bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graph metric learning quantifies morphological differences between two genotypes of shoot apical meristem cells inArabidopsis
Authors: Scott Cory Braker , Mjolsness Eric , Oyen Diane , Kodera Chie , Uyttewaal Magalie , Bouchez David 
Published: January 2023

AbstractWe present a method for learning ‘spectrally descriptive’ edge weights for graphs. We generalize a previously known distance measure on graphs (graph diffusion distance [GDD]), thereby allowing it to be tuned to minimize an arbitrary loss function. Because all steps involved in calculating this modified GDD are differentiable, we demonstrate that it is possible for a small neural network model to learn edge weights which minimize loss. We apply this method to discriminate between graphs constructed from shoot apical meristem images of two genotypes of Arabidopsis thaliana specimens: wild-type and trm678 triple mutants with cell division phenotype. Training edge weights and kernel parameters with contrastive loss produce a learned distance metric with large margins between these graph categories. We demonstrate this by showing improved performance of a simple k-nearest-neighbour classifier on the learned distance matrix. We also demonstrate a further application of this method to biological image analysis. Once trained, we use our model to compute the distance between the biological graphs and a set of graphs output by a cell division simulator. Comparing simulated cell division graphs to biological ones allows us to identify simulation parameter regimes which characterize mutant versus wild-type Arabidopsis cells. We find that trm678 mutant cells are characterized by increased randomness of division planes and decreased ability to avoid previous vertices between cell walls.
The accuracy of the Global Trigger Tool is higher for the identification of adverse events of greater harm: a diagnostic test study
Authors: Moraes Sara Monteiro , Ferrari Teresa Cristina Abreu , Beleigoli Alline 
Published: January 2023

Abstract
Global Trigger Tool (GTT) of the Institute for Healthcare Improvement (IHI) has been used as a measurement strategy for patient safety by several institutions and national programs. Although the greater ability of the GTT to identify adverse events (AEs) compared to other methods has already been demonstrated, there are few data on its accuracy, and studies suggest lower sensitivity for minor AEs. This study aimed to assess the accuracy of the GTT for identifying AEs in adult inpatients for all AEs and for the subgroup of AEs with greater harm to the patient, classified as F–I on the IHI-GTT adapted version of the National Coordinating Council for Medication Error Reporting and Prevention (NCC MERP) Index for Categorizing Errors. In this diagnostic test study, GTT is the index test and identification of AEs (yes/no) represents the condition of interest. Due to the lack of a gold standard test, a composite reference standard method was developed. Reference standard method combined real-time (during hospitalizations) and retrospective search of medical records and administrative data for screening criteria and AEs. Both tests were applied to a random sample of 211 hospitalizations of adult inpatients during October–November 2016 in a large public hospital in Belo Horizonte, Brazil. The accuracy of the GTT was evaluated using sensitivity, specificity, and global accuracy. A total of 176 AEs were identified in 67 admissions using reference standard method and 129 AEs in 76 admissions using GTT, resulting in rates of 126 and 93 AEs/1000 patient-days, respectively. Sensitivity, specificity, and global accuracy of the GTT for the identification of individual AEs were, respectively, 0.41 (95% confidence interval [CI] 0.34; 0.49), 0.68 (95% CI 0.60; 0.74), and 0.54 (95% CI 0.49; 0.60) for all AEs, regardless of the harm categorization, and 0.85 (95% CI 0.72; 0.93), 0.88 (95% CI 0.82; 0.92), and 0.87 (95% CI 0.82; 0.91) for the subgroup of AEs categorized as harm F–I. Among the main AEs missed by the GTT are AEs related to nursing care, such as those related to peripheral venous access and gastric/enteric catheters. GTT proved to be a valid method for identifying AEs in adult inpatients. Its accuracy increases when minor harm AEs are not counted. Among the main AEs missed by the GTT are those related to nursing care. Therefore, the GTT should be used in conjunction with other measurement strategies to achieve results that are representative of the quality profile of the care provided and, thus, guide the best improvement strategies.
The influence of a probiotic/prebiotic supplement on microbial and metabolic parameters of equine cecal fluid or fecal slurry in vitro
Authors: MacNicol Jennifer L , Renwick Simone , Ganobis Caroline M , Allen-Vercoe Emma , Weese Jeffery S , Pearson Wendy 
Published: January 2023

