bluuebunny/crossref_metadata_2025 huggingface dataset:
Neutron transmission imaging system with a superconducting kinetic inductance detector
Authors: Dang Vu The , Shishido Hiroaki , Aizawa Kazuya , Oku Takayuki , Oikawa Kenichi , Harada Masahide , Kojima Kenji M. , Miyajima Shigeyuki , Soyama Kazuhiko , Koyama Tomio , Hidaka Mutsuo , Suzuki Soh Y. , Tanaka Manobu M. , Machida Masahiko , Kawamata Shuichi , Ishida Takekazu
Published: June 2024

We optimized the design and operating conditions of our superconducting neutron detector to improve spatial resolution. We obtained the best spatial resolution of 10 μm when a Gd Siemens star pattern was mounted in close contact with the detector. Although there is a trade-off between a spatial resolution and an easiness of replacing samples, we built our superconducting neutron imaging system for measuring in both the room-temperature samples with a proper collimation ratio L/D for achieving a reasonable spatial resolution and a cryogenic temperature with the best spatial resolution for certain purposes. In this study, we obtained neutron transmission images of various samples when they were cooled down with the superconducting neutron detector. We compared the effect of a different sample-detector distance on a spatial resolution when the samples were placed either at cryogenic temperature or at room temperature. We also confirmed that our CB-KID sensor was able to observe the neutron transmission coefficient over wider energies of pulsed neutrons. We found the appearance of clear Bragg dips by the measurements of natural FeS2 single crystals and succeeded in mapping the distribution of differently-oriented crystals by choosing several Bragg dips of the FeS2 crystals to compose the transmission images.
Bio-inspired design of hard-bodied mobile robots based on arthropod morphologies: a 10 year systematic review and bibliometric analysis
Authors: Cornejo José , Sierra-Garcia J Enrique , Gomez-Gil Francisco Javier , Weitzenfeld Alfredo , Acevedo Flor E , Escalante Ignacio , Recuero Ernesto , Wehrtmann Ingo S
Published: June 2024

This research presents a 10-year systematic review based on bibliometric analysis of the bio-inspired design of hard-bodied mobile robot mechatronic systems considering the anatomy of arthropods. These are the most diverse group of animals whose flexible biomechanics and adaptable morphology, thus, it can inspire robot development. Papers were reviewed from two international databases (Scopus and Web of Science) and one platform (Aerospace Research Central), then they were classified according to: Year of publication (January 2013 to April 2023), arthropod group, published journal, conference proceedings, editorial publisher, research teams, robot classification according to the name of arthropod, limb’s locomotion support, number of legs/arms, number of legs/body segments, limb’s degrees of freedom, mechanical actuation type, modular system, and environment adaptation. During the screening, more than 33 000 works were analyzed. Finally, a total of 174 studies (90 journal-type, 84 conference-type) were selected for in-depth study: Insecta—hexapods (53.8%), Arachnida—octopods (20.7%), Crustacea—decapods (16.1%), and Myriapoda—centipedes and millipedes (9.2%). The study reveals that the most active editorials are the Institute of Electrical and Electronics Engineers Inc., Springer, MDPI, and Elsevier, while the most influential researchers are located in the USA, China, Singapore, and Japan. Most works pertained to spiders, crabs, caterpillars, cockroaches, and centipedes. We conclude that ‘arthrobotics’ research, which merges arthropods and robotics, is constantly growing and includes a high number of relevant studies with findings that can inspire new methods to design biomechatronic systems.
Can CGCMs under CMIP5/6 simulate present-day sea level rise in western Maritime Continent?
Authors: Djamil Y S , Maharani A , Solihuddin T , Setiawati M D , Muslim A M , Eguchi T , Chatterjee U , Alifatri L O
Published: June 2024

Trends of present-day sea level anomaly (SLA) in western Maritime Continent based on the combination of global thermal expansion and ocean dynamics (steric/dynamic), simulated by Coupled Global Climate Models (CGCMs) under the Climate Model Intercomparison Project phase-5 and 6 (CMIP5/6), are evaluated by using satellite observation. Trends of SLA based on the steric/dynamic component of sea level underestimate the one observed by the satellite for the interior seas of western Maritime Continent. However, satellite observation is also known to overestimate the rate of sea level rise in this shallow basin. Thus, the actual trends of SLA in this area could be approximated based on its steric/dynamic component simulated by CGCMs such as ACCESS1-0 and MIROC-ESM.
Designing sustainable ocean infrastructure using reliability based design optimization: a case study of three-legged jacket offshore platform
Authors: Prastianto R W , Syarifudin M R , Hastuti  , Syalsabila F , Rosyid D M
Published: June 2024

