bluuebunny/crossref_metadata_2025 huggingface dataset:
What is Life? The Artistic Aspect of the Embodied Intelligence and Soft Robotics: Life in Sonic Arts, Audio-Visual Programming, and Handicrafts Design
Authors: Yang Shu
Published: November 2023

The artistic aspect is the ‘dancer’ (Gary Zukav) [7] in the machine. There is an embryonic potentiality for embodied intelligence, soft robotics, and engineering if we emphasise the artistic aspect and employ it as an indispensable element. Art is less weighted in science, technology, and engineering than functionalities and applications. Equivalently, there is a potential under-explored advantage of science and technology-based artistic creation instead of individualistic improvisation, interpretation, and expression. Starting from the philosophical and scientific question, What is life? this paper reviewed influential theories from entropy, ‘code-script’ by Erwin Schrödinger, ‘wetware’, cell compartmentation by Paul Nurse, sentient machine by Anil Seth, to the ‘Dance’ by Gary Zukav, the ‘30 000’ organ by Denis Noble, the 100,000 protein sonification by Markus Buehler, and a bio-inspired composition by Alberto Carretero using P-system. With my research on cell-inspired audio-visual works The Cell Planet using Touch Designer, music creation for the Protein Misfolding project, and the soft-robotic inspired biomimetic textiles and art, this paper provides solutions for integrating technology, science, engineering, and art from a deeper, experimental, and philosophical context.
Open to Evolve Embodied Intelligence
Authors: Langdon W B
Published: November 2023

For the goal of automatically evolving Embodied Intelligence (EI), we investigate an open software architecture inspired by the high surface area to volume ratio of animal lungs, which aims to avoid information theoretic limits on long term evolution experiments (LTEE) encountered with monolithic genetic programming trees. Instead individuals are teams composed of 1023 trees whose inputs and outputs are linked by a low entropy loss branching data (air) pathway. Most trees are shallow and software engineering’s failed disruption propagation (FDP) is observed in the small fraction of deep trees. After initial search, most improvements are at intermediate depths and performance is still rising even after 100 000 generations.

Despite the use of double precision for the bifurcating data interconnect, some information loss is seen, particularly in early generations. The static optimisation benchmark, appears to encourage early convergence, which locks the population into possibly sub-optimal phenotypes. Later thousands of small improvements, sometimes in large bloated ensemble members, appear to compensate for early overfitting.

Using tournament fitness selection and subtree crossover, we target pure nested side-effect free floating point functions, which are known to have low FDP, and high fidelity data paths, in the hope of generating code which is not too robust so as to prevent on going improvement. However, we again find genetic changes deep within trees are silent. For single precision, we find a maximum evolvability sweet spot with trees of depth 10 to 100. Accordingly, we suggest to evolve very large very complex programs needed for Embodied Intelligence, an open structure with a high surface area permitting most mutation sites to be within 10-100 levels of the organism’s environment, and many better placed test oracles to monitor the impact of mutated code, will be needed.
Crystal structure, morphology and enhancement of luminescence properties of Cr3+-doped KZnF3 phosphor by using a HF-free hydrothermal method with different chromium sources
Authors: Yang Yifan , Zhu Yongqi , Wu Shuang , Li Xinyue , Mao Qinan , Chen Yifan , Zhong Jiasong , Zhu Yiwen
Published: November 2023

In this study, a series of near-infrared (NIR) KZnF3:Cr3+ phosphors was prepared by different chromium sources using a HF-free hydrothermal method. The influence of different chromium sources on the crystal structure, morphology, and luminescence properties of Cr3+-doped KZnF3 phosphors were systematically investigated. The results showed that the chromium source changed from CrF3·xH2O to (NH4)3CrF6 and leaded to an increased crystal field, resulting in a blue shift of the emission peak position from 803 nm to 753 nm, accompanied by the full-width half maximum (FWHM) reduced from 140 nm to 122 nm. Moreover, KZnF3:0.03Cr3+ (CrF3·xH2O) and KZnF3:0.03Cr3+ ((NH4)3CrF6) phosphors maintained 58% and 87% of their initial room-temperature intensity at 423 K, respectively. These results indicated that altering the synthetic raw materials provided new insights for designing NIR phosphors with highly thermal stability.
Non-destructive analysis of Pb-acid battery positive plates, based on neutron tomography
Authors: Bozzini Benedetto , Cazzanti Silvia , Hippoliti Raimondo , Kis Zoltán , Rovatti Ludovica , Tavola Francesco
Published: November 2023

