bluuebunny/crossref_metadata_2025 huggingface dataset:
Subcutaneous leiomyosarcoma in a cynomolgus macaque (Macaca fascicularis)
Authors: Lee Dong‐Ho , Mo Jun Won , Yoon Seung‐Bin , Kwon Jeongwoo , Jo Yu‐Jin , Lee Sang Il , Kwon Taeho , Kwon Jungkee , Kim Ji‐Su
Published: January 2024

Leiomyosarcoma, a malignant tumour originating from smooth muscle cells, has rarely been documented in non‐human primates. In this case study, a 7‐year‐old female cynomolgus macaque (Macaca fascicularis) presented with a rapidly growing mass overlying the left elbow joint. Radiographs indicated the presence of a soft tissue neoplasm without any associated bone involvement. The mass was surgically resected. Histological and immunohistochemical analyses revealed spindle‐shaped cells with eosinophilic cytoplasm that resembled smooth muscle cells, exhibiting positive immunoreactions for vimentin, desmin and smooth muscle actin and a negative reaction for pan‐cytokeratin. This is the first reported case of subcutaneous leiomyosarcoma in a cynomolgus macaque and provides important insights into the incidence and characteristics of this condition in this species.
Effect of an Escherichia coli–derived phytase and a carbohydrase–protease cocktail derived from Bacillus spp. on performance, digestibility, bone mineralization and gut morphology in broilers fed different nutrient density diets
Authors: Ahmadi Mostafa , Ghasemi Hossein Ali , Hajkhodadadi Iman , Khaligh Farhad
Published: January 2024

Background

Enzyme combinations, particularly phytase (PHY) with various carbohydrases and proteases, are utilized in commercial broiler production to enhance nutrient and energy bioavailability.

Objective

A feeding study was undertaken to determine whether the efficiency of an Escherichia coli–derived PHY and a feed enzyme complex (FEC) derived from Bacillus spp. containing carbohydrase and protease as main activities in broiler chickens is dependent on diet quality. A total of 900 male one‐day‐old broiler chickens (Ross 308) were assigned to a 2 × 3 factorial arrangement of the treatments with 2 different nutrient density diets, standard nutrient diet (SN diet) and a low‐nutrient diet (LN diet; −100 kcal/kg for AMEn and −5% for crude protein [CP] and limiting amino acids), and 3 enzyme treatments (control [no enzymes], PHY and PHY + FEC). Each treatment group was composed of 6 replicates of 25 birds each.

Results

The LN diet caused a decrease in performance index, tibia length and diameter, tibia calcium content and jejunal villus surface area (VSA). The interaction effects between diet and enzyme supplementation were observed (p < 0.05) on overall average daily gain (ADG), performance index, tibia ash content and jejunal villus height (VH) and VSA, with the favourable benefits of PHY + FEC treatment being more pronounced in the LN diets. Regardless of dietary nutrient density, supplementation with PHY alone or combined with FEC enhanced (p < 0.05) final body weight, overall ADG and jejunal villus height (VH)/crypt depth, with the highest values observed in the PHY + FEC group. The PHY + FEC treatment also improved (p < 0.05) overall feed conversion ratio, apparent ileal digestibility of dry matter, organic matter, CP, and energy, and tibia phosphorus content compared to the control treatment.

Conclusions

The results indicate that the simultaneous addition of PHY and FEC to the LN diets improved the growth rate, bone mineralization and gut morphology.
Genetic variants in the TAC1 transcriptional regulatory region affect on trainability and excitability levels in Belgian Malinois dogs
Authors: Fallahi Mohammad , Masoudi Ali Akbar , Torshizi Rasoul Vaez
Published: January 2024

Background

Trainability in dogs is affected by learning aptitude and memory capacity. While this trait has a heritable basis in canines, the specific genetic loci responsible for it remain unknown. Our previous results suggested that the BDNF, CCK and TAC1 genes are associated with learning and memory in canines. Experimental validation is crucial to confirm the effects of these candidate genes on trainability. Understanding the genetic foundation of this trait would offer insight into the inheritance pattern of complex behavioural characteristics.

Objective

This study aimed to assess the genetic variations within candidate genes and explore their potential associations with behavioural phenotypes in dogs.

Methods

The behavioural characteristics of 123 male Belgian Malinois dogs were assessed using a customised questionnaire. Target regions of candidate genes were screened for genetic variation by single‐strand conformational polymorphism (SSCP). Following that, SSCP banding patterns were sequenced, and putative transcription factor binding sites were predicted using bioinformatics tools. Quantitative association analysis between identified genetic variants and behavioural trait scores was performed using the general linear model (GLM).

Results

Sequencing the coding and flanking regions revealed three mutations (c.‐89C>T, c.‐162G>C and c.*33T>A) in the dog TAC1 gene. Bioinformatics analysis predicted two single nucleotide polymorphisms (SNPs) were located within the putative TAC1 promoter and could disrupt transcription factor binding sites. Statistical tests revealed that the c.‐89C>T was significantly associated with excitability (p < 0.01), while the c.‐162G>C was significantly associated with trainability level (p < 0.05).

