cementoenamel junction. We compared 63 participants with NCCLs with 63 controls without NCCLs, matched for sex, age (±1 year) and toothbrushing‐related factors (e.g., type of bristle and brushing patterns, frequency and strength). All participants were asked to complete a questionnaire about self‐administered daily diet habits and health condition. Univariate and multivariate logistic regression analyses were conducted to determine the risk factors for NCCLs.ResultsSignificant variables in the univariate analysis (i.e., p < .2) included frequency of carbonated beverage consumption, sella‐nasion‐point B angle (SNB) and Frankfort‐mandibular plane angle (FMA). Multivariate logistic regression demonstrated that the consumption frequency of carbonated beverages (odds ratio [OR] = 3.147; 95% confidence interval [CI], 1.039–9.532), FMA (OR = 1.100; 95% CI, 1.004–1.204) and SNB (OR = 0.896; 95% CI, 0.813–0.988) was independent influencing factors. The area under the receiver operating characteristic curve (AUC) value of regression Model 1 (established with the frequency of carbonated beverage consumption, FMA, SNB and sleep bruxism) was 0.700 (95% CI, 0.607–0.792; p < .001), and that of regression Model 2 (established using the frequency of carbonated beverage consumption, FMA and SNB) was 0.704 (95% CI, 0.612–0.796; p < .001).ConclusionsThe consumption frequency of carbonated beverages and FMA was risk factors for NCCLs; the higher the frequency of carbonated beverage consumption and FMA, the higher was the probability of NCCLs. SNB was a protective factor for NCCL occurrence; the larger the SNB, the lower was the probability of NCCL occurrence. These findings have further clarified the aetiology of NCCLs and provided clinicians with valuable insights into strategies for preventing the loss of dental tissue.
Verbatim theatre as a creative approach to health professions education research translation
Authors: Brand Gabrielle , Peters Sarah , Dart Janeane 
Published: June 2024

AbstractContextTraditionally, the impact and outcomes from health professions education research (HPER) have focused on academic outputs, whereas in the humanities, research translation is conceptualised more broadly and creatively, including research‐based performances like verbatim theatre. Translating HPER findings through the emotive and embodied nature of a verbatim theatre performance provides a unique opportunity to translate research data and create alternative learning spaces for rich and valuable insights that aligns with transformative pedagogy.ApproachIn this paper, we describe the background of verbatim theatre, a form of performance, which draws on a research participants' testimony and lived experience and how we used this creative approach to translate HPER findings. We discuss the experiential process of bringing an interdisciplinary team together, health professions academics and an academic playwright to craft a verbatim theatre script that provided space to honour the breadth, depth and diversity of participant voices from a large (n = 100) qualitative research study exploring professionalism and sociocultural factors in health professions education (HPE). Furthermore, we discuss the powerful potential of drawing on research‐based performance to create alternative, safe and non‐threatening learning spaces to resonate with and experience HPER in new and transformative ways. Finally, we offer reflexive insights on the key opportunities and challenges we encountered in translating HPER into a verbatim theatre performance.ConclusionsVerbatim theatre presents an innovative and creative way to communicate and translate HPER. This paper offers research and pedagogical insights in translating research into verbatim theatre to support transformative pedagogy and practice in HPE. In conclusion, we encourage other health professions researchers to consider this dynamic and creative approach to transforming HPE.
Dehydration and rehydration differently affect photosynthesis and volatile monoterpenes in bryophytes with contrasting ecological traits
Authors: Esteban Raquel , Pollastri Susanna , Brilli Federico , García‐Plazaola José Ignacio , Odriozola Iñaki , Michelozzi Marco , Loreto Francesco 
Published: June 2024