AbstractThe microbes that reside within the equine hindgut create a complex and dynamic ecosystem. The equine hindgut microbiota is intimately associated with health and, as such, represents an area which can be beneficially modified. Synbiotics, supplements that combine probiotic micro-organisms with prebiotic ingredients, are a potential means of influencing the hindgut microbiota to promote health and prevent disease. The objective of the current study was to evaluate the influence of an equine probiotic/prebiotic supplement on characteristics of the microbiota and metabolite production in vitro. Equine cecal fluid and fecal material were collected from an abattoir in QC, CAN. Five hundred milliliters of cecal fluid was used to inoculate chemostat vessels maintained as batch fermenters (chemostat cecal, N = 11) with either 0 g (control) or 0.44 g of supplement added at 12 h intervals. One hundred milliliters of cecal fluid (anaerobic cecal, N = 15) or 5% fecal slurry (anaerobic fecal, N = 6) were maintained in an anaerobic chamber with either 0 g (control) or 0.356 g of supplement added at the time of vessel establishment. Samples were taken from vessels at vessel establishment (0), 24, or 48 h of incubation. Illumina sequencing of the V4 region of the 16S rRNA gene and bioinformatics were performed for microbiome analysis. Metabolite data was obtained via NMR spectroscopy. All statistical analyses were run in SAS 9.4. There was no effect of treatment at 24 or 48h on alpha or beta diversity indices and limited taxonomic differences were noted. Acetate, propionate, and butyrate were higher in treated compared to untreated vessels in all methods. A consistent effect of supplementation on the metabolic profile with no discernable impact on the microbiota of these in vitro systems indicates inoculum microbe viability and a utilization of the provided fermentable substrate within the systems. Although no changes within the microbiome were apparent, the consistent changes in metabolites indicates a potential prebiotic effect of the added supplement and merits further exploration.
An in vitro and in vivo approach to characterize digesta from pigs fed different forms of pea flour
Authors: Grundy Myriam M L , Labarre Julien , Mayeur-Nickel Frederique , van Milgen Jaap , Renaudeau David 
Published: January 2023

AbstractIn vitro models of digestion are useful tools to explore the behavior of dietary fiber sources in gastrointestinal conditions. To evaluate the validity of our digestion model, digesta obtained in vivo and in vitro were characterized and the impact of cell wall integrity on protein bioaccessibility and digestibility evaluated. Six cannulated barrows [Pietrain × (Large White × Landrace)] were included in a 2 × 2 Latin square design where they were fed two diets identical in chemical composition but differing in nutrient bioaccessibility. Pea was given either as flour (R1, most proteins encapsulated by intact cell walls) or reconstituted flour (R2, mixture of proteins and purified, broken cell walls). Digesta were collected at the duodenal and ileal cannulas at regular interval and after slaughtering, following ingestion of either R1 or R2. The two diets were also digested in vitro using a static gastrointestinal model. The original pea ingredients as well as the digesta collected in vivo and in vitro were characterized (i.e., particle size measurement, microscopy observations and gel electrophoresis) and then compared with each other. The degradation of the pea ingredients differed greatly between the two forms of flour, where particles filled with nutrients were recovered at the latest stage of R1 intestinal digestion as observed with the particle size distribution and the microscopy images. These results were consistent with the in vivo and in vitro digestibility analysis that showed lower protein hydrolysis for R1 than that for R2 (about 19% difference in protein digestion regardless of the method). Overall, great similarities were found between the digesta collected in vivo and in vitro, especially regarding the particle size measurements. To summarize, a substantial proportion of the proteins contained in R1 was retained within the pea cells following gastrointestinal digestion. These encapsulated proteins reduced the amount of amino acids and small peptides available for absorption. This mechanism will have consequences on postprandial metabolism of amino acids and bacterial population based on the delivery form of the dietary fiber.
A Review of Petrol Burns in Australia and New Zealand
Authors: Savage Nicholas , Doherty Zakary , Singer Yvonne , Menezes Hana , Cleland Heather , Goldie Stephen J 
Published: January 2023

