bluuebunny/crossref_metadata_2025_split huggingface dataset:
Control Co-Design With Performance-Robustness Trade-Off Using Tube-Based Stochastic Model Predictive Control
Authors: Tsai Ying-Kuan , Malak, Jr. Richard J. 
Published: January 2025

Abstract
Control co-design (CCD) has been demonstrated to achieve superior solutions for closed-loop systems. However, limited work has addressed CCD problems under probabilistic disturbances. This article addresses this gap by formulating a finite-horizon optimal control problem with chance constraints and proposing a novel CCD approach. This approach integrates tube-based stochastic model predictive control with constraint-tightening techniques to optimize performance and robustness while preventing instability and infeasibility. A nested CCD framework is introduced, along with a constrained multi-objective optimization algorithm that enables the performance-robustness trade-off. A method for quantifying the robustness of closed-loop systems under stochastic disturbances is presented. The proposed CCD approach is demonstrated on a numerical example and an engineering case of the satellite attitude control system. Results show that CCD can generate more well-spread Pareto fronts that cannot be reached by other design strategies. This helps designers explore more potential solutions with different dynamic characteristics. Selected nondominated solution trajectories are visualized for qualitative comparisons. Future work will extend this to nonlinear applications.
The Ripple Effect: The Impact of Narrative on Team Culture and Lifelong Exercise Adherence
Authors: Busanich Rebecca , Nelson Paige E. , Koren Amber 
Published: January 2025

This case study narratively explores a high school cross-country team in a small U.S. Midwestern town from 1992 to 1999. Results of this study revealed how the team coconstructed discovery and relational nonperformance narratives, with the head coach adopting aligning narrative practices (i.e., newsletters and team journals), which together socially constructed a team culture built on love (i.e., for running, for one’s own self, and for one another). This case study highlights what a discovery and relational narrative are, how they vary from the more dominant performance narrative, and the ways in which these narratives were drawn upon, used, and reproduced over time and ultimately changed the meanings around exercise and sport for the members of this team. The outcomes associated with these narrative practices, and the meanings embedded within them, led to a successful program, greater exercise enjoyment, the development of lifelong friendships and healthy habits, long-term exercise adherence, and a ripple effect of many of the young athletes on this team going on to become future exercise and/or sport leaders (i.e., fitness coaches, personal trainers, and sport coaches) as adults. The long-term implications and implementation recommendations are explored.
Diversity and dynamics of multiple symbionts contribute to early development of broadcast spawning reef-building coral
Dipsastraea veroni
Authors: Guo Minglan , Jiang Lei , Zhou Guowei , Lian Jiansheng , Yu Xiaolei , Huang Hui 
Published: January 2025

ABSTRACT

Sexual reproduction and recruitment enhance the genetic diversity and evolution of reef-building corals for population recovery and coral reef conservation under climate change. However, new recruits are vulnerable to physical changes and the mechanisms of symbiosis establishment remain poorly understood. Here,
Dipsastraea veroni
, a broadcast spawning hermaphrodite reef-building coral, was subjected to settlement and juvenile growth in flow-through
in situ
seawater at 27.93 ± 0.96°C. Symbiosis of Symbiodiniaceae, bacteria, and/or archaea by horizontal acquisition and/or hypothetical vertical transmission through the mucus with symbionts from the parent appears to be a heritable process of selection and adaptation in
D. veroni
at the egg, larva, juvenile (5 days post settlement, d p.s. and 32 d p.s.) stages. Symbiodiniaceae was dominated by the genera
Cladocopium
,
Durusdinium
,
Symbiodinium,
with increasing relative abundance of
Durusdinium
at 5 d p.s. and
Symbiodinium
at 32 d p.s. Mixed acquisition of the dominant phyla Pseudomonadota, Bacteroidota, Cyanobacteriota, Bacillota, Planctomycetota, and Actinomycetota in egg, larva, and/or juvenile showed a winnowing and regulated bacterial diversity and dynamics, resulting in stage-abundant orders Pseudomonadales and Bacillales in egg and Rhodobacterales, Rhodospirillales, Cyanobacteria, and Cyanobacteriales in larva and/or juvenile. The photoautotrophic Chloroflexales, Cyanobacteriales, and Chlorobiales were abundant in adults. The stable archaeal community contained predominant Crenarchaeota, Halobacterota, Nanoarchaeia Thermoplasmatota, and eight rare phyla, with increased relative abundance of the genera
Bathyarchaeota
,
Candidatus_Nitrosopumilus
,
Candidatus_Nitrocosmicus
,
Nitrosarchaeum
,
Candidatus_Nitrosotenuis
,
Candidatus_Nitrosopelagicus
,
Cenarchaeum
,
Haladaptatus
,
Halogranum
,
Halolamina,
and
Woesearchaeales
and
GW2011-AR15
in juveniles. All results revealed flexible symbiotic mechanisms in
D. veroni
during early ontogeny for coral survival and evolution.

