bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐wide transcriptomic and functional analyses provide new insights into the response of spring barley to drought stress
Authors: Elakhdar Ammar , El‐Naggar Ahmed A. , Kubo Takahiko , Kumamaru Toshihiro 
Published: December 2023

AbstractDrought is a major abiotic stress that impairs the physiology and development of plants, ultimately leading to crop yield losses. Drought tolerance is a complex quantitative trait influenced by multiple genes and metabolic pathways. However, molecular intricacies and subsequent morphological and physiological changes in response to drought stress remain elusive. Herein, we combined morpho‐physiological and comparative RNA‐sequencing analyses to identify core drought‐induced marker genes and regulatory networks in the barley cultivar ‘Giza134’. Based on field trials, drought‐induced declines occurred in crop growth rate, relative water content, leaf area duration, flag leaf area, concentration of chlorophyll (Chl) a, b and a + b, net photosynthesis, and yield components. In contrast, the Chl a/b ratio, stoma resistance, and proline concentration increased significantly. RNA‐sequence analysis identified a total of 2462 differentially expressed genes (DEGs), of which 1555 were up‐regulated and 907 were down‐regulated in response to water‐deficit stress (WD). Comparative transcriptomics analysis highlighted three unique metabolic pathways (carbohydrate metabolism, iron ion binding, and oxidoreductase activity) as containing genes differentially expressed that could mitigate water stress. Our results identified several drought‐induced marker genes belonging to diverse physiochemical functions like chlorophyll concentration, photosynthesis, light harvesting, gibberellin biosynthetic, iron homeostasis as well as Cis‐regulatory elements. These candidate genes can be utilized to identify gene‐associated markers to develop drought‐resilient barley cultivars over a short period of time. Our results provide new insights into the understanding of water stress response mechanisms in barley.
The effect of hair type and texture on electroencephalography and event‐related potential data quality
Authors: Lees Ty , Ram Nilam , Swingler Margaret M. , Gatzke‐Kopp Lisa M. 
Published: December 2023

AbstractResearch utilizing event‐related potential (ERP) methods is generally biased with regard to sample representativeness. Among the myriad of factors that contribute to sample bias are researchers' assumptions about the extent to which racial differences in hair texture, volume, and style impact electrode placement, and subsequently, study eligibility. The current study examines these impacts using data collected from n = 213 individuals ages 17–19 years, and offers guidance on collection of ERP data across the full spectrum of hair types. Individual differences were quantified for hair texture using a visual scale, and for hair volume by measuring the amount of gel used in cap preparation. Electroencephalography data quality was assessed with multiple metrics at the preprocessing, post‐processing, and variable generation stages. Results indicate that hair volume is associated with small, but systematic differences in signal quality and signal amplitude. Such differences are highly problematic as they could be misattributed to cognitive differences among groups. However, inclusion of gel volume as a covariate to account for individual differences in hair volume significantly reduced, and in most cases eliminated, group differences. We discuss strategies for overcoming real and perceived technical barriers for researchers seeking to achieve greater inclusivity and representativeness in ERP research.
Amyloodiniosis in aquaculture: A review
Authors: Moreira Márcio , Costas Benjamín , Rodrigues Pedro M. , Lourenço‐Marques Cátia , Sousa Rui , Schrama Denise , de Magalhães Cláudia Raposo , Farinha Ana Paula , Soares Florbela 
Published: December 2023

