Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Epidemics of Citrus Tristeza Virus (CTV) in Young Citrus Groves Exposed to Aphid Infestation under Different Climatic Conditions in Reunion Island

Le virus de la Tristeza des agrumes (CTV) est tres repandu a l'ile de la Reunion ou Toxoptera citricidus, vecteur le plus efficace de la maladie ainsi que d'autres especes d'aphides sont presents. Des souches severes du virus affectant la longevite et la productivite d'especes d'agrumes sensibles au virus ont ete signalees. Afin de suivre l'etendue naturelle du CTV sous differentes conditions ecologiques, diverses parcelles experimentales ont ete plantees avec des agrumes issus de pepinieres indemnes de Tristeza en quatre emplacements differents et des aphides ont ete signales sur les jeunes pousses vegetatives. Le pourcentage d'arbres infectes une annee apres plantation a varie de 21 a 100% dans 6 vergers ou a ete utilise le test ELISA pour la detection du CTV. La distribution spatiale des arbres malades a l'interieur des parcelles s'est faite generalement au hasard. Les aphides predominants infestant les jeunes limettiers a basse altitude (150 m) ont ete T. citricidus, tandis que Aphis sp. et Macrosiphum euphorbiae ont ete plus frequents a des altitudes plus elevees (800 m)
Group-level Speech Emotion Recognition Utilising Deep Spectrum Features

The objectives of this challenge paper are two fold: first, we apply a range of neural network based transfer learning approaches to cope with the data scarcity in the field of speech emotion recognition, and second, we fuse the obtained representations and predictions in a nearly and late fusion strategy to check the complementarity of the applied networks. In particular, we use our Deep Spectrum system to extract deep feature representations from the audio content of the 2020 EmotiW group level emotion prediction challenge data. We evaluate a total of ten ImageNet pre-trained Convolutional Neural Networks, including AlexNet, VGG16, VGG19 and three DenseNet variants as audio feature extractors. We compare their performance to the ComParE feature set used in the challenge baseline, employing simple logistic regression models trained with Stochastic Gradient Descent as classifiers. With the help of late fusion, our approach improves the performance on the test set from 47.88 % to 62.70 % accuracy.
Fractionated small cell‐free DNA increases possibility to detect cancer‐related gene mutations in advanced colorectal cancer

Liquid biopsy is a method that can efficiently detect tumor genetic abnormalities from body fluids such as blood and urine. Detection sensitivity and the available number of mutations in cell‐free DNA (cfDNA) are limited. In this study, we develop a highly sensitive and comprehensive method to detect mutations from cfDNA by concentrating tumor fractions of small cfDNA in advanced colorectal cancers.
Autocrine signaling by receptor tyrosine kinases in urothelial carcinoma of the bladder

Comprehensive characterizations of bladder cancer (BCa) have established molecular phenotype classes with distinct alterations and survival trends. Extending these studies within the tyrosine kinase (TK) family to identify disease drivers could improve our use of TK inhibitors to treat specific patient groups or individuals. We examined the expression distribution of TKs as a class (n = 89) in The Cancer Genome Atlas (TCGA) muscle invasive BCa data set (n >400). Patient profiles of potentially oncogenic alterations (overexpression and/or amplification) clustered TKs into 3 groups; alterations of group 1 and 3 TKs were associated with significantly worse patient survival relative to those without alterations. Many TK pathways induce epithelial-to-mesenchymal transition (EMT), which promotes tumor invasiveness and metastasis. Overexpression and/or amplification among 9 EMT transcriptional activators occurred in 43% of TCGA cases. Co-occurring alterations of TKs and EMT transcriptional activators involved most group 1 TKs; 24% of these events were associated with significantly worse patient survival. Co-occurring alterations of receptor TKs and their cognate ligands occurred in 16% of TCGA cases and several BCa-derived cell lines. Suppression of GAS6, MST1 or CSF1, or their respective receptors (AXL, MST1R and CSF1R), in BCa cell lines was associated with decreased receptor activation, cell migration, cell proliferation and anchorage independent cell growth. These studies reveal the patterns and prevalence of potentially oncogenic TK pathway-related alterations in BCa and identify specific alterations associated with reduced BCa patient survival. Detection of these features in BCa patients could better inform TK inhibitor use and improve clinical outcomes.
Multivariate distributions of behavioural, morphological, and ontogenetic traits in hybrids bring new insights into the divergence of sympatric Arctic charr morphs

