Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear aging in polyglutamine-induced neurodegeneration

Machado-Joseph disease (MJD) is an autosomal dominantly-inherited neurodegenerative disorder characterized by an over-repetition of the CAG trinucleotide of the ATXN3 gene, conferring a toxic gain-of-function to the resulting ataxin-3 protein. Despite the significant advances produced over the last years, the molecular mechanisms involved in MJD are still unclear and no treatment able to modify the disease progression is available. Aging is the major risk factor for neurodegenerative disorders, being associated with the occurrence and progression of several diseases, such as Alzheimer’s, Huntington’s, among others. The nuclear membrane proteins - lamins - and lamin-processing related proteins, such as ZMPSTE24, have been shown to be altered, not only during normal aging, but also in neurodegenerative disorders, such as Alzheimer’s disease. Taking this into account, we aimed at investigating the role of aging in MJD by evaluating the presence of age-related markers in human and animal MJD models. Decreased levels of lamins B and C, together with decreased ZMPSTE24 levels were identified in the different MJD models. Accordingly, abnormalities in nuclear circularity, a hallmark of aging, were also observed in a N2a MJD cellular model, supporting an age-related phenotype. Furthermore, overexpressing progerin, the abnormal lamin A, generated in Hutchinson Guilford Progeria Syndrome patients that present premature and accelerated aging, in a relevant brain area of a lentiviral MJD mouse model, induced an aggravation of MJD-associated neuropathology. Our results suggest that aging is a key player in the context of MJD pathogenesis, unveiling new pathways for the development of future therapies for the disease.
PP2A-B55SUR-6 promotes nuclear envelope breakdown in C. elegans embryos

Nuclear envelope (NE) disassembly during mitosis is critical to ensure faithful segregation of the genetic material. NE disassembly is a phosphorylation-dependent process wherein mitotic kinases hyper-phosphorylate lamina and nucleoporins to initiate nuclear envelope breakdown (NEBD). In this study, we uncover an unexpected role of the PP2A phosphatase B55SUR-6 in NEBD during the first embryonic division of Caenorhabditis elegans embryo. B55SUR-6 depletion delays NE permeabilization and stabilizes lamina and nucleoporins. As a result, the merging of parental genomes and chromosome segregation is impaired. This NEBD defect upon B55SUR-6 depletion is not due to delayed mitotic onset or mislocalization of mitotic kinases. Importantly, we demonstrate that microtubule-dependent mechanical forces synergize with B55SUR-6 for efficient NE disassembly. Finally, our data suggest that the lamin LMN-1 is likely a bona fide target of PP2A-B55SUR-6. These findings establish a model highlighting biochemical cross-talk between kinases, PP2A-B55SUR-6 phosphatase, and microtubule-generated mechanical forces in timely NE dissolution.
Using a Riemannian elastic metric for statistical analysis of tumor cell shape heterogeneity

We examine how a specific instance of the elastic metric, the Square Root Velocity (SRV) metric, can be used to study and compare cellular morphologies from the contours they form on planar surfaces. We process a dataset of images from osteocarcoma (bone cancer) cells that includes different treatments known to affect the cell morphology, and perform a comparative statistical analysis between the linear and SRV metrics. Our study indicates superior performance of the SRV at capturing the cell shape heterogeneity, with a better separation between different cell groups when comparing their distance to their mean shape, as well as a better low dimensional representation when comparing stress statistics. Therefore, our study suggests the use of a Riemannian metric, such as the SRV as a potential tool to enhance morphological discrimination for large datasets of cancer cell images.
CHPF boosts proliferation and invasion of clear cell renal cell carcinoma

