bluuebunny/crossref_metadata_2025 huggingface dataset:
+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

Identification 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

Abundant 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

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

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

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 > activator-to-precursor mass ratio > curing temperature for the AS case and curing temperature > activating solution concentration > 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.
The Addition of Thoracic Spine Manipulation or Mobilization to Exercise in Adults With Subacromial Impingement Syndrome: A Critically Appraised Topic
Authors: Vicente Joan , Wooley Ryan
Published: January 2025

Clinical Scenario: Shoulder pain is the third most common musculoskeletal complaint. The most common type of shoulder pain is subacromial impingement syndrome (SIS). The concept of regional interdependence demonstrates that body regions are interrelated, affecting how they function. Previous studies have reported the influence of the thoracic spine on the shoulder. Clinical Question: Does adding thoracic spine manipulation or mobilization to exercise in adults with SIS improve shoulder range of motion (ROM), pain, and disability? Summary of Key Findings: The literature was searched for level 2 evidence or higher that examined the effects of the addition of thoracic mobilization or manipulation to exercises in shoulder ROM, pain, and disability in SIS. Twenty articles related to the clinical question, but only 3 met the inclusion and exclusion criteria. Two studies reported that the combination of thoracic mobilization or manipulation and exercises resulted in more significant improvements in shoulder ROM, pain, and disability compared to exercises alone. One study concluded that the combination of thoracic or shoulder mobilization to exercises was superior to ultrasound or exercises alone. Clinical Bottom Line: There is moderate evidence to support the addition of thoracic manipulation or mobilization to exercise in treating SIS to improve shoulder ROM, pain, and disability. Strength of Recommendation: Grade B evidence supports a multimodal approach using the combination of thoracic mobilization or manipulation and exercises in adults with SIS.
Principals’ Perspectives on Quality Physical Education in Australian Primary Schools
Authors: Henderson Pip , Pill Shane , Telford Richard , Telford Rohan
Published: January 2025

Purpose: This study examined principals’ perceptions of quality physical education (PE). Principals’ perceptions are important due to their positions in schools and their influence over teacher improvement and student learning. Insights into principal’s perceptions are needed as, in Australia, PE is often marginalized, and afforded less time, and resourcing than “academic” subjects. Methods: Interview data from 14 primary school principals across Kaurna Yerta (Adelaide, South Australia) were thematically analyzed to identify attributes ascribed to quality PE. Results: Principals reported teacher attributes as personal and interpersonal abilities, and pedagogical and content knowledge. School-based attributes relating to resources, specifically facilities and equipment, were also reported. Data pertaining to pedagogy revealed that principals were unfamiliar with the PE curriculum structure, content, and student achievement standards, nor did they recognize unique pedagogical requirements for PE. Conclusion: Responses indicated principals do not necessarily understand or comprehend unique PE-specific pedagogies that enhance PE, nor have deep familiarity with PE.
Physical Education as a Pathway to Sustainability: Implementing the Personal and Social Responsibility Model to Meet Sustainable Development Goals
Authors: Baena-Morales Salvador , Rocamora Irene , Manzano-Sánchez David , González-Víllora Sixto
Published: January 2025

Reflecting on the urgent need for planetary sustainability and the United Nations’ 17 Sustainable Development Goals for 2030, this study investigates the critical role of physical education in the educational system toward achieving these objectives. It specifically examines how the Sustainable Development Goals can be integrated with the Personal and Social Responsibility Model to enhance sustainability in education. By presenting a didactic approach and practical examples, like active commuting, and plogging, tailored to suit various levels of Personal and Social Responsibility Model, the study aims to engage students in sustainability efforts. The findings reveal that such activities not only encourage health and well-being but also foster a sense of social and environmental responsibility, promote gender equality, and aim to reduce inequalities among students. Ultimately, incorporating this model into physical education shows considerable promise in instilling important values and responsibilities in students, equipping them to apply these principles in real-world scenarios and positively contributing toward achieving the Sustainable Development Goals.
Hippocampal coding of identity, sex, hierarchy, and affiliation in a social group of wild fruit bats
Authors: Ray Saikat , Yona Itay , Elami Nadav , Palgi Shaked , Latimer Kenneth W. , Jacobsen Bente , Witter Menno P. , Las Liora , Ulanovsky Nachum
Published: January 2025

