Miracle-dz/UniFAR-FTUs huggingface dataset:
Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil.

Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4T and GMJ5T, were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4T and GMJ5T were both positive for catalase and oxidase. Strain PBS4-4T grew at 15-37 °C and pH 5.0-12.0. Strain GMJ5T grew at 15-37 °C and pH 5.0-11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4T and GMJ5T form a closely related cluster with the genus Chryseobacterium. The average nucleotide identity and digital DNA-DNA hybridization values between strain PBS4-4T and its closely related strains were 79.4-84.5% and 23.2-28.7 %, respectively. For GMJ5T, the values were 78.3-79.3% and 22.0-22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Strain GMJ5T had one other major fatty acid: iso-C17 : 0 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4T and GMJ5T represent novel species within the genus Chryseobacterium, and the names Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov. are proposed, respectively. The type strain of C. edaphi is PBS4-4T (=KACC 22882T=TBRC 17052T) and the type strain of C. gilvum is GMJ5T (=KACC 22883T=TBRC 17053T).
Clinical implications of gallbladder enlargement in Kawasaki disease

Kawasaki disease (KD) presents with gallbladder enlargement (GBE) or hydrops in the acute phase. Although GBE is highly specific to KD, epidemiological data on GBE have not been updated. In this study we evaluated the occurrence rate of GBE in KD and characterized the clinical features of patients who developed GBE.
Explorative Synthetic Biology in AI: Criteria of Relevance and a Taxonomy for Synthetic Models of Living and Cognitive Processes

Abstract This article tackles the topic of the special issue “Biology in AI: New Frontiers in Hardware, Software and Wetware Modeling of Cognition” in two ways. It addresses the problem of the relevance of hardware, software, and wetware models for the scientific understanding of biological cognition, and it clarifies the contributions that synthetic biology, construed as the synthetic exploration of cognition, can offer to artificial intelligence (AI). The research work proposed in this article is based on the idea that the relevance of hardware, software, and wetware models of biological and cognitive processes—that is, the concrete contribution that these models can make to the scientific understanding of life and cognition—is still unclear, mainly because of the lack of explicit criteria to assess in what ways synthetic models can support the experimental exploration of biological and cognitive phenomena. Our article draws on elements from cybernetic and autopoietic epistemology to define a framework of reference, for the synthetic study of life and cognition, capable of generating a set of assessment criteria and a classification of forms of relevance, for synthetic models, able to overcome the sterile, traditional polarization of their evaluation between mere imitation and full reproduction of the target processes. On the basis of these tools, we tentatively map the forms of relevance characterizing wetware models of living and cognitive processes that synthetic biology can produce and outline a programmatic direction for the development of “organizationally relevant approaches” applying synthetic biology techniques to the investigative field of (embodied) AI.
Ontogeny reveals the origin of Gemminger bones in Mormyridae

Mormyridae are well known and intensively studied for their weak electric organ discharges, which facilitate communication and orientation. The Gemminger bones of Mormyridae are located next to the electrical organ in the caudal peduncle; however, they have not attracted much interest until recently. Therefore, we investigated the diversity of Gemminger bones in mormyrids and studied their ontogenetic development in Mormyrus rume proboscirostris. Gemminger bones are paired, thin, elongated ossifications lying on the dorsal and ventral sides of the caudal peduncle, and usually reach anterior well below the dorsal and anal fin bases. Ontogeny revealed that they are not intermuscular ossifications, as suspected based on the anatomical position of this structure and the systematic position of the mormyrids. Instead, they are membrane ossifications that originate from the fin stays of the dorsal and anal fins.
Infrared and visible images fusion based on visual saliency map and NSCT

A fusion algorithm of infrared and visible images based on visual saliency map (VSM) and nonsubsampled contourlet transform (NSCT) was proposed. Usually, the visual salient region of infrared image is directed towards the targets which interpret the most important information in the image. For the given registered infrared and visible images, firstly, the frequency-tuned (FT) saliency detection algorithm is used to calculate the visual saliency map of infrared and visible images. Then the size of each salient region is obtained by maximizing entropy. In order to capture the details of the infrared and visible images, the low and high frequency fusion coefficients of nonsubsampled contourlet transform (NSCT) are selected based on region saliency, region energy (RE) and region sharpness (RS). Four different data sets from TNO, Human Factors are employed, and experimental results indicate that the proposed method can achieve a superior performance compared with other fusion methods in both subjective and objective assessments.
Feline herpesvirus 1 (FHV-1) enters the cell by receptor-mediated endocytosis