Conclusion

In summary, we identified two regulatory SNPs in the 5'‐UTR promoter region of the TAC1 gene that are associated with excitability and trainability in Belgian Malinois dogs. These genetic variations have the potential to alter the binding sites of transcription factors NRF1 and OTX1, consequently influencing TAC1 expression and related behavioural characteristics. Our findings implicate TAC1 polymorphisms as candidates influencing breed‐specific behavioural characteristics in canines. Further studies on diverse breeds of dogs are necessary to validate these SNPs' effects.
Natural halloysite nanotubes decorated with organophosphorous for highly flame‐resistant epoxy composites
Authors: Ruan Li , Hu Dechao , Ma Wenshi
Published: January 2024

Highly flame‐resistant epoxy composites have important application value in many industrial fields. Unfortunately, epoxy resins (EPs) are inherently flammable materials and exhibit great fire hazard. In this study, the commercially available 9,10‐dihydro‐9‐oxa‐10‐phosphaphenanthrene‐10‐oxide (DOPO) was chemically immobilized on the surface of natural halloysite nanotubes (HNTs) via the linkage of vinyltrimethoxysilane to obtain a novel flame‐retardant VD@HNTs containing P/Si/Al elements. It was found that the flame‐retardant VD@HNTs can effectively improve the thermal stability and flame resistance of epoxy composites. Typically, when 10% of VD@HNTs is added in EP, the limiting oxygen index of as‐prepared VD@HNTs/EP composites reaches 30.3%, and it also successfully reaches V‐0 classification in the UL‐94 test. Besides, the ignition time of VD@HNTs/EP composites was enhanced from 42 s for pure EP to 60 s, and the maximum heat release rate was reduced from 1221 to 758 kW∙m−2. These great findings promise an innovative and efficient strategy for improving the fire safety of EP products and may also offer valuable insight toward fabricating various novel organic–inorganic flame retardants as well as highly flame‐resistant polymer composites.

Highlights

A novel flame‐retardant VD@HNTs containing P/Si/Al elements was prepared by the chemical decoration of HNTs with organophosphorous.

The VD@HNT can effectively improve the thermal stability and flame resistance of epoxy composites.

Synergistic flame‐retardant mechanism of phosphorus‐based flame retardants and natural HNTs was classified.
Ascomycetes yeasts: The hidden part of human microbiome
Authors: Nenciarini Stefano , Renzi Sonia , di Paola Monica , Meriggi Niccolò , Cavalieri Duccio
Published: January 2024

The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host–microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture‐dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal‐specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease.

This article is categorized under:

Immune System Diseases > Genetics/Genomics/Epigenetics

Immune System Diseases > Environmental Factors

Infectious Diseases > Environmental Factors
Condensation and evaporation of boson stars
Authors: Chan James Hung-Hsu , Sibiryakov Sergey , Xue Wei
Published: January 2024

Abstract

Axion-like particles, including the QCD axion, are well-motivated dark matter candidates. Numerical simulations have revealed coherent soliton configurations, also known as boson stars, in the centers of axion halos. We study evolution of axion solitons immersed into a gas of axion waves with Maxwellian velocity distribution. Combining analytical approach with controlled numerical simulations we find that heavy solitons grow by condensation of axions from the gas, while light solitons evaporate. We deduce the parametric dependence of the soliton growth/evaporation rate and show that it is proportional to the rate of the kinetic relaxation in the gas. The proportionality coefficient is controlled by the product of the soliton radius and the typical gas momentum or, equivalently, the ratio of the gas and soliton virial temperatures. We discuss the asymptotics of the rate when this parameter is large or small.
Effective field theory bootstrap, large-N χPT and holographic QCD
Authors: Li Yue-Zhou
Published: January 2024

Abstract

We review the effective field theory (EFT) bootstrap by formulating it as an infinite-dimensional semidefinite program (SDP), built from the crossing symmetric sum rules and the S-matrix primal ansatz. We apply the program to study the large-N chiral perturbation theory (χPT) and observe excellent convergence of EFT bounds between the dual (rule-out) and primal (rule-in) methods. This convergence aligns with the predictions of duality theory in SDP, enabling us to analyze the bound states and resonances in the ultra-violet (UV) spectrum. Furthermore, we incorporate the upper bound of unitarity to uniformly constrain the EFT space from the UV scale M using the primal method, thereby confirming the consistency of the large-N expansion. In the end, we translate the large-N χPT bounds to constrain the higher derivative corrections of holographic QCD models.
Newly emerged bumblebees are highly susceptible to gut parasite infection
Authors: Wolmuth-Gordon Hannah S , Nakabayashi Kazumi , Brown Mark JF
Published: January 2024

