bluuebunny/crossref_metadata_2025_split huggingface dataset:
LOX1- and PLP1-dependent transcriptional reprogramming is essential for injury-induced conidiophore development in a filamentous fungus
Authors: Camargo-Escalante Martín O. , Balcázar-López Edgar , Albores Méndez Exsal M. , Winkler Robert , Herrera-Estrella Alfredo 
Published: November 2023

ABSTRACT

Fungi use oxylipins (oxidized lipids) as signaling molecules to induce asexual development. These molecules play an essential role in the response to wounding, exerting a protective effect against plant pathogens, and are part of the inflammatory process in animals. However, the physiological and molecular mechanisms triggered by oxylipins that lead to asexual development in fungi are not well understood. Using a genetic approach, mass spectrometry, and phenotypic analysis, we describe the functional role of a patatin-like phospholipase (
plp1
) and a unique lipoxygenase (
lox1
) in the response to injury in the model fungus
Trichoderma atroviride. lox1
and
plp1
are co-expressed and regulated by damage signaling and sensing components. Phenotypic analysis revealed an essential defect in the emergence of aerial hyphae in the
lox1
and
plp1
null mutant strains, blocking injury-induced conidiation. In addition, functional loss analysis demonstrated that both genes are essential for wound-associated linoleic acid-derived oxylipin 13-hydroxy-9Z,11E-octadecadienoic acid (13-HODE) production and the transcriptional reprogramming required for conidiation.
T. atroviride
requires LOX1 and PLP1 to induce transcription factors involved in asexual development such as
brlA
,
hox2
, and
azf1
homologs at the early stages of the response and at a later stage to activate lipid metabolism and the structural proteins involved in aerial mycelium emergence. Our study shows how the cooperative function of
lox1
and
plp1
, during the response to wounding, regulates the molecular and physiological processes of damaged-sensitized cells that lead to reproductive aerial mycelium development and consequently, ensure survival through asexual reproduction.

IMPORTANCE

In addition to being considered a biocontrol agent, the fungus
Trichoderma atroviride
is a relevant model for studying mechanisms of response to injury conserved in plants and animals that opens a new landscape in relation to regeneration and cell differentiation mechanisms. Here, we reveal the co-functionality of a lipoxygenase and a patatin-like phospholipase co-expressed in response to wounding in fungi. This pair of enzymes produces oxidized lipids that can function as signaling molecules or oxidative stress signals that, in ascomycetes, induce asexual development. Furthermore, we determined that both genes participate in the regulation of the synthesis of 13-HODE and the establishment of the physiological responses necessary for the formation of reproductive aerial mycelium ultimately leading to asexual development. Our results suggest an injury-induced pathway to produce oxylipins and uncovered physiological mechanisms regulated by LOX1 and PLP1 to induce conidiation, opening new hypotheses for the novo regeneration mechanisms of filamentous fungi.
‘More than likely the men come first. That’s just very frustrating’. A qualitative exploration of contextual factors affecting the implementation of injury prevention initiatives and the provision of effective injury management in elite-level women’s club football in Ireland
Authors: Horan Dan , Delahunt Eamonn , Roe Mark , Hägglund Martin , Blake Catherine , Kelly Seamus 
Published: November 2023

Objectives
The aim of our study was to explore the contextual factors that affect the implementation of football injury prevention initiatives and the provision of effective injury management in the Irish Women’s National League (WNL).

Methods
We used a criterion-based purposive sampling approach to recruit coaches (n=7), players (n=17) and medical personnel (n=8) representing eight of the nine clubs in the WNL to participate in one-to-one semistructured interviews. Our study was located within an interpretivist, constructivist research paradigm. The interview data were analysed using reflexive thematic analysis.

Results
The participants identified academic and work pressures, financial challenges, conflict with college football, inadequate facilities and gender inequity as being barriers to the implementation of injury prevention initiatives and the provision of effective injury management. Financial constraints within clubs were perceived to limit the provision of medical care and strength and conditioning (S&C) support and this was deemed to be associated with a heightened risk of injuries.