ABSTRACT Feline herpesvirus type 1 (FHV-1) is an enveloped dsDNA virus belonging to the Herpesviridae family and is considered one of the two primary viral etiological factors of feline upper respiratory tract disease. In this study, we investigated the entry of FHV-1 into host cells using two models: the AK-D cell line and primary feline skin fibroblasts (FSFs). We employed confocal microscopy, siRNA silencing, and selective inhibitors of various entry pathways. Our observations revealed that the virus enters cells via pH and dynamin-dependent endocytosis, as the infection was significantly inhibited by NH4Cl, bafilomycin A1, dynasore, and mitmab. Additionally, genistein, nystatin, and filipin treatments, siRNA knock-down of caveolin-1, as well as FHV-1 and caveolin-1 colocalization suggest the involvement of caveolin-mediated endocytosis during the entry process. siRNA knock-down of clathrin heavy chain and analysis of virus particle colocalization with clathrin indicated that clathrin-mediated endocytosis also takes part in the primary cells. This is the first study to systematically examine FHV-1 entry into host cells, and for the first time, we describe FHV-1 replication in AK-D and FSFs. IMPORTANCE Feline herpesvirus 1 (FHV-1) is one of the most prevalent viruses in cats, causing feline viral rhinotracheitis, which is responsible for over half of viral upper respiratory diseases in cats and can lead to ocular lesions resulting in loss of sight. Although the available vaccine reduces the severity of the disease, it does not prevent infection or limit virus shedding. Despite the clinical relevance, the entry mechanisms of FHV-1 have not been thoroughly studied. Considering the limitations of commonly used models based on immortalized cells, we sought to verify our findings using primary feline skin fibroblasts, the natural target for infection in cats. Feline herpesvirus 1 (FHV-1) is one of the most prevalent viruses in cats, causing feline viral rhinotracheitis, which is responsible for over half of viral upper respiratory diseases in cats and can lead to ocular lesions resulting in loss of sight. Although the available vaccine reduces the severity of the disease, it does not prevent infection or limit virus shedding. Despite the clinical relevance, the entry mechanisms of FHV-1 have not been thoroughly studied. Considering the limitations of commonly used models based on immortalized cells, we sought to verify our findings using primary feline skin fibroblasts, the natural target for infection in cats.
Midfrontal theta as an index of conflict strength in approach–approach vs avoidance–avoidance conflicts

Abstract The seminal theory of motivational conflicts distinguishes between approach–approach (AP-AP) conflicts, in which a decision is made between desirable alternatives, and avoidance–avoidance (AV-AV) conflicts, in which a decision is made between undesirable alternatives. The behavioral differences between AP-AP and AV-AV conflicts are well documented: abundant research showed that AV-AV conflicts are more difficult to resolve than AP-AP ones. However, there is little to no research looking into the neural underpinnings of the differences between the two conflict types. Here, we show that midfrontal theta, an established neural marker of conflict, distinguished between the two conflict types such that midfrontal theta power was higher in AV-AV conflicts than in AP-AP conflicts. We further demonstrate that higher midfrontal theta power was associated with shorter decision times on a single-trial basis, indicating that midfrontal theta played a role in promoting successful controlled behavior. Taken together, our results show that AP-AP and AV-AV conflicts are distinguishable on the neural level. The implications of these results go beyond motivational conflicts, as they establish midfrontal theta as a measure of the continuous degree of conflict in subjective decisions.
Loss of Mtm1 causes cholestatic liver disease in a model of X-linked myotubular myopathy

X-linked myotubular myopathy (XLMTM) is a fatal congenital disorder caused by mutations in the MTM1 gene. Currently, there are no approved treatments, although AAV8-mediated gene transfer therapy has shown promise in animal models and preliminarily in patients. However, 4 patients with XLMTM treated with gene therapy have died from progressive liver failure, and hepatobiliary disease has now been recognized more broadly in association with XLMTM. In an attempt to understand whether loss of MTM1 itself is associated with liver pathology, we have characterized what we believe to be a novel liver phenotype in a zebrafish model of this disease. Specifically, we found that loss-of-function mutations in mtm1 led to severe liver abnormalities including impaired bile flux, structural abnormalities of the bile canaliculus, and improper endosome-mediated trafficking of canalicular transporters. Using a reporter-tagged Mtm1 zebrafish line, we established localization of Mtm1 in the liver in association with Rab11, a marker of recycling endosomes, and canalicular transport proteins and demonstrated that hepatocyte-specific reexpression of Mtm1 could rescue the cholestatic phenotype. Last, we completed a targeted chemical screen and found that Dynasore, a dynamin-2 inhibitor, was able to partially restore bile flow and transporter localization to the canalicular membrane. In summary, we demonstrate, for the first time to our knowledge, liver abnormalities that were directly caused by MTM1 mutation in a preclinical model, thus establishing the critical framework for better understanding and comprehensive treatment of the human disease.
Reliable Multi-label Classification: Prediction with Partial Abstention

