bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of long‐term oral administration of the flavonoid quercetin on the antioxidant profile of young and adult reproductive rabbit does
Authors: Vicente‐Carrillo A. , Jordán‐Rodríguez D. , Cáceres‐Martín E. , Gómez‐León A. , Rebollar P. G. , Lorenzo P. L. , García‐García R. M. , Arias‐Álvarez M. 
Published: October 2024

AbstractIn industrialized farms, rabbit does undergo intensive production rhythms which overlap lactation and gestation, leading to a high energy mobilization and increasing oxidative stress. Accordingly, we hypothesize that administration of the flavonoid quercetin (QUR) may improve the antioxidant status of young and adult rabbit reproductive females. In this study, the effect of daily oral administration of 300 mg/kg QUR for 8 weeks was assessed on the antioxidant profile of 24 New Zealand × Californian rabbit does, assigned to 4 experimental groups: rearing young (8–16 weeks old) and adult does at the end of their reproductive life (12–14 months old, with at least 3–4 reproductive cycles) treated (YQ and AQ) or not (YC and AC) with QUR, respectively. Plasma glutathione (GSH), as well as serum superoxide dismutase (SOD) and malondialdehyde (MDA) were measured during the experimental period. To assess the health status of the animals, a physical examination was also performed. GSH plasma concentrations were significantly higher in young does at weeks 1 and 4, but not at week 8 of the experiment, irrespectively of QUR administration. An increase in GSH plasma concentration was observed during the 8‐week experiment in both AQ and AC groups. Furthermore, QUR administration did not alter either SOD or MDA serum activity and concentration in any group during the experimental period. Physical examination revealed no differences between the experimental groups. In conclusion, under our experimental conditions, QUR did not modify the general clinical or the antioxidant profile of young and adult reproductive rabbit females.
Media viscosity affects post‐thaw ram sperm rheotactic behaviour
Authors: Martín‐Maestro A. , Abril‐Parreño L. , Soler A. J. , Fair S. 
Published: October 2024

AbstractThe aim of this experiment was to assess the effect of media viscosity on ram sperm motility, kinematics and rheotaxis in vitro by using methylcellulose as a media thickener. Frozen–thawed semen of three rams was thawed and diluted in Tyrode's albumin lactate pyruvate (TALP) media supplemented with 0%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6% and 0.7% w/v of methylcellulose. Sperm motility and kinematic characteristics were analysed using computer‐assisted sperm analysis (CASA). The rheotactic behaviour was assessed in a microfluidic channel, and the number of spermatozoa that passed the 10 mm point of a microfluidic channel over a 2min period against a flow rate of 30 μm/sec was assessed. The use of media with higher viscosity (higher levels of methylcellulose) resulted in significantly lower (p < .05) sperm motility and kinematic parameters. Moreover, higher levels of methylcellulose reduced (p < .05) the number of spermatozoa that exhibited positive rheotaxis. In conclusion, viscosity affected the kinematic properties and rheotactic behaviour of ram sperm.
Effect of silver nanoparticles on donkey sperm parameters and ultrastructure
Authors: Pérez Verónica , Crespo Francisco , López Angela I. , Cárdenas Soledad , Bautista María José , Hidalgo Manuel , Dorado Jesus , Ortiz Isabel 
Published: October 2024

AbstractThe aim of this study was to determine the effect of silver nanoparticles (AgNPs) on donkey sperm parameters and ultrastructure. AgNPs were synthesized, purified and resuspended in the extender. Nine frozen–thawed donkey sperm samples were exposed to different concentrations of AgNPs (0, 1.25, 2.5, 5, 12.5, 25 and 50 μg/mL). Sperm parameters: total (TMOT, %) and progressive (PMOT, %) sperm motility, plasma (LIVE, %) and acrosomal membrane integrity (AIS, %), and sperm morphology (MORF, %) were evaluated immediately after AgNPs exposure (T0) and after 2 h of incubation (T2). The interaction beween AgNPs and spermatozoa was visualized by transmission electron microscopy (TEM). At T0, sperm motility and AIS were reduced (p < .05) when using concentrations ≥50 and ≥25 μg/mL, respectively. At T2, sperm motility and LIVE were significantly decreased (p < .05) in concentrations ≥25 and ≥50 μg/mL, respectively. TEM analysis revealed nanoparticle adhesion to the acrosomal region of the plasma membrane. In conclusion, AgNPs at concentrations ≥25 μg/mL impair motility, acrosome and plasma membrane integrity of donkey sperm, which may be mediated by adhesion to the acrosomal region of the sperm surface membrane.
Ethical aspects associated with genome alteration techniques applied to animal reproduction research
Authors: Montoliu Lluis 
Published: October 2024

