bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence, Clinical and Imaging Characteristics of Superior Ophthalmic Vein Periphlebitis in Thyroid Eye Disease
Authors: Goodyear Kendall , Ghiam Sean , Strawbridge Jason , Oh Angela J. , Singh Pallavi , Roelofs Kelsey A. , Rootman Daniel B. 
Published: January 2024

Purpose:
To determine the prevalence, clinical features, and radiographic findings of superior ophthalmic vein periphlebitis (SOVP) in thyroid eye disease (TED).

Methods:
Patients with a clinical diagnosis of thyroid eye disease and contrast-enhanced imaging were included. Imaging was reviewed for the presence of SOVP, and patients with SOVP were compared to those without. A random eye was determined to be the affected eye in patients without SOVP.

Results:
A total of 212 patients met the inclusion criteria. Unilateral SOVP was identified in 4.7% of cases. There was no significant difference in age (p = 0.22), gender (p = 0.09), or disease duration (p = 0.14) between patients with and without SOVP. There was a significant (p < 0.05) difference in stage classification and clinical activity core between the groups. The affected eye in patients with SOVP had significantly (p < 0.05) greater margin reflex distance 1, degree of relative proptosis, horizontal motility restriction, and vertical motility restriction than in patients without SOVP. There was no significant difference in horizontal strabismus (p = 1.0), vertical strabismus (p = 0.87), or relative intraocular pressure (p = 0.77). On imaging, the maximal diameter of the SR and IR were found to be significantly (p < 0.05) larger in the affected eye of patients with periphlebitis; however, there was no difference in measured diameter of the medial rectus and (p = 0.30) or lateral rectus (p = 0.78).

Conclusions:
SOVP is an under-reported imaging finding of thyroid eye disease. It is associated with significantly greater margin reflex distance 1, relative proptosis, and motility restriction on exam as well as larger superior rectus and inferior rectus diameter on imaging. These patients tend to present in the active stage of disease with greater clinical activity score.
Interindividual variability in cold-pressor pain sensitivity is not explained by peripheral vascular responding and generalizes to a C-nociceptor–specific pain phenotype
Authors: Martel Richard D. , Papafragou Georgios , Weigand Sylvia , Rolke Roman , Prawitt Dirk , Birklein Frank , Treede Rolf-Detlef , Magerl Walter 
Published: January 2024

Abstract
Pain sensitivity of healthy subjects in the cold-pressor (CP) test was proposed to be dichotomously distributed and to represent a pain sensitivity trait. Still, it has not been systematically explored which factors influence this pain sensitivity readout. The aim of this study was to distinguish potential contributions of local tissue-related factors such as perfusion and thermoregulation or gain settings in nociceptive systems. Cold-pressor–sensitive and CP-insensitive students screened from a medical student laboratory course were recruited for a CP retest with additional cardiovascular and bilateral local vascular monitoring. In addition, comprehensive quantitative sensory testing according to Deutscher Forschungsverbund Neuropathischer Schmerz standards and a sustained pinch test were performed. Cold pressor was reproducible across sessions (Cohen kappa 0.61 ± 0.14, P < 0.005). At 30 seconds in ice water, CP-sensitive subjects exhibited not only more pain (78.6 ± 26.3 vs 29.5 ± 17.5, P < 0.0001) but also significantly stronger increases in mean arterial blood pressure (12.6 ± 9.3 vs 5.6 ± 8.1 mm Hg, P < 0.05) and heart rate (15.0 ± 8.2 vs 7.1 ± 6.2 bpm, P < 0.005), and lower baroreflex sensitivity, but not local or vasoconstrictor reflex–mediated microcirculatory responses. Cold-pressor–sensitive subjects exhibited significantly lower pain thresholds also for cold, heat, and blunt pressure, and enhanced pain summation, but no significant differences in Aδ-nociceptor–mediated punctate mechanical pain. In conclusion, differences in nociceptive signal processing drove systemic cardiovascular responses. Baroreceptor activation suppressed pain and cardiovascular responses more efficiently in CP-insensitive subjects. Cold-pressor sensitivity generalized to a pain trait of C-fiber–mediated nociceptive channels, which was independent of local thermal and vascular changes in the ice-water–exposed hand. Thus, the C-fiber pain trait reflects gain setting of the nociceptive system.
Improving risk models for patients having emergency bowel cancer surgery using linked electronic health records: a national cohort study
Authors: Blake Helen A. , Sharples Linda D. , Boyle Jemma M. , Kuryba Angela , Moonesinghe Suneetha R. , Murray Dave , Hill James , Fearnhead Nicola S. , van der Meulen Jan H. , Walker Kate 
Published: January 2024

