bluuebunny/crossref_metadata_2025 huggingface dataset:
Unraveling the molecular dissociation between aging and atherosclerosis: A bioinformatics approach
Authors: Kamihara Takahiro , Kinoshita Tomoyasu , Kawano Reo , Tanaka Seiya , Omura Takuya , Tanaka Ken , Hirashiki Akihiro , Kokubo Manabu , Arai Hidenori , Shimizu Atsuya
Published: December 2024

Aim

In clinical practice, cardiologists frequently note substantial differences in coronary artery health among patients of the same age bracket. This observation led to our investigation into identifying genes that are shared between atherosclerosis and aging, as well as those that are specifically amplified in atherosclerosis alone.

Methods

Our study leveraged existing gene expression datasets from the Gene Expression Omnibus (GEO), avoiding the need for new experimental research involving human or animal subjects. We focused on analyzing two specific datasets: one comprising artery samples from individuals with and without atherosclerosis, and the other featuring samples from people in middle age versus those in older age groups. To identify significant genes, we applied a technique known as the weighted average difference (WAD).

Results

Our analysis identified 14 genes that were upregulated in both aging and atherosclerosis, hinting at the involvement of the type I interferon response in both conditions. Conversely, 408 genes that exhibited heightened activity within atherosclerotic lesions indicated an augmentation in lysosome‐related processes. While aging might create a groundwork that predisposes individuals to atherosclerosis, the progression of atherosclerosis also involves distinct factors such as type I interferon response and an increase in lysosomal activity.

Conclusions

Aging encompasses more than just the senescence of vascular cells; it is significantly affected by extracellular factors such as type I interferon. The onset of atherosclerosis, therefore, cannot be attributed solely to aging. Instead, it likely involves enhanced mechanisms such as phagocytosis and heighted lysosomal activity. Geriatr Gerontol Int 2025; 25: 108–115.
Limited impact of weekend admissions on hip fracture outcomes in elderly patients: A study from a Japanese nationwide medical claims database
Authors: Mori Yu , Tarasawa Kunio , Tanaka Hidetatsu , Mori Naoko , Fushimi Kiyohide , Aizawa Toshimi , Fujimori Kenji
Published: December 2024

Aim

The effectiveness of early surgery in preventing complications in elderly Japanese hip fracture patients and the impact of weekend hospitalization need further investigation. The purpose of this study was to determine whether weekend hospitalization affects the incidence of various sequelae and death during hospitalization in elderly hip fracture patients using a comprehensive Japanese hip fracture case database.

Methods

We retrospectively analyzed the Japanese National Administrative DPC (Diagnosis Procedure Combination) database from April 2016 to March 2022. During this period, approximately 1100 DPC‐affiliated hospitals consistently provided medical records with consent for the study. The study focused on weekend hospitalizations and investigated the associations with postoperative pneumonia, pulmonary embolism, myocardial infarction, urinary tract infection, acute renal dysfunction, dementia, and in‐hospital mortality after propensity score matching. Owing to the large population size of the study, significance levels were strictly enforced, and a P‐value < 0.001 was considered statistically significant.

Results

After performing propensity score matching based on age, sex, and comorbidities, 111 035 patient pairs were identified, comparing those admitted on weekends versus weekdays. The analysis showed no heightened risk of sequelae for those admitted during the weekend compared with weekdays. Additionally, there was a slight trend toward higher mortality risk during weekend hospital stays; however, the increase was insignificant, with a hazard ratio of 1.071 (95% confidence interval: 1.005–1.140, P = 0.03).

Conclusion

The results of this study indicate that weekend hospitalization for elderly patients with hip fractures is not definitively associated with an increase in various sequelae or in‐hospital mortality and that the importance of early surgery for elderly patients with hip fractures may be recognized and promoted in Japan. Geriatr Gerontol Int 2025; 25: 75–81.
Use and application of geographical restrictions in systematic reviews with the aim of including studies about Germany: An update of a methodological review
Authors: Muente Catharina , Pachanov Alexander , Hirt Julian , Hoffmann Falk , Palm Rebecca , Munschek Silvan , Pieper Dawid
Published: December 2024

Background

In systematic reviews (SRs), geographical limitations in literature searches can aid in focussing research efforts. A methodological review published in 2016 examined the approaches SR authors use to identify studies about Germany, analysing 36 SRs.

Objective

The aim of this study was to update the original review.

Methods

We conducted a literature search on PubMed for SRs synthesising evidence from studies about Germany published between 22 January 2016 and 7 June 2022. Two reviewers independently performed study selection and data extraction. We evaluated the application of search syntax for restricting studies to those about Germany using the peer review of electronic search strategies criteria. The updated findings were reported and summarised alongside those of the original review.

Results

Thirty‐two additional SRs were newly included (total = 68). Geographic restrictions were applied in 57 SRs, representing 72% in the original review and increasing to 97% in the newly included SRs. Moreover, there was an increased use of truncations and field tags.