AbstractThe revolution in biology triggered by the different genome‐editing tools has of course arrived to the research field of animal reproduction. Yeast meganucleases, zinc‐finger nucleases, TALEN and, particularly, the several generations of CRISPR tools have landed in animal reproduction thereby providing novel strategies to optimize or modify some of the features and capabilities of the recipient animals. All these genome‐editing proposals and activities are associated with ethical considerations regarding how those planned genome alterations might affect important animal welfare issues. The ethical dimension of all these genome editing must be seriously considered. Hence, all ethical aspects bound to any given genome‐edited allele in animals should be discussed in order to ensure that we are maximizing benefits and reducing any potential risk or negative considerations of these modifications. In this review, I will summarize some of the experiments reported aiming to investigate or improve animal reproduction and I will address the ethics issues that should also be considered.
A direct approach for solving the cubic Szegö equation
Authors: Matsuno Yoshimasa 
Published: October 2024

AbstractWe study the cubic Szegö equation which is an integrable nonlinear nondispersive and nonlocal evolution equation. In particular, we present a direct approach for obtaining the multiphase and multisoliton solutions as well as a special class of periodic solutions. Our method is substantially different from the existing one which relies mainly on the spectral analysis of the Hankel operator. We show that the cubic Szegö equation can be bilinearized through appropriate dependent variable transformations and then the solutions satisfy a set of bilinear equations. The proof is carried out within the framework of an elementary theory of determinants. Furthermore, we demonstrate that the eigenfunctions associated with the multiphase solutions satisfy the Lax pair for the cubic Szegö equation, providing an alternative proof of the solutions. Last, the eigenvalue problem for a periodic solution is solved exactly to obtain the analytical expressions of the eigenvalues.
The histone chaperones ASF1 and HIRA are required for telomere length and 45S rDNA copy number homeostasis
Authors: Machelová Adéla , Dadejová Martina Nešpor , Franek Michal , Mougeot Guillaume , Simon Lauriane , Le Goff Samuel , Duc Céline , Bassler Jasmin , Demko Martin , Schwarzerová Jana , Desset Sophie , Probst Aline V. , Dvořáčková Martina 
Published: October 2024

SUMMARYGenome stability is significantly influenced by the precise coordination of chromatin complexes that facilitate the loading and eviction of histones from chromatin during replication, transcription, and DNA repair processes. In this study, we investigate the role of the Arabidopsis H3 histone chaperones ANTI‐SILENCING FUNCTION 1 (ASF1) and HISTONE REGULATOR A (HIRA) in the maintenance of telomeres and 45S rDNA loci, genomic sites that are particularly susceptible to changes in the chromatin structure. We find that both ASF1 and HIRA are essential for telomere length regulation, as telomeres are significantly shorter in asf1a1b and hira mutants. However, these shorter telomeres remain localized around the nucleolus and exhibit a comparable relative H3 occupancy to the wild type. In addition to regulating telomere length, ASF1 and HIRA contribute to silencing 45S rRNA genes and affect their copy number. Besides, ASF1 supports global heterochromatin maintenance. Our findings also indicate that ASF1 transiently binds to the TELOMERE REPEAT BINDING 1 protein and the N terminus of telomerase in vivo, suggesting a physical link between the ASF1 histone chaperone and the telomere maintenance machinery.
Putting the Ghost in the Machine: Emulating Cognitive Style in Large Language Models
Authors: Agarwal Vasvi , Jablokow Kathryn , McComb Christopher 
Published: October 2024

Abstract
Large Language Models (LLMs) have emerged as pivotal technology in the evolving world. Their significance in design lies in their transformative potential to support engineers and collaborate with design teams throughout the design process. However, it is not known whether LLMs can emulate the cognitive and social attributes which are known to be important during design, such as cognitive style. This research evaluates the efficacy of LLMs to emulate aspects of Kirton’s Adaption–Innovation theory, which characterizes individual preferences in problem-solving. Specifically, we use LLMs to generate solutions for three design problems using two different cognitive style prompts (adaptively framed and innovatively framed). Solutions are evaluated with respect to feasibility and paradigm relatedness, which are known to have discriminative value in other studies of cognitive style. We found that solutions generated using the adaptive prompt tend to display higher feasibility and are paradigm-preserving, while solutions generated using the innovative prompts were more paradigm-modifying. This aligns with prior work and expectations for design behavior based on Kirton's Adaption–Innovation theory. Ultimately, these results demonstrate that LLMs can be prompted to accurately emulate cognitive style.
Deep Learning-Driven Analysis of a Six-Bar Mechanism for Personalized Gait Rehabilitation
Authors: Khan Naveed Ahmad , Hussain Shahid , Spratford Wayne , Goecke Roland , Kotecha Ketan , Jamwal Prashant K. 
Published: October 2024