Background Clear cell renal cell carcinoma (ccRCC) is a malignant tumor most commonly seen in the urinary system, featuring quick progression, invasive behavior, frequent recrudesce, and bad prognosis, whereas Chondroitin polymerizing factor (CHPF) is an essential glycosyl transferase of biosynthesis involved chondroitin sulphate. But the relationship between the two has not been fully understood so far. The present research will probe into the relationship between CHPF and ccRCC. Methods Explore the CHPF expression level in renal ccRCC tissues through bioinformatics analysis of The Cancer Genome Atlas (TCGA) and the real-time quantitative polymerase chain reaction detection system (qPCR); acquire relevant clinical data from the TCGA data-base and use Kaplan-Meier survival analysis to verify the relevance of CHPF expression to the clinical prognosis of ccRCC patients; then, effectively silence CHPF in ccRCC 786-O cells by a lentivirus-mediated approach; next, observe the effects of CHPF on tumor cell proliferation, cell cycle progression, and apoptosis. Results In ccRCC tissues, CHPF expression has been significantly upregulated; the higher expression, the shorter survival of ccRCC patients. CHPF downregulation in the 786-O cell can effectively hold back the proliferation, apoptosis and cycle of cancer cells. Conclusion Based on the above results, we arrive at a conclusion that CHPF expression contributes markedly to the development of human ccRCC cells. Therefore, CHPF may act as a potential prognostic marker of ccRCC and provide a new target for ccRCC treatment. Simple Summary Chondroitin polymerizing factor (CHPF) is an important glycosyltransferase involved in the biosynthesis of chondroitin sulfate, which is thought to have some pro-carcinogenic effects. However, the role and mechanism of CHPF in clear cell renal cell carcinoma (ccRCC) have not been reported. The aim of this study was to investigate the relationship between CHPF and ccRCC. In this study, we found that CHPF was highly expressed in ccRCC and knocking out CHPF can greatly inhibit the proliferation and cell cycle progression of ccRCC and accelerate its apoptosis, suggesting that CHPF can predict the prognosis of ccRCC and a potential target for treatment.
The effects of data leakage on connectome-based machine learning models

Predictive modeling has now become a central technique in neuroimaging to identify complex brain-behavior relationships and test their generalizability to unseen data. However, data leakage, which unintentionally breaches the separation between data used to train and test the model, undermines the validity of predictive models. Previous literature suggests that leakage is generally pervasive in machine learning, but few studies have empirically evaluated the effects of leakage in neuroimaging data. Although leakage is always an incorrect practice, understanding the effects of leakage on neuroimaging predictive models provides insight into the extent to which leakage may affect the literature. Here, we investigated the effects of leakage on machine learning models in two common neuroimaging modalities, functional and structural connectomes. Using over 400 different pipelines spanning four large datasets and three phenotypes, we evaluated five forms of leakage fitting into three broad categories: feature selection, covariate correction, and lack of independence between subjects. As expected, leakage via feature selection and repeated subjects drastically inflated prediction performance. Notably, other forms of leakage had only minor effects (e.g., leaky site correction) or even decreased prediction performance (e.g., leaky covariate regression). In some cases, leakage affected not only prediction performance, but also model coefficients, and thus neurobiological interpretations. Finally, we found that predictive models using small datasets were more sensitive to leakage. Overall, our results illustrate the variable effects of leakage on prediction pipelines and underscore the importance of avoiding data leakage to improve the validity and reproducibility of predictive modeling.
African Swine Fever Virus major capsid p72 Trimers function as a pH sensor during uncoating process of virus endocytosis

African swine fever virus (ASFV) belongs to nucleocytoplasmic large DNA viruses (NCLDVs), the only member of Asfarviridae. So far, it is revealed that the ASFV uncoating is a pH-dependent process undergone in late endosomes. But, the research on how pH affects capsid stability is limited, and which protein plays an essential role in pH sensing remains unknown. In this study, we identified the main component of the ASFV capsid -- major capsid protein p72, as a pH sensitive residue abundance protein, and it is speculated that the conformational change of the p72 trimer is possibly responsible for the ASFV uncoating process. To test this speculation, we obtained recombinant p72 trimers, treated with the acidic environment that simulated endosomes and displayed structural analysis. The results showed that the p72 trimer depolymerized at low pH. The depolymerization of trimers rationally explains the disassembly mechanism of the ASFV icosahedral capsid in endosomes.
Assessing annual trends, monthly fluctuations and between‐station relationship of sulphate deposition in the Turkey Lakes Watershed