Studying the development of fitness related traits in hybrids from populations diverging in sympatry is a fundamental approach to understand the processes of speciation. However, such traits are often affected by covariance structures that complicate the comprehension of these processes, especially because the interactive relationships between traits of different nature (e.g. morphology, behaviour, life-history) remain largely unknown in this context. In a common garden setup, we conducted an extensive examination of phenotypic traits suspected to be involved in the divergence of two recently evolved morphs of Arctic charr (Salvelinus alpinus), and investigated the consequences of potential patterns of trait covariance on the phenotype of their hybrids. We observed differences among morphs in overall phenotypic variance and in trait correlations. Phenotypic contrainsts also tended to be reduced in the hybrids, which corroborates the narrative of hybridization facilitating adaptive divergence by relaxing trait covariance. However, the hybrids were associated with reduced phenotypic variance at different scales (i.e. at the scale of the entire P matrix and in different parts of the multivariate space), and we identified stronger correlations between several ontogenetic and morphological traits in the hybrids than in both morphs. These findings suggest a limited potential for hybridization to generate phenotypic novelty, and emphasise the need for multivariate approaches conciliating ontogenetic, morphological and behavioural processes to study the processes of adaptive divergence and speciation.
Friends’ Closeness and Intimacy From Adolescence to Adulthood: Art Captures Implicit Relational Representations in Joint Drawing: A Longitudinal Study

This longitudinal study, employing a mixed-methods explanatory design, explored the power of art to express aspects of one’s inner world using the joint drawing technique, which allows for observation and treatment of implicit representations of relationships. At Time 1 (T1, 1977–1978), 200 adolescents created a joint drawing with either a good friend or with a classmate who was not a friend and filled out the Intimate Friendship Scale (IFS) in relation to their best friend. In 2014 (T2), 36 women and 21 men from the original cohort completed the IFS with regard to a good friend and with regard to their spouse. The drawings were analyzed qualitatively to define pictorial phenomena that may be indicative of closeness. The analysis was conducted in accordance with the phenomenological approach to art therapy and with the principles of thematic analysis. Fourteen pictorial phenomena were defined, and a scale was constructed to quantitatively evaluate the extent to which each phenomenon was present in the joint drawing. This yielded a closeness score for each drawing. Quantitatively, no correlations were found between intimacy as measured by IFS at T1 and at T2. In contrast, there was a correlation between the degree of closeness in the joint drawing at T1, and the IFS score with the partner in T2, suggesting continuity over the 36-year time span. This correlation was likewise found when examined separately among participants who drew with a friend. The multivariate ANOVA (MANOVA) results showed a marginally significant effect for the interaction between closeness in drawing and drawing with a friend/non-friend – on IFS. An ANOVA showed that the IFS regarding the participant’s best friend and their romantic partner at T2 was higher when the closeness in the drawing at T1 was higher. There was also a significant interaction between closeness in the drawings and the participant’s IFS score regarding their best friend at T1. The differences between the joint drawing with the close friend and the non-friend are discussed. These findings, from a span of over 36 years, thus contribute to the validity of the IFS and the joint drawing technique when assessing closeness and intimacy.
Influences of Environmental and Social Factors on Perceived Bio-Cultural Services and Disservices