Conclusion

Although geographical restriction methods are increasingly utilised, additional tools are necessary to enhance the robustness of search strategies. The development of a dedicated geographical search filter would facilitate the identification of studies about Germany.
Disentangling the ‘digital’: A critical review of information technology capabilities, information technology–enabled capabilities and digital capabilities in business research
Authors: Grego Marica , Bartosiak Marcin , Palese Biagio , Piccoli Gabriele , Denicolai Stefano
Published: December 2024

Business and management scholars have always placed a strong emphasis on the study of capabilities. As digital technology moves from the back office to the forefront of digital innovation and transformation, organizations increasingly recognize the vital role of their digital‐related capabilities. Yet, despite the attention, substantial confusion remains in the cross‐disciplinary management and business literature, caused by conflating related, yet distinct, constructs: information technology (IT) capabilities, IT‐enabled capabilities and digital capabilities. Our objective in this article is twofold. First, we analyse the capability literature across business research areas to identify weaknesses, contradictions, controversies or inconsistencies regarding ‘IT’ and ‘digital’ constructs. We do so by conducting a theory‐driven critical review encompassing 360 studies in fields ranging from accounting to strategy. Second, our article advances a theoretical framework that clarifies the differences across IT capabilities, IT‐enabled capabilities and digital capabilities. It also provides solid ground for future inquiry by ensuring reliable knowledge accumulation while pointing research attention to unique and novel research questions.
The role of acoustic telemetry in assessing fish connectivity within marine seascapes: A global review
Authors: Welch Rebecca J. , Childs Amber‐Robyn , Murray Taryn S. , Darnaude Audrey M. , James Nicola C.
Published: December 2024

The study of aquatic animal movements is a rapidly growing field of research, with tracking methodology ever developing and refining. Acoustic telemetry is arguably the most popular method used to study the movements of fish. Despite this method being able to elucidate many aspects of movement behavior, including residency, home range, and migration, among others, one aspect that remains challenging is the study and definition of connectivity, particularly within marine seascapes. As such, this review assesses published literature on acoustic telemetry studies, which have specifically assessed some aspect of fish connectivity, and discusses these in terms of study distribution and overall trends, the diversity of taxa and life stage assessed, the role that large‐scale acoustic telemetry networks plays in assessing connectivity of marine fishes, how connectivity studies have been used in an applied context, and proposes definitions linked to specific types of connectivity, which will assist future researchers when conceptualizing studies. Further, methods that can be used in conjunction with acoustic telemetry to complement the data are discussed. Given that marine resources and habitats are intricately connected, this review highlights the critical role that acoustic telemetry can play in assessing this link. It is envisaged that our developed framework of connectivity definitions will assist future studies and stakeholders in assessing ecosystem functioning and ultimately contribute to improved conservation and management of marine fish populations and ecosystems.
Increase Incidence and Prevalence of Eosinophilic Gastrointestinal Disorders in Israel During the Last Decade
Authors: Ben‐Tov Amir , Melzer‐Cohen Cheli , Yahalom Roni , Yarden Adva , Livnat Idit , Patalon Tal , Gazit Sivan
Published: December 2024

Background

Eosinophilic gastrointestinal disorders (EGIDs) are primary immune‐mediated disorders, with significant morbidity and long‐term sequelae. Temporal trends in incidence and prevalence are on the rise, but studies outside Europe and North America are sparse.

Methods

Based on retrospective Electronic Medical Records (EMR) data, we studied a large population cohort during the years 2014–2021 of all patients diagnosed with EGIDs. Incidence rate and prevalence were calculated for each year during the study cohort stratified by disease location, age, and sex.

Results

Between 2014 and 2021, among a population of 2.4 million persons, the incidence rate of EGIDs tripled from 2.51 (95% CI: 1.78–3.23) to 7.88 (95% CI: 6.75–9.01) per 100 000 person‐years. Most (85.1%) were patients with eosinophilic esophagitis (EoE). The increased temporal trend was almost identical among all subgroups, including patients with EoE, patients with non‐EoE EGIDs, and patients with EGIDs with esophageal involvement. The prevalence of EGIDs increased from 14.53 (95% CI: 12.80–16.26) to 51.43 (95% CI: 48.60–54.26) per 100 000 persons. In 2021, at the end of the study, the prevalence of EoE was 39.54 (95% CI: 37.05–42.02) per 100 000 persons, and the prevalence of non‐EoE EGID was 11.89 (95% CI: 10.53–13.26) per 100 000 persons.

Conclusions

The incidence and prevalence of EGIDs in Israel have risen steeply during the last decade. The main contribution came from the increased incidence rate of patients with EoE. By the end of the surveillance period, the increased temporal trends did not reach a plateau.
Comparative Analysis of Early Caregiver–Child Interaction Patterns in Infants and Toddlers: Evaluating Down Syndrome vs. Typical Development
Authors: Fernández Ana Karen , Aparicio Andrés , Tenorio Marcela
Published: December 2024

Background

The dynamic, reciprocal, and bidirectional relationships in encounters between infants and their caregivers are called early interactions. Evidence shows that these interactions influence cognitive, emotional, and social development beyond the early years. While some studies have examined these interactions in dyads with infants with Down syndrome, they have mostly focused on parents in small samples. This study explores these interactions by considering parental, infant, and interaction variables.