One factor that can affect infection susceptibility is host age, the effects of which vary in a range of ways. For example, susceptibility may increase with age, due to senescence or decrease with age as a result of maturation of the immune system. If certain ages are more susceptible to infection, populations with contrasting demographics, such as same-age cohorts versus a mixture of ages, will exhibit differing disease prevalence. We use the bumblebee, Bombus terrestris, and its interaction with the gut trypanosome Crithidia sp. as a model system to investigate age-related susceptibility in a social insect. Crithidia sp. are widespread and prevalent parasites of bumblebees that are spread between colonies via faeces on flowers when foraging, and within colonies via contact with infected bees and contaminated surfaces and resources. In the field, Bombus spp. live for approximately three weeks. Here, we inoculated bumblebees at 0, 7, 14 and 21 days of age and measured their infection after one week. We also measured the level of gene expression of two antimicrobial peptides important in the defence against Crithidia bombi in bumblebees. We found that younger bumblebees are more susceptible to infection by Crithidia sp. than their older siblings. Specifically, individuals inoculated on their first day of emergence had infection intensities seven days later that were four-fold higher than bees inoculated at 21 days of age. In contrast, the gene expression of two AMPs known to protect against the trypanosome, abaecin and defensin, did not significantly vary with age. These results suggest that age does affect susceptibility to Crithidia sp. infection in B. terrestris. The higher susceptibility of callows may have implications for the susceptibility of colonies at different stages of their lifecycle, due to the contrasting age demography of workers in the colony.
Insight into the mechanism of action of ORG27569 at the cannabinoid type one receptor utilising a unified mathematical model
Authors: Green Hayley M. , Yang Liang , Zhu Xiao , Finlay David B. , Duffull Stephen B. , Glass Michelle
Published: January 2024

Allosteric modulation of CB1 is therapeutically advantageous compared to orthosteric activation as it potentially offers reduced on-target adverse effects. ORG27569 is an allosteric modulator that increases orthosteric agonist binding to CB1 but decreases functional signalling. ORG27569 is characterised by a delay in disinhibition of agonist-induced cAMP inhibition (lag); however, the mechanism behind this kinetic lag is yet to be identified. We aimed to utilise a mathematical model to predict data and design in vitro experiments to elucidate mechanisms behind the unique signalling profile of ORG27569. The established kinetic ternary complex model includes the existence of a transitional state of CB1 bound to ORG27569 and CP55940 and was used to simulate kinetic cAMP data using NONMEM 7.4 and Matlab R2020b. These data were compared with empirical cAMP BRET data in HEK293 cells stably expressing hCB1. The pharmacometric model suggested that the kinetic lag in cAMP disinhibition by ORG27569 is caused by signal amplification in the cAMP assay and can be reduced by decreasing receptor number. This was confirmed experimentally, as reducing receptor number through agonist-induced internalisation resulted in a decreased kinetic lag by ORG27569. ORG27569 was found to have a similar interaction with CP55940 and the high efficacy agonist WIN55,212-2, and was suggested to have lower affinity for CB1 bound by the partial agonist THC compared to CP55940. Allosteric modulators have unique signalling profiles that are often difficult to interrogate exclusively in vitro. We have used a combined mathematical and in vitro approach to prove that ORG27569 causes a delay in disinhibition of agonist-induced cAMP inhibition due to large receptor reserve in this pathway. We also used the pharmacometric model to investigate the common phenomenon of probe dependence, to propose that ORG27569 binds with higher affinity to CB1 bound by high efficacy orthosteric agonists.
Disease Manifestations and Complications in Dutch X-Linked Hypophosphatemia Patients
Authors: Bosman A. , Appelman-Dijkstra N. M. , Boot A. M. , de Borst M. H. , van de Ven A. C. , de Jongh R. T. , Bökenkamp A. , van den Bergh J. P. , van der Eerden B. C. J. , Zillikens M. C.
Published: January 2024

X-linked hypophosphatemia (XLH) is the most common monogenetic cause of chronic hypophosphatemia, characterized by rickets and osteomalacia. Disease manifestations and treatment of XLH patients in the Netherlands are currently unknown. Characteristics of XLH patients participating in the Dutch observational registry for genetic hypophosphatemia and acquired renal phosphate wasting were analyzed. Eighty XLH patients, including 29 children, were included. Genetic testing, performed in 78.8% of patients, showed a PHEX mutation in 96.8%. Median (range) Z-score for height was − 2.5 (− 5.5; 1.0) in adults and − 1.4 (− 3.7; 1.0) in children. Many patients were overweight or obese: 64.3% of adults and 37.0% of children. All children received XLH-related medication e.g., active vitamin D, phosphate supplementation or burosumab, while 8 adults used no medication. Lower age at start of XLH-related treatment was associated with higher height at inclusion. Hearing loss was reported in 6.9% of children and 31.4% of adults. Knee deformities were observed in 75.0% of all patients and osteoarthritis in 51.0% of adult patients. Nephrocalcinosis was observed in 62.1% of children and 33.3% of adults. Earlier start of XLH-related treatment was associated with higher risk of nephrocalcinosis and detection at younger age. Hyperparathyroidism longer than six months was reported in 37.9% of children and 35.3% of adults. This nationwide study confirms the high prevalence of adiposity, hearing loss, bone deformities, osteoarthritis, nephrocalcinosis and hyperparathyroidism in Dutch XLH patients. Early start of XLH-related treatment appears to be beneficial for longitudinal growth but may increase development of nephrocalcinosis.
Phosphate-Solubilizing Bacillus sp. Modulate Soil Exoenzyme Activities and Improve Wheat Growth
Authors: Iqbal Zafar , Ahmad Maqshoof , Raza Muhammad Ali , Hilger Thomas , Rasche Frank
Published: January 2024

