bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marine heatwave duration and intensity interact to reduce physiological tipping points of kelp species with contrasting thermal affinities
Authors: Leathers Tayla , King Nathan G , Foggo Andy , Smale Dan A 
Published: November 2023

Abstract

Background and Aims
Marine heatwaves (MHWs) are widely recognized as pervasive drivers of ecosystem change, yet our understanding of how different MHW properties mediate ecological responses remains largely unexplored. Understanding MHW impacts on foundation species is particularly important, given their structural role in communities and ecosystems.

Methods
We simulated a series of realistic MHWs with different levels of intensity (Control: 14 °C, Moderate: 18 °C, Extreme: 22 °C) and duration (14 or 28 d) and examined responses of two habitat-forming kelp species in the southwest UK. Here, Laminaria digitata reaches its trailing edge and is undergoing a range contraction, whereas Laminaria ochroleuca reaches its leading edge and is undergoing a range expansion.

Key Results
For both species, sub-lethal stress responses induced by moderate-intensity MHWs were exacerbated by longer duration. Extreme-intensity MHWs caused dramatic declines in growth and photosynthetic performance, and elevated bleaching, which were again exacerbated by longer MHW duration. Stress responses were most pronounced in L. ochroleuca, where almost complete tissue necrosis was observed by the end of the long-duration MHW. This was unexpected given the greater thermal safety margins assumed with leading edge populations. It is likely that prolonged exposure to sub-lethal thermal stress exceeded a physiological tipping point for L. ochroleuca, presumably due to depletion of internal reserves.

Conclusions
Overall, our study showed that exposure to MHW profiles projected to occur in the region in the coming decades can have significant deleterious effects on foundation kelp species, regardless of their thermal affinities and location within respective latitudinal ranges, which would probably have consequences for entire communities and ecosystems.
Independent, cooperative regulation of cellulolytic genes by paralogous transcription factors ClbR and ClbR2 in Aspergillus aculeatus
Authors: Kunitake Emi , Kawaguchi Takashi , Tani Shuji 
Published: November 2023

ABSTRACT
The cellobiose-responsive regulator ClbR, a Zn(II)2Cys6 binuclear-cluster transcription factor, is a positive regulator of carbohydrate-active enzyme (CAZyme) genes responsive to cellulose in Aspergillus aculeatus. Because Zn(II)2Cys6 transcription factors tend to dimerize with proteins of the same family, we searched for a counterpart of ClbR and identified ClbR2, which is 42% identical to ClbR, as an interacting partner of ClbR by yeast two-hybrid screening. Genetic analyses suggested that ClbR and ClbR2 cooperatively regulate the expression of CAZyme genes in response to cellulose and 1,4-β-mannobiose in A. aculeatus. CAZyme genes under the control of the transcription factor ManR were regulated by ClbR and ClbR2, whereas those controlled by the transcription factor XlnR were regulated by ClbR, but not ClbR2. These findings suggest that ClbR participates in multiple regulatory pathways in A. aculeatus by altering an interacting factor.
syntenyPlotteR: a user-friendly R package to visualize genome synteny, ideal for both experienced and novice bioinformaticians
Authors: Quigley Sarah , Damas Joana , Larkin Denis M , Farré Marta 
Published: November 2023

Abstract

Motivation
The rapid increase in the number of chromosome-scale genome assemblies has renewed interest in chromosome evolution studies. The visualization of syntenic relationships between genomes is a crucial initial step in the study of chromosome rearrangements and evolution. There are few tools available that serve this purpose, and they can be difficult to learn. Moreover, these tools are limited in the number of species comparisons that can be visualized and the size of chromosome rearrangements identified. Thus, the development of novel visualization tools is in strong need.

Results
Here, we present syntenyPlotteR, an R package developed to visualize homologous synteny blocks in a pairwise or multispecies manner. This package contains three functions that allow users to generate publication-quality representations of syntenic relationships easily and quickly between genomes of interest.