AbstractFish ectoparasites are one of the pathogens groups that pose great concern to the aquaculture industry. The dinoflagellate Amyloodinium ocellatum is responsible for amyloodiniosis, a parasitological disease with a strong economic impact in temperate and warm water aquaculture, mainly in earthen pond semi‐intensive systems. Amyloodiniosis represents one of the most important bottlenecks for aquaculture and, with the predictable expansion of the area of influence of this parasite to higher latitudes due to global warming it might also be a threat to other aquaculture species that are not yet parasitized by A. ocellatum. This review made a compilation of the existing knowledge about this parasite and the disease associated with it. It was noticed that, except from the life cycle characterisation, detection methods, histopathological analysis, and treatments, there are still a lot of areas that need a further investment in research. Areas like parasite–host interactions, epidemiological models, taxonomy, host physiological responses to parasitism, and genome sequencing, amongst others, can contribute to a better understanding of this disease. These proposed approaches and routes of investigation will enhance and contribute to a more standardised knowledge, creating the opportunity for a better understanding of amyloodiniosis impacts on fish and contributing for the development of new tools against A. ocellatum, that may reduce fish mortality in aquaculture production due to amyloodiniosis outbreaks.
Average and heterogeneous effects of smallholder farm sizes on dietary diversity in northern Ghana
Authors: Addai Kwabena Nyarko , Ng'ombe John N. , Temoso Omphile 
Published: December 2023

AbstractThe relationship between farm size and dietary diversity has recently gained attention among development practitioners and policymakers. To study this issue, we utilized cross‐sectional data from 900 farm households in Northern Ghana. The analysis employs three econometric approaches—ordinary least squares, two‐stage least squares, and instrumental variable (IV) quantile regression. We subjected our estimates to Conley‐Hansen‐Rossi bound tests to assess the validity of total farmland under household control as an IV for farm size, which serves to illustrate the robustness of the causal inferences linking farm size to household dietary diversity. The results show that a 1‐ha increase in cultivated land improves household dietary diversity score by 3.221 units. The effect of cultivated land on dietary diversity is enhanced by market information, use of improved seeds, chemical fertilizers and herbicides, and overall household asset value. In conclusion, the results indicate that farm size increases household dietary diversity when moving along the dietary diversity distribution. This highlights the importance of considering the influence of farm size at different points along the conditional dietary diversity score distribution, as relying solely on mean effects may obscure important counteracting effects.
Phylogenomic species delimitation of the twisted‐winged parasite genus Stylops (Strepsiptera)
Authors: Lähteenaro Meri , Straka Jakub , Forshage Mattias , Hovmöller Rasmus , Nakase Yuta , Nilsson Anders L. , Smit John T. , Nylander Johan A. A. , Bergsten Johannes 
Published: December 2023

AbstractThe twisted‐winged parasite genus Stylops has a history of different species concepts with varying host specificity resulting in diverse species diversity estimates in different regions of the Holarctic. The adoption of a supergeneralist species concept in Europe, proposing synonymization of all Western Palaearctic Stylops species, did not facilitate taxonomic clarity and obscured the available life‐history data in the region for decades. Lack of molecular data has allowed divergent opinions on species hypotheses and little opportunity for evaluating them in this morphologically challenging genus. To solve these discrepancies and gain novel information about host associations, we applied whole‐genome sequencing to 163 specimens, representing a significant portion of putative European species. We evaluate the existing and conflicting species hypotheses with molecular species delimitation using Species bOundry Delimitation using Astral (SODA) and use a maximum likelihood phylogeny to investigate host associations of the species. Furthermore, we evaluate the effect of a number of loci used in SODA for the number of inferred species. We find justification for synonymization of multiple species and indications of undescribed species, as well as new host–parasite relationships. We show that the number of inferred species in SODA is exceedingly and positively correlated with the number of loci used, urging for cautious application. The results of our study bring clarity to the Western Palaearctic species diversity of Stylops. Furthermore, the comprehensive molecular dataset generated in this study will be a valuable resource for future studies on Stylops and the evolution of parasites in general.
Cosmetic gynaecology
Authors: Bugeja Roberta , McConnell James , Jha Swati 
Published: December 2023