Phosphorus (P) is a vital mineral nutrient in agriculture and its deficiency results in reduced growth, yield, and grain quality in cereals. Much of the applied P in agriculture becomes fixed in soils, limiting its accessibility to plants. Thus, investigating sustainable strategies to release fixed P resources and enhance plant uptake is crucial. This study explored how plant-associated bacteria employ phosphate solubilizing mechanisms to improve P availability. The growth patterns of four bacterial strains, namely Bacillus subtilis ZE15 and ZR3, along with Bacillus megaterium ZE32 and ZR19, were examined in Pikovskaya’s broth culture with and without the addition of insoluble phosphorus (P). In the absence of P amendment, most strains reached a stationary growth phase by the fourth day. However, their responses diverged when exposed to P-amended media. Particularly, ZE15 demonstrated the highest P solubilization capability, achieving up to 130 µg mL−1 solubilization in vitro. All strains produced organic acids in Pikovskaya’s broth culture. A comparison of the influence of Ca3(PO4)2 revealed significantly greater organic acid quantities in the presence of insoluble P. Notably, strain ZE15 exhibited the highest phosphate esterase activity (3.65 nmol g−1 dry matter), while strain ZE32 showed the highest ß-D glucosidase activity (2.81 nmol g−1 dry matter) in the presence of insoluble P. The ability of Bacillus species to solubilize P in combination with increased exoenzyme activity in the rhizosphere could be used in future studies to support P uptake through enhanced solubilization and mineralization.
Dieback and Replacement of Riparian Trees May Impact Stream Ecosystem Functioning
Authors: Alonso Alberto , Boyero Luz , Solla Alejandro , Ferreira Verónica
Published: January 2024

Alders are nitrogen (N)-fixing riparian trees that promote leaf litter decomposition in streams through their high-nutrient leaf litter inputs. While alders are widespread across Europe, their populations are at risk due to infection by the oomycete Phytophthora ×alni, which causes alder dieback. Moreover, alder death opens a space for the establishment of an aggressive N-fixing invasive species, the black locust (Robinia pseudoacacia). Shifts from riparian vegetation containing healthy to infected alder and, eventually, alder loss and replacement with black locust may alter the key process of leaf litter decomposition and associated microbial decomposer assemblages. We examined this question in a microcosm experiment comparing three types of leaf litter mixtures: one representing an original riparian forest composed of healthy alder (Alnus lusitanica), ash (Fraxinus angustifolia), and poplar (Populus nigra); one with the same species composition where alder had been infected by P. ×alni; and one where alder had been replaced with black locust. The experiment lasted six weeks, and every two weeks, microbially driven decomposition, fungal biomass, reproduction, and assemblage structure were measured. Decomposition was highest in mixtures with infected alder and lowest in mixtures with black locust, reflecting differences in leaf nutrient concentrations. Mixtures with alder showed distinct fungal assemblages and higher sporulation rates than mixtures with black locust. Our results indicate that alder loss and its replacement with black locust may alter key stream ecosystem processes and assemblages, with important changes already occurring during alder infection. This highlights the importance of maintaining heathy riparian forests to preserve proper stream ecosystem functioning.
3000 leagues under the sea: the voyages of vagrant walruses (Odobenus rosmarus) in temperate Europe
Authors: Chiacchio Michele , Aae Rune
Published: January 2024

Sightings of vagrant walruses in Europe have been known since historic times, yet whether this phenomenon remains constant or changes over time is unclear. In this study, we conducted a comprehensive cross-reference of information on vagrant walruses observed in temperate Europe (below 61° N) between 1923 and 2022 utilising data from the Global Biodiversity Information Facility depository. In addition, we conducted an online search of records from the last ten years, resulting in a detailed reconstruction of the movements of the most recently observed individuals. We estimated that between 31 and 36 different individuals have been observed over the last century, with most of these likely originating from the Svalbard region and only a few from Greenland. A comparison in the yearly number of records showed a significant increase over time, suggesting that vagrant walruses reach Europe as a result of a combination of climatic and meteorological events as well as of demographic changes in the populations of the North Atlantic.
Truthful cake sharing
Authors: Bei Xiaohui , Lu Xinhang , Suksompong Warut
Published: January 2024

The classic cake cutting problem concerns the fair allocation of a heterogeneous resource among interested agents. In this paper, we study a public goods variant of the problem, where instead of competing with one another for the cake, the agents all share the same subset of the cake which must be chosen subject to a length constraint. We focus on the design of truthful and fair mechanisms in the presence of strategic agents who have piecewise uniform (i.e., approval) utilities over the cake. On the one hand, we show that the leximin solution is excludably truthful (meaning it is truthful when it can block each agent from accessing parts of the cake that the agent does not claim to desire) and moreover maximizes the guaranteed normalized egalitarian welfare among all excludably truthful and position oblivious mechanisms. On the other hand, we demonstrate that the maximum Nash welfare solution is excludably truthful for two agents (as it coincides with leximin in that case) but not in general. We also provide an impossibility result on truthfulness when blocking is not allowed, and adapt notions of representation to our setting.
Elevated Eosinophil Counts in Acute Exacerbations of Bronchiectasis: Unveiling a Distinct Clinical Phenotype
Authors: Chen Weixin , Ran Siyi , Li Chenchang , Li Zhixin , Wei Nili , Li Jing , Li Naijian
Published: January 2024

Background

Non-cystic fibrosis bronchiectasis is a chronic respiratory disease characterized by bronchial dilation. However, the significance of elevated eosinophil counts in acute exacerbations of bronchiectasis remains unclear.