Availability and implementation
SyntenyPlotteR can be installed from CRAN with the documentation found in https://farre-lab.github.io/syntenyPlotteR/.
Can Social Workers Estimate the Likelihood of Future Actions and Events? A Forecasting Accuracy Study
Authors: Wilkins David , Meindl Melissa 
Published: November 2023

Abstract
Social workers routinely make decisions and formulate care plans in the course of their work with children and families. These decisions and care plans are based at least in part on the professional judgement of the worker. An important component of judgemental quality is the extent to which explicit or implicit forecasts about the likelihood of different future actions and events are made with accuracy. In this article, we report an analysis of 21,193 forecasts made by 581 child and family social workers in England about the likelihood of different future actions and events following referrals to children’s services. We found that the more likely social workers said an action or event was to happen (as the forecast likelihood increased towards 100 per cent), the more often it occurred. However, we also found that social workers tend to over-estimate the likelihood of almost all specified future actions and events. Social workers were most accurate when forecasting something to be very unlikely, and less accurate when they forecast something to be likely or very likely. We consider these findings in relation to false positive and negative errors in child protection, and the theory of judgemental rationalism.
Validation of the Medical Research Council prion disease rating scale in France
Authors: Brandel Jean-Philippe , Welaratne Arlette , Denouel Angeline , Haïk Stéphane 
Published: November 2023

Abstract
The development of assessment tools other than survival time is necessary to conduct therapeutic trials in prion diseases (also known as subacute transmissible encephalopathies). The Medical Research Council Prion Disease Rating Scale published by Thompson et al. (The Medical Research Council prion disease rating scale: A new outcome measure for prion disease therapeutic trials developed and validated using systematic observational studies. Brain. 2013; 136: 1116–27.) is the first attempt at a specific evaluation of prion diseases to avoid the floor effect seen in other scales. Validation of this scale in other countries is essential because, given the rarity of these diseases, therapeutic trials are likely to be multi-centre and international. After translation into French, we assessed by phone 173 cases classified as sporadic Creutzfeldt–Jakob disease out of 852 patients notified to the French national surveillance network between November 2014 and May 2021. Data showed that the natural history of the disease is similar in the UK and France. Patients who have a heterozygous genotype at codon 129 of the prion protein gene have a slower decline than homozygous patients. In rapidly progressing patients, death occurs shortly after reaching a low score or after a ‘pre-terminal plateau’ at a very low score. The similarities of disease progression profile observed in France and the UK with somewhat different surveillance systems and by distinct procedures highlight the robustness of the Medical Research Council Prion Disease Rating Scale that can be thus used to define primary endpoints of future trials at the international level.
Prevalence and localization of nocturnal epileptiform discharges in mild cognitive impairment
Authors: Ciliento Rosario , Gjini Klevest , Dabbs Kevin , Hermann Bruce , Riedner Brady , Jones Stephanie , Fatima Safoora , Johnson Sterling , Bendlin Barbara , Lam Alice D , Boly Melanie , Struck Aaron F 
Published: November 2023

Abstract
Recent evidence shows that identifying and treating epileptiform abnormalities in patients with Alzheimer’s disease could represent a potential avenue to improve clinical outcome. Specifically, animal and human studies have revealed that in the early phase of Alzheimer’s disease, there is an increased risk of seizures. It has also been demonstrated that the administration of anti-seizure medications can slow the functional progression of the disease only in patients with EEG signs of cortical hyperexcitability. In addition, although it is not known at what disease stage hyperexcitability emerges, there remains no consensus regarding the imaging and diagnostic methods best able to detect interictal events to further distinguish different phenotypes of Alzheimer’s disease. In this exploratory work, we studied 13 subjects with amnestic mild cognitive impairment and 20 healthy controls using overnight high-density EEG with 256 channels. All participants also underwent MRI and neuropsychological assessment. Electronic source reconstruction was also used to better select and localize spikes. We found spikes in six of 13 (46%) amnestic mild cognitive impairment compared with two of 20 (10%) healthy control participants (P = 0.035), representing a spike prevalence similar to that detected in previous studies of patients with early-stage Alzheimer’s disease. The interictal events were low-amplitude temporal spikes more prevalent during non-rapid eye movement sleep. No statistically significant differences were found in cognitive performance between amnestic mild cognitive impairment patients with and without spikes, but a trend in immediate and delayed memory was observed. Moreover, no imaging findings of cortical and subcortical atrophy were found between amnestic mild cognitive impairment participants with and without epileptiform spikes. In summary, our exploratory study shows that patients with amnestic mild cognitive impairment reveal EEG signs of hyperexcitability early in the disease course, while no other significant differences in neuropsychological or imaging features were observed among the subgroups. If confirmed with longitudinal data, these exploratory findings could represent one of the first signatures of a preclinical epileptiform phenotype of amnestic mild cognitive impairment and its progression.
Alpha and SSVEP power outperform gamma power in capturing attentional modulation in human EEG
Authors: Das Aritra , Nandi Nilanjana , Ray Supratim 
Published: November 2023