Social animals live in groups and interact volitionally in complex ways. However, little is known about neural responses under such natural conditions. Here, we investigated hippocampal CA1 neurons in a mixed-sex group of five to 10 freely behaving wild Egyptian fruit bats that lived continuously in a laboratory-based cave and formed a stable social network. In-flight, most hippocampal place cells were socially modulated and represented the identity and sex of conspecifics. Upon social interactions, neurons represented specific interaction types. During active observation, neurons encoded the bat’s own position and head direction, together with the position, direction, and identity of multiple conspecifics. Identity-coding neurons encoded the same bat across contexts. The strength of identity coding was modulated by sex, hierarchy, and social affiliation. Thus, hippocampal neurons form a multidimensional sociospatial representation of the natural world.
Ancient genomics and the origin, dispersal, and development of domestic sheep
Authors: Daly Kevin G. , Mullin Victoria E. , Hare Andrew J. , Halpin Áine , Mattiangeli Valeria , Teasdale Matthew D. , Rossi Conor , Geiger Sheila , Krebs Stefan , Medugorac Ivica , Sandoval-Castellanos Edson , Özbaşaran Mihriban , Duru Güneş , Gülcür Sevil , Pöllath Nadja , Collins Matthew , Frantz Laurent , Vila Emmanuelle , Zidarov Peter , Stoddart Simon , Boldgiv Bazartseren , Orlando Ludovic , Pearson Mike Parker , Mullville Jacqui , Askeyev Igor V. , Askeyev Arthur O. , Askeyev Oleg V. , Shaymuratova Dilyara N. , Van den Hurk Youri , Zeeb-Lanz Andrea , Arbogast Rose-Marie , Hemmer Helmut , Davoudi Hossein , Amiri Sarieh , Doost Sanaz Beizaee , Decruyenaere Delphine , Fathi Homa , Khazaeli Roya , Hassanzadeh Yousef , Sardari Alireza , Lhuillier Johanna , Abdolahi Mostafa , Summers Geoffrey D. , Marro Catherine , Bahshaliyev Veli , Berthon Rémi , Çakirlar Canan , Benecke Norbert , Scheu Amelie , Burger Joachim , Sauer Eberhard , Horwitz Liora Kolska , Arbuckle Benjamin , Buitenhuis Hijlke , Gourichon Lionel , Bulatović Jelena , O’Connor Terry , Orton David , Jalabadze Mindia , Rhodes Stephen , Chazan Michael , Özkaya Vecihi , Zeder Melinda , Atıcı Levent , Mashkour Marjan , Peters Joris , Bradley Daniel G.
Published: January 2025

The origins and prehistory of domestic sheep (
Ovis aries
) are incompletely understood; to address this, we generated data from 118 ancient genomes spanning 12,000 years sampled from across Eurasia. Genomes from Central Türkiye ~8000 BCE are genetically proximal to the domestic origins of sheep but do not fully explain the ancestry of later populations, suggesting a mosaic of wild ancestries. Genomic signatures indicate selection by ancient herders for pigmentation patterns, hornedness, and growth rate. Although the first European sheep flocks derive from Türkiye, in a notable parallel with ancient human genome discoveries, we detected a major influx of Western steppe–related ancestry in the Bronze Age.
Scratching promotes allergic inflammation and host defense via neurogenic mast cell activation
Authors: Liu Andrew W. , Zhang Youran R. , Chen Chien-Sin , Edwards Tara N. , Ozyaman Sumeyye , Ramcke Torben , McKendrick Lindsay M. , Weiss Eric S. , Gillis Jacob E. , Laughlin Colin R. , Randhawa Simran K. , Phelps Catherine M. , Kurihara Kazuo , Kang Hannah M. , Nguyen Sydney-Lam N. , Kim Jiwon , Sheahan Tayler D. , Ross Sarah E. , Meisel Marlies , Sumpter Tina L. , Kaplan Daniel H.
Published: January 2025