Methods

This retrospective case-control study included 169 hospitalized patients with acute exacerbations of non-cystic fibrosis bronchiectasis. Based on blood eosinophil levels, patients were categorized into eosinophilic and non-eosinophilic bronchiectasis groups. Various clinical variables, including lung function, comorbidities and clinical features were collected for analysis. The study aimed to examine the differences between these groups and their clinical phenotypes.

Results

Eosinophilic bronchiectasis (EB) was present in approximately 22% of all hospitalized patients with bronchiectasis, and it was more prevalent among male smokers (P < 0.01). EB exhibited greater severity of bronchiectasis, including worse airway obstruction, higher scores in the E-FACED (FACED combined with exacerbations) and bronchiectasis severity index (BSI), a high glucocorticoids medication possession ratio, and increased hospitalization cost (P < 0.05 or P < 0.01). Furthermore, we observed a significant positive correlation between blood eosinophil count and both sputum eosinophils (r = 0.49, P < 0.01) and serum total immunoglobulin E levels (r = 0.21, P < 0.05). Additional analysis revealed that patients with EB had a higher frequency of shortness of breath (P < 0.05), were more likely to have comorbid sinusitis (P < 0.01), and exhibited a greater number of lung segments affected by bronchiectasis (P < 0.01).

Conclusions

These findings suggest that EB presents a distinct pattern of bronchiectasis features, confirming the notion that it is a specific phenotype.
Why identification matters: an explorative study on six cases of family reunification
Authors: Franceschetti Lorenzo , Mazzarelli Debora , Ragni Chiara , Paltenghi Francesca , Pecoraro Andrea , Albani Denise , Giuffrida Roberto , Siccardi Cecilia , Polizzi Nicolò , Di Simone Paola , D’Apuzzo Annalisa , Mandrioli Daniele , Buscemi Martina , D’Amico Marilisa , Viarengo Ilaria , Cattaneo Cristina
Published: January 2024

The escalating phenomenon of migration, accompanied by a disturbing surge in associated tragedies, has persistently violated internationally protected human rights. Absence of physical evidence, namely the presence of adequately identified corpses, may impede the full enjoyment of human rights and—in some cases—the course of justice as it obstructs the initiation of legal proceedings against individuals implicated in causing such catastrophes. It also presents administrative obstacles, as death certificates are indispensable in legitimizing statuses like orphanhood and widowhood. Family reunification, particularly for orphans, plays a significant role for those attempting to reconnect with their relatives all over the world. Likewise, for mothers, the acknowledgment of their marital status or widowhood can be a pathway to regain their marginalized right to social life. To elucidate this issue, we analyzed six representative cases from the tragic October 3, 2013, shipwreck near the Italian island of Lampedusa, where 366 individuals were retrieved dead from the sea. These cases underscore the practical challenges involved, highlighting the compelling need for continued efforts to ensure that this burdensome problem transcends from being a mere ethical, moral, and legal discourse. Although considerable progresses, these cases also reveal that substantial work still lies ahead. There is a pressing need for improved mechanisms to certify kinship ties, which are often the limiting factor in many reunifications, and can hinder the granting of custody to children. The severity and far-reaching implications of this problem necessitate thoughtful attention and action, especially considering the ongoing escalation in migration and related fatalities.
Brecciation and fracturing by water ingress into the Genbudo basaltic andesitic lava flow, Iwate volcano, northeastern Japan
Authors: Hoshide Takashi , Ishibashi Nao , Iwahashi Keisuke
Published: January 2024

The Genbudo lava, the late Pleistocene basaltic-andesitic lava flow in the southwestern part of Iwate Volcano, Japan, is a 70 m thick columnar jointed flow that can be divided into three parts from bottom to top: the colonnade, the entablature, and the partly-brecciated uppermost part. Two main types of fractures developed in the entablature: pseudopillow fractures that formed in a branching network-like pattern throughout the entablature, and sheet fractures with curved surfaces that are nearly parallel to each other. At the uppermost part of the flow, finger-like structures of lava extend upward from the coherent lava, and cogenetic autoclastic rocks form between the fingers. This occurrence suggests that hyaloclastites were generated during emplacement in the uppermost part of the flow, apparently when water from a dammed river valley covered the flow. The texture of the lava near the pseudopillow fractures in the entablature is commonly hypocrystalline, while the texture in other parts is holocrystalline. There are two types of pyroxene microlites, large prismatic (average size ~ 30 µm) and dendritic (< 10 µm in length) crystals in the lava near the pseudopillow fractures. These suggest that the cooling rate of the lava was greatest in the vicinity of the pseudopillow fractures. Networks of palagonite-filled micro-fractures (less than 10 µm in width) are found in this part of the flow, and many bubbles are observed along the fractures. This is clear evidence that the rapid cooling of the lava was caused by water infiltration through the pseudopillow fractures. From the measurement of Fe-rich droplet sizes that formed due to liquid immiscibility within the lava, we estimate the cooling rate within the colonnade as about 49 °C/h and within the entablature as 642 °C/h, consistent with much more rapid cooling by water infiltration from above.
Neural network classification of eigenmodes in the magnetohydrodynamic spectroscopy code Legolas
Authors: De Jonghe J. , Kuczyński M. D.
Published: January 2024