Conclusion
Specific contextual factors were identified which curtail the implementation of injury prevention initiatives and the provision of effective injury management in elite-level women’s club football in Ireland. Gender inequity was identified as one of the factors impacting the availability of high-quality medical care, S&C support, as well as access to training and match facilities. Our results provide new insights that could be used to inform the design and implementation of injury prevention and management initiatives for women football players in Ireland.
Mapping nutrition within medical curricula in Australia and New Zealand: a cross-sectional content analysis
Authors: King Ryan E , Palermo Claire , Wilson Alyce N 
Published: November 2023

ObjectiveTo systematically map nutrition content in medical curricula across all 23 medical schools in Australia and New Zealand accredited by the Australian Medical Council (AMC).MethodsA cross-sectional content analysis was conducted. Learning outcomes for 20 AMC-accredited medical curricula were extracted from online repositories and directly from universities in February to April 2021. Nutrition relevant learning outcomes or equivalent learning objectives/graduate attributes were identified. Nutrition learning outcomes were analysed according to Bloom’s revised taxonomy to determine whether outcomes met cognitive, psychomotor or affective domains and at what level.ResultsOf the total 23 AMC-accredited medical curricula, 20 medical schools had learning outcomes able to be sourced for analysis. A total of 186 nutrition learning outcomes were identified within 11 medical curricula. One medical school curriculum comprised 129 of 186 (69.4%) nutrition learning outcomes. The majority of outcomes (181, 97.3%) were in the cognitive domain of Bloom’s revised taxonomy, predominantly at level 3 ‘applying’ (90, 49.7%). The psychomotor domain contained five nutrition learning outcomes (5, 2.7%), while the affective domain contained none. New Zealand medical curricula (153, 82.3%) contained 4.6-fold more nutrition learning outcomes than Australian curricula (33, 17.7%). When comparing clinical and preclinical years across curricula, the proportion of learning outcomes in the psychomotor domain was 3.7-fold higher in clinical years (4.08%) versus preclinical years (1.15%).ConclusionThere is wide variation across medical curricula regarding the number of nutrition learning outcomes. This may lead to varying competency of medical graduates to provide nutrition care in Australia and New Zealand.
Diagnosis of Acute Aortic Syndrome in the Emergency Department (DAShED) study: an observational cohort study of people attending the emergency department with symptoms consistent with acute aortic syndrome
Authors: McLatchie Rachel , Reed Matthew J , Freeman Nicola , Parker Richard A , Wilson Sarah , Goodacre Steve , Cowan Alicia , Boyle Jessica , Clarke Benjamin , Clarke Ellise 
Published: November 2023

BackgroundThe diagnosis of acute aortic syndrome (AAS) is commonly delayed or missed in the ED. We describe characteristics of ED attendances with symptoms potentially associated with AAS, diagnostic performance of clinical decision tools (CDTs) and physicians and yield of CT aorta angiogram (CTA).MethodsThis was a multicentre observational cohort study of adults attending 27 UK EDs between 26 September 2022 and 30 November 2022, with potential AAS symptoms: chest, back or abdominal pain, syncope or symptoms related to malperfusion. Patients were preferably identified prospectively, but retrospective recruitment was also permitted. Anonymised, routinely collected patient data including components of CDTs, was abstracted. Clinicians treating prospectively identified patients were asked to record their perceived likelihood of AAS, prior to any confirmatory testing. Reference standard was radiological or operative confirmation of AAS. 30-day electronic patient record follow-up evaluated whether a subsequent diagnosis of AAS had been made and mortality.Results5548 patients presented, with a median age of 55 years (IQR 37–72; n=5539). 14 (0.3%; n=5353) had confirmed AAS. 10/1046 (1.0%) patients in whom the ED clinician thought AAS was possible had AAS. 5/147 (3.4%) patients in whom AAS was considered the most likely diagnosis had AAS. 2/3319 (0.06%) patients in whom AAS was considered not possible did have AAS. 540 (10%; n=5446) patients underwent CT, of which 407 were CTA (7%). 30-day follow-up did not reveal any missed AAS diagnoses. AUROC (area under the receiver operating characteristic) curve for ED clinician AAS likelihood rating was 0.958 (95% CI 0.933 to 0.983, n=4006) and for individual CDTs were: Aortic Dissection Detection Risk Score (ADD-RS) 0.674 (95% CI 0.508 to 0.839, n=4989), AORTAs 0.689 (95% CI 0.527 to 0.852, n=5132), Canadian 0.818 (95% CI 0.686 to 0.951, n=5180) and Sheffield 0.628 (95% CI 0.467 to 0.788, n=5092).ConclusionOnly 0.3% of patients presenting with potential AAS symptoms had AAS but 7% underwent CTA. CDTs incorporating clinician gestalt appear to be most promising, but further prospective work is needed, including evaluation of the role of D-dimer.Trial registration numberNCT05582967;NCT05582967.
Injury-related emergency department use among people with intellectual and developmental disabilities insured by Medicaid from 2010 to 2016
Authors: Williams Jessica , Royer Julie , Lauer Emily , Kurth Noelle K , Horner-Johnson Willi , McDermott Suzanne , Levy Anna , Hall Jean P 
Published: November 2023