Abstract
Petrol-related thermal burns cause significant morbidity and mortality worldwide and it has been established that they affect young males disproportionately. Beyond this, we sought to identify the difference in the characteristics and outcomes of burns between males and females in an international population. Such differences may highlight areas for future preventative strategies. The Burns Registry of Australia and New Zealand was used. Petrol burns that resulted in a hospital admission in those 16 years or older between January 2010 and December 2019 were included. A total of 2833 patients were included. The median age was 35 years with most patients being male (88%). Burns from a campfire or burnoffs were most common. Females were more likely to suffer burns due to assault or from deliberate self-harm. The total body surface area affected by burns was higher for females than males (10% vs 8%). Furthermore, females more frequently required ICU admission, escharotomies, and had a longer hospital length of stay. The unadjusted mortality rate for females was more than double the rate for males (5.8% vs 2.3%). This international study demonstrates that whilst men more frequently suffer petrol burns, women suffer more severe burns, require more intensive and longer hospitalizations and have a higher mortality rate. These findings may inform changes in preventative health policies globally to mitigate against these concerning findings.
Examination of Hivetop Incubator Efficacy for Emerging Osmia lignaria (Hymenoptera: Megachilidae) and the Impact on Apis mellifera (Hymenoptera: Apidae) Colonies
Authors: McCabe Lindsie M , Cox-Foster Diana , Pitts-Singer Theresa L 
Published: January 2023

Abstract
Osmia lignaria Say is used in combination with Apis mellifera L. to pollinate U.S. orchard crops. The deployment of O. lignaria requires artificial warming to synchronize adult bee emergence with crop bloom. However, current methods for emerging bees are time consuming and inefficient; the Hivetop Incubator (HTI) invention creates a space atop an A. mellifera hive whose heat flows through the screened bottom of the HTI to incubate cocooned O. lignaria adults therein. In response to HTI heat, O. lignaria adults chew out of cocoons, find an exit hole, and fly away to nest in provided nesting sites and, thereby, pollinate a crop. Objectives for studies performed in Utah and Washington were to: 1) determine whether HTIs inhibit A. mellifera thermoregulation or colony growth, 2) compare O. lignaria emergence duration from an HTI with and without hive heat, and 3) assess whether O. lignaria females leave HTIs located at the orchard edge to nest throughout the orchard. We found no significant differences between the internal temperatures of A. mellifera colonies with and without HTIs and no impact on A. mellifera food storage or brood production. Osmia lignaria in hive-heated HTIs emerged 3× faster than bees in unheated HTIs. Heated HTIs were significantly cooler than hive temperatures but significantly warmer than HTIs atop empty hive boxes. Osmia lignaria nest distribution was not correlated to the location of HTIs at the orchard edge. Overall, HTIs were effective for timely, on-site emergence of O. lignaria for orchard pollination without negatively impacting A. mellifera colonies.
Anthropogenic Influence on the Distribution of the Longlegged Ant (Hymenoptera: Formicidae)
Authors: Lum Jun-Yin , Chiu Ming-Chung , Tseng Shu-Ping , Scotty Yang Chin-Cheng , Lee Chow-Yang 
Published: January 2023

Abstract
The longlegged ant Anoplolepis gracilipes (Smith) is a highly invasive tramp ant species known for its deleterious effects on native ecosystems. While tramp ants are associated with human activity, information on how different intensities of human activity affect their distribution is limited. This study investigated how anthropogenic activities affected the distribution of A. gracilipes in Penang, a tropical island in northern peninsular Malaysia. Three study sites (Youth Park, Sungai Ara, and Bukit Jambul/Relau) were selected, containing four sub-locations corresponding to different levels of human activity (low, moderate, high, and very high), determined by the average number of passersby observed over 30 min. Baited index cards were placed at each sub-location to evaluate ant abundance and distribution. The results demonstrated that A. gracilipes worker abundance was highest in areas of moderate human activity, as opposed to areas with low and higher human activity. The low abundance of A. gracilipes in comparatively undisturbed localities may be attributed to unsuitable microclimate, lack of propagule pressure, and diminished honeydew availability. In contrast, its exclusion from more urbanized localities could be explained by high interspecific competition with other tramp species and the absence of preferred nesting sites.
Internalized transphobia predicts worse longitudinal trend of body uneasiness in transgender persons treated with gender affirming hormone therapy: a 1-year follow-up study
Authors: Castellini Giovanni , Rossi Eleonora , Cassioli Emanuele , Sanfilippo Giulia , Ristori Jiska , Vignozzi Linda , Maggi Mario , Ricca Valdo , Fisher Alessandra Daphne 
Published: January 2023