AbstractBryophytes desiccate rapidly when relative humidity decreases. The capacity to withstand dehydration depends on several ecological and physiological factors. Volatile organic compounds (VOCs) may have a role in enhancing tolerance to desiccating bryophytes. However, the functions of VOCs in bryophytes have received little attention so far. We aimed to investigate the impact of a dehydration‐rehydration treatment on primary carbon metabolism and volatile terpenes (VTs) in three bryophytes with contrasting ecological traits: Vessicularia dubyana, Porella platyphylla and Pleurochaete squarrosa. First, we confirmed the desiccation sensitivity gradient of the species. Under fully hydrated conditions, the photosynthetic rate (A) was inversely associated with stress tolerance, with a lower rate in more tolerant species. The partial recovery of A in P. platyphylla and P. squarrosa after rehydration confirmed the desiccation tolerance of these two species. On the other hand, A did not recover after rehydration in V. dubyana. Regarding VT, each species exhibited a distinct VT profile under optimum hydration, with the highest VT pool found in the more desiccation‐sensitive species (V. dubyana). However, the observed species‐specific VT pattern could be associated with the ecological habitat of each species. P. squarrosa, a moss of dry habitats, may synthesize mainly non‐volatile secondary metabolites as stress‐defensive compounds. On the other hand, V. dubyana, commonly found submerged, may need to invest photosynthetically assimilated carbon to synthesize a higher amount of VTs to cope with transient water stress occurrence. Further research on the functions of VTs in bryophytes is needed to deepen our understanding of their ecological significance.
The role of phytomelatonin in plant homeostasis, signaling, and crosstalk in abiotic stress mitigation
Authors: Sati Hansika , Chinchkar Ajay V. , Kataria Priyanka , Pareek Sunil 
Published: June 2024

AbstractIn recent years, there has been an increase in the study of phytomelatonin. Having numerous functions in animals, melatonin produced by plants (phytomelatonin) is also a multi‐regulatory molecule with great potential in plant physiology and in mitigating abiotic stresses, such as drought, salinity, chilling, heat, chemical contamination, and UV‐radiation stress. This review highlights the primary functions of phytomelatonin as an anti‐stress molecule against abiotic stress. We discuss the role of phytomelatonin as a master regulator, oxidative stress manager, reactive oxygen species and reactive nitrogen species regulator, and defense compounds inducer. Although there exist a handful of reviews on the crosstalk of phytomelatonin with other signaling molecules like auxin, cytokinin, gibberellin, abscisic acid, ethylene, nitric oxide, jasmonic acid, and salicylic acid, this review looks at studies that have reported a few aspects of phytomelatonin with newly discovered signaling molecules along with classical signaling molecules with relation to abiotic stress tolerance. The research and applications of phytomelatonin with hydrogen sulfide, strigolactones, brassinosteroids, and polyamines are still in their nascent stage but hold a promising scope for the future. Additionally, this review states the recent developments in the signaling of phytomelatonin with nitrogen metabolism and nitrosative stress in plants.
DYNamic Assessment of Multi‐Organ level dysfunction in patients recovering from COVID‐19: DYNAMO COVID‐19
Authors: Gupta Ayushman , Nicholas Rosemary , McGing Jordan J. , Nixon Aline V. , Mallinson Joanne E. , McKeever Tricia M. , Bradley Christopher R. , Piasecki Mathew , Cox Eleanor F. , Bonnington James , Lord Janet M. , Brightling Christopher E. , Evans Rachael A. , Hall Ian P. , Francis Susan T. , Greenhaff Paul L. , Bolton Charlotte E. 
Published: June 2024

AbstractWe evaluated the impacts of COVID‐19 on multi‐organ and metabolic function in patients following severe hospitalised infection compared to controls. Patients (n = 21) without previous diabetes, cardiovascular or cerebrovascular disease were recruited 5–7 months post‐discharge alongside controls (n = 10) with similar age, sex and body mass. Perceived fatigue was estimated (Fatigue Severity Scale) and the following were conducted: oral glucose tolerance (OGTT) alongside whole‐body fuel oxidation, validated magnetic resonance imaging and spectroscopy during resting and supine controlled exercise, dual‐energy X‐ray absorptiometry, short physical performance battery (SPPB), intra‐muscular electromyography, quadriceps strength and fatigability, and daily step‐count. There was a greater insulin response (incremental area under the curve, median (inter‐quartile range)) during the OGTT in patients [18,289 (12,497–27,448) mIU/min/L] versus controls [8655 (7948–11,040) mIU/min/L], P < 0.001. Blood glucose response and fasting and post‐prandial fuel oxidation rates were not different. This greater insulin resistance was not explained by differences in systemic inflammation or whole‐body/regional adiposity, but step‐count (P = 0.07) and SPPB scores (P = 0.004) were lower in patients. Liver volume was 28% greater in patients than controls, and fat fraction adjusted liver T1, a measure of inflammation, was raised in patients. Patients displayed greater perceived fatigue scores, though leg muscle volume, strength, force‐loss, motor unit properties and post‐exercise muscle phosphocreatine resynthesis were comparable. Further, cardiac and cerebral architecture and function (at rest and on exercise) were not different. In this cross‐sectional study, individuals without known previous morbidity who survived severe COVID‐19 exhibited greater insulin resistance, pointing to a need for physical function intervention in recovery.
Physics-Guided Bayesian Neural Networks and Their Application in ODE Problems
Authors: Xu Xinyue , Paneru Suman , Russcher Sez A. , Wang Julian 
Published: June 2024