ObjectivesData on non-fatal injuries and visits to the emergency department (ED) for injuries are not readily available. The objective of this paper is to describe injury-related ED visits for people with intellectual and developmental disabilities who are covered by the Medicaid insurance programme.MethodsWe aggregated 2010–2016 Medicaid claims data from eight states. Using these data, we identified individuals with intellectual and developmental disabilities and then determined an all-cause ED visit rate, ED visit due to injury rate and admission from ED due to injury rate. Data were stratified by sex and age group. Results were compared with national rates.ResultsMedicaid members with intellectual and developmental disabilities visited EDs at approximately 1.8 times the rate of the general population. The ED visit rate due to injury was approximately 1.5 times that observed in the population overall. When ED visits due to injury data were stratified by age and sex, the largest discrepancy was observed in women ages 45–64, who visited EDs due to injury at a rate 2.1 times that of women of the same age in the general population. The admission rate from ED due to injury increased over the study period most notably in the older age groups.ConclusionsWhile rates and patterns of ED utilisation among Medicaid members with intellectual and developmental disabilities vary by age and gender, our findings suggest this group visits the ED due to injury at rates well above the general population.
Exploring the potential utility of AI large language models for medical ethics: an expert panel evaluation of GPT-4
Authors: Balas Michael , Wadden Jordan Joseph , Hébert Philip C , Mathison Eric , Warren Marika D , Seavilleklein Victoria , Wyzynski Daniel , Callahan Alison , Crawford Sean A , Arjmand Parnian , Ing Edsel B 
Published: November 2023

Integrating large language models (LLMs) like GPT-4 into medical ethics is a novel concept, and understanding the effectiveness of these models in aiding ethicists with decision-making can have significant implications for the healthcare sector. Thus, the objective of this study was to evaluate the performance of GPT-4 in responding to complex medical ethical vignettes and to gauge its utility and limitations for aiding medical ethicists. Using a mixed-methods, cross-sectional survey approach, a panel of six ethicists assessed LLM-generated responses to eight ethical vignettes.The main outcomes measured were relevance, reasoning, depth, technical and non-technical clarity, as well as acceptability of GPT-4’s responses. The readability of the responses was also assessed. Of the six metrics evaluating the effectiveness of GPT-4’s responses, the overall mean score was 4.1/5. GPT-4 was rated highest in providing technical (4.7/5) and non-technical clarity (4.4/5), whereas the lowest rated metrics were depth (3.8/5) and acceptability (3.8/5). There was poor-to-moderate inter-rater reliability characterised by an intraclass coefficient of 0.54 (95% CI: 0.30 to 0.71). Based on panellist feedback, GPT-4 was able to identify and articulate key ethical issues but struggled to appreciate the nuanced aspects of ethical dilemmas and misapplied certain moral principles.This study reveals limitations in the ability of GPT-4 to appreciate the depth and nuanced acceptability of real-world ethical dilemmas, particularly those that require a thorough understanding of relational complexities and context-specific values. Ongoing evaluation of LLM capabilities within medical ethics remains paramount, and further refinement is needed before it can be used effectively in clinical settings.
Observational study on occupational exposure of dairy farmers to formaldehyde
Authors: Janssen Esmée Rianne , Nielen Mirjam , Spithoven Jacobus Jochem Gerardus , van Werven Tine , Wouters Inge Maria 
Published: November 2023