AbstractBackgroundGiven the relationship between interiorized stigma and body image, it could be hypothesized that high levels of internalized transphobia (IT) might predict higher levels of body uneasiness in subjects with gender dysphoria (GD) and worse improvement of body image after gender affirming hormone therapy (GAHT).AimWe sought to evaluate the relationship between IT and body uneasiness in subjects with GD and the role of IT in moderating the improvement of body image after GAHT.MethodsIn total, 200 individuals with GD performed the baseline assessment; 99 were re-evaluated 12 months after starting GAHT. At baseline participants were evaluated through a face-to-face interview and filled self-administered questionnaires to evaluate GD (Utrecht Gender Dysphoria Scale [UGDS]), IT attitudes (Attitudes Toward Transgendered Individuals [ATTI] Scale), body uneasiness (Body Uneasiness Test, part A [BUT-A]), and general psychopathology (Symptom Checklist 90-Revised [SCL 90-R]). The same questionnaires, except ATTI, were readministered at follow-ups.OutcomesOutcomes were based on measures of the associations between IT and baseline characteristics of the sample, the longitudinal trends of GD, body uneasiness, and general psychopathology; and IT as a moderator of the longitudinal trend of body uneasiness.ResultsAt baseline, IT correlated with lower level of education, higher GD, and more severe body uneasiness. Longitudinal analyses showed significant improvements in GD, body uneasiness, and general psychopathology during GAHT. Moderation analysis confirmed that participants with more transphobic attitudes showed less improvement after GAHT with regard to body uneasiness (bTime*ATTI = −.002, P = .040). The Johnson-Neyman technique revealed that no significant improvement in body uneasiness was found for participants with ATTI scores lower than 71.14.Clinical ImplicationsThe presence of IT should be investigated in subjects with GD who require gender affirming treatments to provide specific interventions aimed at targeting this dimension.Strengths and LimitationsStrengths of this study include the mixed cross-sectional and longitudinal design and the dimensional evaluation of the investigated constructs. Limitations include the small sample size and the limited follow-up. Furthermore, the effects of gender affirming surgery were not evaluated.ConclusionThe association of IT with both baseline body uneasinessand the longitudinal course of this dimension highlighted the clinical significance of body uneasiness and the importance of making continuous efforts to improve education and information to fight societal stigmas.
Differential sensitivities of photosynthetic processes and carbon loss mechanisms govern N-induced variation in net carbon assimilation rate for field-grown cotton
Authors: Parkash Ved , Snider John L , Sintim Henry Y , Hand Lavesta C , Virk Gurpreet , Pokhrel Amrit 
Published: January 2023

Abstract
Nitrogen (N) deficiency limits the net carbon assimilation rate (AN), but the relative N sensitivities of photosynthetic component processes and carbon loss mechanisms remain relatively unexplored for field-grown cotton. Therefore, the objective of the current study was to define the relative sensitivity of individual physiological processes driving N deficiency-induced declines in AN for field-grown cotton. Among the potential diffusional limitations evaluated, mesophyll conductance was the only parameter substantially reduced by N deficiency, but this did not affect CO2 availability in the chloroplast. A number of metabolic processes were negatively impacted by N deficiency, and these effects were more pronounced at lower leaf positions in the cotton canopy. Ribulose bisphosphate (RuBP) regeneration and carboxylation, AN, and gross photosynthesis were the most sensitive metabolic processes to N deficiency, whereas photosynthetic electron transport processes, electron flux to photorespiration, and dark respiration exhibited intermediate sensitivity to N deficiency. Among thylakoid-specific processes, the quantum yield of PSI end electron acceptor reduction was the most sensitive process to N deficiency. It was concluded that AN is primarily limited by Rubisco carboxylation and RuBP regeneration under N deficiency in field-grown cotton, and the differential N sensitivities of the photosynthetic process and carbon loss mechanisms contributed significantly to photosynthetic declines.
A novel mutant allele of AtCNGC15 reveals a dual function of nuclear calcium release in the root meristem
Authors: Tipper Emily , Leitão Nuno , Dangeville Pierre , Lawson David M , Charpentier Myriam 
Published: January 2023