Infrastructure is essential in utilizing maritime resources and requires reliability, resilience, and cost-effectiveness. In the design phase, recent developments in computational approaches have led to design optimization that relies more on science than on the engineering judgment of designers. However, the final result of design optimization is sometimes impractical and has a lower expected lifetime due to drastic reduction. Therefore, reliability is considered during the optimization process as part of the structural evaluation. The case study for this investigation was an offshore jacket platform with three legs. Within the context of the optimization process, reliability serves as a constraint. The goal is to bring down the overall weight of the structure. The tubular elements of the jacket construction are referred to as variables. Variables are separated into several different groupings. The results show that considering the reliability index does not reduce the weight of the structure as much as deterministic optimization. However, the structure’s reliability is not violated, and yet the structure is more economical and still reliable.
Fostering Resilient Communities and Sustainable Tourism against Climate-Driven Disaster Risk in Gili Islands
Authors: Handayani A P , Muhammad M F , Sujatmiko K A
Published: June 2024

Climate change exacerbates natural conditions and disasters. It increased the frequency and severity of droughts, rising sea levels leading to coastal erosion and flooding, more intense and unpredictable weather patterns, and the potential for stronger storm surges and tropical cyclones. These changes have significant impacts on the local ecosystems, water resources, and agriculture and ultimately affect the lives and livelihoods of the island’s residents. Additionally, the changes in ocean temperature and acidity due to climate change can disrupt marine ecosystems, affecting fisheries and coral reefs, which are vital for the island’s tourism industry. This research investigates the consequences of climate change-induced disaster risks on the Gili Islands, particularly drought and their implications for local tourism. Utilizing qualitative methods, the study focuses on developing strategies for sustainable tourism and bolstering community capacity across the islands. Prioritizing the establishment of a strong nexus and resilient community, the research underscores the essential role of collaboration and education. It highlights the importance of active engagement from well-resourced hotels and resorts in addressing these challenges. The study also proposes innovative business processes to enhance connections between hotels, resorts, the government, and the local community. Ultimately, the research aims to provide a roadmap for sustainable tourism practices, fostering a resilient community and facilitating effective cooperation among stakeholders to mitigate the impacts of climate change in the Gili Islands.
Quantification of the Coastal Exposure Index (CEI) in the Kangean Islands using GIS Based Modelling
Authors: Rachman H A , Hidayah Z , As-syakur A R , Nandika M R
Published: June 2024

Climate change has become an important issue in recent years, especially in the context of threats to small islands. This phenomenon causes a rise in sea surface and surface temperatures that endanger coastal ecosystems. Therefore, studies related to the calculation of coastal exposure levels are very important in an effort to mitigate and reduce these impacts. In this study, the calculation of Coastal Exposure Index (CEI) was carried out on the entire coastal area of the Kangean Islands, both large and small islands. We quantified the CEI using Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) Modeling. Parameters used in this analysis include coastal topography, bathymetry, waves, surges, natural habitats (mangrove, coral, and seagrass), geomorphology, and sea level rise. The results of the analysis were then classified into fives categories using natural break point as very low, low, moderate, high, and very high. The results show that about 9.76% (58.03 km) of the coastline has a very high vulnerability level, 19.18% is categorized as high (114.04 km), and about 144.85 km or 24.37%, is a moderate category. Locations with very high and high vulnerability level dominate the northern part of Kangean Island. This area is more exposed to the open ocean and has relatively low natural habitat cover and high exposure of wave and surge potential. While the southern part of the island is dominated by mangrove cover, which is protected from exposure in the open ocean area. This condition is probably causing this area to dominantly have low and moderate CEI categories. In the Sepanjang Island area, areas with coral reef and seagrass cover have a lower CEI. The existence of natural habitats is one of the important components of coastal area exposure and reduces the level of vulnerability. The results of this study can be used as a reference in the Kangean Islands management programme as a response to climate change disasters.
Risk Exposure of Coastal Inundation from Storm Surge in the Northern part of Malaysian Borneo
Authors: Osman N F , Saleh E , Sentian J
Published: June 2024

Coastal communities heavily rely on marine resources for their livelihoods. The rising occurrence of extreme weather events have affected both the coastal ecosystems and socio-economic activities. One of the most prevalent extreme events in Malaysia is the storm surge. This study aims to assess the extent of coastal inundation based on three storm surge scenarios (categories by Meteorological Department of Malaysia) and to determine the risk exposure ranking of nine study sites. Field trips and interviews were conducted from March 2020 to March 2023 in Kudat located at the northern part of Malaysian Borneo. One hundred respondents were surveyed using semi-structured open-ended questionnaires to evaluate the risk exposure of coastal inundation caused by storm surges. The findings revealed that Category 1 flooded certain sites of west (Kimihang) and east (Tajau Laut) sides of Kudat. The Category 2 have significantly flooded one site in the west side (Simpang Mengayau) of Kudat. While, for Category 3 of coastal inundation affected two sites in east sides of Kudat (Tanjong Kapor and Landung Ayang). These two sites in east sides of Kudat also experienced a high level of risk exposure due to the lack of diverse coastal ecosystems and high population density. While three sites in west side of Kudat (Kimihang, Kelambu and Simpang Mengayau) faced significant impacts on social services, particularly within the tourism sector. Despite relying on multiple livelihoods, these sites were susceptible to storm surges. Additionally, the increasing development for tourism purposes posed a threat to the richness of the ecosystem. This study suggests that certain sites in east side of Kudat (Tanjong Kapor and Landung Ayang) are highly exposed to risk and require measures for adaptation and mitigation.
Instrumentation for Monitoring and Early Warning of Tidal Flood Using ESP32S2 Microcontroller and A01NYUB Ultrasonic Sensor in Tambakrejo, Semarang
Authors: Susanti A F S , Putranto R T , Rahmadani M A , Mustaqim I , Saliyo A D S , Sazidah H , Hutahaean C A , Putri S A , Iriani R N , Mulyawan Z W , Kurniawan M W , Alimatunnisa I , Ginanjar S , Adiningsih S , Wirasatriya A , Kunarso  , Sugianto D N , Trianto A
Published: June 2024