Itch is a dominant symptom in dermatitis, and scratching promotes cutaneous inflammation, thereby worsening disease. However, the mechanisms through which scratching exacerbates inflammation and whether scratching provides benefit to the host are largely unknown. We found that scratching was required for skin inflammation in mouse models dependent on FcεRI-mediated mast cell activation. Scratching-induced inflammation required pain-sensing nociceptors, the neuropeptide substance P, and the mast cell receptor MrgprB2. Scratching also increased cutaneous inflammation and augmented host defense to superficial
Staphylococcus aureus
infection. Thus, through the activation of nociceptor-driven neuroinflammation, scratching both exacerbated allergic skin disease and provided protection from
S. aureus
, reconciling the seemingly paradoxical role of scratching as a pathological process and evolutionary adaptation.
Pre-exposure antibody prophylaxis protects macaques from severe influenza
Authors: Kanekiyo Masaru , Gillespie Rebecca A. , Cooper Kristine , Canedo Vanessa Guerra , Castanha Priscila M. S. , Pegu Amarendra , Yang Eun Sung , Treaster Luke , Yun Gabin , Wallace Megan , Kettenburg Gwenddolen , Williams Connor , Lundy Jeneveve , Barrick Stacey , O’Malley Katherine , Midgett Morgan , Martí Michelle M. , Chavva Hasitha , Corry Jacqueline , Treat Benjamin R. , Lipinski Abby , Batsche Lucia Ortiz , Creanga Adrian , Ritter Isabella , Walker Reagan , Olsen Emily , Laughlin Amanda , Perez Daniel R. , Mascola John R. , Boritz Eli A. , Loo Yueh-Ming , Blair Wade , Esser Mark , Graham Barney S. , Reed Douglas S. , Barratt-Boyes Simon M.
Published: January 2025

Influenza virus pandemics and seasonal epidemics have claimed countless lives. Recurrent zoonotic spillovers of influenza viruses with pandemic potential underscore the need for effective countermeasures. In this study, we show that pre-exposure prophylaxis with broadly neutralizing antibody (bnAb) MEDI8852 is highly effective in protecting cynomolgus macaques from severe disease caused by aerosolized highly pathogenic avian influenza H5N1 virus infection. Protection was antibody dose–dependent yet independent of Fc-mediated effector functions at the dose tested. Macaques receiving MEDI8852 at 10 milligrams per kilogram or higher had negligible impairment of respiratory function after infection, whereas control animals were not protected from severe disease and fatality. Given the breadth of MEDI8852 and other bnAbs, we anticipate that protection from unforeseen pandemic influenza A viruses is achievable.
The monster in the room
Humans: A Monstrous History
Surekha Davies
University of California Press, 2025. 336 pp.
Authors: Finn Ed
Published: January 2025

A historian interrogates the mythical creatures we create to dehumanize and devalue others
Catching carbon fixation without fixing
Authors: Feng Xiang , Rees Douglas C.
Published: January 2025

Structural snapshots of an enzyme complex reveal missing pieces of a biological process
Taking responsibility: Asilomar and its legacy
Authors: Hurlbut J. Benjamin
Published: January 2025

A reappraisal of the constitutional position of science in American democracy is needed
Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy
Authors: Cross Kayla , Beckman Noelle , Jahnes Benjamin , Sabree Zakee L.
Published: January 2025

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

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

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

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

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.
Safety and efficacy of filgotinib in patients with rheumatoid arthritis: final results of the DARWIN 3 long-term extension study
Authors: Westhovens Rene , Winthrop Kevin L , Kavanaugh Arthur , Greenwald Maria , Dagna Lorenzo , Cseuz Regina , Besuyen Robin , de Vries Dick , Modgill Vikas , Le Ly Huong , Genovese Mark C , Emery Paul , Verschueren Patrick , Alten Rieke
Published: January 2025

Objectives

DARWIN 3 (ClinicalTrials.gov:NCT02065700) assessed the safety and efficacy of filgotinib in a long-term extension (LTE) of two phase II randomised controlled rheumatoid arthritis (RA) trials.