Methods

A total of 128 dyads participated, with 64 infants with Down syndrome and 64 typically developing infants, matched one‐by‐one by developmental age. During home visits, socio‐demographic and developmental information was collected, development and dyadic interactions were assessed using standardised instruments. Descriptive analyses, MANOVAs, and ANOVAs were conducted comparing the group of dyads that included infants and toddler with Down syndrome and those with typical development. Infant and toddler gender showed significant differences and was included as a relevant factor in the analyses.

Results

Key findings include lower scores in parental sensitivity and non‐directiveness in dyads with children with Down syndrome. Children with Down syndrome also showed lower scores in attention to the caregiver. Interactions with children with Down syndrome exhibited less mutuality and engagement. Significant gender‐based interactions were found, showing that parents are more sensitive and less directive with girls with Down syndrome, who also show greater expression of negative affect and better attention to the caregiver.

Conclusions

This study suggests different qualities in early interactions when a child with Down syndrome is involved. These interactions are characterised by lower sensitivity and greater directiveness, possibly in response to the lower attention towards the caregiver observed in these children. This results in less mutual interaction. The findings' alignment with previous research and implications for clinical work are discussed. Given the observed effect of the child's gender, future research should further explore this aspect.
Robotic salvage radical hysterectomy for locally recurrent cervical cancer: A comparison with open surgery in a single‐surgeon series
Authors: Mabuchi Seiji , Maeda Michihide , Sakata Mina , Matsuzaki Shinya , Matsumoto Yuri , Kamiura Shoji , Kimura Tadashi
Published: December 2024

Aim

To compare the surgical and oncologic outcomes between patients with locally recurrent cervical cancer undergoing robotic‐assisted salvage radical hysterectomy (RH) and those undergoing conventional open salvage RH, performed by a single surgeon.

Methods

This retrospective comparative observational study utilized data obtained from consecutive patients with locally recurrent cervical cancer, developed after definitive radiotherapy. These patients either underwent robot‐assisted RH (robotic group) or conventional open RH (open group). Clinicopathological characteristics, surgical outcomes, and oncological outcomes were compared between the two groups.

Results

The operative time was slightly longer in the robotic group; however, this difference was not statistically significant. Estimated blood loss was significantly lower in the robotic group (median; 0 mL [robotic group] vs. 700 mL [open group]: p < 0.01). The incidence of intraoperative and early and late complications did not statistically differ between the two groups. The mean follow‐up was 29.0 and 17.1 months in the open and robotic groups, respectively. Disease recurrence rates were similar between the two groups (40% [robotic group] vs. 44.4% [open group]). Kaplan–Meier survival analysis for progression‐free survival and overall survival did not show statistically significant differences between the two groups.

Conclusion

Robot‐assisted salvage RH in women with locally recurrent cervical cancer showed perioperative and oncological outcomes comparable to those of the open procedure. Although our results suggest that the robot‐assisted approach is as good as or better than the open approach, further investigation is required to establish a more robust conclusion.
Morphology, biology and molecular characterisation of the endemic Canary Islands blowfly Calliphora splendens Macquart, 1838 (Diptera: Calliphoridae)
Authors: Martínez‐Sánchez Anabel , Szpila Krzysztof , Villet Martin H. , Ståhls Gunilla , Thomas‐Cabianca Arianna , Velásquez Yelitza , Parrott Jonathan J. , Rojo Santos
Published: December 2024

The Canary Islands are an excellent natural laboratory for understanding ecological and evolutionary processes such as biogeographical colonisation. The morphology of the larva, puparium and adult of the endemic Canarian copper fly, Calliphora splendens, is described, illustrated and contrasted with those of the other species of Calliphora that occur in Africa, the Iberian Peninsula and Macaronesia. Partial cytochrome oxidase I sequences show a connection between C. splendens, Calliphora vicina, Calliphora loewi and Calliphora croceipalpis, but more distant relationship with Calliphora vomitoria. Calliphora splendens produced unisexual offspring in captivity. This work confirms the relict character of the Canarian copper fly associated with the endemic laurel forest habitat.
Clinical Research Practitioner: Transformation to a Competent Professional Through Reflective Practice
Authors: Sadare Ibiyemi
Published: December 2024

The National Institute for Health and Care Research (NIHR) has significantly contributed to the growth of clinical research activities in the United Kingdom. Central to this expansion is the pivotal role of Clinical Research Practitioners (CRPs) within the healthcare organization. This narrative explores reflective practice as a dynamic tool and essential requirements for their transformation and development into competent CRPs. Additionally, this article adds to the growing literature to highlight the benefits of having a professionally registered CRP for NHS organizations. By weaving together personal insights, professional development, and the integration of acquired knowledge, the narrative illuminates the profound impact of reflective practice on the evolution of a skilled and adept CRP. This review adds to the current literature on the importance of reflective practice in improving professionalism and competency for registered CRPs. The narrative emphasizes lifelong learning and reflective practice integration in clinical research training programs. It suggests further research on workplace reflection for knowledge integration. This resource is valuable for CRPs, organizations, and policymakers, emphasizing professionalism, competency development, and reflective practice in clinical research.
Trajectory and determinants of intensive care unit–acquired weakness in critical illness: A multicentre, prospective, longitudinal study
Authors: Chen Xue‐Xian , Xiong Jing , Chen Jin‐Xia , Luo Chen‐Juan , Zhuang Yao‐Ning , Xu Mei‐Lian , Li Hong , Wu Ting‐Ting
Published: December 2024