A tidal flood early warning system is crucial to minimize the impact and loss in tidal flood-prone areas. This research proposes an instrumentation and information system for tidal flood early warning monitoring by optimizing tidal data in the local area. The efficiency of the instrumentation depends on the accuracy of the sensors installed. This research presents the testing and application of The A01NYUB ultrasonic sensor with The ESP32S2 microcontroller for real-time technology-based water level monitoring and The Internet of Things concept. The collected sensor data is analyzed with an algorithm that has also been proposed in this research. The results show that the ultrasonic sensors can provide a reliable and adequate tide monitoring scheme with an accuracy of RMSE value of 0.08943 and bias value of – 2×10−16. The developed system provides early warning when the sea level reaches 260-280 cm with the MSL datum reference value range of -20 cm to 40 cm. The system has been tested at the Fisherman Boat Harbor, Tambakrejo, Semarang, Central Java, Indonesia. The test has shown the system’s accuracy and has proven that the developed system will help minimize the impact of the tidal flood disaster.
Characteristics of internal waves in the Bali Sea from Sentinel-1A data and ocean modeling
Authors: Lukman A , Atmadipoera A S , Nugroho D , Harsono G
Published: June 2024

Internal waves (IWs) that propagate into the Bali Sea are supposed to originate from the generating sill area in the southern part of the Lombok Strait. This study aims to investigate surface features and mechanism of IWs formation and propagation into the Bali Sea. The datasets are acquired from the Sentinel-1A imageries and CROCO model simulation. The results showed that solitary wave packets are spread over two areas: near Lombok Strait as generating area, and in the western and northern parts of the Bali Sea as propagating area. The length of IWs crests increased as they moved into the propagation area. The model showed that mixed semidiurnal tidal currents near the sill flow northward (southward) alternately during the flood (ebb) tidal period, resulting in the pycnocline deepening down to ~400 m near the northern sill area during the flood tide. Furthermore, the model demonstrated an alternating upward and downward movement of vertical currents components, associated with propagation of IWs’ crests and troughs along IWs pathway.
Silver nanoparticles alleviate the impact of soil contamination and wastewater irrigation on rosemary plants: modulating of gene expression and secondary metabolites
Authors: Al Kashgry Najla Amin T , Darwish Hadeer , Aljomiha Nouf A , Alharthi Sarah , Alayafi Aisha A M , Fallatah Ahmed M , El-Deeb Bahig A , Abd El-Gawad Hany G , Hewidy Mohammed , Al-Harbi Nadi Awad , Al-Qahtani Salem Mesfir , Alotaibi Modhi O , Algotiml Rabaa Abdullah , Noureldeen Ahmed
Published: June 2024

A number of obstacles, including irrigated wastewater and soil contamination, arise in the growth of aromatic and medicinal plants. This study aimed to reduce the effects of contaminated soil and wastewater irrigation on rosemary (Rosmarinus officinalis L.) plants by using biosynthesized silver nanoparticles (AgNPs) produced by the ginger (Zingiber officinale) plant extract. The AgNPs were characterized using Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR). The experimental design involved three distinct groups of plants: one group was irrigated with regular tap water, another group was rooted in soil contaminated by sewage-wastewater and irrigated with processed wastewater, and the final group consisted of plants grown in wastewater-contaminated soil, irrigated with processed wastewater, and sprayed with 200 mM l−1 AgNPs. The study also examined the impact of different treatments on gene expression and secondary metabolite levels in rosemary plants. According to HPLC investigations, nineteen phenol compounds and flavonoids were identified in a methanolic extract of rosemary that was grown in contaminated soil, irrigated with wastewater, and sprayed with AgNPs. Plants treated with wastewater and nanoparticles produced quantities of secondary compounds, including resvertol, vanillic acid, and gallic acid with 1.11, 0.15, and 0.01 mg g−1 respectively, which are all regarded as significant antioxidants employed in the pharmaceutical industry. Hexokinase synthase (HK), geranyl diphosphate synthase (GPPS), and linalool synthase (LS) coding genes were found to have highly expressed expressions when plants grown in contaminated soil, wastewater-irrigated plants, and nanoparticle-sprayed plants, respectively, at a 23.2- and 5.54-fold level, where the HK gene was 8.7 times more strongly expressed. Conversely, plants grown in contaminated soil and irrigated with treated wastewater showed downregulation of these genes. Conclusively, using silver nanoparticles significantly reduced the influence of wastewater pollution on secondary metabolites in rosemary plants, which was increased by the gene expression results and was completely consistent with HPLC analysis.
On 𝑝-adic 𝐿-functions for Hilbert modular forms
Authors: Bergdall John , Hansen David
Published: June 2024

