bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ozone as a method for decontamination of dissolving microneedles for clinical use
Authors: Requena Michelle B. , Corrêa Thaila Q. , Bejar Dianeth Sara L. , Barreiro Juliana C. , de Paula Kelly T. , Bagnato Vanderlei S. 
Published: January 2025

AbstractDissolving microneedles (DMNs) is a promising technology for transdermal and intradermal drug delivery. However, effective decontamination protocols are necessary to ensure safety and efficacy in clinical applications. The challenge is to use a technique that preserves mechanical properties, does not introduce chemicals, and can decontaminate DMNs without affecting the drug. With its potent antimicrobial properties and minimal residual effects, ozone presents a novel and safe method for decontaminating DMNs. Specifically, the present study assesses ozone's efficacy in decontaminating DMNs loaded with aminolevulic acid, intended for photodynamic therapy in skin cancer treatment. The results showed that it effectively decontaminates E. coli and S. aureus without compromising the polymer properties or promoting drug degradation. Overall, ozone represents an approach that can be adopted to decontaminate DMNs, offering a safer and effective strategy that enhances their potential to translate to clinical application.
+SSLIP: Automated Radon‐Assisted and Rotation‐Corrected Identification of Complex HCP Slip System Activity Fields from DIC Data
Authors: Vermeij T. , Slokker G. , Mornout C. J. A. , König D. , Hoefnagels J. P. M. 
Published: January 2025

ABSTRACTIdentification of crystallographic slip in metals and alloys is crucial to understand and improve their mechanical behaviour. Recently, a novel slip system identification framework, termed SSLIP (for slip system–based local identification of plasticity), was introduced to leap from conventional trace‐based identification to automated, point‐by‐point identification, exploiting the full deformation kinematics. Using sub‐micron‐scale digital image correlation (DIC) deformation fields aligned to electron backscatter diffraction (EBSD) data, SSLIP matches the measured in‐plane displacement gradient tensor to the kinematics of the optimal combination of multiple slip system activities, at each DIC datapoint. SSLIP was demonstrated to be successful on virtual and experimental case studies of FCC and BCC metals. However, for more challenging HCP crystal structures, the complete identification of all slip systems was found to be more challenging, posing limitations on automation and flexibility. To extend the capabilities of SSLIP, we propose an extended framework, hereinafter referred to as the +SSLIP method, which includes (i) a preselection of slip systems using a Radon transform, (ii) robustness to measured rigid body rotation by simultaneous identification of the local rotation field, (iii) identification of the two best matching slip systems for each data point and (iv) a procedure to determine groups of slip systems with in‐plane displacement gradient tensors that cannot be discriminated. This procedure yields the full (HCP) slip system activity maps for every slip system in each grain. The resulting objective identification method does not rely on the Schmid factor to select which slip system is active at each point. We show how slip systems from multiple slip families are successfully identified on virtual and real experiments on a Zn polycrystalline coating.
Sedentary lifestyle induces oxidative stress and atrophy in rat skeletal muscle
Authors: Gungor‐Orhan Irem , Akin Senay , Powers Scott K. , Olgaz‐Bingol Seda , Demirel Haydar A. 
Published: January 2025

AbstractAbundant evidence indicates that skeletal muscle plays a key role in regulating metabolic homeostasis. Therefore, maintaining healthy skeletal muscles is essential to good health. While prolonged muscle inactivity is known to cause oxidative stress and muscle loss, it remains unclear whether a shift from an active to a sedentary lifestyle induces similar effects. This study tested the hypothesis that transitioning to a sedentary lifestyle rapidly leads to oxidative stress and muscle loss in the load‐bearing soleus muscle. Adult Wistar rats were randomly divided into control (CON; n = 8) and sedentary (SED; n = 8) groups. During a 7‐day experimental period, CON rats were housed in standard cages allowing free movement, while SED rats were confined to smaller cages promoting sedentary behaviour. Soleus muscles were analysed for antioxidant enzyme activities (superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX)), as well as two oxidative stress biomarkers (advanced protein oxidation products (AOPPs) and 4‐hydroxynonenal (4‐HNE)). Sedentary behaviour caused a 17.2% reduction in the soleus‐to‐body weight ratio (P < 0.001). Moreover, the activities of SOD, CAT and GPX were significantly lower in the soleus muscle of SED animals (P < 0.05), while AOPPs and 4‐HNE levels were higher (P < 0.001 and P < 0.05) compared to CON animals. These findings provide the first evidence that transitioning from an active to a sedentary lifestyle leads to the rapid onset of oxidative stress and atrophy in the soleus muscle. Importantly, the results suggest that impaired antioxidant defences contribute to sedentary behaviour‐induced oxidative stress in load‐bearing muscles.
Inverse Problem of Parameter Estimation in Natural Convection of an Iron Oxide—Distilled Water Nanofluid
Authors: Bermeo Leonardo A. , Pereira da Silva Nilton , Orlande Helcio R. B. 
Published: January 2025