Background

Intensive care unit–acquired weakness (ICU‐AW) is prevalent and adversely affects patient outcomes. Muscle strength progression and response to rehabilitation differ across ICU populations. However, the trajectories, determinants and prognoses of muscle strength changes remain unclear.

Aim

This study aimed to investigate the trajectory and determinants of ICU‐AW in critical illness and its impact on 60‐day postadmission mortality.

Study design

A multicentre prospective cohort study was conducted, involving critically ill patients from 10 ICUs across five tertiary hospitals in Fujian Province, China. Patients were evaluated using the Medical Research Council (MRC) scale at three time points: within 48 h of ICU admission or within 24 h of regaining consciousness (T1), within 24 h of ICU discharge (T2) and at the time of hospital discharge (T3). The latent class growth mixed model was utilized for data analysis, and multivariable logistic regression was employed to examine the determinants of muscle strength trajectories.

Results

This study encompassed 343 patients from five tertiary hospitals. Three latent trajectory groups were identified: a low‐level decline group (5.83%), a medium‐level stability group (25.36%) and a high‐level recovery group (68.81%). Multivariable logistic regression revealed that Charlson comorbidity index (CCI) and alcohol consumption significantly influenced the trajectory of muscle strength development in ICU patients (p < .05). The mortality rate at 60 days was significantly higher in both the low‐level decline and medium‐level stability groups compared with the high‐level recovery groups (p < .05).

Conclusions

This study identified three muscle strength trajectories in ICU patients: low‐level decline, medium‐level stability and high‐level recovery. CCI and alcohol consumption significantly influenced these trajectories. The lower 60‐day mortality rate in the high‐level recovery group underscores the need for early intervention and tailored care.

Relevance to Clinical Practice

Developing targeted rehabilitation strategies for those at risk of low‐level decline or medium‐level stability group is challenging and may potentially improve recovery and outcomes.
Molecular allergen sensitization drives phenotypes of severe asthma in children: Evidence from a megacity cohort (SAMP)
Authors: Bourgoin‐Heck Mélisande , Wolff‐Goldnadel Victoria , Chantran Yannick , Saf Sarah , Guiddir Tamazoust , Amat Flore , Rancière Fanny , Momas Isabelle , Wanin Stéphanie , Rose Thierry , Saint‐Pierre Philippe , Just Jocelyne
Published: December 2024

Background

Several major sensitization profiles have been described in children with asthma, but it remains unclear how these profiles relate to asthma phenotypes. The aim of this study was to determine allergenic sensitization profiles in a megacity cohort (SAMP).

Methods

This was a cross‐sectional analysis performed from 2011 to 2015 including preschool and school‐age children with severe and moderate asthma from the SAMP cohort. We performed ALEX multiplex array and carried out cluster analysis.

Results

Data from 367 children were analyzed: 224 of preschool age and 143 of school age, respectively 84 (38%) and 114 (80%) presented at least one allergic sensitization. At preschool age, three clusters were identified: Cluster 1, Few sensitizations to inhaled allergen molecular families and non‐type 2 (T2) inflammation (n = 61); Cluster 2, Predominant sensitization to HDM molecular families (n = 16); Cluster 3, Severe asthma with multiple sensitizations to inhaled and food allergen molecular families (n = 7). At school age, five clusters were identified: Cluster 1, Few sensitizations to inhaled allergen molecular families and non‐T2 inflammation (n = 43); Cluster 2, Predominant sensitization to HDM molecular families (n = 31); Cluster 3, Predominant sensitization to PR‐10 protein family (n = 25); Cluster 4, Severe asthma with predominant sensitization to tropomyosin family (n = 11); Cluster 5, Severe asthma with multiple sensitizations to inhaled and food allergen molecular families (n = 4).