Abstract
Attention typically reduces power in the alpha (8–12 Hz) band and increases power in gamma (&gt;30 Hz) band in brain signals, as reported in macaque local field potential (LFP) and human electro/magneto-encephalogram (EEG/MEG) studies. In addition, EEG studies often use flickering stimuli that produce a specific measure called steady-state-visually-evoked-potential (SSVEP), whose power also increases with attention. However, effectiveness of these neural measures in capturing attentional modulation is unknown since stimuli and task paradigms vary widely across studies. In a recent macaque study, attentional modulation was more salient in the gamma band of the LFP, compared to alpha or SSVEP. To compare this with human EEG, we designed an orientation change detection task where we presented both static and counterphasing stimuli of matched difficulty levels to 26 subjects and compared attentional modulation of various measures under similar conditions. We report two main results. First, attentional modulation was comparable for SSVEP and alpha. Second, non-foveal stimuli produced weak gamma despite various stimulus optimizations and showed negligible attentional modulation although full-screen gratings showed robust gamma activity. Our results are useful for brain-machine-interfacing studies where suitable features are used for decoding attention, and also provide clues about spatial scales of neural mechanisms underlying attention.
Mining the Gap: Deriving Pregnancy Reference Intervals for Hematology Parameters Using Clinical Datasets
Authors: Barakauskas Vilte E , Bohn Mary Kathryn , Branch Emma , Boutin Amelie , Albert Arianne , Luke Sabrina , Dittrick Michelle , Higgins Victoria , Adeli Khosrow , Vallance Hilary , Jung Benjamin , Dooley Kent , Dahlgren-Scott Leanne , Chan Wee-Shian 
Published: November 2023

Abstract

Background
Physiological changes during pregnancy invalidate use of general population reference intervals (RIs) for pregnant people. The complete blood count (CBC) is commonly ordered during pregnancy, but few studies have established pregnancy RIs suitable for contemporary Canadian mothers. Prospective RI studies are challenging to perform during pregnancy while retrospective techniques fall short as pregnancy and health status are not readily available in the laboratory information system (LIS). This study derived pregnancy RIs retrospectively using LIS data linked to provincial perinatal registry data.

Methods
A 5-year healthy pregnancy cohort was defined from the British Columbia Perinatal Data Registry and linked to laboratory data from two laboratories. CBC and differential RIs were calculated using direct and indirect approaches. Impacts of maternal and pregnancy characteristics, such as age, body mass index, and ethnicity, on laboratory values were also assessed.

Results
The cohort contained 143 106 unique term singleton pregnancies, linked to &gt;972 000 CBC results. RIs were calculated by trimester and gestational week. Result trends throughout gestation aligned with previous reports in the literature, although differences in exact RI limits were seen for many tests. Trimester-specific bins may not be appropriate for several CBC parameters that change rapidly within trimesters, including red blood cells (RBCs), some leukocyte parameters, and platelet counts.