In contrast to conventional (single-label) classification, the setting of multilabel classification (MLC) allows an instance to belong to several classes simultaneously. Thus, instead of selecting a single class label, predictions take the form of a subset of all labels. In this paper, we study an extension of the setting of MLC, in which the learner is allowed to partially abstain from a prediction, that is, to deliver predictions on some but not necessarily all class labels. We propose a formalization of MLC with abstention in terms of a generalized loss minimization problem and present first results for the case of the Hamming loss, rank loss, and F-measure, both theoretical and experimental.
Subjective Visual Vertical test with the 3D virtual reality system: effective factors and cybersickness

Abstract Background 3D Virtual Reality (VR) offers new opportunities in vestibular science. It also presents new challenges and problems. Aims/objectives The study aimed to evaluate the effective factors in the 3D VR Subjective Visual Vertical (SVV) test and the impact of cybersickness on the test results. Material and methods The effect of the foam surface, head position in the yaw axis, moving background, and arm position holding the controller was tested. Cybersickness was evaluated using the Simulator Sickness Questionnaire (SSQ). Results The head position and controller holding style significantly affected the results. The foam surface and the moving background did not have a significant effect. Although 61.4% of the patients fell into the bad category according to the symptoms of the SSQ score, cybersickness did not significantly affect the SVV results. Conclusions and significance In 3D VR SVV, additional factors should be considered: the headset’s weight, head position, and how we hold the controller. The A-effect emerged when the head was 45 degrees turned on the yaw axis. A significant shift was detected in the test, with the arm holding the controller at 90 degrees. Most subjects felt cybersickness at a considerable level. Cybersickness should always be taken into account in VR when planning new applications.
Structure of Our Galactic Bulge from CN Measurements

The double red clumps (DRCs) are now dominantly believed to be the strong observational line of evidence of the so-called X-shaped Galactic bar structures. Recently, Lee et al. reported a subtle mean δCN(3839) difference between the DRCs and suggested a dichotomic picture that can be seen in globular clusters: the faint red clump is the first generation, while the bright red clump corresponds to the second generation (SG). They argued that the magnitude difference between the DRCs is due to different stellar populations, and is not due to the geometric difference between the DRCs. Our reanalysis shows that their data do not appear to support the idea of multiple population-induced DRCs in our Galactic bulge. We perform fully empirical Monte Carlo simulations and find that the shape of the δCN(3839) distributions is the most stringent evidence to pursue. Our results strongly suggest that the CN distributions toward the Galactic bulge are qualitatively consistent with the X-shaped Galactic bulge with a minor fraction of the SG of about 2%–3%.
Simulation of dielectric properties of poly(vinylidene fluoride)

ABSTRACT The dynamic Monte-Carlo method for three-dimensional lattice model of rotators with anisotropic intra- and interchain interactions of dipole type is used to investigate dielectric properties of poly(vinylidene fluoride) in β-phase. Hysteresis curves are calculated. It is shown that the area of hysteresis curve in strong electric fields increases with the increase of interchain interactions.
Factors Mediating or Moderating the Effects of Obesity on Walking: Targeting Areas for Rehabilitation

Abstract Increased physical activity, such as walking, is often prescribed to address obesity. Several factors that may influence the connection between obesity and walking include the biomechanics of gait, pain, depressive symptoms, physical health, and activity. The objective of this study was to assess the moderation and mediation effects of knee pain and buckling, depressive symptoms, physical activity, and physical health on spatiotemporal gait parameters in individuals with obesity. Forty participants with obesity performed a task in which they walked on flat ground and crossed an obstacle. Measures of knee pain and buckling, depressive symptoms, physical activity, and physical health were collected. We conducted mediation analyses with knee buckling and pain as mediators of the effect of the BMI on spatiotemporal gait parameters. Moderation analyses were performed with depressive symptoms, physical activity, and physical health as moderators of the effect of BMI on spatiotemporal gait parameters. We found that depressive symptoms and physical health moderated the relationship between BMI and Step Width in people with obesity. These effects were pronounced when participants crossed an obstacle. In conclusion, depressed mood and physical health influence the relationship between obesity and walking. These factors present potential avenues for rehabilitation interventions to aid individuals with obesity.
Epistasis-based Basis Estimation Method for Simplifying the Problem Space of an Evolutionary Search in Binary Representation

An evolutionary search space can be smoothly transformed via a suitable change of basis; however, it can be difficult to determine an appropriate basis. In this paper, a method is proposed to select an optimum basis can be used to simplify an evolutionary search space in a binary encoding scheme. The basis search method is based on a genetic algorithm and the fitness evaluation is based on the epistasis, which is an indicator of the complexity of a genetic algorithm. Two tests were conducted to validate the proposed method when applied to two different evolutionary search problems. The first searched for an appropriate basis to apply, while the second searched for a solution to the test problem. The results obtained after the identified basis had been applied were compared to those with the original basis, and it was found that the proposed method provided superior results.
The rat Achilles and patellar tendons have similar increases in mechanical properties but become transcriptionally divergent during postnatal development