Methods

Eligible patients completing the 24-week DARWIN 1 (filgotinib plus methotrexate) and DARWIN 2 (filgotinib monotherapy) trials could enrol. Patients received filgotinib 200 mg/day, except 15 men who received filgotinib 100 mg/day. The primary endpoints were safety and tolerability, which were assessed by the incidence of treatment-emergent adverse events (TEAEs). Safety and efficacy analyses included all enrolled patients who received ≥1 dose of filgotinib in DARWIN 3.

Results

739 patients entered the LTE. The total patient-years of exposure (PYE) to filgotinib was 3706.3 years; the mean exposure duration was 259.8 weeks. 497 patients (67.3%) discontinued prematurely (including 266 TEAEs and 172 withdrawals due to the patient’s decision or ‘sponsor request’). Overall exposure-adjusted incidence rate (EAIR) was 67 (95% CI 62 to 72.2)/100 PYE for TEAEs and 3.8 (95% CI 3.2 to 4.5)/100 PYE for serious TEAEs. EAIR of infections was 23.3 (95% CI 21.2 to 25.6)/100 PYE, 1.3 (95% CI 0.9 to 1.7)/100 PYE for serious infections and 1.3 (95% CI 0.9 to 1.7)/100 PYE for herpes zoster. EAIRs of major adverse cardiovascular events (0.19 (95% CI 0.8 to 0.39)/100 PYE) and malignancies (0.6 (95% CI 0.4 to 0.9)/100 PYE) were low. Disease response assessed using non-responder imputation plateaued at LTE week 12 before slowly declining over time, with overall American College of Rheumatology (ACR)20/50/70 response rates of 26.9%/20.2%/14.7% at week 396.

Conclusion

Filgotinib was well tolerated in patients with RA for up to 8 years. Safety and efficacy profiles were maintained in patients previously receiving either filgotinib plus methotrexate or filgotinib monotherapy.
Knowledge management for product innovation design based on dual-layer concept network
Authors: Liu Qiyu , Zhang Jingyu , Fang Pan , Shi Qingtian , Liu Xiaoming , Li Dengsong
Published: January 2025

Creative design has become the core of competitiveness for enterprises, and the design process is an activity based on multi-domain knowledge. Designers need to have a lot of interdisciplinary knowledge in this activity, and there may be a burden on understanding. To alleviate understanding burden and promote knowledge integration, a dual-layer concept network is established based on complex networks. Knowledge association in the network originates from the perspective of innovation and product design, facilitating in providing designers with creative and content-related knowledge. This paper takes function, invention principle and scientific principle as the label to build a creative attribute network, and uses the semantic similarity between knowledge texts to build a semantic association network. Combining creative attributes and content semantics of knowledge, a novel knowledge management and browsing method based on a dual-layer concept network is proposed. Meanwhile, due to the ambiguity and uncertainty of design activity and knowledge demand, designers repeatedly query knowledge based on a dual-layer concept network. During this process, designers’ think of diverges and associates, which inspire them to integrate knowledge and generate creative ideas. Finally, this paper takes the problem of vibrating screens as an example to verify the practicability and effectiveness of this method. The methodology is expected to be served as an essential supporting tool for sparking innovation.
Pharmacokinetics and Biological Activities of Notoginsenoside R1: A Systematical Review
Authors: Wen Chao , Liao Xiaofei , Ye Xinyun , Lai Wentao
Published: January 2025