ObjectivesTo provide insights into exposure of Dutch dairy farmers to formaldehyde derived from formalin footbaths used for cows. Dutch safety norms are set at a limit of 0.122 ppm during an 8-hour time-weighted average (TWA) and 0.407 ppm for a 15-min TWA.MethodsAt 20 farms formaldehyde air concentrations were determined using stationary active air sampling with impingers next to the footbath and in the milking parlour during footbath usage. Formalin footbath concentrations were tested and meteorological conditions were collected using a climate monitor to assess associations with formaldehyde concentrations. A structured interview inquired on potential exposure routes and exposure duration.ResultsFormaldehyde concentrations next to the footbath ranged from <0.003 to 0.316 ppm, with seven measurements exceeding the 8-hour TWA threshold. None of the measurements exceeded the 15-min TWA threshold at either location. Formaldehyde air concentrations in the milking parlour were generally lower, yet at two farms exceeded the 8-hour TWA limit during sampling. Self-reported exposure time of the dairy farmers to the formalin footbath never exceeded 15 min. Although due to the small sample size, no significant associations between most predictor variables and formaldehyde levels in the air were found, the direction of effects were as expected.ConclusionsThe exposure of Dutch dairy farmers presumably falls within the established safety norms. Nonetheless, substantial levels of formaldehyde could be detected. This study further emphasises the importance of substitution of formalin in dairy practice and the relevance of informing dairy farmers on proper handling of formalin to reduce exposure.
Cosmological singularities in $$f(T,\phi ) $$ gravity
Authors: Trivedi Oem , Khlopov Maxim , Said Jackson Levi , Nunes Rafael 
Published: November 2023

AbstractThe pursuit of understanding the mysteries surrounding dark energy has sparked significant interest within the field of cosmology. While conventional approaches, such as the cosmological constant, have been extensively explored, alternative theories incorporating scalar field-based models and modified gravity have emerged as intriguing avenues. Among these, teleparallel theories of gravity, specifically the $$f(T,\phi )$$

f
(
T
,
ϕ
)

formulation, have gained prominence as a means to comprehend dark energy within the framework of teleparallelism. In this study, we investigate two well-studied models of teleparallel dark energy and examine the presence of cosmological singularities within these scenarios. Using the Goriely–Hyde procedure, we examine the dynamical systems governing the cosmological equations of these models. Our analysis reveals that both models exhibit Type IV singularities, but only for a limited range of initial conditions. These results could indicate a potential edge for teleparallel cosmological models over their other modified gravity counterparts, as the models we examine seem to be only allowing for weak singularities that too under non general conditions.
Learning from Very Little Data: On the Value of Landscape Analysis for Predicting Software Project Health
Authors: Lustosa Andre , Menzies Tim 
Published: November 2023

When data is scarce, software analytics can make many mistakes. For example, consider learning predictors for open source project health (e.g., the number of closed pull requests in 12 months time). The training data for this task may be very small (e.g., 5 years of data, collected every month means just 60 rows of training data). The models generated from such tiny datasets can make many prediction errors.

Those errors can be tamed by a
landscape analysis
that selects better learner control parameters. Our
niSNEAK
tool (a) clusters the data to find the general landscape of the hyperparameters, then (b) explores a few representatives from each part of that landscape.
niSNEAK
is both faster and more effective than prior state-of-the-art hyperparameter optimization algorithms (e.g., FLASH, HYPEROPT, OPTUNA).

The configurations found by
niSNEAK
have far less error than other methods. For example, for project health indicators such as
C
= number of commits,
I
= number of closed issues, and
R
= number of closed pull requests,
niSNEAK
’s 12-month prediction errors are {I=0%, R=33% C=47%}, whereas other methods have far larger errors of {I=61%,R=119% C=149%}. We conjecture that
niSNEAK
works so well since it finds the most informative regions of the hyperparameters, then jumps to those regions. Other methods (that do not reflect over the landscape) can waste time exploring less informative options.

Based on the preceding, we recommend landscape analytics (e.g.,
niSNEAK
) especially when learning from very small datasets. This article only explores the application of
niSNEAK
to project health. That said, we see nothing in principle that prevents the application of this technique to a wider range of problems.