IMPORTANCE

Flexible symbioses of Symbiodiniaceae, bacteria, and archaea appear to be a heritable process of selection and adaptation in
Dipsastraea veroni
in the field, benefiting early coral development and facilitating coral population recovery and reef conversation.
Two NADPH-dependent 2-ketogluconate reductases involved in 2-ketogluconate assimilation in
Gluconobacter
sp. strain CHM43
Authors: Nakashima Sakura , Matsutani Minenosuke , Kataoka Naoya , Adachi Osao , Yamashita Riku , Matsushita Kazunobu , Tippayasak Uraiwan , Theeragool Gunjana , Yakushi Toshiharu 
Published: January 2025

ABSTRACT

Incomplete oxidation of glucose by
Gluconobacter
sp. strain CHM43 produces gluconic acid and then 2- or 5-ketogluconic acid. Although 2-keto-D-gluconate (2KG) is a valuable compound, it is sometimes consumed by
Gluconobacter
itself via an unknown metabolic pathway. We anticipated that 2KG reductase (2KGR) would be a key enzyme in 2KG metabolism.
GLF_0478
and
GLF_1777
were identified in the genome of strain CHM43, which encode proteins with 70% and 48% amino acid sequence identity, respectively, to the 2KGR of
Gluconobacter oxydans
strain 621H. Constructed mutant derivatives of strain CHM43 lacking
GLF_0478
,
GLF_1777
, or both were examined for their 2KG consumption ability. Strains ∆
GLF_0478
and ∆
GLF_1777
consumed 2KG like the parental strain. However, the double-deletion (∆∆) strain did not consume 2KG at all, although it produced 2KG like the parental strain. Strains ∆
GLF_0478
and ∆
GLF_1777
each showed decreased 2KGR activity compared with the parental strain, and strain ΔΔ lost 2KGR activity. These results suggest that reduction of 2KG catalyzed by GLF_0478 and GLF_1777 is the committed step in 2KG metabolism in
Gluconobacter
sp. strain CHM43. The two 2KGRs showed high activity at neutral pH and lower
K
M
values for NADPH than NADH. Results of induction experiments suggest that GLF_0478 is constitutively expressed at a low level but induced by 2KG, and GLF_1777 is also inducible by 2KG but repressed in the absence of an inducer. Our study that characterizes the key genes for 2KG consumption in
Gluconobacter
gives insights for improvement of biological 2KG production systems.

IMPORTANCE

2-Keto-D-gluconate (2KG), a product of incomplete oxidation of glucose by acetic acid bacteria including
Gluconobacter
spp., is used for various purposes, including in the food industry.
Gluconobacter
also consumes 2KG via an unclear metabolic pathway. It is reported that
Pseudomonas
spp. and
Cupriavidus necator
phosphorylate 2KG in the first step of 2KG metabolism, but some enteric bacteria including
Escherichia coli
reduce 2KG. This study evaluated the 2KG consumption ability of a mutant derivative of a strain of
Gluconobacter
that lacks two putative 2KGR-encoding genes. The mutant strain did not consume 2KG at all; the two 2KGRs were each found to catalyze 2KG reduction. It is concluded that reduction of 2KG is the committed step in 2KG metabolism in
Gluconobacter
. The results presented here give insights that might facilitate improvement of 2KG production systems that use
Gluconobacter
.
Pathogen genomic surveillance and the AI revolution
Authors: Lytras Spyros , Lamb Kieran D. , Ito Jumpei , Grove Joe , Yuan Ke , Sato Kei , Hughes Joseph , Robertson David L. 
Published: January 2025