Notwithstanding the in-depth understanding of lead-acid battery degradation processes developed in a time-honored field of science, there is still wide scope for knowledge-based technological advancements, in particular, targeting positive plate (PP) durability. Non-destructive imaging of the internal morphology, structure and chemistry of these components, enabled by neutron-based methods, is capable of disclosing otherwise inaccessible observables, that can form the factual basis for new pathways to device improvement. In this study, we propose a post mortem investigation of as-formed and electrochemically aged PPs, centered on neutron tomography and complemented by x-ray radiography and scanning-electron microscopy. These complementary imaging methods, thriving on different contrast mechanisms, allow 2D/3D position-sensitive morphological analyses of the nature and evolution of the positive active material (PAM) and of the spines of the PP, including: morphology variation, crack location, porosity distribution and identification of hydrogenated compounds. Specifically, in this work, we have pinpointed the differences in degradation modes—resulting from the application of a standard ageing protocol—of PPs fabricated in two technologically alternative ways: punching and gravity-casting, showing the superiority of the formed in terms of electrode stability upon charging abuse conditions.
A novel generalized multi input boosting multi-level inverter (MIB-MLI) for high-frequency AC (HFAC) power distribution
Authors: Sinha Rajiv Ranjan , Mandal Rajib Kumar
Published: November 2023

The simplified topology for the high-frequency ac (HFAC) power distribution method with a multi-level inverter (MLI) hybrid switched capacitor (SC) is introduced. Capacitors, switches, diodes, and DC sources are among the components that are reduced in the designed MIB-MLI (Multi Input Boosting Multi-level Inverter). Where asymmetric dc voltage sources are available, such as in renewable energy farm-based ac microgrids and current electric vehicle, this architecture is advantageous. The proposed inverter has the feature of self-balancing the capacitor voltages and voltage boosting by using the series-parallel conversion scheme. The quality of output power is increased when a dc source array is connected with the unidirectional switched converter. Moreover, if a major phase variation betwixt the output current along with the voltage is no more mandatory, multiple alive switches may be recouped with diodes. In the switched capacitor group ripple volatge is reciprocal to the output frequency, so the MIB-MLI is favorable for HFAC implementations. Also, this paper clarifies the operating theory of the complete network and switching condition covered by the sinusoidal pulse width modulation (SPWM) technique. Mathematical equation related to power loss and capacitor voltages are provided. The modeling and simulation results of the proposed seventeen-level (17-L) inverter are depicted in this paper. The findings have shown that the proposed inverter is superior at HFAC along with the power efficiency of the inverter is adequate with SPWM technique.
Machine-learning based optimization of a biomimiced herringbone microstructure for superior aerodynamic performance
Authors: Patel Rushil Samir , Akolekar Harshal D
Published: November 2023

Biomimicry involves drawing inspiration from nature’s designs to create efficient systems. For instance, the unique herringbone riblet pattern found in bird feathers has proven effective in minimizing drag. While attempts have been made to replicate this pattern on structures like plates and aerofoils, there has been a lack of comprehensive optimization of their overall design and of their constituent individual repeating structures. This study attempts to enhance the performance of individual components within the herringbone riblet pattern by leveraging computational fluid dynamics (CFD) and supervised machine learning to reduce drag. The paper outlines a systematic process involving the creation of 107 designs, parameterization, feature selection, generating targets using CFD simulations, and employing regression algorithms. From CFD calculations, the drag coefficients (C

d
) for these designs are found, which serve as an input to train supervised learning models. Using the trained transformed target regressor model as a substitute to CFD, C

d
values for 10,000 more randomly generated herringbone riblet designs are predicted. The design with the lowest predicted C

d
is the optimized design. Notably, the regressed model exhibited an average prediction error rate of 6% on the testing data. The prediction of C

d
for the optimized design demonstrated an error of 4% compared to its actual C

d
value calculated through CFD. The study also delves into the mechanics of drag reduction in herringbone riblet structures. The resulting optimized microstructure design holds the potential for reducing drag in various applications such as aerospace, automotive, and marine crafts by integrating it onto their surfaces. This innovative approach could significantly transform drag reduction and open pathways to more efficient transportation systems.
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