Conclusions
Combining information from comprehensive clinical databases with LIS data provides a robust and reliable means for deriving pregnancy RIs. The present analysis also illustrates limitations of using conventional trimester bins during pregnancy, supporting use of gestational age or empirically derived bins for defining CBC normal values during pregnancy.
A generating-function approach to modelling complex contagion on clustered networks with multi-type branching processes
Authors: Keating Leah A , Gleeson James P , O’Sullivan David J P 
Published: November 2023

Abstract
Understanding cascading processes on complex network topologies is paramount for modelling how diseases, information, fake news and other media spread. In this article, we extend the multi-type branching process method developed in Keating et al., (2022), which relies on networks having homogenous node properties, to a more general class of clustered networks. Using a model of socially inspired complex contagion we obtain results, not just for the average behaviour of the cascades but for full distributions of the cascade properties. We introduce a new method for the inversion of probability generating functions to recover their underlying probability distributions; this derivation naturally extends to higher dimensions. This inversion technique is used along with the multi-type branching process to obtain univariate and bivariate distributions of cascade properties. Finally, using clique-cover methods, we apply the methodology to synthetic and real-world networks and compare the theoretical distribution of cascade sizes with the results of extensive numerical simulations.
Revascularization strategies for multivessel coronary artery disease based on sex and age
Authors: Sulaiman Samian , Harik Lamia , Merz C Noel Bairey , Fremes Stephen E , Masterson Creber Ruth , Rong Lisa Q , Alkhouli Mohamad , Gaudino Mario 
Published: November 2023

Abstract

OBJECTIVES
This study describes coronary revascularization strategies used by sex and age in the USA.

METHODS
A sex-stratified cohort study from the National Inpatient Sample from the Agency for Healthcare Research and Quality (USA) including patients admitted for coronary revascularization with primary or secondary diagnoses of chronic coronary syndrome or non-ST elevation myocardial infarction who underwent ≥3-vessel coronary artery bypass grafting or percutaneous coronary intervention from January 2019 to December 2020. The primary outcome was the use rate of coronary artery bypass grafting or multivessel percutaneous coronary intervention. Prespecified subgroups included age and non-ST elevation myocardial infarction.

RESULTS
Among 121 150 patients (21.7% women), there were no sex differences in age (women: 66.6 [66.5–66.7], men: 67.6 [67.5–67.7], standardized mean difference: 0.1) or non-ST elevation myocardial infarction incidence (women: 37.4%, men: 45.7%, standardized mean difference: 0.17). The majority of women (74.2%) and men (84.9%) underwent bypass grafting, which was unaffected by age, race or non-ST elevation myocardial infarction. Women were less likely to undergo bypass grafting than percutaneous intervention (adjusted odds ratio 0.49, 95% confidence interval 0.44–0.54; P &lt; 0.001) and a disparity most pronounced in patients &gt;80 years old (adjusted odds ratio 0.31, 95% confidence interval 0.22–0.45; P &lt; 0.001).

CONCLUSIONS
Most patients with multivessel coronary artery disease needing revascularization undergo bypass grafting, irrespective of sex, age or clinical presentation. The sex disparity in the use of bypass grafting is mostly seen among patients &gt;80 years old.
Pain
Authors: de C Williams Amanda C 
Published: November 2023

Abstract
An evolutionary perspective offers insights into the major public health problem of chronic (persistent) pain; behaviours associated with it perpetuate both pain and disability. Pain is motivating, and pain-related behaviours promote recovery by immediate active or passive defence; subsequent protection of wounds; suppression of competing responses; energy conservation; vigilance to threat; and learned avoidance of associated cues. When these persist beyond healing, as in chronic pain, they are disabling. In mammals, facial and bodily expression of pain is visible and identifiable by others, while social context, including conspecifics’ responses, modulate pain. Studies of responses to pain emphasize onlooker empathy, but people with chronic pain report feeling disbelieved and stigmatized. Observers frequently discount others’ pain, best understood in terms of cheater detection—alertness to free riders that underpins the capacity for prosocial behaviours. These dynamics occur both in everyday life and in clinical encounters, providing an account of the adaptiveness of pain-related behaviours.
Dynamics of Thioalkalivibrio species in a co-culture under selective pressure of ampicillin
Authors: Ahn Anne-Catherine , Schuurmans J Merijn , Sorokin Dimitry , Muyzer Gerard 
Published: November 2023