Conclusion

These results underline the heterogeneity of sensitization profiles in severe allergic childhood asthma. The most severe asthma phenotypes were associated with multiple sensitizations to both inhaled and food allergen molecular families as expected, and to the tropomyosin molecular family, a novel finding.
Plant Architecture Optimizes the Trait‐Based Description and Classification of Vegetation
Authors: Liu Biying , Yuan Sihao , Chen Zhihui , Zhao Panpan , Wang Yi , Chu Wei , Zhang Shuo , Zhao Wensheng , Tan Shiqin , Zhou Ting , Peng Shaolin
Published: December 2024

Trait‐based approaches offer valuable perspectives for vegetation classification, but functional traits struggle to capture resource allocation among competing plants, showing limitations across scales. This study aimed to introduce plant architecture to enhance trait‐based vegetation classification. Based on a forest transect survey along China's eastern coast from 2021 to 2023, data from 32 plots of coastal dwarf forests (CDF), characterized primarily by reduced plant height, and normal noncoastal dwarf forests (NCDF) were obtained. Their community characteristics were quantified, and classification and clustering models assessed the advantages of plant architecture in distinguishing these communities. The results indicated plant architecture traits are more critical for distinguishing different community types than leaf‐based functional traits. Additionally, plant architecture traits are effective in clustering plant associations within the same community type. Because plant architectural traits are closely linked to habitat, phylogeny and community structure, providing a comprehensive description of vegetation. In contrast, traditional plant functional traits primarily reflect habitat information related to soil nutrients. Our findings underscore the importance of plant architecture in optimizing trait‐based vegetation classification and suggest that variations in the plasticity of plant architecture traits may support the classification of CDF as a distinct vegetation unit.
Microplastics and Nanoplastics Alter the Physicochemical Properties of Willow Trees and Lead to Mortality in Leaf Beetle Larvae
Authors: Zhu Peipei , Zhang Yanping , Deng Mengqi , Zhang Yuxin , Luo Jing , Han Runhua , Xu Letian
Published: December 2024

Polystyrene micro‐ and nanoplastics (MNPs) are increasingly found in terrestrial environments, posing risks across the food web. However, the potential impacts of MNPs transfer on plant‐insect interactions remains largely unknown. In this study, consumption of willow plants (Salix maizhokunggarensis) exposed to 10.0 mg/L MNPs for 21 days inhibited survival and reduced body weight in Plagiodera versicolora larvae unlike those exposed to lower concentrations or shorter durations (0.1, 1.0 and 10.0 mg/L MNPs for 7 or 14 days). MNPs exposure increased lignin content and leaf thickness in willows, leading to decreased leaf consumption and increased mouthpart wear in P. versicolora larvae. Transcriptome and gut microbiota analyses revealed significant downregulation of genes related to digestion, intestinal homoeostasis, immunity, and growth/development along with profound alterations in gut microbiota composition. Notably, the abundance of the pathogenic bacterium Pseudomonas increased significantly. The gut barrier was disrupted, allowing gut bacteria to translocate into the haemolymph, accelerating larval mortality. Overall, MNPs altered plant physiology, making willow plants unsuitable for herbivore consumption and indirectly influenced herbivore survival by modulating gut bacteria. These findings offer novel insights into the cascading ecological effects and risks of MNPs, highlighting potential impacts on plant‐herbivore interactions, biodiversity, and ecosystem health in terrestrial ecosystems.
Caminos de la prosa, bajo el signo del arte contemporáneo: más allá de lo documental
Authors: Manzi Jorge
Published: December 2024

En la primera parte de este artículo, en diálogo con la noción de nominalismo de Theodor Adorno y de novelización de Mijaíl Bajtín, se identifica un posible vaso comunicante entre prosa, novela y arte contemporáneo, basado en una compleja dialéctica entre arte y antiarte. En la segunda parte, con base en una discusión sobre la orientación documental de la prosa contemporánea y en un análisis de Baroni: un viaje de Sergio Chejfec, se identifica una nueva modalidad de la prosa contemporánea, que, en lugar de crear ficciones novelescas a partir de material documental, apuesta por transfigurarlo en arte a partir de sutiles procedimientos de exhibición y encuadre.
Los nombres en la poesía temprana de Ramón López Velarde y Alfonso Reyes
Authors: Vital Díaz Alberto
Published: December 2024

Las figuras de Alfonso Reyes y de Ramón López Velarde pueden parecer disímiles a pesar de compartir las mismas coordenadas temporales; sin embargo, la producción poética de cada uno demuestra que no es así, pues hay puntos de convergencia entre sus estilos. Por ello, en el presente artículo se aplicarán diferentes estrategias onomásticas para analizar las obras poéticas de Ramón López Velarde y de Alfonso Reyes, desde sus etapas iniciales hasta sus textos de madurez, lo cual permitirá advertir la importancia de los nombres en la literatura y cómo cada uno se apropia de los antropónimos y topónimos para generar diferentes efectos en sus obras. Asimismo, la utilización de diferentes nombres permite que cada autor pueda formar, poco a poco, un lenguaje que los distinguirá en la literatura mexicana del siglo XX.
Speckled Laser Pump–Thermoreflectance Microscopy Probe to Measure and Study Micro/Nanoscale Thermal Transport: Numerical Simulation
Authors: Zhang Yifan , Luo Zuni , Xie Zhikun , Wang Jingwen , Cao Kun , Chen Ke
Published: December 2024