Water deposition of pollutants can be a good indicator of both air and water quality in a region of interest. In this paper, we study sulphate deposition change over time in a network of multiple monitoring stations in the Turkey Lakes Watershed in Sault Ste. Marie, Ontario, Canada. As there is generally substantial correlation among sulphate deposition observed over time and space, we incorporate temporally correlated multivariate random effects into Gamma regression models to account for the temporal dependence within each station and between‐station dependence in space. We applied our new approach to analyse monthly average sulphate depositions between 1983 and 2003. We found the observed increase of sulphate deposition between 1994 and 2003 was not significant, that is, annual trends in sulphate deposition had stabilized since 1994. Our analysis also quantified increasing sulphate deposition from upstream to downstream and its monthly fluctuations from higher in winter to lower in summer. Understanding of these sulphate deposition trends is of great policy relevance to environmental conservation. Copyright © 2016 John Wiley & Sons, Ltd.
Gender, Values and Power in Local Environmental Conflicts: The Case of Grassroots Organisations in North Catalonia

Not much attention has been paid to gender in environmental management and decision-making. This article explores how a gender dimension can contribute to the environmental debate by means of a comparative study of three environmental grassroots organisations in the North of Catalonia (Spain). The study shows that gender is significant for distinguishing different priorities between women and men in local conflicts and in environmental interests in general. The analysis of unequal power relations between genders in grassroots organisations leads us to discuss how women have fewer opportunities to influence the environmental debate and to advance their ideas. The concluding thoughts stress the need for developing a gender dimension in environmental management and decision-making, considering the opportunities that are presented by emerging governance practices, and particularly by participatory processes.
Jet noise computation based on enhanced DES formulations accelerating the RANS-to-LES transition in free shear layers

The paper presents jet noise computations performed using the original and some recently proposed modified formulations of detached-eddy simulation, based on alternative definitions of the subgrid length-scale and/or a modified version of the subgrid Spalart-Allmaras model, which involves the Wall-Adapting Local Eddy-viscosity model. The modifications are aimed at the elimination or, at least, a significant weakening of a known flaw of detached-eddy simulation, namely, the severe delay of the Kelvin–Helmholtz instability and transition from fully modeled to mostly resolved turbulence in the free and separated shear layers. This flaw makes the original detached-eddy simulation formulation, in fact, non-applicable to the prediction of the noise of high Reynolds number jet flows when typical grids are used, and has led to the use of Implicit Large-Eddy Simulation instead. Based on examples of application of these modifications to such flows, already available in the literature, they were found capable of resolving the issue and providing quite accurate predictions of the aerodynamic characteristics and turbulent statistics of the high-Re jets. The study performed in the present work allows us to draw a similar conclusion regarding the accuracy of the enhanced detached-eddy simulation formulations in terms of jet-noise prediction. The new formulation gives noise results very close to those of ILES except at the highest frequencies, while being more general and less sensitive to grid resolution. In addition, it removes a (1–3) dB underestimation of the noise spectral maximums for the peak radiation direction, which is typical of ILES on fine grids.
GAMs and functional kriging for air quality data

In environmental sciences data having spatio-temporal structure are often observed. They can be considered as discrete observations from curves along time and/or space and treated as functional. Generalized Additive Models (GAMs)represent a useful tool for modelling, for example, pollutant concentrations and describing their spatial and/or temporal trends.Very often the prediction of a curve at an unmonitored site is necessary. At this aim we extend kriging for functional data to a multivariate context. Actually, even if we are interested only in predicting a single pollutant, for example PM10, exploiting its correlation with the other pollutants can improve the estimation. Cross validation is used to test the performance of the proposed procedure.
Integrating Compassion and Theoretical Premises of Caring Science into Undergraduate Health Professions Education