Panax notoginseng (PN) root is a renowned nutritional supplement, health food additive, and traditional medicine that maintains homeostasis within the human microcirculatory system. Notoginsenoside R1 (NG-R1), an active compound derived from PN root, has been reported to possess various pharmacological activities, including anti-inflammatory, antioxidant, anticancer, antimicrobial, and angiogenic effects. However, NG-R1’s pharmacokinetic properties and pharmacological activities have not been systematically elucidated. In this paper, the pharmacokinetic properties of NG-R1, its pharmacological effects, mechanisms of actions, and structure-activity relationship have been reviewed. Notably, NG-R1 inhibits tumor necrosis factor α (TNF-α) expression, enhances the expression of nuclear factor erythroid 2-related factor 2 (NRF2), and enhances the expression of vascular endothelial growth factor receptor (VEGFR). The pharmacological effects of NG-R1 are associated with the modulation of several signaling pathways, such as mitogen-activated protein kinase (MAPK)/nuclear factor κ-B (NF-κB), NRF2/antioxidant response element (ARE), Wnt/β-catenin, and phosphoinositide-3 kinase (PI3K)/protein kinase B (AKT). NG-R1 offers potentially protective effects against numerous diseases, including cardiovascular, neurological, renal, pulmonary, bone, and diabetes-related conditions. Although the pharmacological activities and diverse effects of NG-R1 have been demonstrated in various diseases, its clinical applications are limited by poor bioavailability. Several strategies have been explored to improve the pharmacokinetic profile of NG-R1, making it a promising candidate for drug development.
The Critical Role of Self-Inhibition in Epileptic Seizures Based on Dynamic Analysis of the Corticothalamic Model
Authors: Wang Zhihui , Wei Xindan , Duan Lixia
Published: January 2025

Studies have shown that inhibitory interneurons include inhibitory interneurons on fast time scales (I1) and inhibitory interneurons on slow time scales (I2), both of which can modulate epileptic activities. Based on this, we improve the corticothalamic model by introducing self-inhibition of I1 and I2 to explore the onset and transitions of epileptic activities from the dynamic perspective. First, we investigate the case that the excitatory loop between the excitatory pyramidal neurons (PY) and the thalamic relay neurons (TC) induces epileptic activities in the absence of self-inhibition. The emergence of multistability drives the system to produce a variety of epileptic activities, such as m-spike-wave discharges, tonic and clonic oscillations. Subsequently, we introduce self-inhibition of inhibitory interneurons and find that the advancement or disappearance of the Hopf bifurcation leads to a reduction in the area of epileptic discharges. Finally, we explore epileptic activities induced by the self-inhibition of I1 and the excitability of TC on I1. The strong self-inhibition can effectively modulate seizures, but excessive exchange of information between TC and I1 induces absence seizures. In addition, the paper focuses on revealing the loop mechanisms and related bifurcation characteristics in various situations. Besides Hopf and fold limit cycle bifurcations, period-doubling and homoclinic bifurcations are also key factors leading to the state transitions. These may provide some theoretical guidance for the generation and evolution of seizures.
SPONDYLODISCITIS WITH ONSET FROM A SIGMO-RETTAL FISTULA CAUSED BY A FOREIGN BODY: CASE REPORT
Authors: Geronimo Alessandro , Piazzolla Andrea , Bizzoca Davide , Cassano Giuseppe Danilo , Solarino Giuseppe
Published: January 2025

Spondylodiscitis is a infective processes of the spinal column, that can affect the vertebrae in isolation (spondylitis), the discs (discitis) or both (spondylodiscitis). Three infection pathways are described from a pathogenetic perspective: endogenous, exogenous, and per continuitatem. The hematogenic form is the most common (about 60%), but cases of direct inoculation following surgical procedures on the spine (15%) or contamination by contiguity (12%) are not rare. Diagnosis is based on clinical, laboratory, radiological, microbiological and histopathological data, where the magnetic resonance imaging is the technique of choice for the diagnosis. Treatment may be medical using antibiotics to eliminate the infection or surgery using spinal fixation to prevent spinal instability and ample debridement of infected tissue. We report on a patient who had spondylodiscitis due to a sigmo-rettal fistula caused by a intrarectal penetration of a toothpick which was accidentally swallowed by the patient; which was successfully treated with targeted antibiotic therapy and immobilization.
Sentiment Classification from Social Media Data with Gaussian Conditional Rule-Based Deep Convolutional Neural Network
Authors: Vinod Priya , Sheeja S.
Published: January 2025