Nondiffusive thermal transport in solids and their micro/nanostructures is a key subject in the research of micro/nanoscale heat conduction. A number of laser and optical techniques to measure or capture the nondiffusive behaviors of heat carriers have been developed, such as transient thermoreflectance, time-domain thermoreflectance (TDTR), transient thermal grating (TTG), and so on. Here, we propose a novel method to study micro/nanoscale heat transport, namely, speckled laser pump–thermoreflectance microscopy probe. In this technique, micrometer to few hundred nanometer size random heat spots are generated by a speckled laser pump pulse, and the time–space evolution of heat spots are recorded by thermoreflectance microscopy images of the probe pulses arriving at different delay times. Fourier transform is applied to analyze the thermoreflectance images and extract the thermal decaying time for different spatial frequencies and along different in-plane directions. Thermal conductivity at different spatial frequencies, which includes the nondiffusive transport information, is obtained in this way. By numerically performing simulation of anisotropic Brownian motion and solving phonon Boltzmann transport equations under the initial condition of random heat spots, we retrieve the preset anisotropic thermal conductivity and the nondiffusive behavior of reduced thermal conductivity with increasing spatial frequencies, proving the validity of this technique. The innovative method can also be applied to study electron and spin transports, and holds the potential to facilitate the experimental research and understanding of nanoscale energy transport.
Computational Analysis of Flow and Transport Suggests Reduced Oxygen Levels Within Intracranial Aneurysms, Especially in Individuals With Sickle-Cell Disease
Authors: Bazzi Marisa S. , Wiputra Hadi , Wood David K. , Barocas Victor H.
Published: December 2024

Sickle cell disease (SCD) is a genetic condition characterized by an abundance of sickle hemoglobin in red blood cells. SCD patients are more prone to intracranial aneurysms (ICA) compared to the general population, with distinctive features such as multiple intracranial aneurysms: 66% of SCD patients with ICAs have multiples ICAs, compared to 20% in nonsickle patients. The exact mechanism behind these associations is not fully understood, but there is a hypothesized link between hypoxic conditions in blood vessels and impaired synthesis of extracellular matrix, which may weaken the vessel walls, favoring aneurysm formation and rupture. SCD patients experience reduced oxygen levels in their blood, potentially exacerbating hypoxia in intracranial aneurysms, and potentially creating a feedback loop that could contribute to aneurysm development and early onset in these patients. In this work, we performed a series of computational studies (Fluent) using idealized geometries to investigate the key differences in the oxygen transport and blood flow dynamics inside an aneurysm formation for sickle and nonsickle cases. We found that using sickle cell disease parameters resulted in a 14% to 68% reduction in blood flow and a 37% to 70% reduction in oxygen availability within the aneurysm, depending on the vessel curvature and the aneurysm throat diameter, due to factors including oxygen-dependent viscosity and alteration in the oxygen transport. The results indicate that depending on geometry and flow characteristics, some degree of hypoxia maybe present in aneurysm bulb and would be more severe in sickle-cell disease patients. This study hopes to bring into attention the potential presence of hypoxic environment in the aneurysm bulb.
A Generalized Machining Process Damping Model for Orthogonal Cutting
Authors: Theraroz Jonathan , Tuysuz Oguzhan
Published: December 2024

Chatter vibrations in machining degrade the surface quality, cause premature tool and machine failures, and reduce the productivity. The dynamic interference between the cutting tool and the wavy part surface damps the machining process in the presence of vibrations. Machining process damping improves the chatter stability especially for difficult-to-cut materials and is even more pronounced via optimized cutting edge geometries. However, there is not any analytical model that can consider arbitrary edge profiles in modeling the process damping. This study introduces a new generalized analytical model to predict the process damping forces for any two-dimensional cutting edge geometries by taking the vibration parameters, work material properties, cutting conditions, and cutting edge geometry into account. That is achieved by discretizing the tool–workpiece contact using a series of springs with a nonlinear Winkler foundation and by employing a material constitutive model to describe the behavior of the deformed springs beyond elasticity. The process damping force is calculated from the contact pressure between the edge and the work material and linearized with an equivalent viscous damper dissipating the same energy. The proposed model has been verified experimentally and numerically for different tool geometries. It is demonstrated that the model can eliminate the time-intensive experimental and numerical identification of process damping coefficients and can digitalize the design phase of cutting tools by rapidly evaluating their machining dynamics performance in place of physical tests.
Computational Model for Hot Deformation Behavior of AA2024/SiC Composites Emphasizing the Effect of Volume Fraction and Particle Size
Authors: Hashmi Anisah Farooq , Li Fuguo , Zhao Qian , Li Qinghua , Zhu E. , Tanveer Muhammad , Gopi K. R.
Published: December 2024