We construct

p
p

-adic

L
L

-functions associated with

p
p

-refined cohomological cuspidal Hilbert modular forms over any totally real field under a mild hypothesis. Our construction is canonical, varies naturally in

p
p

-adic families, and does not require any small slope or non-criticality assumptions on the

p
p

-refinement. The main new ingredients are an adelic definition of a canonical map from overconvergent cohomology to a space of locally analytic distributions on the relevant Galois group, and a smoothness theorem for certain eigenvarieties at critically refined points.
Horses, gender, and (queer) masculine desire, or how experimental found footage film recycles three Hollywood films
Authors: Boczkowska Kornelia
Published: June 2024

Although the experimental found footage film recycles Hollywood films so that the outcome may radically differ from the original story, there are no accounts on how it adapts images from mainstream cinema to represent human–animal relations, linking to gender and masculinity. To fill this gap, I discuss how experimental film Horsey recycles footage from three Hollywood productions—Reflections in a Golden Eye, The Swimmer, and The Black Stallion—to construct a new narrative, which displays a very close conformity to the prior text, shifting the focus to human–horse interactions. Raising questions about the traditional understanding, scope, and limits of adaptation in avant-garde film studies, Horsey fits in with the broader tradition of cinematic recycling of mainstream cinema as it exemplifies intertextuality as a direct form of quotation, taking quotation as appropriation through cuts, detournement, compilation and free association. Particularly, following Guy Barefoot’s understanding of adaptation as an intertextual form of recycling, Horsey is distinctive in its sole use of found footage from the three Hollywood films as it fully acknowledges the recycled material, strongly alluding to the original stories, and simultaneously re-processes them through a collage of pre-used footage, slow motion, washed-out colours, and an altered soundtrack. Despite appearing to merely extract images and sounds from Reflections, The Swimmer, and The Black Stallion, Horsey emerges as a productive site for recycling Hollywood cinema, placing it into new contexts and audio-visual configurations and offering more complex, engaging ways of looking at how humans connect to horses.
High Blood Pressure Is Associated With Lower Brain Volume and Cortical Thickness in Healthy Young Adults
Authors: Won Junyeon , Ashley John , Cardim Danilo , Vongpatanasin Wanpen , Zhang Rong
Published: June 2024

BACKGROUND

High blood pressure (BP) in middle-aged and older adults is associated with lower brain volume and cortical thickness assessed with structural magnetic resonance imaging (MRI). However, little evidence is available on young adults. We investigated the associations of high BP with brain volumes and cortical thickness in healthy young adults.

METHODS

This cross-sectional study included 1,095 young adults (54% women, 22–37 years) from the Human Connectome Project (HCP) who self-reported not having a history of hypertension or taking antihypertensive medications. Brachial systolic (SBP) and diastolic BP (DBP) were measured with a semi-automatic or manual sphygmomanometer during study visits. Structural MRI was used to measure gray matter (GM) and white matter (WM) volume and mean cortical thickness. Associations of BP and hypertension stage with total and regional brain volumes and cortical thickness were analyzed using linear regression and analysis of covariance (ANCOVA) after adjusting for age, sex, education years, body mass index (BMI), smoking, alcohol consumption history, zygosity, and total intracranial volume.

RESULTS

SBP and DBP were (mean ± SD) 123.6 ± 14.2 and 76.5 ± 10.6 mm Hg, respectively, (n = 1,095). High DBP was associated with lower total GM (P = 0.012), cortical GM (P = 0.004), subcortical GM (P = 0.012), and total WM volumes (P = 0.031). High SBP and DBP were associated with lower regional cortical volume and cortical thickness.

CONCLUSIONS

These findings suggest that high BP may have deleterious effects on brain health at the early stage of adulthood.
Adaptive Steroid Tapering Impedes Corticosteroid-free Remissions Compared with Forced Tapering in Clinical Trials of Ulcerative Colitis
Authors: Narula Neeraj , Hamam Hasan , Liu Jasmine , Wong Emily C L , Marshall John K , Jairath Vipul , Hanauer Stephen B , Reinisch Walter , Dulai Parambir S
Published: June 2024

Introduction

It is unclear if steroid tapering protocols can affect clinical trial outcomes in ulcerative colitis [UC], particularly fixed versus adaptive steroid tapering. Fixed steroid tapering involves incremental dose decreases at prespecified intervals, and adaptive steroid tapering uses investigator discretion as determined by the patient’s response.

Methods

In this post-hoc analysis from six clinical trials of UC [VARSITY, ACT 1, PURSUIT, GEMINI1, OCTAVE, and ULTRA2], responders to induction therapy with baseline corticosteroid use were considered as the primary population of interest. Adjustments were made to account for treat-through versus re-randomisation designs, and multivariate regression was performed to account for other potential confounding variables. The primary outcome was corticosteroid-free clinical remission [CR] at 1 year, and secondary outcomes were CR and endoscopic improvement.