Social media platforms share several emotions in the form of text, audio, and images, where the text-shared data are less convincing to understand the emotions. The classification of the sentiments should be accurate to achieve a better understanding of the values in the commercial industry. Twitter has proven to be an effective instrument for text-based sentiment analysis when compared to other traditional assessments like surveys and stock market performance records. Though the existing research on sentiment analysis achieved good results of performance, the techniques had drawbacks such as long-term sentence prediction, less robustness, high computational resources, lack of complementary feature extraction, and so on. In this research, the Gaussian conditional rule-based deep convolutional neural network (DCNN) (Gaussian conditional rule-based DCNN) is proposed to tackle the limitation of the existing techniques, where the Gaussian distribution is applied for the selection of the kernel filters in the formation of the feature maps, and the classifier parameters are adaptively trained using the proposed adaptive nature optimizer (ANO). Through the integration of the conditionality of the random forest algorithm into the developed architecture, the model attains the potential to adapt the processing concerning the supplementary contextual information or features. Utilizing the prominent word embedding approach maximizes the input quality, converts words into continuous vector representations in a high-dimensional space, and captures both syntactic and semantic associations between words. In addition, the Graph embedding preserves some of the graph’s structural characteristics and effectively captures the syntactic dependencies, co-occurrences, semantic similarities, as well as pertinent linguistic correlations among the texts. Specifically, the proposed ANO algorithm and the conditional rule exploited in the model provide stable as well as robust performance in the classification of sentiments. The experimental results demonstrate that the Gaussian conditional rule-based DCNN model achieves 98.36 %, 98.80%, and 97.44% for accuracy, specificity, and sensitivity, respectively.
The Application of Data Mining Models in Personal Credit Risk Control
Authors: Liang Ruilin , Hou Yuke , Liang Xin , Li Bo , Yao XiaoXuan
Published: January 2025

This study employs LendingClub data in the field of personal credit risk control as an illustrative case. Various data mining models, and support vector machine, are utilized for training purposes. Additionally, a Stacking model is integrated into the analysis to forecast customer default likelihood. Subsequently, lending decisions are made in accordance with these predictions. The outcomes indicate a reduction in customer default rates compared to scenarios without the application of data mining models, thereby achieving our goal of risk control.
Efficient finite difference method for two-dimensional diffusion equation in comb structure with fractional derivative boundary conditions
Authors: Bu Weiping , Xu Xiaohong , Zhao Yue
Published: January 2025

In [Liu L., Chen S., Feng L., Wang J., Zhang S., Chen Y., Si X., Zheng L., Analysis of the anomalous diffusion in comb structure with absorbing boundary conditions, J. Comput. Phys. 490:112315, 2023], an anomalous diffusion model in comb structure is simulated by finite difference method, which exhibits a low convergence rate in time compared to space. It inspires us to enhance temporal convergence accuracy for this interesting problem. In this paper, we first consider the finite difference method of normal diffusion equation in comb structure which can be viewed as a natural generalization of the anomalous diffusion case. Then we use finite difference method to solve the above anomalous diffusion problem. Unlike the existed work which employs L1 method to discrete the fractional derivative of the considered equation, the Crank–Nicolson method is used for integer-order problem and L2-1[Formula: see text] method is used for fractional problem here. For these two proposed numerical schemes, their stability and convergence are discussed, respectively. For the fractional problem, the present convergence result shows that the accuracy in time has been obviously improved compared with the existed work. Finally, the obtained theoretical results are verified by some numerical tests.