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

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

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

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

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

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

Attention typically reduces power in the alpha (8–12 Hz) band and increases power in gamma (>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

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 >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

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

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 < 0.001) and a disparity most pronounced in patients >80 years old (adjusted odds ratio 0.31, 95% confidence interval 0.22–0.45; P < 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 >80 years old.
Pain
Authors: de C Williams Amanda C
Published: November 2023

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

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

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.
Informative community structure revealed using Arabidopsis time series transcriptome data via partitioned local depth
Authors: Khoury Maleana G , Berenhaut Kenneth S , Moore Katherine E , Allen Edward E , Harkey Alexandria F , Mühlemann Joëlle K , Craven Courtney N , Xu Jiayi , Jain Suchi S , John David J , Norris James L , Muday Gloria K
Published: November 2023

Transcriptome studies that provide temporal information about transcript abundance facilitate identification of gene regulatory networks (GRNs). Inferring GRNs from time series data using computational modeling remains a central challenge in systems biology. Commonly employed clustering algorithms identify modules of like-responding genes but do not provide information on how these modules are interconnected. These methods also require users to specify parameters such as cluster number and size, adding complexity to the analysis. To address these challenges, we used a recently developed algorithm, partitioned local depth (PaLD), to generate cohesive networks for 4 time series transcriptome datasets (3 hormone and 1 abiotic stress dataset) from the model plant Arabidopsis thaliana. PaLD provided a cohesive network representation of the data, revealing networks with distinct structures and varying numbers of connections between transcripts. We utilized the networks to make predictions about GRNs by examining local neighborhoods of transcripts with highly similar temporal responses. We also partitioned the networks into groups of like-responding transcripts and identified enriched functional and regulatory features in them. Comparison of groups to clusters generated by commonly used approaches indicated that these methods identified modules of transcripts that have similar temporal and biological features, but also identified unique groups, suggesting that a PaLD-based approach (supplemented with a community detection algorithm) can complement existing methods. These results revealed that PaLD could sort like-responding transcripts into biologically meaningful neighborhoods and groups while requiring minimal user input and producing cohesive network structure, offering an additional tool to the systems biology community to predict GRNs.
A comparison of empirical and mechanistic models for wheat yield prediction at field level in Moroccan rainfed areas
Authors: Mamassi Achraf , Lang Marie , Tychon Bernard , Lahlou Mouanis , Wellens Joost , El Gharous Mohamed , Marrou Hélène
Published: November 2023

In the context of climate change, in-season and longer-term yield predictions are needed to anticipate local and regional food crises and propose adaptations to farmers’ practices. Mechanistic models and machine learning are two modelling options to consider from this perspective. In this study, multiple regression (MR) and random forest (RF) models were calibrated for wheat yield prediction in Morocco, using data collected from 125 farmers’ wheat fields. Additionally, MR and RF models were calibrated both with or without remotely sensed leaf area index (LAI), while considering all farmers’ fields, or specifically to agroecological zoning in Morocco. The same farmers’ fields were simulated using a mechanistic model (APSIM-wheat). We compared the predictive performances of the empirical models and APSIM-wheat. Results showed that both MR and RF showed rather good predictive quality (normalized root mean square errors (NRMSEs) below 35 %), but were always outperformed by the APSIM model. Both RF and MR selected remotely sensed LAI at heading, climate variables (maximal temperatures at emergence and tillering), and fertilization practices (amount of nitrogen applied at heading) as major yield predictors. Integration of remotely sensed LAI in the calibration process reduced NRMSE by 4.5 % and 1.8 % on average for MR and RF models, respectively. Calibration of region-specific models did not significantly improve the predictive. These findings lead to the conclusion that mechanistic models are better at capturing the impacts of in-season climate variability and would be preferred to support short-term tactical adjustments to farmers’ practices, while machine learning models are easier to use in the perspective of mid-term regional prediction.
Reverse Flow Injection Spectrophotometric Determination of Total Acidity in Beverages Using Butterfly Pea Flower Extract
Authors: Deecharoenchaiyakul Patpitcha , Tangtreamjitmun Napa
Published: November 2023

Background

Monitoring total acidity during beverage production is crucial for quality control (QC). The standard acid–base titration, though widely used, is slow and generates hazardous waste through the use of acid–base indicators.