Results

There was a total of 861 patients who had achieved clinical response after induction and were using corticosteroids. Within multivariate analysis, patients using adaptive steroid tapering regimens were less likely to achieve corticosteroid-free CR at 1 year (odds ratio [OR] 0.66 [95% confidence interval, CI, 0.48-0.92], p = 0.015) but had increased odds for achieving CR at 1 year (OR 1.9 [95% CI 1.43-2.52], p < 0.001). The steroid tapering regimen was not associated with achievement of endoscopic improvement at 1 year.

Conclusions

Among patients with UC on corticosteroids in clinical trials, patients using adaptive steroid weaning regimens were less likely to achieve corticosteroid-free CR at 1 year but more likely to achieve CR at 1 year. Consideration should be given to implementing mandatory fixed steroid weaning protocols in future clinical trials of UC.
Global Englishes-oriented teacher education: lasting shifts
Authors: Schreiber Brooke R , Jansz Mihiri
Published: June 2024

Despite a growing body of research demonstrating the pluralistic nature of English today, ELT globally still tends to uphold traditional ‘native-speaker’ norms. A Global Englishes language teaching (GELT) approach to teacher education is one way of breaking down that gap, yet it is not well known how the effects of this approach might hold up over time. This article reports on a study of three Sri Lankan teachers who participated in a GELT-oriented pedagogic innovation in 2017 communicating with a diverse group of speakers in the United States. Using interview data, this article discusses how, three years later, their experiences may have affected their pedagogic beliefs and practices. The teachers reported changes such as greater tolerance for informal language, a desire to bring ‘real world’ communication into language classrooms, and an openness to diversity in pronunciation as a means of reducing student anxiety about speaking. These small, meaningful shifts support the value of small-scale GELT teacher education innovations in the long term.
Home Through Their Eyes: A Qualitative Exploration of the Meaning of Home for Persons With Dementia and Impact of Physical Environment During Meaning-Making
Authors: Wang Wenjin , Roumell Elizabeth , Xu Chuanyue , Lu Zhipeng
Published: June 2024

Objectives

This study aimed to examine the meaning of home for persons with dementia and the role of the physical environment during their meaning-making process. In response to a growing number of persons with dementia, there has been a strong advocacy for prioritizing the development of dementia-friendly environments within design practice and research agendas, for which “home” has become one of the important loci. However, of the limited studies on the meaning of home from the perspective of those individuals who continue to live in their own homes after developing dementia, even fewer addressed this issue within the Chinese context.

Methods

Five dyads, persons with dementia and their family caregivers, participated in the qualitative phenomenology study. Ten home visits–2 visits per dyad–were conducted, during which interview data, photographs, and field notes were collected. Phenomenological analysis was applied within and across the data sets.

Results

Three key themes emerged—“Three Dimensions of Home” revealed that “home” goes beyond physical residence and immediate family connections, including meaningful objects and places, enduring relationships, self-identity, and lived experiences.; “The Impact of Physical Environment” and “The Impact of Cognitive Impairment” showed the complex interactions between the environment, cognitive impairment, and meaning-making.

Discussion

An exploration of the essence of meaning of home within the Chinese context, in person–environment relationships with dementia progression, and implications for future research and practice on dementia-related environments and care were further discussed. This study contributes insights into enhancing the well-being of persons with dementia and benefiting their caregivers.
Target Trial Emulation: Improving the Quality of Observational Studies in Inflammatory Bowel Disease Using the Principles of Randomized Trials
Authors: Honap Sailish , Danese Silvio , Peyrin-Biroulet Laurent
Published: June 2024

The past decade has seen a substantial increase in the number of randomized controlled trials (RCTs) conducted in inflammatory bowel disease (IBD). Randomized controlled trials are the gold standard method for generating robust evidence of drug safety and efficacy but are expensive, time-consuming, and may have ethical implications. Observational studies in IBD are often used to fill the gaps in evidence but are typically hindered by significant bias. There are several approaches for making statistical inferences from observational data with some that focus on study design and others on statistical techniques. Target trial emulation is an emerging methodological process that aims to bridge this gap and improve the quality of observational studies by applying the principles of an ideal, or “target,” randomized trial to routinely collected clinical data. There has been a rapid expansion of observational studies that have emulated trials over the past 5 years in other medical fields, but this has yet to be adopted in gastroenterology and IBD. The wealth of nonrandomized clinical data available through electronic health records, patient registries, and administrative health databases afford innumerable hypothesis-generating opportunities for IBD research. This review outlines the principles of target trial emulation, discusses the merits to IBD observational studies in reducing the most common biases and improving confidence in causality, and details the caveats of using this approach.
Burrowing Constrains the Phenotypic Diversity of Fossorial Crayfish
Authors: Delekta Emmy M , Kolmann Matthew A
Published: June 2024