Background:
Life-saving emergency major resection of colorectal cancer (CRC) is a high-risk procedure. Accurate prediction of postoperative mortality for patients undergoing this procedure is essential for both healthcare performance monitoring and preoperative risk assessment. Risk-adjustment models for CRC patients often include patient and tumour characteristics, widely available in cancer registries and audits. The authors investigated to what extent inclusion of additional physiological and surgical measures, available through linkage or additional data collection, improves accuracy of risk models.

Methods:
Linked, routinely-collected data on patients undergoing emergency CRC surgery in England between December 2016 and November 2019 were used to develop a risk model for 90-day mortality. Backwards selection identified a ‘selected model’ of physiological and surgical measures in addition to patient and tumour characteristics. Model performance was assessed compared to a ‘basic model’ including only patient and tumour characteristics. Missing data was multiply imputed.

Results:
Eight hundred forty-six of 10 578 (8.0%) patients died within 90 days of surgery. The selected model included seven preoperative physiological and surgical measures (pulse rate, systolic blood pressure, breathlessness, sodium, urea, albumin, and predicted peritoneal soiling), in addition to the 10 patient and tumour characteristics in the basic model (calendar year of surgery, age, sex, ASA grade, TNM T stage, TNM N stage, TNM M stage, cancer site, number of comorbidities, and emergency admission). The selected model had considerably better discrimination compared to the basic model (C-statistic: 0.824 versus 0.783, respectively).

Conclusion:
Linkage of disease-specific and treatment-specific datasets allowed the inclusion of physiological and surgical measures in a risk model alongside patient and tumour characteristics, which improves the accuracy of the prediction of the mortality risk for CRC patients having emergency surgery. This improvement will allow more accurate performance monitoring of healthcare providers and enhance clinical care planning.
Role of the revised Baux score in predicting mortality among burn patients in an African low-income country: a multicentre prospective cohort
Authors: Baraka Samuel Mandro , Kiswezi Ahmed , Olasinde Anthony Ayotunde , Edyedu Isaac , Molen Selamo Fabrice , Muhumuza Joshua , Zawadi Gift Vulwaghe , Okedi Francis Xaviour 
Published: January 2024

Introduction:
Burn injury is a major cause of mortality. Majority of the burns occur in low and middle-income countries like Uganda. Uganda has a limited number of burn centres and medical resources, making a predictor of mortality necessary in allocation of the limited resources. Although the revised Baux (r-Baux) score has been validated and used in many high income countries, no study has assessed its role in an African low-income country; the reason this study was done.

Methods:
This was a prospective multicentre cohort that enroled 101 burn patients with moderate and severe burns admitted in three tertiary hospitals in western Uganda. Follow-up was done until discharge, documenting mortality. A receiver operator characteristic curve was used to determine the role of r-Baux score in predicting mortality.

Results:
This study included 101 patients, with a mean age of 21.3 (SD=16.8) years. The majority of the participants were male (69.3%). The area under the curved for r-Baux score’s prediction of mortality was 0.943 (P<0.001). The most appropriate cut-off was determined to be 74.5. At this cut-off, r-Baux score predicted mortality with a sensitivity of 100% and specificity of 83.5%. After controlling for burn severity using Poisson regression, a patient with r-Baux score greater than 74.5 was 1.358 times more likely to die (adjusted risk ratio=1.358, 95% CI=1.195–1.543, P<0.001).