The hot deformation behavior of AA2024/SiC composite was investigated by experimental and finite element simulation (FEM) methods. The influence of different particle volume fractions (VFs) and sizes on the mechanical behavior of AA2024/SiC composites was studied. An integrated numerical model was developed using a modified Johnson–Cook model for the AA2024 matrix implemented via VUHARD subroutine and the Johnson–Holmquist model 2 for the SiC particles. Simulations were performed at higher temperatures (673–753 K) and varying strain rates (0.01–1 s−1) within a random microstructure-based FEM framework using abaqus. The FEM results are in close agreement with the experimental data, particularly in the true stress–strain curves, indicating that the developed FEM model effectively captures the hot workability of AA2024/SiC composites under varying temperature conditions, SiC volume fractions, and particle sizes (PSs). The results showed that the reinforcement of SiC particles into the AA2024 matrix significantly improved its hot workability by reducing dislocation mobility. The flow stress of composites increased with SiC content and decreased with the reinforcement particle size. The composites reinforced with 5 µm SiC particles had a higher peak flow stress of 145.945 MPa than the others at 673 K and a strain rate of 1 s−1. Similarly, at constant temperature and strain rate, the peak flow stress of the composite material increased from 87 MPa to 145.945 MPa (PS = 5 µm at 673 K and strain rate 1 s−1) as the VF increased from 1% to 20%.
Simulation Study of the Upper-Limb Isometric Wrench Feasible Set With Glenohumeral Joint Constraints
Authors: Rezzoug Nasser , Skuric Antun , Padois Vincent , Daney David
Published: December 2024

The aim of this work is to improve musculoskeletal-based models of the upper-limb wrench feasible set (WFS), i.e., the set of achievable maximal wrenches at the hand for applications in collaborative robotics and computer aided ergonomics. In particular, a recent method performing wrench capacity evaluation called the iterative convex hull method (ICHM) is upgraded in order to integrate nondislocation and compression limitation constraints at the glenohumeral (GH) joint not taken into account in the available models. Their effects on the amplitude of the force capacities at the hand, glenohumeral joint reaction forces and upper-limb muscles coordination in comparison to the original iterative convex hull method are investigated in silico. The results highlight the glenohumeral potential dislocation for the majority of elements of the wrench feasible set with the original iterative convex hull method and the fact that the modifications satisfy correctly stability constraints at the glenohumeral joint. Also, the induced muscles coordination pattern favors the action of stabilizing muscles, in particular the rotator-cuff muscles, and lowers that of known potential destabilizing ones according to the literature.
Programming tissue-sensing T cells that deliver therapies to the brain
Authors: Simic Milos S. , Watchmaker Payal B. , Gupta Sasha , Wang Yuan , Sagan Sharon A. , Duecker Jason , Shepherd Chanelle , Diebold David , Pineo-Cavanaugh Psalm , Haegelin Jeffrey , Zhu Robert , Ng Ben , Yu Wei , Tonai Yurie , Cardarelli Lia , Reddy Nishith R. , Sidhu Sachdev S. , Troyanskaya Olga , Hauser Stephen L. , Wilson Michael R. , Zamvil Scott S. , Okada Hideho , Lim Wendell A.
Published: December 2024

To engineer cells that can specifically target the central nervous system (CNS), we identified extracellular CNS-specific antigens, including components of the CNS extracellular matrix and surface molecules expressed on neurons or glial cells. Synthetic Notch receptors engineered to detect these antigens were used to program T cells to induce the expression of diverse payloads only in the brain. CNS-targeted T cells that induced chimeric antigen receptor expression efficiently cleared primary and secondary brain tumors without harming cross-reactive cells outside of the brain. Conversely, CNS-targeted cells that locally delivered the immunosuppressive cytokine interleukin-10 ameliorated symptoms in a mouse model of neuroinflammation. Tissue-sensing cells represent a strategy for addressing diverse disorders in an anatomically targeted manner.
Climate change extinctions
Authors: Urban Mark C.
Published: December 2024

Climate change is expected to cause irreversible changes to biodiversity, but predicting those risks remains uncertain. I synthesized 485 studies and more than 5 million projections to produce a quantitative global assessment of climate change extinctions. With increased certainty, this meta-analysis suggests that extinctions will accelerate rapidly if global temperatures exceed 1.5°C. The highest-emission scenario would threaten approximately one-third of species, globally. Amphibians; species from mountain, island, and freshwater ecosystems; and species inhabiting South America, Australia, and New Zealand face the greatest threats. In line with predictions, climate change has contributed to an increasing proportion of observed global extinctions since 1970. Besides limiting greenhouse gases, pinpointing which species to protect first will be critical for preserving biodiversity until anthropogenic climate change is halted and reversed.
In Other Journals
Authors: Lavine Marc S. , Simonti Corinne , Smith Keith T. , Ash Caroline , Nusinovich Yevgeniya , Suleymanov Yury , Ray L. Bryan
Published: December 2024

Editors’ selections from the current scientific literature
‘Brutal’ math test raises the bar for AI
Authors: Savitsky Zack
Published: December 2024

Model-stumping benchmark shows human experts remain on top—for now
The fourth-stage autoinfective larva of
Strongyloides stercoralis
: redescription and diagnostic implications
Authors: Zhao Huan , Koehler Anson V. , Truarn Cameron , Bradford Damien , New David W. , Speare Rick , Gasser Robin B. , Sheorey Harsha , Bradbury Richard S.
Published: December 2024