Abstract
Deterministic Neural Networks (NNs) have been widely adopted to represent system behaviors in various engineering problems, which have been criticized for providing overconfident predictions. This challenge, i.e., overfitting, refers to a model that captures data patterns and random noise during the learning process, leading to an inferior predictive capability in the unobserved domains. As known to all, Bayesian inference offers an effective way for uncertainty quantification (UQ) to help enhance model predictions and offer informed decision-making. Integrating deterministic NN models with Bayesian inference provides a way to fast simulate and quantify both data and model uncertainty simultaneously. Thereby, Bayesian Neural Networks (BNNs), a combination of standard NNs with Bayesian philosophy, introduce probability to the network parameters, i.e., biases and weights. In BNNs, predictive uncertainty reflects how confident model predictions are regarding the corresponding credible intervals, which helps identify overfitting and interpreting abnormal predictions. Another advantage is that BNNs naturally implement regularization by integrating over the weights such that BNNs can reach good generalization when data availability is limited. BNNs rely heavily on observations as a purely data-driven approach. Besides, standard BNNs have relatively complex network structures, which makes it hard to provide detailed interpretability on model predictions. Researchers share concerns about their predictions that may violate real-world phenomena. The combination of physics knowledge with the optimization objective can improve the adherence of predictions with the known physical principles. Physics laws are usually embedded as constraint functions in the process of optimization. With the help of constrained optimization, model predictions keep consistent with the known physical principles.
The authors refine BNNs with physics-guided information, i.e., Physics-Guided BNNs (PG-BNNs), to reduce dependence on data, improve model interpretability, and offer reliable model predictions. PG-BNNs interpret the known physics knowledge as constraint functions to better guide optimization processes, especially for case studies with sparse and limited data sets. A case study of an ordinary differential equation (ODE) problem is carried out to compare the performance of PG-BNN and unconstrained BNN models and demonstrate the effectiveness of PG-BNN.
Uncertainty Quantification of Drill Collar Fatigue Performance Due to Manufacturing Tolerances
Authors: Ghosh Pritha , Du Michael H. 
Published: June 2024

Abstract
The bottomhole assembly (BHA), the lower part of the drillstring on an oil drilling rig, extends from the drillpipe to the drill bit. High dogleg severity (DLS) curvatures during directional drilling can create fatigue issues in the drillstring because of high alternating stresses and strains around the porthole in the collar. The manufacturing tolerances affect the collar-chassis and plug-porthole clearances, as well as the porthole dimensions and can cause significant variability or uncertainty in evaluating the drill tool fatigue life.
The 3D finite element analysis (FEA) method was used for stress and strain predictions of the drill tool under the effect of pressure and DLS. The rotating bending fatigue life of the drill collar was calculated using these prediction results and the life-strain model that was created through testing the collar material. The FEA models were verified with the developed analytical calculation models for stress predictions under the effect of pressure and DLS. The relevant manufacturing tolerance ranges for the collar, chassis, porthole, and port plug were considered. The uncertainty in the fatigue life of the tool was quantified for each of these variables at the expected operating bending moment to evaluate their contributing role in the fatigue performance of the tool.
For a drill tool with a nominal diameter size of 8.25 in, it was found that the collar could show up to 76% uncertainty in fatigue life when the chassis-collar clearances were increased from the minimum to the maximum within the manufacturing tolerance bands. Similarly, the collar showed up to 38% uncertainty in fatigue life when the plug-pothole clearances were changed from the minimum to the maximum. This uncertainty quantification study provides insight into the mechanics of structural fatigue from collar assembly components and their manufacturing tolerance conditions. This helps eliminate time-consuming design iterations and expensive fatigue testing.