Abstract
Recent advances in robotics and artificial intelligence have highlighted the potential for the integration of computational intelligence in enhancing the functionality and adaptability of robotic systems, particularly in rehabilitation. Designing robotic exoskeletons for the lower limb rehabilitation of post-stroke patients requires frequent adjustments to accommodate individual differences in leg anatomy. This complex engineering challenge necessitates a deep understanding of human physiology, robotics, and optimization to develop adaptive robotic systems and also to swiftly quantify the required adjustments and implement them for each patient. The conventional approaches, which mostly rely on heuristics and manual tuning, often struggle to achieve optimal results. This paper presents a novel method that integrates a genetic algorithm with a deep learning approach to generate a gait trajectory of the ankle joint from a six-bar linkage mechanism of fixed dimensions. Later, using the same approach, the inverse kinematics solution for this mechanism is also devised whereby, the set of the link dimensions of the six-bar linkage mechanism is obtained for the given gait trajectory of an individual to achieve customization. We simulated the kinematic behavior of the six-bar linkage mechanism within defined mechanical constraints and utilized the generated data for training a feedforward neural network and long short-term memory models. The proposed model, when trained, can produce accurate lengths for the desired gait trajectories in the sagittal plane and vice versa, which further validates our proposed approach for inverse kinematics solution. Moreover, to evaluate the efficiency of deep learning models, we have conducted an extensive error-based, comparative, and sensitivity analysis using different performance indices. The results highlight the potential of the proposed deep-learning-driven approach in the design analysis of gait rehabilitation robots.
Co-Simulation of CFD and Hydraulic System for Wireline Deep Transient Test
Authors: Chang Yong , Tao Chen , Gisolf Adriaan 
Published: October 2024

Abstract
In a recent deep transient test field job, the pressure discrepancy between the pressure gauge readings from the two flowlines was observed. To investigate and understand such discrepancies, a CFD and hydraulic system co-simulation method was implemented to simulate different scenarios of events that happened in the downhole testing tool. CFD using Star-CCM+ performs flow simulation of miscible multispecies fluids in the rock and in the tool annulus sealed by the dual packers. The hydraulic model is fully coupled with the CFD simulation, with consideration of the variations of the fluid density and viscosity through the tool hydraulic system, as well as the tool operations uncertainties from the valve controls, the pump-out flow rate variations, etc. The simulations help in understanding the fluids flow through the tool annulus and local convection in the annulus. It is concluded that the discrepancy of build-up pressures most likely results from the plugging of the guard valve. When the guard valve is plugged, the flow rate at the guard inlet is much smaller. Therefore, the mixed fluid density in the guard line is higher, which leads to a larger pressure discrepancy for the build-up pressure.
The co-simulation approach implemented in this study provides a solid way to model the downhole tool operations and enables engineers to perform more realistic what-if analyses for pre-job planning and post-job troubleshooting.
High-quality draft genome of
Lactiplantibacillus plantarum
strain APC2688 isolated from human feces
Authors: Valderrama Benjamin , Daly Isabelle , Gunnigle Eoin , Rea Mary C. , Kenny John , Coakley Mairead , Cryan John F. , Clarke Gerard , Nagpal Jatin 
Published: October 2024

ABSTRACT

Lactiplantibacillus plantarum
is a commensal bacterial species often found within the human gut. To expand our knowledge about this human-associated taxon with potential probiotic properties, here we present the draft genome sequence of
Lactiplantibacillus plantarum
strain APC2688, isolated from a human fecal sample.
Coding complete genomes of an iridovirus and two parvoviruses identified in lab-reared social spiders (
Stegodyphus dumicola
)
Authors: Millerwise Sydney , Lund Michael C. , Schimidlin Kara , Kraberger Simona , Pinter-Wollman Noa , Varsani Arvind 
Published: October 2024

ABSTRACT

Coding complete genomes of an iridovirus (194,403 nts) and two parvoviruses (4,689, 3,764 nts) were identified in social spiders (
Stegodyphus dumicola
). The iridovirus and one of the parvovirus are most closely related to those from house crickets (
Acheta domesticus
), whereas the other is most closely related to one from a social spider.
Complete genome sequence of deformed wing virus isolated from honeybees (
Apis mellifera
L.) in Iraq
Authors: Sadiq Ali , Alisawi Osamah , Mansor Mohammed Shakir 
Published: October 2024