A neural network is employed to address a non-binary classification problem of plasma instabilities in astrophysical jets, calculated with the code. The trained models exhibit reliable performance in the identification of the two instability types supported by these jets. We also discuss the generation of artificial data and refinement of predictions in general eigenfunction classification problems.
Patients with a large ossification of the posterior longitudinal ligament have a higher incidence of arteriosclerosis in the carotid artery
Authors: Oshima Yasushi , Doi Toru , Ohtomo Nozomu , Ito Yusuke , Nakajima Koji , Nagata Kosei , Kato So , Taniguchi Yuki , Matsubayashi Yoshitaka , Tanaka Sakae
Published: January 2024

Purpose

This study aimed to investigate the impact of the severity of cervical ossification of the posterior longitudinal ligament (OPLL) on the incidence of arteriosclerosis in the carotid artery.

Methods

Patients with OPLL-induced cervical myelopathy were prospectively enrolled. The study involved analyzing patient characteristics, blood samples, computed tomography scans of the spine, and intima-media thickness (IMT) measurements of the common carotid artery. Patients were divided into two groups based on the size of the cervical OPLL to compare demographic data, comorbidities, and the presence of thickening of the carotid intima-media (max IMT ≥ 1.1 mm).

Results

The study included 96 patients (mean age: 63.5 years; mean body mass index: 26.9 kg/m2; 71.8% male; 35.4% with diabetes mellitus). The mean maximum anteroposterior (AP) diameter of the OPLL was 4.9 mm, with a mean occupancy ratio of 43%. The mean maximum IMT was 1.23 mm. Arteriosclerosis of the carotid artery was diagnosed in 62.5% of the patients. On comparing the two groups based on OPLL size, the group with larger OPLL (≥ 5 mm) had a higher BMI and a greater prevalence of carotid intima-media thickening. This significant difference in the prevalence of carotid intima-media thickening persisted even after adjusting for patient backgrounds using propensity score matching.

Conclusions

Patients with a larger cervical OPLL showed a higher frequency of intima-media thickening in the carotid artery.
Microsatellites reveal high levels of genetic admixture in the natural populations of Laurus azorica, Lauraceae
Authors: Rego Rúben M. C. , Vieira Ângela F. , Silva Luís , Elias Rui , Silva Carlos , Resendes Roberto , Moura Mónica
Published: January 2024

Laurus (Lauraceae) species are currently restricted to isolated refugia in the southern Black Sea, Mediterranean Basin, southern Morocco, and Macaronesian archipelagos. One to three species of Laurus has been recognized: the Azorean endemic Laurus azorica, L. nobilis from the Mediterranean, and L. novocanariensis from Madeira and the Canary Islands. This study aims to determine the population structure, genetic diversity, and associated patterns of gene flow within and between Azorean populations, using eight existing SSR markers. We also included plant material from L. nobilis populations found in the Azores, for comparison. Amplification was performed in 212 samples of L. azorica and in 30 samples of L. nobilis. For L. azorica, 78 alleles were amplified (average 9.75 alleles per loci). Bayesian analysis with STRUCTURE unveiled five genetic groups for the Azorean accessions, with high level of genetic admixture. Genetic diversity was generally high, with moderate levels of genetic differentiation among L. azorica populations. Moreover, high gene flow levels, likely mediated by past human translocations and naturally, by birds, might have contributed to the high level of genetic admixture observed possibly reflecting hybridization events between L. nobilis and L. azorica. Conservation measures should be applied to some populations of São Miguel, Santa Maria, and Flores Islands, based on the number of private alleles, and further, ad hoc translocation events should be avoided. Conservation in situ and the preservation of laurel forest remains are recommended. The study of this species’ taxonomy, genetics, and population dynamics in the Macaronesian region should be continued.
Flexible active-site loops fine-tune substrate specificity of hyperthermophilic metallo-oxidases
Authors: Brissos Vânia , Borges Patrícia T. , Sancho Ferran , Lucas Maria Fátima , Frazão Carlos , Conzuelo Felipe , Martins Lígia O.
Published: January 2024

Hyperthermophilic (‘superheat-loving’) archaea found in high-temperature environments such as Pyrobaculum aerophilum contain multicopper oxidases (MCOs) with remarkable efficiency for oxidizing cuprous and ferrous ions. In this work, directed evolution was used to expand the substrate specificity of P. aerophilum McoP for organic substrates. Six rounds of error-prone PCR and DNA shuffling followed by high-throughput screening lead to the identification of a hit variant with a 220-fold increased efficiency (kcat/Km) than the wild-type for 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) without compromising its intrinsic activity for metal ions. The analysis of the X-ray crystal structure reveals four proximal mutations close to the T1Cu active site. One of these mutations is within the 23-residues loop that occludes this site, a distinctive feature of prokaryotic MCOs. The increased flexibility of this loop results in an enlarged tunnel and one additional pocket that facilitates bulky substrate-enzyme interactions. These findings underscore the synergy between mutations that modulate the dynamics of the active-site loop enabling enhanced catalytic function. This study highlights the potential of targeting loops close to the T1Cu for engineering improvements suitable for biotechnological applications.