Abstract
Nanofluids have been used to facilitate the transport of nanoparticles to tumor regions for different purposes, such as drug delivery, promotion of antioxidant effects, and selective absorption of energy from external sources for thermal treatments. The characterization of nanofluids by solving an inverse parameter estimation problem was the main objective of this work. A nanofluid of Fe2O3 nanoparticles dissolved in distilled water was heated by a diode laser, causing natural convection currents during the experiment. The parameter estimation problem was solved within the Bayesian framework of statistics by applying the Metropolis–Hastings algorithm of the Markov Chain Monte Carlo method, thus demanding large computational times associated with stochastic simulations of a natural convection problem. A multivariate linear regression model was then trained with the high-fidelity natural convection model, to speed up calculations during the solution of the inverse problem. It is shown that the multivariate linear regression low-fidelity model can be used as an accurate representation of the temperatures at the heated surface of the nanofluid, thus resulting in estimated parameters with small uncertainties.
Production of Middle Distillate Through Hydrocracking of Paraffin Wax
Authors: Özgür Büyüksakallı Kader , Aksoy Parvana , Işık-Gülsaç Işıl , Sayar Aslı , Üresin Ersin 
Published: January 2025

Abstract
A significant challenge in the hydrocracking (HC) process is managing the complex reaction path to adjust product selectivity. In this study, the hydrocracking ability of two different catalysts over model paraffin wax was investigated, where the HC activity was analyzed through process conditions for the selectivity of middle distillates. Catalysts containing different metals and support compositions were selected to analyze the effects on product distribution and chemical composition. According to the results, high wax conversion ratios from C21+ cracking were obtained during HC, with primary cracking identified as the main process for the Ni/W-containing catalyst. Furthermore, the Ni/W-containing catalyst is more favorable for middle distillates production, while the Pt-containing catalyst is more reactive for light product yield, such as the gasoline range. Additionally, the latter is more prone to produce i-paraffin compositions under all process parameters compared to the former. Higher temperatures positively affect the production of middle distillates in the case of Ni/W catalyst; namely, the maximum middle distillate (C10–C20) yield of 49 wt% was obtained under 450 °C, 45-min reaction time, and 30 bar initial hydrogen pressure.
Modeling and Optimization of the Compressive Strength of an Alkali-Activated Material Using a Mixed Full Factorial Design
Authors: Sarri Arezki , Oualit Mehena , Cherfi Abdelhamid 
Published: January 2025

Abstract
The aim of the present work is to carry out a technical study on blast furnace slag-based alkali-activated binders, using the design of experiments methodology. A four-factor, mixed-level (two and three) full factorial design was employed to evaluate and model the significance and interactions of four independent factors on the compressive strength: curing environment, activator type (alkali silicate (AS) and alkali hydroxide (AH)), activator content, and curing time. The experimental compressive strength data were adequately fitted by empirical models with determination coefficients (R2) of 0.89 and 0.93 for AS and AH activators, respectively. The most significant effects of factors on the compressive strength are classed according to this order: curing time &gt; activator-to-precursor mass ratio &gt; curing temperature for the AS case and curing temperature &gt; activating solution concentration &gt; curing time for the AH case. The most favorable situation corresponding to maximum compressive strength is obtained with a minimum curing temperature of 20 °C, an activator-to-precursor mass ratio of 0.42, and a maximum curing duration of 28 days, for a desirability value of 0.95, in the case of the AS activator. When using the AH activator: a desirability function-based optimization targeting a compressive strength above 50 MPa showed that this could be achieved beyond 16 days of curing, with a minimum concentration of the alkaline solution worth 5 M (considering its corrosive nature), and a medium temperature representative of North African countries (≈30 °C), for a desirability value of 0.35.
Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy
Authors: Cross Kayla , Beckman Noelle , Jahnes Benjamin , Sabree Zakee L. 
Published: January 2025

ABSTRACT

Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous
Periplaneta americana
over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome “service outages” due to functional redundancy.