ABSTRACT

Here, we report the complete genome sequence of deformed wing virus (DWV) isolated from honeybees (
Apis mellifera
L.) in Iraq, named the Tikrit isolate. The phylogeny revealed that the Tikrit isolate has a close relationship to the Iraqi isolate DWV-Iraq-2023 and related to isolates from France, the United Kingdom, and Israel.
Genome sequence of
Mycoplasma gallisepticum
strain A5969
Authors: Leigh Spencer A. , Evans Jeff D. 
Published: October 2024

ABSTRACT

Mycoplasma gallisepticum
strain A5969 is one of the earliest identified and studied avian mycoplasma strains, valued for its ease of growth and production of uniformly sized colonies. Here, we report the genomic sequence of the A5969 strain.
Complete genome sequencing of four marine bacteria,
Gilvimarinus japonicus
NBRC 111987
T
,
Halioxenophilus aromaticivorans
JCM 19134
T
,
Maricurvus nonylphenolicus
JCM 17778
T
, and
Simiduia litorea
JCM 19759
T
belonging to the family
Cellvibrionaceae
Authors: Miura Takamasa , Miyakawa Tomoyo , Kusuya Yoko , Kamino Kei 
Published: October 2024

ABSTRACT

We report on the complete genomes of
Gilvimarinus japonicus
NBRC 111987
T
,
Halioxenophilus aromaticivorans
JCM 19134
T
,
Maricurvus nonylphenolicus
JCM 17778
T
, and
Simiduia litorea
JCM 19759
T
, isolated from the sea. Strains JCM 19134
T
, JCM 17778
T
, and JCM 19759
T
contain genes predicted to be polyhydroxyalkanoate-degrading enzymes.
Complete genome sequence of marine prosthecate bacterium
Fretibacter rubidus
type strain JCM 15585
Authors: LaSarre Breah , Watson Mark L. , Corby Emma M. , Randich Amelia M. 
Published: October 2024

ABSTRACT

Fretibacter rubidus
is a dimorphic, prosthecate member of the family
Maricaulaceae
, order Caulobacterales, in the class Alphaproteobacteria. Here, we report the genome of type strain JCM 15585
T
(JC2236
T
), sequenced with Oxford Nanopore Technology.
Development of a droplet digital PCR assay for the detection of BK polyomavirus
Authors: Ai Lu , Zhao Yating , Tan Chianru , Bai Lu , Huang Gang , Wang Ruizhi , Huang Hao , Yu Xuegao , Guo Yong , Chen Peisong 
Published: October 2024

ABSTRACT

The objective of this study was to establish a more sensitive and specific diagnostic method for detecting plasma BK polyomavirus (BKPyV) DNA load in patients after renal transplantation using droplet digital polymerase chain reaction (ddPCR) and to validate the methodology. The linear range, lower limit of detection, accuracy, precision, and specificity of the detection system were evaluated by using the WHO BKPyV standard (7.2 log
10
IU/mL) as a reference, in accordance with the relevant documents of the Clinical and Laboratory Standards Institute. Plasma samples were collected from 74 renal transplantation patients with urinary BKPyV-DNA levels exceeding 7 log
10
copies/mL. Quantitative PCR (qPCR) and ddPCR were performed, and their diagnostic efficacy for BKPyV-DNA in the diagnosis of BK polyomavirus-associated nephropathy was evaluated using a receiver operating characteristic (ROC) curve. The coefficients of variation for the repeated detection of BKPyV standard DNA were 2.55 and 4.71 at concentrations of 6.2 and 3.2 log
10
IU/mL, respectively. The linear range was 2.2–6.2 log
10
IU/mL, and the lowest detection limit was 100 IU/mL. By utilizing histopathological examination of renal biopsy as the gold standard for BKPyV diagnosis, the area under the ROC curve of 74 post-transplantation plasma samples detected by the ddPCR system was found to be 0.875 (95% CI: 0.797–0.953,
P
< 0.01). The optimal threshold was 512.86 copies/mL, with a sensitivity of 90.0% and a specificity of 67.6%. In comparison, the area under the ROC curve for qPCR was 0.668 (95% CI: 0.583–0.752,
P
< 0.01), with an optimal threshold of 11,481.54 copies/mL, a sensitivity of 35.0%, and a specificity of 100.0%. Pairwise comparison (Delong test) of the ROC curves of the two systems showed a significant difference in the area under the curve, with a difference of 0.207 and a
P
-value <0.01. The BKPyV nucleic acid detection system, based on ddPCR, is appropriate for the regular monitoring of the BK polyomavirus, specifically in plasma samples containing low viral DNA loads while it provides the benefits of both absolute quantification and high sensitivity.