Graphical Abstract
Development and Validation of a 3D Resnet Model for Prediction of Lymph Node Metastasis in Head and Neck Cancer Patients
Authors: Lin Yi-Hui , Lin Chieh-Ting , Chang Ya-Han , Lin Yen-Yu , Chen Jen-Jee , Huang Chun-Rong , Hsu Yu-Wei , You Weir-Chiang
Published: January 2024

The accurate diagnosis and staging of lymph node metastasis (LNM) are crucial for determining the optimal treatment strategy for head and neck cancer patients. We aimed to develop a 3D Resnet model and investigate its prediction value in detecting LNM. This study enrolled 156 head and neck cancer patients and analyzed 342 lymph nodes segmented from surgical pathologic reports. The patients’ clinical and pathological data related to the primary tumor site and clinical and pathology T and N stages were collected. To predict LNM, we developed a dual-pathway 3D Resnet model incorporating two Resnet models with different depths to extract features from the input data. To assess the model’s performance, we compared its predictions with those of radiologists in a test dataset comprising 38 patients. The study found that the dimensions and volume of LNM + were significantly larger than those of LNM-. Specifically, the Y and Z dimensions showed the highest sensitivity of 84.6% and specificity of 72.2%, respectively, in predicting LNM + . The analysis of various variations of the proposed 3D Resnet model demonstrated that Dual-3D-Resnet models with a depth of 34 achieved the highest AUC values of 0.9294. In the validation test of 38 patients and 86 lymph nodes dataset, the 3D Resnet model outperformed both physical examination and radiologists in terms of sensitivity (80.8% compared to 50.0% and 91.7%, respectively), specificity(90.0% compared to 88.5% and 65.4%, respectively), and positive predictive value (77.8% compared to 66.7% and 55.0%, respectively) in detecting individual LNM + . These results suggest that the 3D Resnet model can be valuable for accurately identifying LNM + in head and neck cancer patients. A prospective trial is needed to evaluate further the role of the 3D Resnet model in determining LNM + in head and neck cancer patients and its impact on treatment strategies and patient outcomes.
Detecting Avascular Necrosis of the Lunate from Radiographs Using a Deep-Learning Model
Authors: Wernér Krista , Anttila Turkka , Hulkkonen Sina , Viljakka Timo , Haapamäki Ville , Ryhänen Jorma
Published: January 2024

Deep-learning (DL) algorithms have the potential to change medical image classification and diagnostics in the coming decade. Delayed diagnosis and treatment of avascular necrosis (AVN) of the lunate may have a detrimental effect on patient hand function. The aim of this study was to use a segmentation-based DL model to diagnose AVN of the lunate from wrist postero-anterior radiographs. A total of 319 radiographs of the diseased lunate and 1228 control radiographs were gathered from Helsinki University Central Hospital database. Of these, 10% were separated to form a test set for model validation. MRI confirmed the absence of disease. In cases of AVN of the lunate, a hand surgeon at Helsinki University Hospital validated the accurate diagnosis using either MRI or radiography. For detection of AVN, the model had a sensitivity of 93.33% (95% confidence interval (CI) 77.93–99.18%), specificity of 93.28% (95% CI 87.18–97.05%), and accuracy of 93.28% (95% CI 87.99–96.73%). The area under the receiver operating characteristic curve was 0.94 (95% CI 0.88–0.99). Compared to three clinical experts, the DL model had better AUC than one clinical expert and only one expert had higher accuracy than the DL model. The results were otherwise similar between the model and clinical experts. Our DL model performed well and may be a future beneficial tool for screening of AVN of the lunate.
Mixta mediterraneensis as a novel and abundant gut symbiont of the allergen-producing domestic mite Blomia tropicalis
Authors: Erban Tomas , Sopko Bruno , Klimov Pavel B. , Hubert Jan
Published: January 2024

Blomia tropicalis is an allergen-producing mite in the human environment in tropical regions. The microbiome of B. tropicalis was described using the barcode sequencing region of V4 16S rDNA and genome assemblage. Mixta mediterraneensis, previously isolated from human skin swabs, was identified as a B. tropicalis gut symbiont based on genome assembly. The microbiome contains two bacteria, Staphylococcus and M. mediterraneensis. The number of M. mediterraneensis 16S DNA copies was 106 per mite and 109 per feces in the rearing chamber based on qPCR quantification. The profile of this bacterium reached 50% of reads in the mite gut and feces. Genomic analyses revealed that the bacterium has several metabolic pathways that suggest metabolic cooperation with the mite host in vitamin and amino acid synthesis, nitrogen recycling, and antimicrobial defense. Lysozyme is present in the symbiotic bacterium but absent in the mite. The B. tropicalis microbiome contained Staphylococcus, which accelerates mite population growth. Mites can digest Staphylococcus by using specific enzymes with hydrolytic functions against bacterial cell walls (chitinases and cathepsin D), leading to endocytosis of bacteria and their degradation in lysosomes and phagosomes. Gene expression analysis of B. tropicalis indicated that phagocytosis was mediated by the PI3-kinase/Akt pathway interacting with the invasins produced by M. mediterraneensis. Moreover, the symbiont had metabolic pathways that allowed it to recycle the mite metabolic waste product guanine, known as a mite attractant. The mite host symbiont enhances mite aggregation in the feces, and the fecal–oral transmission route is excepted.
Key Grazing Behaviours of Beef Cattle Identify Specific Genotypes of the Glutamate Metabotropic Receptor 5 Gene (GRM5)
Authors: Moreno García Cristian Anibal , Perelman Susana Beatríz , Dynes Robyn , Maxwell Thomas M. R. , Zhou Huitong , Hickford Jonathan
Published: January 2024