Human strongyloidiasis is often underdiagnosed or misdiagnosed, which can relate to a lack of knowledge or recognition of the importance of particular developmental/larval stages of
Strongyloides stercoralis
in making an accurate diagnosis using parasitological methods (a morphological approach or morphological features/characters). Here, we report the identification of
S. stercoralis
autoinfective fourth-stage larvae (L4a) in naturally infected humans, encountered in two clinical cases in Australia. These larvae were identified in sputum (Case 1) and bronchoalveolar lavage (Case 2) specimens by direct wet-mount microscopy. The L4a of
S. stercoralis
can be morphologically differentiated from autoinfective third-stage larvae by its conical and pointed tail and a relatively mature genital primordium with an enlarged genital rudiment and the formation of a vulva within cuticle layers. This study emphasizes the need to consider these morphological features of the L4a stage for an accurate diagnosis of
S. stercoralis
infection. A detailed morphological description of this stage is given to guide laboratory practitioners and researchers in the identification and differentiation of this unique but neglected life-cycle stage of
S. stercoralis
.
Analysis of the ubiquitin-modified proteome identifies novel host factors in Kaposi’s sarcoma herpesvirus lytic reactivation
Authors: Causey Amerria , Constantine Mathew , Oswald Jessica , Dellomo Anna , Masters Bronwyn , Omorogbe Esosa , Admon Arie , Garzino-Demo Alfredo , Ehrlich Elana
Published: December 2024

Kaposi’s sarcoma herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma and is associated with primary effusion lymphoma (PEL), multicentric Castleman’s disease, and two inflammatory diseases. KSHV-associated cancers are primarily associated with genes expressed during latency, while other pathologies are associated with lytic gene expression. The major lytic switch of the virus, Replication and Transcription Activator (RTA), interacts with cellular machinery to co-opt the host ubiquitin proteasome system to evade the immune response as well as activate the program of lytic replication. Through stable isotope labeling using amino acids in cell culture (SILAC) labeling, ubiquitin remnant enrichment, and mass spectrometry, we have analyzed the RTA-dependent ubiquitin-modified proteome. We identified RTA-dependent changes in the populations of polyubiquitin chains, as well as changes in ubiquitinated proteins in both cells expressing RTA and naturally infected cells following lytic reactivation. We observed an enrichment of proteins that are also reported to be SUMOylated, suggesting that RTA, a small ubiquitin-like modifier (SUMO) targeting ubiquitin ligase, may function to alleviate a SUMO-dependent block to lytic reactivation. RTA targeted substrates directly through a ubiquitin ligase domain-dependent mechanism as well as indirectly through cellular ubiquitin ligase RAUL. Our ubiquitome analysis revealed an RTA-dependent mechanism of immune evasion. We provide evidence of inhibition of transporter associated with antigen processing (TAP)-dependent peptide transport, resulting in decreased human leukocyte antigen (HLA) complex stability. The results of this analysis increase our understanding of mechanisms governing the latent to lytic transition in addition to the identification of a novel RTA-dependent mechanism of immune evasion.

IMPORTANCE

Kaposi’s sarcoma herpesvirus, an AIDS-associated pathogen, is associated with multiple cancers and inflammatory syndromes. This virus has a latent and lytic lifecycle, each associated with pathogenesis and oncogenesis. Here, we identify proteins that display differential abundance in different phases of the lifecycle. We provide evidence supporting a new model of viral immune evasion. These findings increase our understanding of how the virus manipulates the host cell and provides new targets for intervention.
A more significant role for insertion sequences in large-scale rearrangements in bacterial genomes
Authors: Ngan Wing Y. , Parab Lavisha , Bertels Frederic , Gallie Jenna
Published: December 2024

Insertion sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element and a short duplication at the target site. It has been noted that, for some extant IS copies, no target site duplications (TSDs) are readily identifiable. TSD absence has been attributed to degeneration of the TSD after the insertion event, recombination between identical ISs, or adjacent deletions. Indeed, the latter two—recombination between ISs and adjacent deletions—are frequent causes for the absence of TSDs, which we demonstrate here in an analysis of genome sequence data from the Lenski long-term evolution experiment. Furthermore, we propose that some IS movements—namely, those that occur in association with large-scale genomic rearrangements—do not generate TSDs, and occur without evidence for recombination between ISs or adjacent deletions. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS
5
movement plus a large deletion in
Escherichia coli
C, and an IS
481
movement occurring with a large duplication in
Pseudomonas fluorescens
SBW25. Although unlikely, it is possible that the observed deletion and associated IS movement occurred in two successive events in one overnight culture. However, an IS at the center of a large-scale duplication is not readily explained, suggesting that IS element activity may promote both large-scale deletions and duplications.

IMPORTANCE

Insertion sequences are the most common mobile genetic elements found in bacterial genomes, and hence they significantly impact bacterial evolution. We observe insertion sequence movement at the center of large-scale deletions and duplications that occurred during laboratory evolution experiments with
Escherichia coli
and
Pseudomonas fluorescens
, involving three distinct types of transposase. We raise the possibility that the transposase does not mediate DNA cleavage but instead inserts into existing DNA breaks. Our research highlights the importance of insertion sequences for the generation of large-scale genomic rearrangements and raises questions concerning the mechanistic basis of these mutations.