Synopsis

Strong selective pressure on phenotype can arise when habitat transitions fundamentally alter the physical media in which animals live, such as the invasion of land by lobe-finned fishes and insects. When environmental gradients differ drastically among habitats and multiple lineages transition between these habitats, we expect phenotypic convergence to be prevalent. One transition where widespread convergence has been observed is the shift from aboveground to subterranean environments in fossorial animals. Subterranean environments are low-light, confined spaces and tend to be hypoxic or anoxic, not to mention that the act of burrowing itself demands morphological specializations for excavation. Research suggests burrowing promotes morphological convergence in crayfish, with non-burrowing forms having a dorsoventrally compressed carapace and long, slender claws (chelae), while primary burrowing forms have a dorsolaterally compressed carapace and shorter, more powerful claws. However, earlier ecomorphological comparisons relied on qualitative rather than quantitative assessments of phenotypic differences. This study tested for convergence in North American crayfishes using a geometric morphometric approach. We photographed the carapace and claw for representative species across 13 North American genera. We hypothesized that crayfishes that occur in similar habitats and exhibit similar burrowing behaviors, would converge in their carapace and claw shapes. We found evidence for convergence in carapace and claw morphologies in burrowing crayfishes. However, claw phenotypes did not converge as strongly as carapace shape, an example of “imperfect” or “incomplete” convergence we attribute to the multiple competing demands on claw form and function. We argue that nuances in habitat characteristics, like soil type or compaction, make complete convergence unlikely for range- and dispersal-limited fossorial crayfishes.
miRNome Profiling of Extracellular Vesicles in Patients With Severe COVID-19 and Identification of Predictors of Mortality
Authors: Sánchez-de Prada Laura , García-Concejo Adrián , Tamayo-Velasco Álvaro , Martín-Fernández Marta , Gonzalo-Benito Hugo , Gorgojo-Galindo Óscar , Montero-Jodra A , Peláez María Teresa , Martínez Almeida Iciar , Bardají-Carrillo Miguel , López-Herrero Rocío , Román-García Patricia , Eiros José María , Sanz-Muñoz Iván , Aydillo Teresa , Jiménez-Sousa María Ángeles , Fernández-Rodríguez Amanda , Resino Salvador , Heredia-Rodríguez María , Bernardo David , Gómez-Sánchez Ester , Tamayo Eduardo
Published: June 2024

Background

Extracellular vesicles (EVs), containing microRNAs (miRNAs) and other molecules, play a central role in intercellular communication, especially in viral infections caused by SARS-CoV-2. This study explores the miRNA profiles in plasma-derived EVs from patients with severe COVID-19 vs controls, identifying potential mortality predictors.

Methods

This prospective study included 36 patients with severe COVID-19 and 33 controls without COVID-19. EV-derived miRNAs were sequenced, and bioinformatics and differential expression analysis between groups were performed. The plasma miRNA profile of an additional cohort of patients with severe COVID-19 (n = 32) and controls (n = 12) was used to compare with our data. Survival analysis identified potential mortality predictors among the significantly differentially expressed (SDE) miRNAs in EVs.

Results

Patients with severe COVID-19 showed 50 SDE miRNAs in plasma-derived EVs. These miRNAs were associated with pathways related to inflammation and cell adhesion. Fifteen of these plasma-derived EV miRNAs were SDE in the plasma of severe cases vs controls. Two miRNAs, hsa-miR-1469 and hsa-miR-6124, were identified as strong mortality predictors with an area under the receiver operating characteristic curve of 0.938.

Conclusions

This research provides insights into the role of miRNAs within EVs in severe COVID-19 and their potential as clinical biomarkers for mortality.
Biology, ecology, host range, and management approaches for Monolepta spp. (Coleoptera: Chrysomelidae), emerging threats to crops
Authors: Ramzan Muhammad , Khashaveh Adel , Yi Chaoqun , Shan Shuang , Tang Ziyi , Liu Wentao , Khan Khalid Ali , Zhang Yongjun
Published: June 2024

Monolepta signata, Monolepta hieroglyphica, and Monolepta quadriguttata are highly destructive agricultural pests in East and Southeast Asia, causing considerable economic losses by damaging a variety of crops in China, including soybeans, corn, cotton, rice, and vegetables. Despite numerous studies to prevent and control their spread, these pests continue to pose a severe agricultural issue demanding attention. This review focuses on the latest research concerning the biology, hosts, and prevention of these beetles. We also explore the biotic and abiotic factors influencing the population dynamics of these pests. While insecticides are commonly employed to manage these beetles, options for suppressing adult beetles and grubs are limited. Despite ongoing regulatory efforts, these beetles remain a significant threat to several crops, including cotton and corn. Researching the pests’ interactions with predators, parasitoids, and host plants in their ecosystem can provide valuable insights into their ecological roles and potential control methods.
A nomogram to predict the pathological complete response in patients with breast cancer based on the TILs-US score
Authors: Shigematsu Hideo , Fukui Kayo , Kanou Akiko , Fujimoto Mutsumi , Suzuki Kanako , Ikejiri Haruka , Amioka Ai , Hiraoka Emiko , Sasada Shinsuke , Emi Akiko , Arihiro Koji , Okada Morihito
Published: June 2024

Background

The tumor-infiltrating lymphocytes-ultrasonography score is a calculation system for predicting lymphocyte-predominant breast cancers in surgical specimens. A nomogram based on the tumor-infiltrating lymphocytes-ultrasonography score was developed to predict the pathological complete response in breast cancer treated with neoadjuvant chemotherapy.