ABSTRACT

The unprecedented sequencing efforts during the COVID-19 pandemic paved the way for genomic surveillance to become a powerful tool for monitoring the evolution of circulating viruses. Herein, we discuss how a state-of-the-art artificial intelligence approach called protein language models (pLMs) can be used for effectively analyzing pathogen genomic data. We highlight examples of pLMs applied to predicting viral properties and evolution and lay out a framework for integrating pLMs into genomic surveillance pipelines.
Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism
Authors: Ndovie Wanangwa , Havránek Jan , Leconte Jade , Koszucki Janusz , Chindelevitch Leonid , Adriaenssens Evelien M. , Mostowy Rafal J. 
Published: January 2025

ABSTRACT

Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%. Using a rigorous simulation framework, we demonstrate MANIAC’s accuracy and scalability compared to existing approaches, even to data sets of hundreds of thousands of viral genomes. Applying MANIAC to a curated data set of complete bacterial dsDNA viruses revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap (~90%) but shifted, likely due to viral-specific evolutionary processes such as recombination dynamics and mosaicism. We then evaluated ANI and AF as predictors of genus-level taxonomy using a logistic regression model. We found that this model has strong predictive power (PR-AUC = 0.981), but that it works much better for virulent (PR-AUC = 0.997) than temperate (PR-AUC = 0.847) bacterial viruses. This highlights the complexity of taxonomic classification in temperate phages, known for their extensive mosaicism, and cautions against over-reliance on ANI in such cases. MANIAC can be accessed at
https://github.com/bioinf-mcb/MANIAC
.

IMPORTANCE
We introduce a novel computational pipeline called MANIAC, designed to accurately assess average nucleotide identity (ANI) and alignment fraction (AF) between diverse viral genomes, scalable to data sets of over 100k genomes. Using computer simulations and real data analyses, we show that MANIAC could accurately estimate genetic relatedness between pairs of viral genomes of around 60%–70% ANI. We applied MANIAC to investigate the question of ANI discontinuity in bacterial dsDNA viruses, finding evidence for an ANI gap, akin to the one seen in bacteria but around ANI of 80%. We then assessed the ability of ANI and AF to predict taxonomic genus boundaries, finding its strong predictive power in virulent, but not in temperate phages. Our results suggest that bacterial dsDNA viruses may exhibit an ANI threshold (on average around 80%) above which recombination helps maintain population cohesiveness, as previously argued in bacteria.
TccP4: a novel effector identified in the
Escherichia albertii
strain 1551-2 required for attaching and effacing lesion formation on infected Nck-null cells
Authors: Fernandes Iranildo do A. , Ooka Tadasuke , de Lira Daiany R. P. , Martins Fernando H. , Orsi Henrique , Jones Nina , Elias Waldir P. , Hayashi Tetsuya , Gomes Tânia A. T. , Hernandes Rodrigo T. 
Published: January 2025

ABSTRACT

Escherichia albertii
is a pathogen that causes sporadic cases and outbreaks of diarrhea. The main virulence feature of this bacterium is the attaching and effacing (AE) lesion formation on infected intestinal epithelial cells, which is characterized by the formation of pedestal-like structures that are rich in F-actin. The Brazilian
E. albertii
1551-2 strain can recruit F-actin using both the Nck-dependent and the Nck-independent pathways, the latter of which uses an adaptor protein named Tir-cytoskeleton coupling protein (TccP/EspF
U
). Genome analyses of the 1551-2 strain unveiled the existence of a gene encoding a putative novel TccP subtype in addition to a gene encoding for the TccP3 subtype. Amino-acid sequence comparison with known TccP subtypes (TccP/EspF
U
, TccP2, and TccP3) confirmed that the protein represents a novel TccP subtype—named here TccP4. Lack of TccP4 led to an approximately 96% reduction in the ability of the
tccP3
deletion mutant of strain 1551-2 to induce the F-actin-rich pedestals formation in the infected Nck-null mouse embryonic fibroblasts (MEF) cells. The
tccP4
gene was distributed widely in
E. albertii
, including the strains first separated from other
E. albertii
strains, suggesting that this gene was acquired at a very early stage during the diversification of
E. albertii
. The highly variable genetic organization of the
tccP4
-containing regions and the presence of various mobile genetic elements in this region may explain the lack of
tccP4
in
E. albertii
strains belonging to various lineages.