Objective

To develop an analysis method for beverage samples to determine total acidity using a natural reagent from butterfly pea flower as the colorimetric reagent.

Methods

The determination of total acidity in beverages was based on the reaction of citric acid with anthocyanin extracted from butterfly pea flowers. The decreased absorbance of anthocyanin was measured at 620 nm. A two-line reverse flow injection manifold was used to perform online dilution of samples.

Results

Under optimal conditions, the calibration curve equation 1/A = 0.03782C + 0.00241 (A = absorbance and C = concentration) was linear over a range of 0.050–0.25% (w/v) citric acid. The LOD and LOQ were 0.0123 and 0.0409% (w/v), respectively. The system achieved a throughput of 120 samples per hour with comparable accuracy and precision to the standard titrimetric method.

Conclusion

The injection of butterfly pea flower extract into beverage samples with online dilution in a reverse flow injection system (FIS) was reported for the first time for the determination of total acidity.

Highlights

Use of a green reagent in the method reflects its alignment with the principles of green analytical chemistry, providing a rapid and straightforward solution.
Novel synthetic biological study on intracellular distribution of human GlcNAc-1-phosphotransferase expressed in insect cells
Authors: Kiriyama Kei , Fujioka Keisuke , Kawai Kaito , Mizuno Teru , Shinohara Yasuo , Itoh Kohji
Published: November 2023

Many lysosomal enzymes contain N-glycans carrying mannose 6-phosphate (M6P) residues. Modifying lysosomal enzymes by M6P residues requires a two-step process in the Golgi apparatus. Then the lysosomal enzymes with M6P residues are transported from the trans-Golgi network to endosomes and lysosomes by M6P receptors. In insect cells, M6P residues are not added to N-glycans. Therefore, many insect lysosomal enzymes are transported to lysosomes by the M6P-independent pathway. The expression and subcellular distribution of M6P-modifying enzymes were examined by amplifying DNA fragments of M6P-modifying enzymes, generating the corresponding plasmid constructs, and transfection each construct into Sf9 cells, an insect cell line. The human GlcNac-1-phosphotransferase α/β subunit, one of the M6P-modifying enzymes, was found to differ in maturation and localization between mammalian and insect cells. In mammalian cells, newly biosynthesized α/β subunit localized in the cis-Golgi. In Sf9 cells, most of the α/β subunit was localized in the endoplasmic reticulum, and few mature forms of α/β subunit were observed. However, by the co-expression of the human site-1 protease, the mature forms were observed significantly and co-localization with each protein. Our study indicates new insights into regulating the intracellular distribution of the human GlcNac-1-phosphotransferase α/β subunit in insect cells.
Exploratory comparison of flower visiting behavior and pollination ability of mason bees, bumble bees, and honey bees
Authors: Lyu Zhaoyun , Zhou Ting , Sun Meng , Feng Min , Guo Wenxiu , Nie Lei , Song Yingying , Men Xingyuan , Li Lili , Yu Yi
Published: November 2023

This study explored the flower visiting behaviors and pollination abilities of mason bees (Osmia excavata Alfken (Hymenoptera: Megachilidae)), bumble bees (Bombus terrestris (Linnaeus, 1758) (Hymenoptera: Apidae)), and Italian honey bees (Apis mellifera ligustica Spinola (Hymenoptera: Apidae)) in apple orchards in early spring in Jinan (located in the central region of Shandong) and Yantai (located in the Peninsula of Shandong). We compared the pollen collection patterns, flower visiting behavior, flying speed, and effects on apple pollination of the 3 types of bees. The frequencies of flower visits were significantly higher for mason bees (12.89/min in Jinan and 10.63/min in Yantai) than bumble bees and Italian honey bees in the 2 regions. The single flower residence times were significantly higher for Italian honey bees (8.22 s in Jinan and 9.43 s in Yantai), but Italian honey bees were most affected by the climate. The 3 bees differed significantly in terms of the amount of apple pollen collected and their effects on the fruit setting rate in apples (mason bees > bumble bees > Italian honey bees). The results showed that the mason bee was the most suitable pollinating species for spring apple orchards; Bumble bees were more suitable as alternative pollinators during cloudy and low temperatures; Italian honey bees were able to take advantage of their large number of worker bees in sunny and warm weather. Compared to individual bee species, a combination of 2 or 3 species of bees might be more advantageous in dealing with complex and variable weather conditions.
Rock physics characteristics and their control factors of carbonate in different sedimentary microfacies of the Yingshan Formation, Gucheng Area, Tarim Basin
Authors: Wang Jiaqing , Deng Jixin , Xia Hui , Yan Longlong
Published: November 2023