IMPORTANCE
It was previously believed that droplet digital polymerase chain reaction had limitations, including high cost, limited throughput, and cumbersome operation, which hindered its widespread application in clinical practice. However, the current fully automated digital PCR platform, combined with streamlined operations, can detect 96 samples at once, and the entire process can be completed within an hour, laying a solid foundation for its extensive use.
Nanoemulsion is an effective antimicrobial for methicillin-resistant
Staphylococcus aureus
in infected swine skin burn wounds
Authors: Cao Zhengyi , Chen Jesse , Cannon Jayme , Meyer Zachary , Li Yongqing , Ouyang Wenlu , Baker James , Wang Su He 
Published: October 2024

ABSTRACT

Burns are one of the most common injuries in both civilian and combat settings and are difficult to treat. This is particularly true when the wounds are infected with antibiotic-resistant bacteria such as methicillin-resistant
Staphylococcus aureus
(MRSA). A new generation of safe, broadly effective, and easily applied anti-infection agents is needed to successfully prevent and treat infections. Nanoemulsions (NEs) are nanometer-sized particles with a positively charged surfactant at their oil-water interface. In the current study, we further investigated antimicrobial NEs as a treatment to address burn wounds infected by MRSA. Specifically, using a porcine skin model, we infected partial thickness thermal burn wounds with MRSA and then treated it with the nanoemulsion formulation (NB-201) or placebo controls. Bacterial viability after treatment was determined, and inflammation indexes in wounds were scored by histopathology. Topical treatment of infected wounds with NB-201 resulted in reduced colony-forming units (CFUs) compared to placebo treatment. In addition, NB-201 was effective in significantly alleviating inflammation in the treated wounds and promoting wound healing. These results indicate that NB-201 is a promising new agent to treat skin burn wounds infected with MRSA.

IMPORTANCE

The findings of this study are focused on therapeutic applications of nanotechnology. In the current study, we demonstrated that a nanoemulsion formulation could effectively kill methicillin-resistant
Staphylococcus aureus
(MRSA) infection in porcine skin burn wounds. Infection of MRSA in burn wound is a common threat to public health and is usually difficult to treat due to limited therapies available. NB-201 was effective in significantly alleviating inflammation in the treated wounds and promoting wound healing. Therefore, the finding of this study has a great potential to make this formulation a novel antimicrobial agent against MRSA.
Hand Surgical Operating Room Size Allocation: A Comparative Space Utilisation Study
Authors: WOODS David , ILLING Damian , CAO Jue , BOLSON Rajshri M. , LAUDER Alexander , IPAKTCHI Kyros 
Published: October 2024

Background: This study evaluated operating room (OR) space required for various hand surgical procedures. We analysed the size requirements for hand surgical cases divided into four settings: (1) large OR setting requiring fluoroscopy and microsurgical equipment, (2) medium-sized OR setting for cases requiring fluoroscopy, (3) smaller OR setting and (4) minor procedural room without anaesthesia with the aim to describe room size requirements for hand surgery practices. Methods: A variety of hand surgical cases were selected: large cases (microvascular digit replantation), medium-sized cases (closed reduction percutaneous pinning [CRPP] of phalangeal fractures) and smaller cases (carpal tunnel release [CTR]) with and without anaesthesia. Space requirements were compared to general surgery cases (laparoscopic appendectomy) and general orthopaedic surgery cases (cephalomedullary nail [CMN]). Necessary operative equipment was measured (ft2) to calculate requirements for each procedure. Results: Large hand cases such as digit replantation necessitated the most OR space (125 ft2), followed by general orthopaedic cases (CMN; 118 ft2), medium-sized hand cases (CRPP phalanx; 107 ft2), general surgery laparoscopic appendectomy (68 ft2), small hand cases (CTR; 85 ft2) and minor procedures (49 ft2). Conclusions: Hand procedures can be divided into major procedures requiring significant OR space (125 ft2), medium procedures in standard OR suites (107 ft2), procedures in small ORs with anaesthesia (81 ft2) or office-based setting without anaesthesia (49 ft2). These findings help define space utilisation for hand procedures and may have practical implications related to efficiency, cost and patient safety in the hospital and outpatient setting. Level of Evidence: Level IV (Economic and Decision Analyses)