Conclusion:
The r-Baux score was found to be excellent at predicting mortality among burn patients in Uganda and therefore should be done for all patients at admission, in order to predict mortality and do proper planning.
Combining contextuality and causality: a game semantics approach
Authors: Abramsky Samson , Barbosa Rui Soares , Searle Amy 
Published: January 2024

We develop an approach to combining contextuality with causality, which is general enough to cover causal background structure, adaptive measurement-based quantum computation and causal networks. The key idea is to view contextuality as arising from a game played between Experimenter and Nature, allowing for causal dependencies in the actions of both the Experimenter (choice of measurements) and Nature (choice of outcomes).
This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
On geometrical aspects of the graph approach to contextuality
Authors: Amaral Barbara , Terra Cunha Marcelo 
Published: January 2024

The connection between contextuality and graph theory has paved the way for numerous advancements in the field. One notable development is the realization that sets of probability distributions in many contextuality scenarios can be effectively described using well-established convex sets from graph theory. This geometric approach allows for a beautiful characterization of these sets. The application of geometry is not limited to the description of contextuality sets alone; it also plays a crucial role in defining contextuality quantifiers based on geometric distances. These quantifiers are particularly significant in the context of the resource theory of contextuality, which emerged following the recognition of contextuality as a valuable resource for quantum computation. In this paper, we provide a comprehensive review of the geometric aspects of contextuality. Additionally, we use this geometry to define several quantifiers, offering the advantage of applicability to other approaches to contextuality where previously defined quantifiers may not be suitable.
This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
Causality and signalling of garden-path sentences
Authors: Wang Daphne , Sadrzadeh Mehrnoosh 
Published: January 2024

Sheaves are mathematical objects that describe the globally compatible data associated with open sets of a topological space. Original examples of sheaves were continuous functions; later they also became powerful tools in algebraic geometry, as well as logic and set theory. More recently, sheaves have been applied to the theory of contextuality in quantum mechanics. Whenever the local data are not necessarily compatible, sheaves are replaced by the simpler setting of presheaves. In previous work, we used presheaves to model lexically ambiguous phrases in natural language and identified the order of their disambiguation. In the work presented here, we model syntactic ambiguities and study a phenomenon in human parsing called garden-pathing. It has been shown that the information-theoretic quantity known as ‘surprisal’ correlates with human reading times in natural language but fails to do so in garden-path sentences. We compute the degree of signalling in our presheaves using probabilities from the large language modelBERTand evaluate predictions on two psycholinguistic datasets. Our degree of signalling outperforms surprisal in two ways: (i) it distinguishes between hard and easy garden-path sentences (with ap-value<10−5), whereas existing work could not, (ii) its garden-path effect is larger in one of the datasets (32 ms versus 8.75 ms per word), leading to better prediction accuracies.This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
Hidden variables, free choice, context-independence and all that
Authors: Dzhafarov Ehtibar N. 
Published: January 2024

This paper provides a systematic account of the hidden variable models (HVMs) formulated to describe systems of random variables with mutually exclusive contexts. Any such system can be described either by a model with free choice but generally context-dependent mapping of the hidden variables into observable ones, or by a model with context-independent mapping but generally compromised free choice. These two types of HVMs are equivalent, one can always be translated into another. They are also unfalsifiable, applicable to all possible systems. These facts, the equivalence and unfalsifiability, imply that freedom of choice and context-independent mapping are no assumptions at all, and they tell us nothing about freedom of choice or physical influences exerted by contexts as these notions would be understood in science and philosophy. The conjunction of these two notions, however, defines a falsifiable HVM that describes non-contextuality when applied to systems with no disturbance or to consistifications of arbitrary systems. This HVM is most adequately captured by the term ‘context-irrelevance’, meaning that no distribution in the model changes with context.
This article is part of the theme issue ‘Quantum contextuality, causality and freedom of choice’.
Student experiences with an interactive 3D immersive biotechnology simulation and its impact on motivational beliefs
Authors: Spencer Dan , McKeown Caitlin , Tredwell David , Huckaby Benjamin , Wiedner Andrew , Dums Jacob T. , Cartwright Emily L. , Potts Colin M. , Sudduth Nathan , Brown Evan , Albright Phillips , Jhala Arnav , Srougi Melissa C. 
Published: January 2024