Methods

A retrospective evaluation was conducted on 118 patients with breast cancer treated with neoadjuvant chemotherapy at Hiroshima University Hospital. Tumor-infiltrating lymphocytes-ultrasonography scores ≥4 were classified as high. A nomogram was developed using a stepwise logistic regression model for pathological complete response (ypT0 ypN0), based on the smallest Akaike information criterion. The predictive ability and clinical usefulness of the nomogram were also evaluated.

Results

Among 118 patients, 34 (28.8%) achieved a pathological complete response, and 52 (44.1%) exhibited high tumor-infiltrating lymphocytes-ultrasonography. In multivariate logistic regression analysis, high tumor-infiltrating lymphocytes-ultrasonography (odds ratio, 6.01; P < 0.001), clinical complete response (odds ratio, 4.83; P = 0.004) and hormone receptor (odds ratio, 3.48; P = 0.038) were independent predictors of pathological complete response. A nomogram based on tumor-infiltrating lymphocytes-ultrasonography score, clinical complete response, hormone receptor and clinical N status was developed. The nomogram showed an area under the curve of 0.831 and a bias-corrected area under the curve of 0.809. The calibration plot showed a good fit between the expected and actual pathological complete response values. Decision curve analysis also showed the clinical utility of the nomogram for predicting pathological complete responses.

Conclusions

A nomogram based on the tumor-infiltrating lymphocytes-ultrasonography score exhibited a favorable predictive ability for pathological complete response in patients with breast cancer, which can be useful in predicting the residual disease status after neoadjuvant chemotherapy.
Direct Combat-related U.S. Army Aviation Injuries 2003–2014
Authors: Brozoski Frederick T , Conti Marcy , Dudek Jennifer , Chancey Valeta Carol , Crowley John S
Published: June 2024

Introduction

The U.S. Army Aeromedical Research Laboratory (USAARL), a partner in the Joint Trauma Analysis for the Prevention of Injury in Combat (JTAPIC) partnership, conducted a series of retrospective reviews to investigate injuries sustained by occupants of U.S. Army rotary-wing aircraft involved in combat damage incidents. The reviews were conducted to provide occupant survivability information to the Aviation Survivability Development and Tactics team, an agency within the U.S. Army Aviation Center of Excellence. For these reviews, combat damage incidents that produced casualties were separated into direct events (i.e., events in which an enemy weapon system directly injured occupants) and indirect events (i.e., incidents in which occupants were injured as a result of a crash caused by the enemy weapon system). The previous USAARL reviews provided an overview of injuries sustained during direct and indirect events. The objective of this review was to conduct a detailed analysis of injuries occurring during direct events.

Materials and Methods

A descriptive retrospective review was conducted on injuries sustained by occupants of U.S. Army rotary-wing aircraft involved in combat damage incidents between 2003 and 2014. All Black Hawk, Apache, and Chinook combat aviation damage incidents for the study period were reviewed. Personnel casualty information from the Defense Casualty Information Processing System (DCIPS) was linked to combat damage incident information by matching the aircraft platform, incident date, and circumstantial information found in incident narratives. Injury information for personnel identified in DCIPS as being wounded in action was obtained from the JTAPIC partnership; injury data for personnel killed in action were retrieved from the Armed Forces Medical Examiner System. All injuries were coded using the Abbreviated Injury Scale (AIS). Descriptive statistics were used to describe the frequency and distribution of injuries to personnel involved in direct events.

Results

Overall, the extremities were the most commonly injured body regions, with lower extremities suffering more injuries than upper extremities. Penetrating injuries were identified as the primary injury mechanism for all body regions. Injuries to each AIS body region were predominantly of minor (AIS 1) and moderate (AIS 2) severity.

Conclusions

Although injury severities were generally low (AIS 1 or AIS 2), the results of this effort indicate which body regions may benefit from additional protection during rotary-wing operations in hostile environments. The influence of occupant position within the aircraft and the use and effectiveness of personal protective equipment could not be effectively analyzed due to a lack of information.
Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila
Authors: Brand Cara L , Oliver Genevieve T , Farkas Isabella Z , Buszczak Michael , Levine Mia T
Published: June 2024

Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins (“DNA–protein crosslink repair”). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA–protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.
Analysis of Evolutionary Conservation, Expression Level, and Genetic Association at a Genome-wide Scale Reveals Heterogeneity Across Polygenic Phenotypes
Authors: Giel Ann-Sophie , Bigge Jessica , Schumacher Johannes , Maj Carlo , Dasmeh Pouria
Published: June 2024