The molecular events that drive post‐natal tendon development are poorly characterized. In this study, we profiled morphological, mechanical, and transcriptional changes in the rat Achilles and patellar tendon before walking (P7), shortly after onset of walking (P14), and at motor maturity (P28). The Achilles and patellar tendons increased collagen content and mechanical strength similarly throughout post‐natal development. However, at P28 the patellar tendon tended to display a higher maximal tensile load (MTL) (P = 0.0524) than the Achilles tendon, but a similar ultimate tensile strength (UTS; load relative to cross‐sectional area) probably due to its increased cross‐sectional area during development. The tendons started transcriptionally similar, with overlapping PCA clusters at P7 and P14, before becoming transcriptionally distinct at P28. In both tendons, there was an increase in extracellular matrix (ECM) gene expression and a concomitant decrease in cell cycle and mitochondrial gene expression. The transcriptional divergence at P28 suggested that STAT signalling was lower in the patellar tendon where MTL increased the most. Treating engineered human ligaments with the STAT inhibitor itacitinib increased collagen content and MTL. Our results suggest that during post‐natal development, cellular resources are initially allocated towards cell proliferation before shifting towards extracellular matrix development following the onset of mechanical load and provide potential targets for improving tendon function.
Interaction of Filamin C With Actin Is Essential for Cardiac Development and Function

BACKGROUND: FLNC (filamin C), a member of the filamin family predominantly expressed in striated muscles, plays a crucial role in bridging the cytoskeleton and ECM (extracellular matrix) in cardiomyocytes, thereby maintaining heart integrity and function. Although genetic variants within the N-terminal ABD (actin-binding domain) of FLNC have been identified in patients with cardiomyopathy, the precise contribution of the actin-binding capability to FLNC’s function in mammalian hearts remains poorly understood. METHODS: We conducted in silico analysis of the 3-dimensional structure of mouse FLNC to identify key amino acid residues within the ABD that are essential for FLNC’s actin-binding capacity. Subsequently, we performed coimmunoprecipitation and immunofluorescent assays to validate the in silico findings and assess the impact of these mutations on the interactions with other binding partners and the subcellular localization of FLNC. Additionally, we generated and analyzed knock-in mouse models in which the FLNC-actin interaction was completely disrupted by these mutations. RESULTS: Our findings revealed that F93A/L98E mutations completely disrupted FLNC-actin interaction while preserving FLNC’s ability to interact with other binding partners ITGB1 (β1 integrin) and γ-SAG (γ-sarcoglycan), as well as maintaining FLNC subcellular localization. Loss of FLNC-actin interaction in embryonic cardiomyocytes resulted in embryonic lethality and cardiac developmental defects, including ventricular wall malformation and reduced cardiomyocyte proliferation. Moreover, disruption of FLNC-actin interaction in adult cardiomyocytes led to severe dilated cardiomyopathy, enhanced lethality and dysregulation of key cytoskeleton components. CONCLUSIONS: Our data strongly support the crucial role of FLNC as a bridge between actin filaments and ECM through its interactions with actin, ITGB1, γ-SAG, and other associated proteins in cardiomyocytes. Disruption of FLN-actin interaction may result in detachment of actin filaments from the extracellular matrix, ultimately impairing normal cardiac development and function. These findings also provide insights into mechanisms underlying cardiomyopathy associated with genetic variants in FLNC ABD and other regions.
Promotor methylation in ocular surface squamous neoplasia development: epigenetics implications in molecular diagnosis

ABSTRACT Introduction Cancer is heavily influenced by epigenetic mechanisms that include DNA methylation, histone modifications, and non-coding RNA. A considerable proportion of human malignancies are believed to be associated with global DNA hypomethylation, with localized hypermethylation at promoters of certain genes. Area covered The present review aims to emphasize on recent investigations on the epigenetic landscape of ocular surface squamous neoplasia, that could be targeted/explored using novel approaches such as personalized medicine. Expert opinion While the former is thought to contribute to genomic instability, promoter-specific hypermethylation might facilitate tumorigenesis by silencing tumor suppressor genes. Ocular surface squamous neoplasia, the most prevalent type of ocular surface malignancy, is suggested to be affected by epigenetic mechanisms, as well. Although the exact role of epigenetics in ocular surface squamous neoplasia has mostly been unexplored, recent findings have greatly contributed to our understanding regarding this pathology of the eye.