AbstractThe development and use of virtual laboratories to augment traditional in-person skills training continues to grow. Virtual labs have been implemented in a number of diverse educational settings, which have many purported benefits including their adaptability, accessibility, and repeatability. However, few studies have evaluated the impact of virtual laboratories outside of academic achievement and skills competencies, especially in biotechnology. In this study, an interdisciplinary team of content experts, video game researchers, instructional designers, and assessment experts developed a 3D immersive simulation designed to teach novice scientists the technical skills necessary to perform sterile mammalian cell culture technique. Unique to the simulation development process is the recreation of an immersive experience through the capture of details in the real-world lab where participants have the freedom of choice in their actions, while receiving immediate feedback on their technical skills as well as procedural execution. However, unlike an in-person laboratory course, students are able to iterate and practice their skills outside of class time and learn from their mistakes. Using a mixed-methods study design, over the course of two semesters we evaluated student attitudes of the simulation and their science motivational beliefs including self-efficacy and science identity after engaging with the simulation prior to the physical laboratory. Our results show that students’ science identity remained unchanged while their science self-efficacy increased. Furthermore, students had positive perceptions of the benefits of the virtual simulation. These data suggest that the virtual cell culture simulation can be a useful pedagogical training tool to bolster students’ motivational beliefs that is both accessible and easy to implement.
MYC is sufficient to generate mid-life high-grade serous ovarian and uterine serous carcinomas in a p53-R270H mouse model
Authors: Blackman Alexandra , Rees Amy C , Bowers Robert R , Jones Christian M , Vaena Silvia G , Clark Madison A , Carter Shelby , Villamor Evan D , Evans Della , Emanuel Anthony J , Fullbright George , Long David T , Spruill Laura , Romeo Martin J , Helke Kristi L , Delaney Joe R 
Published: January 2024

AbstractGenetically engineered mouse models (GEMM) have fundamentally changed how ovarian cancer etiology, early detection, and treatment is understood. However, previous GEMMs of high-grade serous ovarian cancer (HGSOC) have had to utilize genetics rarely or never found in human HGSOC to yield ovarian cancer within the lifespan of a mouse.MYC, an oncogene, is amongst the most amplified genes in HGSOC, but it has not previously been utilized to drive HGSOC GEMMs. We coupledMycand dominant negative mutant p53-R270H with a fallopian tube epithelium-specific promoterOvgp1to generate a new GEMM of HGSOC. Female mice developed lethal cancer at an average of 15.1 months. Histopathological examination of mice revealed HGSOC characteristics including nuclear p53 and nuclear MYC in clusters of cells within the fallopian tube epithelium and ovarian surface epithelium. Unexpectedly, nuclear p53 and MYC clustered cell expression was also identified in the uterine luminal epithelium, possibly from intraepithelial metastasis from the fallopian tube epithelium (FTE). Extracted tumor cells exhibited strong loss of heterozygosity at the p53 locus, leaving the mutant allele. Copy number alterations in these cancer cells were prevalent, disrupting a large fraction of genes. Transcriptome profiles most closely matched human HGSOC and serous endometrial cancer. Taken together, these results demonstrate theMycandTrp53-R270Htransgene was able to recapitulate many phenotypic hallmarks of HGSOC through the utilization of strictly human-mimetic genetic hallmarks of HGSOC. This new mouse model enables further exploration of ovarian cancer pathogenesis, particularly in the 50% of HGSOC which lack homology directed repair mutations. Histological and transcriptomic findings are consistent with the hypothesis that uterine serous cancer may originate from the fallopian tube epithelium.
Immune-neuroendocrine phenotypic expression changes through life inCoturnix japonicaquails
Authors: Marozzi Antonela , Correa Silvia G. , Palme Rupert , Cantarelli Veronica I. , Ponzio Marina F. , Marin Raul H. , Nazar F. Nicolas 
Published: January 2024