IMPORTANCE

E. albertii
, one of the new members of the genus
Escherichia,
is a diarrheagenic pathogen. The main characteristic of its pathogenicity is the formation of attaching and effacing (AE) lesions on the surface of infected epithelial cells. Here we identified a novel subtype of the TccP type 3 secretion system (T3SS) effector family (termed TccP4), which is required for the recruitment of F-actin during the AE lesion formation in infected host cells by the
E. albertii
1551-2 strain. We also revealed that TccP4 is unique to
E. albertii
and widely distributed in this species, suggesting that the
tccP4
gene was acquired at a very early stage during the diversification process of
E. albertii
. These findings expand our understanding of the function and diversity of this important T3SS effector family.
Estimation of the Contribution of Size-Fractionated Phytoplankton in the Kara Sea to Primary Production and Chlorophyll a during Different Seasons
Authors: Demidov A. B. , Belevich T. A. , Eremeeva E. V. , Tiurina A. S. , Vorobieva O. V. , Artemiev V. A. , Pronina J. O. , Flint M. V. 
Published: January 2025

Abstract
Based on data obtained during seven Kara Sea expeditions (2017–2023), seasonal variation in the contribution of phytoplankton size groups to the total values of primary production (PP) and chlorophyll a (chl a) are examined for the first time. Micro- and nanophytoplankton (MPh + NPh) (>3 µm) dominated in the community composition during the entire ice-free period (June–October). Its predominance was especially noticeable during the spring bloom immediately after first-year sea-ice retreat (up to 97% for PP and up to 93% for chl a). The role of picophytoplankton (PPh) (<3 µm) increased in summer (July, August) (up to 50% for PP and up to 44% for chl a) and decreased by the end of the growing season (September, October). Seasonal variation in the size composition of phytoplankton during the growing season was determined mainly by variability in water temperature and incoming solar radiation. The contribution of PPh to the total chl a increased (up to 51%) at depths of the deep chlorophyll maximum in July and August. The assimilation activity of PPh was higher than that of MPh + NPh in July–September, with an increase in its contribution to the total PP and chl a. For the first time, annual PP of Kara Sea phytoplankton size groups was assessed: 8 ТgС (65%) for MPh + NPh and 5 ТgС (35%) for PPh.
Infective endocarditis presenting as bilateral ocular choroidal ischaemia and acute visual loss
Authors: Peixoto Ricardo , Zopounidou Eleni , Khoo Jeffrey , Anwar Bhatti Samira 
Published: January 2025

We present a challenging case of infective endocarditis (IE) diagnosed after visual loss from bilateral ocular choroidal infarction in the absence of retinal vasculitis, typical retinal embolic phenomenon, clinical cardiac features or obvious medical history.Our case illustrates the difficulties in diagnosing IE and a high index of clinical suspicion is needed.
Qualitative evaluation of the Rehabilitation Exercise and psycholoGical support After COVID-19 InfectioN (REGAIN) randomised controlled trial (RCT): ‘you are not alone’
Authors: Seers Kate , Nichols Vivien P , Bruce Julie , Ennis Stuart , Heine Peter , Patel Shilpa , Sandhu Harbinder Kaur , Underwood Martin , McGregor Gordon 
Published: January 2025

BackgroundThis qualitative evaluation was embedded in the Rehabilitation Exercise and psycholoGical support After COVID-19 InfectioN (REGAIN) study, a randomised controlled trial (RCT) for those with post-COVID-19 condition (‘long COVID’) after hospital admission for COVID-19, comparing weekly home-based, live online supervised group exercise and psychological support sessions with ‘best practice usual care’ (a single session of advice).ObjectiveTo increase our understanding of how and why the REGAIN programme might have worked and what helped or hindered this intervention.DesignA qualitative evaluation which utilised interviews with participants and practitioners delivering the intervention. Framework and thematic analysis were used to analyse the findings.SettingEngland and Wales, UK.ParticipantsAdults discharged from National Health Service (NHS) hospitals at least 3 months previously after COVID-19, with ongoing physical and/or mental health sequelae.ResultsTwenty intervention participants, 20 control participants and five practitioners were interviewed.The themes from the group support sessions were: (1) you are not alone; (2) sharing experiences and addressing worries; (3) gaining new perspectives; (4) hope for progression; (5) peer support and bonding; (6) integration of facilitation skills; (7) modified activity pacing and goal setting, and (8) giving participants structure. The themes from group exercise were: (1) monitoring and modification of the online exercise; (2) catering for differing abilities; (3) feeling safe and confident to exercise; (4) progression of fitness; (5) optimal timing in the recovery trajectory; (6) group effect; (7) initial apprehension about exercise group; (8) gauging exercise capabilities; (9) translating exercises into life; and (10) on-demand supplementary videos. The 1:1 consultation sessions revealed patients needed to tell their stories.ConclusionBeing listened to and being understood by someone ‘who got it’ was very important to people with post-COVID-19 condition. The group sessions of both exercise and psychological support were valued by participants, working together, and learning from each other in the face of a new disease within a global pandemic.
Sexual and reproductive health from the perspective of patients with autoimmune rheumatic diseases in Mexico: a qualitative study
Authors: Skinner-Taylor Cassandra Michelle , Perez-Barbosa Lorena , Lujano-Negrete Abraham Yair , Arévalo-Nieto Fanny , Corral-Trujillo Maria Eugenia , Aguilar-Leal Andrea , Sandoval-Torres Génesis Guadalupe , Rodríguez-Ruiz Cecilia , Rios-Medina Melanie Gabriela , Manrique de Lara Amaranta , Galarza-Delgado Dionicio Angel , Pelaez-Ballestas Ingris 
Published: January 2025