Abstract
Calcium release to the nucleoplasm of root meristem cells was demonstrated to modulate root development. The calcium channel encoded by cyclic nucleotide-gated channel (CNGC) 15 localizes at the nuclear envelope in young Arabidopsis seedlings. In contrast, at later stages of root growth, overexpression analysis showed that AtCNGC15 can relocalize to the plasma membrane to mediate primary nitrate-induced gene expression. This raises the question as to whether nuclear localized AtCNGC15 is required for root apical meristem development in young Arabidopsis seedlings, and whether nitrate signalling occurs independently of nuclear localized AtCNGC15 at this developmental stage. In this study, we characterize a novel mutant allele of AtCNGC15 and demonstrate that the mutation of a highly conserved aspartic acid in the C-linker domain is sufficient to impair the gating of AtCNCG15. We demonstrate that AtCNGC15 mediates the nuclear calcium release that modulates root apical meristem development and nitrate-induced LBD39 expression. We also show that, in the presence of nitrate, the relocalization of AtCNGC15 at the plasma membrane occurs specifically in the columella cells. Our results further suggest that the induction of LBD37, LBD38, and LBD39 in the presence of nitrate is modulated by different inputs of cytoplasmic or nuclear calcium release.
Relevant epistemic logic with public announcements and common knowledge
Authors: PunČochář Vít , Sedlár Igor , Tedder Andrew 
Published: January 2023

AbstractWe study a version of public announcement logic with common knowledge based on the relevant logic $\textsf {R}$. Public announcements, as represented in our framework, are not necessarily truthful and accepted by all agents, nor is it assumed that beliefs are preserved under announcements. We establish a completeness result with respect to a relational semantics, and we show that an alternative semantics based on information states is dual to the relational one. We add a question-forming inquisitive disjunction operator to the language and prove a completeness result with respect to the information semantics.
Logical Realism and the Riddle of Redundancy
Authors: Monroy Pérez Óscar Antonio 
Published: January 2023

AbstractAccording to an influential view, when it comes to representing reality, some words are better suited for the job than others. This is elitism. There is reason to believe that the set of the best, or elite, words should not be redundant or arbitrary. However, we are often forced to choose between these two theoretical vices, especially in cases involving theories that seem to be mere notational variants. This is the riddle of redundancy: both redundancy and arbitrariness are vicious, but there are cases in which one must be picked. Logical realists admit that there are some logical constants among the elite words. This leads to awkward questions, such as which among conjunction and disjunction is elite. In this paper, I show how the riddle of redundancy arises for logical realists, and offer a solution. This approach requires us to change how we represent negation. Instead of using some particular symbol, we represent negation by flipping formulae over the horizontal axis.
Neo-Logicism and Gödelian Incompleteness
Authors: Pregel Fabian 
Published: January 2023

AbstractThere is a long-standing gap in the literature as to whether Gödelian incompleteness constitutes a challenge for Neo-Logicism, and if so how serious it is. In this paper, I articulate and address the challenge in detail. The Neo-Logicist project is to demonstrate the analyticity of arithmetic by deriving all its truths from logical principles and suitable definitions. The specific concern raised by Gödel’s first incompleteness theorem is that no single sound system of logic syntactically implies all arithmetical truths. I set out some responses that initially seem appealing and explain why they are not compelling. The upshot is that Neo-Logicism either offers an epistemic route only to some truths of arithmetic; or that it has to move from a syntactic to a semantic notion of logical consequence, which risks undermining its epistemic goals. I conclude by considering Crispin Wright’s recent attempt to address Gödelian incompleteness, which I argue is not satisfactory.