AbstractImmune-neuroendocrine characteristics can be used to classify individuals according to their physiological profiles or phenotypes (INPs). In avian models such as quail and domestic chickens, three subgroups based on INPs have been defined: Lewis-like (pro-inflammatory polarization), Fischer-like (anti-inflammatory polarization), and an intermediate INP. This study investigates the stability and alterations of INPs throughout ontogeny, from juvenile to adult stages in four time-points including an exposure to unpredictable and diverse chronic stress (CS) during early adulthood. We measured corticosterone levels, pro-(IFN-γ and IL-1β) and anti-inflammatory (IL-13, IL-4) cytokines, phytohemagglutinin (PHA-P) lymphoproliferative response, anti-sheep red blood cells antibody (Ab SRBC) response, and leukocyte distribution frequency. Cluster analyses were conducted to classify bird based on their similarities across all analyzed variables, to thereby establish their INP at each time point. The extreme Lewis- or Fischer-like profiles were less represented in juvenile and pre-stress adult birds showing a higher proportion of individuals with an intermediate profile. Following CS exposure, the prevalence of Lewis-like and Fischer-like profiles increased. This shift persisted 10 weeks later as birds matured to an advanced egg-laying stage, with females predominantly exhibiting the Fischer-like INP, and males the Lewis-like INP. The observed shift in INP distribution following CS towards more polarized Lewis- and Fisher-like profiles implies a more even representation of the three observed profiles and may reflect inter-individual differences in physiological response to CS associated to particular coping strategies. A more even INPs distribution could provide the population with a greater advantage when facing diverse environmental challenges.
Using splines for point spread function calibration at non-uniform depths in localization microscopy
Authors: Korovin Serafim , Kalisvaart Dylan , Hung Shih-Te , Cnossen Jelmer , de Visser Coen , Smith Carlas S. 
Published: January 2024

ABSTRACTSingle-molecule localization microscopy methods extensively leverage the microscope point spread function (PSF) for fitting the molecules. Calibrating an accurate PSF model is especially difficult in the presence of depth-dependent aberrations which alter the PSF shape depending on the imaging depth. The aberrations at depths of a few micrometers become substantial enough to considerably impoverish the conventional calibration methods’ performance. In our work, we propose a novel spline model which enables the depth-dependent PSF model calibration by interpolating between the beads at arbitrary depths. We show that diffspline reduces the PSF intensity overestimation by 67.8 percentage points and underestimation by 21.8 percentage points. Moreover, it eliminates the depth-dependent bias and improves the localization precision two-fold compared to previous approaches.
CODEX: COunterfactual Deep learning for thein-silicoEXploration of cancer cell line perturbations
Authors: Schrod Stefan , Beißbarth Tim , Zacharias Helena U. , Hauschild Anne-Christin , Altenbuchinger Michael 
Published: January 2024

MotivationHigh-throughput screens (HTS) provide a powerful tool to decipher the causal effects of chemical and genetic perturbations on cancer cell lines. Their ability to evaluate a wide spectrum of interventions, from single drugs to intricate drug combinations and CRISPR-interference, has established them as an invaluable resource for the development of novel therapeutic approaches. Nevertheless, the combinatorial complexity of potential interventions makes a comprehensive exploration intractable. Hence, prioritizing interventions for further experimental investigation becomes of utmost importance.ResultsWe propose CODEX as a general framework for the causal modeling of HTS data, linking perturbations to their downstream consequences. CODEX relies on a stringent causal modeling strategy based on counterfactual reasoning. As such, CODEX predicts drug-specific cellular responses, comprising cell survival and molecular alterations, and facilitates thein-silicoexploration of drug combinations. This is achieved for both bulk and single-cell HTS. We further show that CODEX provides a rationale to explore complex genetic modifications from CRISPR-interferencein silicoin single cells.Availability and ImplementationOur implementation of CODEX is publicly available athttps://github.com/sschrod/CODEX. All data used in this article are publicly available.