Although the value of urban ecological infrastructure (UEI) is widely recognized, insufficient research has investigated how people perceive the wide variety of UEI. To address this gap, we investigated residents’ perceptions of the coupled value of aesthetic and biological qualities as related to diverse UEI and other environmental and social factors (including personal beliefs and demographics), collectively referred to as bio-cultural services and disservices. We evaluated whether people positively view their neighborhood environments as natural-looking while providing diverse plants and wildlife habitat (services), in contrast to negatively perceived disservices that we evaluated as messy-looking with weeds and pests (disservices). We analyzed survey data from residents (n = 495) in metropolitan Phoenix, Arizona, United States, coupled with environmental variables (UEI and vegetative cover) compiled from diverse sources. We ran three regression models to compare the relative influence of social and environmental factors independently and combined on the perception of bio-cultural services and disservices. Our results demonstrate the influence of social factors, particularly place identity, neighborhood cohesion, and income, on both bio-cultural services and disservices. Additionally, environmental factors such as vegetation cover increased perceptions of bio-cultural services while decreasing perceived disservices. The effects of proximity to UEI were more varied. While proximity to cropland increased perceived bio-cultural disservices, proximity to desert parks reduced disservices. Although UEI can promote biodiversity and human well-being, all UEI are not perceived the same. Our results underscore the added value of considering both the form of UEI and perceptions among people who live nearby when designing and implementing infrastructure to promote bio-cultural services that are both ecologically and socially valued.
Corticosteroids Improve Renal Survival: A Retrospective Analysis From Chinese Patients With Early-Stage IgA Nephropathy

Background: The efficacy and safety of corticosteroids and immunosuppressive therapy remain controversial for the treatment of immunoglobulin A nephropathy (IgAN). This study aimed to evaluate the effects of corticosteroid and immunosuppressant therapy in Chinese patients with early-stage IgAN whose estimated glomerular filtration rate (eGFR) was ≥45 ml/min/1.73 m2 and proteinuria was ≥1 g/24 h at biopsy. Methods: Patients with biopsy-proven IgAN were retrospectively enrolled from four study centers between 2007 and 2016. Patients were regularly followed up for at least 1 year or until the study end point. Patients were categorized into three treatment groups: supportive care (SC), steroids alone (CS), and steroids plus immunosuppressants (IT). The observed responses to therapy included complete remission (CR), partial remission (PR), no response (NR), and end-stage renal disease (ESRD). The primary end point of the current study was defined as a 50% decline in eGFR and/or ESRD. Results: A total of 715 patients (male 47% and female 53%) were recruited and followed up for 44.69 ± 24.13 months. The observed CR rate was 81.8% with corticosteroids alone (CS), 62.7% with corticosteroids + immunosuppresants (IT), and 37% with supportive care alone (SC). Renal outcomes were remarkably better in the CS group compared with the SC and IT groups (the percentage of patients reaching the end point in each group was 4.6 vs. 14.4 vs. 11.5%, respectively; p = 0.001). Moreover, 36 and 80-month renal survival were significantly better for the CS group (98.3 and 86.4%) than for the IT (94.2 and 82.4%) and SC (94.0 and 51.6%) groups. Early CKD stage also presented with better kidney survival (p < 0.001). Renal survival of CKD stage 1 patients was relatively good regardless of the specific treatment regimen. CS and IT treatment significantly improved renal survival for CKD stage 2 patients when compared with the SC group (p < 0.001 and 0.007, respectively). However, renal survival of CKD stage 3a patients was not impacted by any of the three treatment regimens. Subgroup analysis also showed that renal survival of patients with proteinuria >3.5 g, M1, E0, S1, T0, and C0 was significantly better in the CS group than in the SC and IT groups. A multivariate model showed that hypertension, serum creatinine, E1 lesion, and T1/T2 lesion remained independent predictors of poor renal survival. Conclusions: Immunosuppressive therapy does not have further benefit beyond that provided by steroids. Corticosteroids plus optimal supportive care may further be beneficial in treating early-stage IgAN patients in that it could significantly improve the short-term renal outcome.
Role of Traditional Chinese Medicine in the Management of Viral Pneumonia

Viral pneumonia is one kind of acute respiratory tract infection caused by the virus. There have been many outbreaks of viral pneumonia with high contagiousness and mortality both in China and abroad, such as the great influenza in 1918, the severe acute respiratory syndrome (SARS) coronavirus in 2003, the Influenza A (H1N1) virus in 2009, and the Middle East Respiratory Syndrome coronavirus (MERS-CoV) in 2012 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019. These outbreaks and/or pandemic have significant impact on human life, social behaviors, and economic development. Moreover, no specific drug has been developed for these viruses. Traditional Chinese medicine (TCM) plays an important role in the treatment of viral pneumonia during these outbreaks especially in SARS and SARS-CoV-2 because studies suggest that TCM formulations may target several aspects of the disease and may have lesser side effects than manufactured pharmaceuticals. In recent years, a lot of clinicians and researchers have made a series of in-depth explorations and investigations on the treatment of viral pneumonia with TCM, which have understood TCM therapeutic mechanisms more specifically and clearly. But critical analysis of this research in addition to further studies are needed to assess the potential of TCM in the treatment of viral pneumonia.
Combined p14ARF and Interferon-β Gene Transfer to the Human Melanoma Cell Line SK-MEL-147 Promotes Oncolysis and Immune Activation