IMPORTANCE
Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.
A high-resolution view of the immune and stromal cell response to
Haemophilus ducreyi
infection in human volunteers
Authors: Brothwell Julie A. , Wei Yuhui , Wang Jia , Guo Tingbo , Zhang Chi , Fortney Kate R. , Duplantier Rory , Chen Li , Batteiger Teresa A. , Kaplan Mark H. , Spinola Stanley M. , Cao Sha 
Published: January 2025

ABSTRACT

Haemophilus ducreyi
causes the genital ulcer disease chancroid and cutaneous ulcers in children. To study its pathogenesis, we developed a human challenge model in which we infect the skin on the upper arm of human volunteers with
H. ducreyi
to the pustular stage of disease. The model has been used to define lesional architecture, describe the immune infiltrate into the infected sites using flow cytometry, and explore the molecular basis of the immune response using bulk RNA-seq. Here, we used single cell RNA-seq (scRNA-seq) and spatial transcriptomics to simultaneously characterize multiple cell types within infected human skin and determine the cellular origin of differentially expressed transcripts that we had previously identified by bulk RNA-seq. We obtained paired biopsies of pustules and wounded (mock infected) sites from five volunteers for scRNA-seq. We identified 13 major cell types, including T- and NK-like cells, macrophages, dendritic cells, as well as other cell types typically found in the skin. Immune cell types were enriched in pustules, and some subtypes within the major cell types were exclusive to pustules. Sufficient tissue specimens for spatial transcriptomics were available from four of the volunteers. T- and NK-like cells were highly associated with multiple antigen presentation cell types. In pustules, type I interferon stimulation was high in areas that were high in antigen presentation—especially in macrophages near the abscess—compared to wounds. Together, our data provide a high-resolution view of the cellular immune response to the infection of the skin with a human pathogen.

IMPORTANCE

A high-resolution view of the immune infiltrate due to infection with an extracellular bacterial pathogen in human skin has not yet been defined. Here, we used the human skin pathogen
Haemophilus ducreyi
in a human challenge model to identify on a single cell level the types of cells that are present in volunteers who fail to spontaneously clear infection and form pustules. We identified 13 major cell types. Immune cells and immune-activated stromal cells were enriched in pustules compared to wounded (mock infected) sites. Pustules formed despite the expression of multiple pro-inflammatory cytokines, such as IL-1β and type I interferon. Interferon stimulation was most evident in macrophages, which were proximal to the abscess. The pro-inflammatory response within the pustule may be tempered by regulatory T cells and cells that express indoleamine 2,3-dioxygenase, leading to failure of the immune system to clear
H. ducreyi
.
Detection of chronic wasting disease prions in the farm soil of the Republic of Korea
Authors: Park Kyung-Je , Park Hoo-Chang , Lee Yu-Ran , Mitchell Gordon , Choi Young Pyo , Sohn Hyun-Joo 
Published: January 2025

ABSTRACT

Chronic wasting disease (CWD) is a highly contagious prion disease occurring in free-ranging and farmed cervids. CWD continues to spread uncontrolled across North America, and cases continue to be detected almost every year in the Republic of Korea. CWD-infected animals contaminate the soil by releasing infectious prions through their excreta, and shed prions accumulate and remain infectious in the soil for years. Given that the upper soil levels can become contaminated with prions and serve as infectivity reservoirs facilitating horizontal transmission of CWD, the ability to detect prions in the soil is needed for monitoring and managing CWD spread. Using the protein misfolding cyclic amplification (PMCA) technique, we investigated whether prions could be amplified and detected in farm soil experimentally exposed to CWD-infected brain homogenate as well as in the soil of CWD-affected farms. From each soil sample, we performed 10 serial extractions and used these 10 extracts as PMCA templates. Here, we show that prion seeding activity was detected in extracts from farm soil following 4 years of incubation with CWD-infected brain homogenate. More importantly, 13 of 38 soil samples collected from six CWD-affected farms displayed prion seeding activity, with at least one soil sample in each farm being PMCA positive. Mouse bioassays confirmed the presence of prion infectivity in the soil extracts in which PMCA seeding activity was detected. This is the first report describing the successful detection of prions in soil collected from CWD-affected farms, suggesting that PMCA conducted on serial soil extracts is a sensitive means for prion detection in CWD-contaminated soil.

IMPORTANCE
Chronic wasting disease (CWD) is a highly contagious prion disease affecting free-ranging and farmed cervids. CWD continues to spread uncontrollably across North America, and multiple cases are detected annually in the Republic of Korea. Prions shed from CWD-infected animals remain infectious in the soil for years, serving as infectivity reservoirs that facilitate horizontal transmission of the disease. Therefore, the ability to detect CWD prions in soil is crucial for monitoring and managing the spread of the disease. In this study, we have demonstrated for the first time that prions in the soil of CWD-affected farms can be reliably detected using a combination of serial soil extraction and a prion amplification technique. Our data, in which at least one soil sample tested positive for CWD in each of the six CWD-affected farms analyzed, suggest that the approach employed in this study is a sensitive method for prion detection in CWD-contaminated soil.
Discovery of viruses and bacteria associated with swine respiratory disease on farms at a nationwide scale in China using metatranscriptomic and metagenomic sequencing
Authors: Huang Xi , Yao Xinzhi , Song Wenbo , Zhao Mengfei , Zhu Zhanwei , Liu Hanyuan , Song Xiaorong , Huang Jingwen , Chen Yongrun , Wang Zihao , Peng Changjiang , Wu Wenqing , Yang Hao , Hua Lin , Chen Huanchun , Wu Bin , Peng Zhong 
Published: January 2025