Abstract
Haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio are highly abundant in microbial communities found in soda lakes and dominant in full-scale bioreactors removing sulfide from industrial waste gases. Despite certain soda lakes being remote and unaffected by anthropogenic activities, haloalkaliphilic microorganisms, including Thioalkalivibrio strains, possess various antibiotic resistance genes. In this study, we investigated the impact of the antibiotic ampicillin on a co-culture of two Thioalkalivibrio species, Tv. thiocyanoxidans ARh2T and Tv. versutus AL2T, both experimentally and through in silico analysis of antibiotic resistance. Cell growth dynamics were monitored over time at increasing ampicillin concentrations using rep- and qPCR. Within ten days after the addition of ampicillin, the co-culture transitioned from a Tv. thiocyanoxidans ARh2T-dominated to a stable Tv. versutus AL2T-dominated culture. This shift was attributed to Tv. versutus AL2T displaying a lower susceptibility to ampicillin, making it more competitive. These results emphasize the potential implications of antibiotic pressure on microbial communities, where a resistant species can outcompete a stable co-culture. This study presents the first evidence of such dynamics in haloalkaliphilic chemolithoautotrophs. By understanding the antibiotic resistance and the competitive dynamics of haloalkaliphilic bacteria like Thioalkalivibrio, we can gain insights into their behaviour and stress response.
Biomarkers of Cellular Senescence Predict the Onset of Mobility Disability and Are Reduced by Physical Activity in Older Adults
Authors: Fielding Roger A , Atkinson Elizabeth J , Aversa Zaira , White Thomas A , Heeren Amanda A , Mielke Michelle M , Cummings Steven R , Pahor Marco , Leeuwenburgh Christiaan , LeBrasseur Nathan K 
Published: November 2023

Abstract
Studies in mice and cross-sectional studies in humans support the premise that cellular senescence is a contributing mechanism to age-associated deficits in physical function. We tested the hypotheses that circulating proteins secreted by senescent cells are (i) associated with the incidence of major mobility disability (MMD), the development of persistent mobility disability (PMMD), and decrements in physical functioning in older adults, and (ii) influenced by physical activity (PA). Using samples and data obtained longitudinally from the Lifestyle Interventions in Elders Study clinical trial, we measured a panel of 27 proteins secreted by senescent cells. Among 1 377 women and men randomized to either a structured PA intervention or a healthy aging (HA) intervention, we observed significant associations between several senescence biomarkers, most distinctly vascular endothelial growth factor A (VEGFA), tumor necrosis factor receptor 1 (TNFR1), and matrix metallopeptidase 7 (MMP7), and the onset of both MMD and PMMD. Moreover, VEGFA, GDF15, osteopontin, and other senescence biomarkers were associated with reductions in short physical performance battery scores. The change in senescence biomarkers did not differ between PA and HA participants. In the whole cohort, higher levels of PA were associated with significantly greater reductions in 10 senescence-related proteins at 12 and/or 24 months. These data reinforce cellular senescence as a contributing mechanism of age-associated functional decline and the potential for PA to attenuate this hallmark of aging.
Clinical Trials Registration Number: NCT01072500
Human Rights Activism and Transitional Justice Advocacy in Northern Ireland
Authors: Bryson Anna , McEvoy Kieran 
Published: November 2023

ABSTRACT∞
This article offers a critical assessment of efforts to address the legacy of the Northern Ireland conflict. We begin with an overview of government-led initiatives since 1998 and then reflect on three underpinning themes: justice, accountability and the tilt towards impunity; the shift from ‘truth’ to ‘information’ recovery; and the instrumentalization of history. We then offer a reflexive assessment of our endeavours to contribute to a ‘from below’ variant of legal, political and historical advocacy. Reflecting on our efforts to contest and critique successive government proposals, we draw out three overlapping ‘ideal types’ of transitional justice advocacy: technical engagement, coalition building and exposition. We conclude by highlighting the very specific challenges of engaging in transitional justice scholarship and advocacy in a ‘post-truth’ era.