Understanding the expression level and evolutionary rate of associated genes with human polygenic diseases provides crucial insights into their disease-contributing roles. In this work, we leveraged genome-wide association studies (GWASs) to investigate the relationship between the genetic association and both the evolutionary rate (dN/dS) and expression level of human genes associated with the two polygenic diseases of schizophrenia and coronary artery disease. Our findings highlight a distinct variation in these relationships between the two diseases. Genes associated with both diseases exhibit a significantly greater variance in evolutionary rate compared to those implicated in monogenic diseases. Expanding our analyses to 4,756 complex traits in the GWAS atlas database, we unraveled distinct trait categories with a unique interplay among the evolutionary rate, expression level, and genetic association of human genes. In most polygenic traits, highly expressed genes were more associated with the polygenic phenotypes compared to lowly expressed genes. About 69% of polygenic traits displayed a negative correlation between genetic association and evolutionary rate, while approximately 30% of these traits showed a positive correlation between genetic association and evolutionary rate. Our results demonstrate the presence of a spectrum among complex traits, shaped by natural selection. Notably, at opposite ends of this spectrum, we find metabolic traits being more likely influenced by purifying selection, and immunological traits that are more likely shaped by positive selection. We further established the polygenic evolution portal (evopolygen.de) as a resource for investigating relationships and generating hypotheses in the field of human polygenic trait evolution.
Clinical Presentation and Outcomes Following Infection With Vibrio spp, Aeromonas spp, Chromobacterium violaceum, and Shewanella spp Water-Associated Organisms in Tropical Australia, 2015–2022
Authors: Campbell Stuart , MacGregor Kirsten , Smith Emma L , Kanitkar Tanmay , Janson Sonja , Baird Robert W , Currie Bart J , Venkatesan Sudharsan
Published: June 2024

Background

Water-associated bacterial infections cause a wide spectrum of disease. Although many of these infections are typically due to human host commensal Staphylococcal or Streptococcal spp, water exposure can result in infections with environmental gram negatives such as Vibrio spp, Aeromonas spp, Chromobacterium violaceum, and Shewanella spp (collectively VACS).

Methods

We performed a retrospective analysis of the epidemiology, clinical presentation, and outcomes of deep and superficial infections associated with VACS organisms in our health service between 1 January 2015 and 31 December 2023.

Results

We identified 317 patient episodes of infection with VACS organisms over this period. Of these, Aeromonas spp (63%) was the most common, followed by Vibrio spp (19%), Shewanella spp (13%), and C violaceum (5%). The majority were isolated from males (74.4%) and involved the lower limb (67.5%). Mild infections were more common than severe presentations, with only 15 (4.7%) admissions to the intensive care unit and 8 (2.5%) deaths. Colonization occurred in 6.9% of patients, in contrast to the perceived severity of some of these bacteria. Copathogens were common and included Staphylococcus aureus (48%) and enteric bacteria (57%). The majority of patients (60%) had no documented water exposure. Initial empiric antimicrobial therapy presumptively covered the susceptibilities of the isolated organisms in 47.3% of patients; however, a lack of VACS-covering empirical therapy was not associated with readmission.

Conclusions

The isolation of a VACS organism in our setting was often not associated with documented water exposure, which has implications for empiric antimicrobial therapy. Severe disease and death were uncommon.
Culture-Free Whole Genome Sequencing of Mycobacterium tuberculosis Using Ligand-Mediated Bead Enrichment Method
Authors: Vasanthaiah Shruthi , Verma Renu , Kumar Ajay , Bandari Aravind K , George John , Rastogi Mona , Manjunath Gowrang Kasaba , Sharma Jyoti , Kumar Abhishek , Subramani Janavi , Chawla Kiran , Pandey Akhilesh
Published: June 2024

Background

Direct whole genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) can be used as a tool to study drug resistance, mixed infections, and within-host diversity. However, WGS is challenging to obtain from clinical samples due to low number of bacilli against a high background.

Methods

We prospectively collected 34 samples (sputum, n = 17; bronchoalveolar lavage, n = 13; and pus, n = 4) from patients with active tuberculosis (TB). Prior to DNA extraction, we used a ligand-mediated magnetic bead method to enrich Mtb from clinical samples and performed WGS on Illumina platform.

Results

Mtb was definitively identified based on WGS from 88.2% (30/34) of the samples, of which 35.3% (12/34) were smear negative. The overall median genome coverage was 15.2% (interquartile range [IQR], 7.7%–28.2%). There was a positive correlation between load of bacilli on smears and genome coverage (P < .001). We detected 58 genes listed in the World Health Organization mutation catalogue in each positive sample (median coverage, 85% [IQR, 61%–94%]), enabling the identification of mutations missed by routine diagnostics. Mutations causing resistance to rifampicin, isoniazid, streptomycin, and ethambutol were detected in 5 of 34 (14.7%) samples, including the rpoB S441A mutation that confers resistance to rifampicin, which is not covered by Xpert MTB/RIF.

Conclusions

We demonstrate the feasibility of magnetic bead–based enrichment for culture-free WGS of Mtb from clinical specimens, including smear-negative samples. This approach can also be integrated with low-cost sequencing workflows such as targeted sequencing for rapid detection of Mtb and drug resistance.