Key content
Female genital cosmetic surgery (FGCS) includes several procedures involving the labia minora, labia majora, clitoris, vagina, mons pubis and genital area; procedures may involve, for example, reduction or augmentation and be surgical or energy based.
Indications for FGCS can be broadly divided into cosmetic and functional reasons.
Counselling on the risks and cosmetic outcomes, as well as sexual and functional results, should be provided, and the woman's expectations discussed.
Learning objectives
To develop a holistic view when discussing cosmetic gynaecology concerns, including psychosexual assessment.
To understand the procedures that are currently available, the evidence‐base behind these procedures, and their risks and benefits.
To understand the implications of genital cosmetic surgery on patients, including their psychosexual wellbeing, and the legality of these procedures with reference to female genital mutilation (FGM).
Ethical issues
The ‘postcode lottery’ in commissioning cosmetic gynaecological procedures in the UK leads to the question: should they be available on the NHS?
Who should be performing cosmetic gynaecological procedures: the plastic surgeons who do little vaginal surgery, or the gynaecologists?
There is currently no formal training in this area for gynaecologists.
Environment rather than breed or body site shapes the skin bacterial community of healthy sheep as revealed by metabarcoding
Authors: Jost Stéphanie M. , Cardona Laëtitia , Rohrbach Emmanuelle , Mathis Alexander , Holliger Christof , Verhulst Niels O. 
Published: December 2023

AbstractBackgroundThe skin is inhabited by a variety of micro‐organisms, with bacteria representing the predominant taxon of the skin microbiome. In sheep, the skin bacterial community of healthy animals has been addressed in few studies, only with culture‐based methods or sequencing of cloned amplicons.ObjectivesThe objectives of this study were to determine the sheep skin bacterial community composition by using metabarcoding for a detailed characterisation and to determine the effect of body part, breed and environment.Materials and MethodsOverall, 267 samples were taken from 89 adult female sheep, belonging to three different breeds and kept on nine different farms in Switzerland. From every individual, one sample each was taken from belly, left ear and left leg and metabarcoding of the 16S rRNA V3–V4 hypervariable region was performed.ResultsThe main phyla identified were Actinobacteriota, Firmicutes, Proteobacteria and Bacteriodota. The alpha diversity as determined by Shannon's diversity index was significantly different between sheep from different farms. Beta diversity analysis by principal coordinate analysis (PCoA) showed clustering of the samples by farm and body site, while breed had only a marginal influence. A sparse partial least squares discriminant analysis (sPLS‐DA) revealed seven main groups of operational taxonomic units (OTUs) of which groups of OTUs were specific for some farms.Conclusions and Clinical RelevanceThese findings indicate that environment has a larger influence on skin microbial variability than breed, although the sampled breeds, the most abundant ones in Switzerland, are phenotypically similar. Future studies on the sheep skin microbiome may lead to novel insights in skin diseases and prevention.
Oscillatory vs. non‐oscillatory subthalamic beta activity in Parkinson's disease
Authors: Pardo‐Valencia Jesús , Fernández‐García Carla , Alonso‐Frech Fernando , Foffani Guglielmo 
Published: December 2023