Understanding the influence of geological characteristics on rock physics properties is crucial for accurately recognizing the relationship between rock physics variation and reservoir characteristics. Unlike the conventional rock species, the rock physics properties of the deep carbonate rocks in the third member of Yingshan Formation (Ying-III Member) in Gucheng area, Tarim Basin are relatively more complex. To address this problem, we investigated the rock physics characteristics and controlling factors of different sedimentary microfacies samples, combined with sedimentological analysis and rock physics experiments. The results show that the sedimentary environment affects the lithology and pore structure by controlling the properties of the primitive rock and early diagenesis. Dolomitized shoal microfacies and shoal top dolomitic flat microfacies primarily form crystalline dolomite and siliceous dolomite, with pores consisting of inter-crystalline pores, dissolution pores, and cracks. Inter-shoal dolomitic flat microfacies develops silty dolomite, with only a few inter-crystalline pores and cracks. Middle- to high-energy shoal microfacies and inter-shoal sea microfacies develop tight calcarenite and micritic limestone. Samples with similar mineral composition have relatively consistent density values and acoustic properties. Soft pores, such as micro-cracks, have a significant impact on the effective pressure and acoustic wave velocity, velocity and velocity ratio, and velocity and porosity relationships. The research shows a new approach for the rock physics characteristics of deep carbonate reservoirs under geological background constraints, as well as the rock physics basis for seismic prediction of the Ying-III Member reservoir.
Electron holography observation of electron spin polarization around charged insulating wire
Authors: Sato Takafumi , Shimada Keiko , Akase Zentaro , Magara Hideyuki , Tomita Takeshi , Shindo Daisuke
Published: November 2023

We report direct observation by electron holography of the spin polarization of electrons in a vacuum region around a charged SiO2 wire coated with Pt–Pd. Irradiating the SiO2 wire with 300 keV electrons caused the wire to become positively charged due to the emission of secondary electrons. The spin polarization of these electrons interacting with the charged wire was observed in situ using a phase reconstruction process under an external magnetic field. The magnetic field of the spin-polarized electrons was simulated taking into account the distribution of secondary electrons and the effect of the external magnetic field.
Loss of Respiratory Syncytial Virus Antibody Functions During the Peak of the COVID-19 Pandemic Mitigation Measures
Authors: Abu-Raya Bahaa , Reicherz Frederic , Michalski Christina , Viñeta Paramo Marina , Majdoubi Abdelilah , Golding Liam , Granoski Madison , Stojic Aleksandra , Marchant David J , Lavoie Pascal M
Published: November 2023

Studies have linked respiratory syncytial virus (RSV) antibody-mediated phagocytosis and complement deposition to severe RSV infection in humans. This study shows waning of these antibody functions in women of childbearing age in 2020-2021 during the implementation of COVID-19 mitigation measures, in absence of RSV circulation. These functions could be explored as correlates of protection against severe RSV disease.
Bayesian design with sampling windows for complex spatial processes
Authors: Buchhorn Katie , Mengersen Kerrie , Santos-Fernandez Edgar , Peterson Erin E , McGree James M
Published: November 2023

Optimal design facilitates intelligent data collection. In this paper, we introduce a fully Bayesian design approach for spatial processes with complex covariance structures, like those typically exhibited in natural ecosystems. Coordinate exchange algorithms are commonly used to find optimal design points. However, collecting data at specific points is often infeasible in practice. Currently, there is no provision to allow for flexibility in the choice of design. Accordingly, we also propose an approach to find Bayesian sampling windows, rather than points, via Gaussian process emulation to identify regions of high design efficiency across a multi-dimensional space. These developments are motivated by two ecological case studies: monitoring water temperature in a river network system in the northwestern United States and monitoring submerged coral reefs off the north-west coast of Australia.