ABSTRACT

Respiratory disease (RD) is a worldwide leading threat to the pig industry, but there is still limited understanding of the pathogens associated with swine RD. In this study, we conducted a nationwide genomic surveillance on identifying viruses, bacteria, and antimicrobial resistance genes (ARGs) from the lungs of pigs with RD in China. By performing metatranscriptomic sequencing combined with metagenomic sequencing, we identified 21 viral species belonging to 12 viral families. Among them, porcine reproductive and respiratory syndrome virus, influenza A virus, herpes virus, adenovirus, and parvovirus were commonly identified. However, emerging viruses, such as Getah virus and porcine respiratory coronaviruses, were also characterized. Apart from viruses, a total of 164 bacterial species were identified, with
Streptococcus
suis,
Mycoplasma hyorhinis
,
Mycoplasma hyopneumoniae
,
Glaesserella parasuis
, and
Pasteurella multocida
being frequently detected in high abundances. Notably,
Escherichia coli
,
Enterococcus faecalis
,
Staphylococcus aureus
, and
Klebsiella pneumoniae
were also highly detected. Our further analysis revealed a complex interaction between the identified pathogens in swine RD. We also conducted retrospectively analyses to demonstrate the prevalent viral genotypes or bacterial serotypes associated with swine RD in China. Finally, we identified 48 ARGs, which conferred resistance to 13 predicted antimicrobial classes, and many of these ARGs were significantly associated with a substantial number of mobile genetic elements, including transposons (e.g.,
tnp
AIS1,
tnp
A1353,
int
3, and
IS
Cau1) and plasmids (e.g., Col(BS512), Col(YC)]. These findings will contribute to further understanding the etiology, epidemiology, and microbial interactions in swine RD, and may also shed a light on the development of effective vaccines.

IMPORTANCE
In this study, we identified viruses and bacteria from the lungs of pigs with RD in China at a nationwide farm scale by performing metatranscriptomic sequencing combined with metagenomic sequencing. We also demonstrated the complex interactions between different viral and/or bacterial species in swine RD. Our work provides a comprehensive knowledge about the etiology, epidemiology, and microbial interactions in swine RD and data reference for the research and development of effective vaccines against the disease.
Comparing sputum, nasopharyngeal swabs, and combined samples for respiratory bacterial detection using multiplex PCR
Authors: Kim Keun Ju , Yun Seung Gyu , Nam Myung-Hyun , Lee Chang Kyu , Cho Yunjung 
Published: January 2025

ABSTRACT

Respiratory tract infections are major global health issues that require rapid and accurate diagnostic methods. Multiplex quantitative PCR (qPCR) is commonly used for pathogen detection in respiratory samples. However, the optimal specimen selection for detecting bacterial pathogens is not well-explored. We evaluated the detection rates of respiratory bacteria from nasopharyngeal swabs (NPS), sputum, and combined NPS and sputum samples using multiplex qPCR (Allplex PneumoBacter Assay, Seegene). Paired NPS and sputum samples from 219 patients with acute respiratory symptoms admitted to Korea University Anam Hospital were analyzed. qPCR was performed to detect seven respiratory bacteria:
Bordetella parapertussis, Bordetella pertussis, Chlamydophila pneumoniae, Haemophilus influenzae, Legionella pneumophila, Mycoplasma pneumoniae,
and
Streptococcus pneumoniae
. Combined NPS and sputum samples (
n
= 92) were created from 46 pairs of positive and 46 pairs of negative signals for NPS-alone and sputum-alone samples. Sputum samples (44.3%; 97/219) had a significantly higher positivity rate compared to NPS samples (21.0%; 46/219) (
P <
0.001). The 92 combined samples identified a total of 65 bacterial nucleic acids. The detection rate for the combined samples was 86.2% (56/65), which was comparable to that of sputum alone (89.2%; 58/65) and higher than that of NPS samples (50.8%; 33/65). Combining NPS and sputum samples for PCR testing may offer an alternative for bacterial pathogen detection, providing rates comparable to those of sputum alone and greater sensitivity than that of NPS alone. This combined approach could be a cost-effective method to maximize diagnostic yield, reduce the need for multiple tests, and improve the management of respiratory infections.

IMPORTANCE
This study offers important insights into refining diagnostic strategies for respiratory bacterial infections using multiplex PCR. This study finds that combining sputum and nasopharyngeal swabs into a single tube could serve as an effective alternative for detecting respiratory bacteria in adults with acute respiratory illness.