AbstractParkinson's disease is characterized by exaggerated beta activity (13–35 Hz) in cortico‐basal ganglia motor loops. Beta activity includes both periodic fluctuations (i.e. oscillatory activity) and aperiodic fluctuations reflecting spiking activity and excitation/inhibition balance (i.e. non‐oscillatory activity). However, the relative contribution, dopamine dependency and clinical correlations of oscillatory vs. non‐oscillatory beta activity remain unclear. We recorded, modelled and analysed subthalamic local field potentials in parkinsonian patients at rest while off or on medication. Autoregressive modelling with additive 1/f noise clarified the relationships between measures of beta activity in the time domain (i.e. amplitude and duration of beta bursts) or in the frequency domain (i.e. power and sharpness of the spectral peak) and oscillatory vs. non‐oscillatory activity: burst duration and spectral sharpness are specifically sensitive to oscillatory activity, whereas burst amplitude and spectral power are ambiguously sensitive to both oscillatory and non‐oscillatory activity. Our experimental data confirmed the model predictions and assumptions. We subsequently analysed the effect of levodopa, obtaining strong‐to‐extreme Bayesian evidence that oscillatory beta activity is reduced in patients on vs. off medication, with moderate evidence for absence of modulation of the non‐oscillatory component. Finally, specifically the oscillatory component of beta activity correlated with the rate of motor progression of the disease. Methodologically, these results provide an integrative understanding of beta‐based biomarkers relevant for adaptive deep brain stimulation. Biologically, they suggest that primarily the oscillatory component of subthalamic beta activity is dopamine dependent and may play a role not only in the pathophysiology but also in the progression of Parkinson's disease.
imageKey points
Beta activity in Parkinson's disease includes both true periodic fluctuations (i.e. oscillatory activity) and aperiodic fluctuations reflecting spiking activity and synaptic balance (i.e. non‐oscillatory activity).
The relative contribution, dopamine dependency and clinical correlations of oscillatory vs. non‐oscillatory beta activity remain unclear.
Burst duration and spectral sharpness are specifically sensitive to oscillatory activity, while burst amplitude and spectral power are ambiguously sensitive to both oscillatory and non‐oscillatory activity.
Only the oscillatory component of subthalamic beta activity is dopamine‐dependent.
Stronger beta oscillatory activity correlates with faster motor progression of the disease.
Electronics-Free Soft Robotic Knee Brace for Dynamic Unloading During Gait for Knee Osteoarthritis: A Proof-of-Concept Study
Authors: Johnson Amanda , Gao Run Ze , Marriott Kendal , Dickerson Clark R. , Maly Monica R. , Ren Carolyn L. 
Published: December 2023

Abstract
We present a novel electronics-free soft robotic knee brace which employs a closed-loop fluidic regenerative (CLFR) system for dynamic unloading in unicompartmental tibiofemoral osteoarthritis (OA). The existing dynamic unloaders are bulky, large, and heavy, and have low compliance likely due to the use of an electrical control box, which is eliminated in the CLFR system. The system consists of a commercial unloading knee brace, a spring-loaded bellow inserted under the heel inside a shoe, a soft-fluidic actuator (bladder), and tubing for fluid transfer. The novelty lies in the fact that the user's body weight (self-powered) compresses the bellow to provide energy to inflate the air bladder placed at the knee. As a result, the yielded pressure unloads the undesirable forces due to knee OA during the stance phase of gait while strategically applying no forces during the swing phase. The knee bladder contact pressure/force, the system response time, and the durability were evaluated via contact pressure measurements for six systems with varying bellow volumes and either pneumatic or hydraulic configurations. All systems produced safe pressure outputs for human skin within a tested bodyweight range of 60–90 kg. Pneumatic and hydraulic systems achieved 250 ms and 400 ms pressurization response times, respectively. During cyclic loading, pneumatic and hydraulic systems demonstrated less than 1% and ∼10% pressure loss, respectively. Overall, the CLFR system created a promising electronics-free solution for dynamically unloading the knee during gait, indicating a potential new paradigm for knee braces.
Why should early-career scientists publish in society journals
Authors: Dolan Stephen K. , Banks Lori D. , Yu Wenqi 
Published: December 2023

ABSTRACT
In this editorial, written by early-career scientists, we advocate for the invaluable role of society journals in our scientific community. By choosing to support these journals as authors, peer reviewers, and as editors, we can reinforce our academic growth and benefit from their re-investment back into the scientific ecosystem. Considering the numerous clear merits of this system for future generations of microbiologists and more broadly, society, we argue that early-career researchers should publish our high-quality research in society journals to shape the future of science and scientific publishing landscape.
An ANI gap within bacterial species that advances the definitions of intra-species units
Authors: Rodriguez-R Luis M. , Conrad Roth E. , Viver Tomeu , Feistel Dorian J. , Lindner Blake G. , Venter Stephanus N. , Orellana Luis H. , Amann Rudolf , Rossello-Mora Ramon , Konstantinidis Konstantinos T. 
Published: December 2023