ObjectivesTo explore the experiences and perspectives of female patients with autoimmune rheumatic diseases (ARDs) regarding sexual and reproductive health, including contraception, family planning, and pregnancy.DesignQualitative descriptive study using semi-structured interviews.SettingSpecialised rheumatology clinic in a tertiary hospital in Monterrey, Mexico.Participants21 female patients aged 18–49 with a confirmed ARD diagnosis who were receiving care at the clinic. Participants were selected using convenience sampling, ensuring diversity in age, disease type and stage, socio-economic and cultural background, sexuality and disability status. All participants completed the study.ResultsFour main themes emerged from the analysis. First, participants expressed confusion and concern about the safety and effectiveness of contraceptive methods in the context of their disease and treatment. Second, many participants shared anxiety about infertility, heredity and the risks of pregnancy associated with their ARDs, leading to uncertainty in pregnancy planning. Third, there was concern about the safety of medications during pregnancy and breastfeeding, indicating a lack of guidance and information from healthcare providers. Lastly, patients often deferred decision-making about contraception and medication to their rheumatologists but recognised the importance of a multidisciplinary care approach for comprehensive sexual and reproductive health management.ConclusionsThe study revealed that women with ARDs experience significant challenges and unmet needs related to sexual and reproductive health, particularly in understanding safe contraception, pregnancy planning and medication use during pregnancy and lactation. These findings emphasise the need for rheumatologists to provide clearer guidance on these issues and collaborate closely with gynaecologists and other specialists to ensure comprehensive, patient-centred care. Enhancing communication and education strategies in rheumatology consultations could address these gaps and improve the sexual and reproductive health outcomes and decision-making processes of women with ARDs.
Barriers and facilitators to improved sedentary behaviour in coronary heart disease patients: a scoping review
Authors: Yang Yuting , Yuan Qiao , Wu Chen , Yang Lili 
Published: January 2025

IntroductionThe majority of patients with coronary heart disease (CHD) are at high sedentary levels, which severely affects patient prognosis and outcome. Despite the proven benefits of reducing sedentary behaviour (SB), intervention studies’ effectiveness has been limited. Thus, the factors influencing SB change in patients with CHD need to be explored. This scoping review aimed to identify barriers and facilitators to improved SB in CHD patients and map these factors to the Capability–Opportunity–Motivation-Behaviour model.MethodsWe conducted a scoping review in accordance with the Arksey and O’Malley framework. Eligibility criteria included qualitative and quantitative studies on SB in patients with CHD. Nine databases were searched (PubMed, Medline, Embase, CINAHL, Web of Science Core Collection, Scopus, CNKI, WanFang and VIP) from inception through 31 December 2023, following the scoping review methodology.ResultsA total of 24 studies, including two qualitative and 22 quantitative studies, were included, with 15 847 patients. Barriers to improved SB in CHD patients included capability (eg, physical characteristics, lack of knowledge to improve SB), opportunity (eg, lack of partnership support, lack of resources to carry out activities) and motivation (eg, maintaining the habit of SB, impaired belief in activities). Facilitators included capability (eg, exercise session, improving understanding of SB), opportunity (eg, utilisation of support, tele-rehabilitation guidance, diversification of living environments) and motivation (perceived benefit).ConclusionsPatients with CHD have unique barriers and facilitators to improving SB. Future research should adequately reduce barriers and promote facilitators to increase the effectiveness of interventions.