Compassion and caring are critical foundational concepts for the education of health professions students. Yet many curricula emphasize skill-based learning and test-taking preparation, which often limits the opportunities for students to practice compassionately caring for themselves and others. In 2019, an elective wellness course was introduced into a School of Nursing and Health Professions curriculum to provide students with the knowledge, understanding, and practice of self-compassion and caring as the foundation for holistically caring for others. The goal of the course is to use ethics, values, and ontological competencies of self-compassion and Caritas literacy to awaken students to their being, not just doing, and how it evolves throughout their professional careers. Narrative feedback from students demonstrated a deeper understanding of the necessity for compassion and caring for self to provide compassionate care to others.
Providing Emotional Support to Parents and Caregivers of Infants and Toddlers With Visual Impairments

When a baby is diagnosed with a visual impairment, parents and caregivers are likely to experience a host of overwhelming feelings. They may have urgent questions about the child’s medical care and concerns about how the child will develop and learn. Early intervention visual impairment practitioners (teachers of students with visual impairments and orientation and mobility specialists who provide early intervention services) may meet families during a vulnerable and uncertain period. According to McMilliam and Scott (2001), early interventionists offer informational, material, and emotional supports to families. Early intervention visual impairment practitioners may provide information about the type and severity of a child’s visual impairment and possible influences of vision loss on overall development. They may share information about ways to promote use of functional vision, compensatory skills, and how to obtain or adapt materials to help the child learn. Practitioners may also assist the family in finding relevant services and resources and in addressing material needs such as food, housing, and financial support. They may help families access emotional support through established services in early intervention and from informal family and community networks. Based on required professional competencies (Division for Early Childhood, 2020) early interventionists prepared by early intervention or early childhood special education programs are likely to feel confident and competent to provide informational and material supports to families. However, they may be less prepared to provide emotional support and be challenged by the complexities of family situations (Brotherson et al., 2010; Lee, 2015). Practitioners in visual impairment are trained to serve children of all ages so may not be adequately prepared for early intervention practices (Anthony, 2014; Ely et al., 2020; Ely & Ostrosky, 2018), unless they have had specific training or professional development. Given these training gaps, the authors reflected on their professional experiences mentoring early interventionists from various disciplines including early intervention visual impairment
“Scanning from Heating” and “Shape from Fluorescence”: Two Non-Conventional Imaging Systems for 3D Digitization of Transparent Objects

3D surface acquisition is a subject which has been studied to a large extent. A significant number of techniques for acquiring shape have been proposed, and a wide range of commercial solutions are available. Nevertheless, today’s systems still have difficulties when digitizing objects with non-Lambertian surfaces in the visible light spectrum, as is the case of transparent, semi-transparent or highly reflective materials (e.g. glass, crystals, some plastics and shiny metals). In this chapter, some of the issues of traditional scanning systems are addressed by considering various approaches using the radioactive properties of materials, the polarization information of the reflected light as well as the generated fluorescence applied D. Fofi Université de Bourgogne, France I. Mohammed Université de Bourgogne, France O. Morel Université de Bourgogne, France C. Stolz Université de Bourgogne, France F. Truchetet Université de Bourgogne, France
Wing flutter calculations with the CAP-TSD unsteady transonic small disturbance program

The paper describes the application and assessment of the recently-developed CAP-TSD transonic small-disturbance code for flutter prediction. The CAP-TSD program has been developed for aeroelastic analysis of complete aircraft configurations and was previously applied lo the calculation of steady and unsteady pressures with favorable results. Flutter calculations are presented for two thin, sweptand-tapered wing planforms with well-defined modal properties. The calculations are for Mach numbers from low subsonic to low supersonic values, including the transonic range. and are compared with subsonic linear theory and experimental flutter data. The CAP-TSD flutter results are generally in good agreement with the experimental values and are in good agreement with subsonic linear theory when wing thickness is neglected.
Translational Models in Glioma Immunotherapy Research