ABSTRACT
Large-scale surveys of prokaryotic communities (metagenomes), as well as isolate genomes, have revealed that their diversity is predominantly organized in sequence-discrete units that may be equated to species. Specifically, genomes of the same species commonly show genome-aggregate average nucleotide identity (ANI) >95% among themselves and ANI <90% to members of other species, while genomes showing ANI 90%–95% are comparatively rare. However, it remains unclear if such “discontinuities” or gaps in ANI values can be observed within species and thus used to advance and standardize intra-species units. By analyzing 18,123 complete isolate genomes from 330 bacterial species with at least 10 genome representatives each and available long-read metagenomes, we show that another discontinuity exists between 99.2% and 99.8% (midpoint 99.5%) ANI in most of these species. The 99.5% ANI threshold is largely consistent with how sequence types have been defined in previous epidemiological studies but provides clusters with ~20% higher accuracy in terms of evolutionary and gene-content relatedness of the grouped genomes, while strains should be consequently defined at higher ANI values (>99.99% proposed). Collectively, our results should facilitate future micro-diversity studies across clinical or environmental settings because they provide a more natural definition of intra-species units of diversity.

IMPORTANCE
Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings.
The peroxisome protein translocation machinery is developmentally regulated in the fungus
Podospora anserina
Authors: Aguirre-López Beatriz , Suaste-Olmos Fernando , Peraza-Reyes Leonardo 
Published: December 2023

ABSTRACT

Peroxisomes are versatile organelles that are essential for diverse developmental processes. Peroxisome function critically depends on its matrix proteins, which are imported from the cytosol by the receptors Pex5 and Pex7. These receptors cycle into and out of peroxisomes through two membrane protein channels. Cargo-loaded Pex5 is imported into peroxisomes through the docking/translocation machinery, which is composed of Pex13 and Pex14. After cargo delivery, Pex5 is exported through the peroxisome ubiquitin ligase complex. This complex also ubiquitinates the receptors dictating their membrane extraction by the peroxisome AAA ATPase complex. In the fungus
Podospora anserina,
peroxisomes are required for meiotic induction. This process relies on PEX13 but not on PEX14. In addition, PEX14 is partially dispensable for peroxisome protein import during meiotic development, suggesting a developmental regulation of the translocation machinery. Here we show that PEX13 abundance in hyphae is maintained at low levels by the activity of the peroxisome ubiquitin ligase complex and the ubiquitin-conjugating enzyme PEX4, in conjunction with PEX14, PEX5, and with the peroxin that bridges the ubiquitination and the docking/translocation machineries, PEX8. Moreover, we found that the AAA ATPase complex and the peroxins that drive peroxisome membrane formation—PEX3 and PEX19—are also required to restrain PEX13 levels and that in their absence PEX13 associates with mitochondria. Furthermore, we found that PEX13 levels are higher throughout sexual development, where they are further increased during meiocyte and meiotic-spore differentiation. Our findings show that the peroxisome protein translocation machinery is subject to complex developmental regulation, which finely modulates PEX13 along sexual development.

IMPORTANCE

Sexual reproduction allows eukaryotic organisms to produce genetically diverse progeny. This process relies on meiosis, a reductional division that enables ploidy maintenance and genetic recombination. Meiotic differentiation also involves the renewal of cell functioning to promote offspring rejuvenation. Research in the model fungus
Podospora anserina
has shown that this process involves a complex regulation of the function and dynamics of different organelles, including peroxisomes. These organelles are critical for meiosis induction and play further significant roles in meiotic development. Here we show that PEX13—a key constituent of the protein conduit through which the proteins defining peroxisome function reach into the organelle—is subject to a developmental regulation that almost certainly involves its selective ubiquitination-dependent removal and that modulates its abundance throughout meiotic development and at different sexual differentiation processes. Our results show that meiotic development involves a complex developmental regulation of the peroxisome protein translocation system.