Genotype-phenotype associations between the bovine genome and grazing behaviours measured over time and across contexts have been reported in the past decade, with these suggesting the potential for genetic control over grazing personalities in beef cattle. From the large array of metrics used to describe grazing personality behaviours (GP-behaviours), it is still unclear which ones are linked to specific genes. Our prior observational study has reported associations and trends towards associations between genotypes of the glutamate metabotropic receptor 5 gene (GRM5) and four GP-behaviours, yet the unbalanced representation of GRM5 genotypes occurring in observational studies may have limited the ability to detect associations. Here, we applied a subsampling technique to create a genotypically-balanced dataset in a quasi-manipulative experiment with free ranging cows grazing in steep and rugged terrain of New Zealand’s South Island. Using quadratic discriminant analysis, two combinations of eleven GP-behaviours (and a total of fifteen behaviours) were selected to build an exploration model and an elevation model, respectively. Both models achieved ∼ 86% accuracy in correctly discriminating cows’ GRM5 genotypes with the training dataset, and the exploration model achieved 85% correct genotype prediction of cows from a testing dataset. Our study suggests a potential pleiotropic effect, with GRM5 controlling multiple grazing behaviours, and with implications for the grazing of steep and rugged grasslands. The study highlights the importance of grazing behavioural genetics in cattle and the potential use of GRM5 markers to select individuals with desired grazing personalities and built herds that collectively utilize steep and rugged rangelands sustainably.
Evaluation of a virtual reality training tool for firefighters responding to transportation incidents with dangerous goods
Authors: Berthiaume Maxine , Kinateder Max , Emond Bruno , Cooper Natalia , Obeegadoo Ishika , Lapointe Jean-François
Published: January 2024

Access to dangerous goods training for firefighters in remote areas is limited for financial and logistical reasons. Virtual reality (VR) is a promising solution for this challenge as it is cost-effective, safe, and allows to simulate realistic scenarios that would be dangerous or difficult to implement in the real world. However, rigorous evaluations of VR training tools for first responders are still scarce. In this exploratory user study, a simple VR training tool involving two dangerous goods scenarios was developed. In each scenario, trainees learned how to safely approach a jackknifed truck with a trailer and how to collect and communicate information about the transported materials. The tool was tested with a group of 24 professional firefighter trainees (n = 22) and instructors (n = 2), who each completed the two training scenarios. The main goal of the study was to assess the usability of the VR tool in the given scenarios. Participants provided feedback on cybersickness, perceived workload, and usability. They also filled out a knowledge test before and after the VR training and gave feedback at the end of the study. The VR tool recorded task completion duration and participants’ navigation and use of tools events. Overall, the tool provided good usability, acceptance, and satisfaction. However, a wide range in individuals’ responses was observed. In addition, no post-training improvement in participants' knowledge was found, likely due to the already high level of knowledge pre-training. Future directions for improving the VR tool, general implications for other VR training tools, and suggestions for future research are discussed.
Mountain masses as a determinant to genetic structure of char distributed in the Chugoku region, Japan
Authors: Kawai Koichiro , Matsuo Mahiro , Fujiwara Kazuki , Tani Shotaro , Tada Shohei , Saito Hidetoshi
Published: January 2024

A mountain mass from which multiple river basins originate is a possible determinant of genetic structure of freshwater fishes. In this study, subspecies composition and genetic structure were examined for Japanese white-spotted char comprising of two subspecies, Salvelinus leucomaenis imbrius (Jordan and McGregor), “Gogi,” and S. l. pluvius (Hilgendorf), “Nikkoiwana,” collected in the 19 river basins originating from 6 mountain masses in the Chugoku Region, Japan, based on mitochondrial DNA sequences. In the western mountain masses, only Gogi was collected, while in the eastern mountain mass, only Nikkoiwana was collected. A total of 27 haplotypes were detected, among which only seven were shared by two subspecies and three were detected only in Nikkoiwana whereas 17 were detected only in Gogi. As many as 11 haplotypes were distributed only in the Oyorogi Mountain mass in the middle region. In the network, one group was exclusively constructed by the samples from the Oyorogi Mountain mass. Furthermore, in a tree of river basins based on average genetic distance of char, the Gono River basin originating from the Asa Mountain mass, situated in the western region, participated in a clade constructed by the rivers originating from the westernmost Sukegatake and the adjacent Asa Mountain masses, whereas the Gono River basin originating from the Oyorogi Mountain mass participated in a different clade constructed by the rivers originating from the Oyorogi to the easternmost Hyonosen Mountain masses. These results suggest that a mountain mass is a determinative factor to subspecies composition and genetic structure of char, with an implication of invasion of fish taking advantage of some geological events or conditions.