Immunotherapy is a promising therapeutic domain for the treatment of gliomas. However, clinical trials of various immunotherapeutic modalities have not yielded significant improvements in patient survival. Preclinical models for glioma research should faithfully represent clinically observed features regarding glioma behavior, mutational load, tumor interactions with stromal cells, and immunosuppressive mechanisms. In this review, we dive into the common preclinical models used in glioma immunology, discuss their advantages and disadvantages, and highlight examples of their utilization in translational research.
Duality and Subgroups

The second author proved, in [27], a duality theorem for general locally compact groups as a generalization of the so-called Tannaka duality theorem for compact groups. In the proof, the regular representation plays an essential role. In order to clarify the role of the regular representation in duality theory, the first author gave, in [23], a characterization of group algebras in terms of a Hopf-von Neumann algebra and showed that the abelian von Neumann algebra L-(G) of all essentially bounded functions on a locally compact group G together with the co-multiplication 6, the involution j and the Haar measure f involves the duality principle for the given group G. In this paper we shall examine, by showing a correspondence between closed subgroups and subalgebras of the Hopf-von Neumann algebra {L-(G), a, j}, how this duality principle works for subgroups. For a locally compact abelian group G, the Pontryagin duality theorem shows that there is a beautiful and complete one-to-one correspondence between a closed subgroup H of G and a closed subgroup H I of the dual group G such that
Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species

Noctuidae is known to have high species diversity, although the genomic diversity of Noctuidae species has yet to be studied extensively. Investigation of transposable elements (TEs) in this family can improve our understanding of the genomic diversity of Noctuidae. In this study, we annotated and characterized genome-wide TEs in ten noctuid species belonging to seven genera. With multiple annotation pipelines, we constructed a consensus sequence library containing 1038–2826 TE consensus. The genome content of TEs showed high variation in the ten Noctuidae genomes, ranging from 11.3% to 45.0%. The relatedness analysis indicated that the TE content, especially the content of LINEs and DNA transposons, is positively correlated with the genome size (r = 0.86, p-value = 0.001). We identified SINE/B2 as a lineage-specific subfamily in Trichoplusia ni, a species-specific expansion of the LTR/Gypsy subfamily in Spodoptera exigua, and a recent expansion of SINE/5S subfamily in Busseola fusca. We further revealed that of the four TE classes, only LINEs showed phylogenetic signals with high confidence. We also examined how the expansion of TEs contributed to the evolution of noctuid genomes. Moreover, we identified 56 horizontal transfer TE (HTT) events among the ten noctuid species and at least three HTT events between the nine Noctuidae species and 11 non-noctuid arthropods. One of the HTT events of a Gypsy transposon might have caused the recent expansion of the Gypsy subfamily in the S. exigua genome. By determining the TE content, dynamics, and HTT events in the Noctuidae genomes, our study emphasized that TE activities and HTT events substantially impacted the Noctuidae genome evolution.
A New Algorithm of Moving Target Detection in Image Sequence Based on the Lifting Scheme

In surveillance system, moving target detection in image sequence is a very significant and difficult problem. The objective of this research was to present a new detection method to enhance the efficiency and accuracy of moving target recognition,and to resolve the difficulties brought by target distortion. The detail theory and algorithm of a new detection method, which was based on the lifting scheme of wavelet and deformable template technique, were described. The multi-scale images were used to improve the target matching efficiency, and the deformable templates were used to tracking the target distortions. The results indicated that the moving objects detected by the new method based on the lifting scheme were more robust than those detected by traditional methods. In addition, the detection speed became more rapid. The results seem to suggest that the new method be with efficiency and accuracy advantages in computer version.