To assist other researchers in repeating, improving, or even refuting our results, all our scripts and data are available on GitHub at https://github.com/zxcv123456qwe/niSneak.
Adherence to 2018 WCRF/AICR Cancer Prevention Recommendations and Risk of Cancer: The Melbourne Collaborative Cohort Study
Authors: Peng Yang , Bassett Julie K. , Hodge Allison M. , Melaku Yohannes Adama , Afshar Nina , Hopper John L. , MacInnis Robert J. , Lynch Brigid M. , Smith-Warner Stephanie A. , Giles Graham G. , Milne Roger L. , Jayasekara Harindra 
Published: November 2023

Abstract

Background:
We examined associations between adherence to adaptations of the 2018 World Cancer Research Fund/American Institute for Cancer Research (WCRF/AICR) cancer prevention recommendations and total, exposure-related and site-specific cancer risk.

Methods:
A total of 20,001 participants ages 40 to 69 years at enrollment into the Melbourne Collaborative Cohort Study in 1990 to 1994, who had diet, body size, and lifestyle reassessed in 2003 to 2007 (“baseline”), were followed-up through June 2021. We constructed diet and standardized lifestyle scores based on core WCRF/AICR recommendations on diet, alcohol intake, body size and physical activity, and additional scores incorporating weight change, sedentary behavior, and smoking. Associations with cancer risk were estimated using Cox regression, adjusting for confounders.

Results:
During follow-up (mean = 16 years), 4,710 incident cancers were diagnosed. For highest quintile (“most adherent”) of the standardized lifestyle score, compared with lowest (“least adherent”), a HR of 0.82 [95% confidence interval (CI): 0.74–0.92] was observed for total cancer. This association was stronger with smoking included in the score (HR = 0.74; 95% CI: 0.67–0.81). A higher score was associated with lower breast and prostate cancer risk for the standardized score, and with lung, stomach, rectal, and pancreatic cancer risk when the score included smoking. Our analyses identified alcohol use, waist circumference and smoking as key drivers of associations with total cancer risk.

Conclusions:
Adherence to WCRF/AICR cancer prevention recommendations is associated with lower cancer risk.

Impact:
With &lt;0.2% of our sample fully adherent to the recommendations, the study emphasizes the vast potential for preventing cancer through modulation of lifestyle habits.
Tool or Actor? Expert Improvisers' Evaluation of a Musical AI “Toddler”
Authors: Erdem Çağrı , Wallace Benedikte , Glette Kyrre , Jensenius Alexander Refsum 
Published: November 2023

Abstract
In this article, we introduce the coadaptive audiovisual instrument, CAVI. This instrument uses deep learning to generate control signals based on muscle and motion data of a performer's actions. The generated signals control time-based live sound-processing modules. How does a performer perceive such an instrument? Does it feel like a machine learning–based musical tool? Or is it an actor with the potential to become a musical partner? We report on an evaluation of CAVI after it had been used in two public performances. The evaluation is based on interviews with the performers, audience questionnaires, and the creator's self-analysis. Our findings suggest that the perception of CAVI as a tool or actor correlates with the performer's sense of agency. The perceived agency changes throughout a performance based on several factors, including perceived musical coordination, the balance between surprise and familiarity, a “common sense,” and the physical characteristics of the performance setting.
Composing the Assemblage: Probing Aesthetic and Technical Dimensions
of Artistic Creation with Machine Learning
Authors: Gioti Artemi-Maria , Einbond Aaron , Born Georgina 
Published: November 2023

Abstract
In this article, we address the role of machine learning (ML) in the composition of two new musical works for acoustic instruments and electronics through autoethnographic reflection on the experience. Our study poses the key question of how ML shapes, and is in turn shaped by, the aesthetic commitments characterizing distinctive compositional practices. Further, we ask how artistic research in these practices can be informed by critical themes from humanities scholarship on material engagement and critical data studies. Through these frameworks, we consider in what ways the interaction with ML algorithms as part of the compositional process differs from that with other music technology tools. Rather than focus on narrowly conceived ML algorithms, we take into account the heterogeneous assemblage brought into play: from composers, performers, and listeners to loudspeakers, microphones, and audio descriptors. Our analysis focuses on a deconstructive critique of data as being contingent on the decisions and material conditions involved in the data-creation process. It also explores how interaction among the human and nonhuman collaborators in the ML assemblage has significant similarities to—as well as differences from—existing models of material engagement. Tracking the creative process of composing these works, we uncover the aesthetic implications of the many nonlinear collaborative decisions involved in composing the assemblage.