Immune evasion is an important cancer hallmark and the understanding of its mechanisms has generated successful therapeutic approaches. Induction of immunogenic cell death (ICD) is expected to attract immune cell populations that promote innate and adaptive immune responses. Here, we present a critical advance for our adenovirus-mediated gene therapy approach, where the combined p14ARF and human interferon-β (IFNβ) gene transfer to human melanoma cells led to oncolysis, ICD and subsequent activation of immune cells. Our results indicate that IFNβ alone or in combination with p14ARF was able to induce massive cell death in the human melanoma cell line SK-MEL-147, though caspase 3/7 activation was not essential. In situ gene therapy of s.c. SK-MEL-147 tumors in Nod-Scid mice revealed inhibition of tumor growth and increased survival in response to IFNβ alone or in combination with p14ARF. Emission of critical markers of ICD (exposition of calreticulin, secretion of ATP and IFNβ) was stronger when cells were treated with combined p14ARF and IFNβ gene transfer. Co-culture of previously transduced SK-MEL-147 cells with monocyte-derived dendritic cells (Mo-DCs) derived from healthy donors resulted in increased levels of activation markers HLA-DR, CD80, and CD86. Activated Mo-DCs were able to prime autologous and allogeneic T cells, resulting in increased secretion of IFNγ, TNF-α, and IL-10. Preliminary data showed that T cells primed by Mo-DCs activated with p14ARF+IFNβ-transduced SK-MEL-147 cells were able to induce the loss of viability of fresh non-transduced SK-MEL-147 cells, suggesting the induction of a specific cytotoxic population that recognized and killed SK-MEL-147 cells. Collectively, our results indicate that p14ARF and IFNβ delivered by our adenoviral system induced oncolysis in human melanoma cells accompanied by adaptive immune response activation and regulation.
Emerging Zoonotic Diseases: Should We Rethink the Animal–Human Interface?

Department of Infectious Diseases and Public Health, City University of Hong Kong, Kowloon, Hong Kong, 2 School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, NSW, Australia, Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, NSW, Australia, UMR ASTRE (Animal, Santé, Territoires, Risques et Ecosystémes), CIRAD-INRAE, Université de Montpellier, Montpellier, France, Department of Philosophy, University of Basel, Basel, Switzerland, 6 Vetsuisse Faculty, Veterinary Public Health Institute, University of Bern, Bern, Switzerland
Hand-selective visual regions represent how to grasp 3D tools for use: brain decoding during real actions

Most neuroimaging experiments that investigate how tools and their associated actions are represented in the brain use visual paradigms where tools or hands are displayed as 2D images and no real movements are performed. These studies have discovered selective responses in occipito-temporal and parietal cortices for viewing pictures of hands or tools which are assumed to reflect action-related processing, but this claim has never been directly investigated. To address this, we examined the responses of independently visually defined category-selective brain areas when participants directly manipulated 3D tools with their hands. Using real action fMRI and multi-voxel pattern analysis, we found that representations about whether a 3D tool is being grasped appropriately for use (e.g., grasp knife by the handle rather than its serrated edge) were decodable from hand-selective areas in occipito-temporal and parietal cortices, but not from tool-, object-, or body-selective areas, even if partially overlapping. These representations were automatically evoked even when there was no requirement for tool use and participants were naïve to object category (tool vs non-tools). We further show that these effects were exclusive for actions with tools, but not for biomechanically matched actions with control non-tools. The lack of effects in tool-selective cortex challenges the long-standing assumption that brain activation for viewing tool images reflects tool manipulation sensorimotor processing. Instead our results show that representations of how to grasp tools for use are automatically evoked in visual regions specialised for representing the human hand, the brain’s primary tool for interacting with the world.
Diagnostic Imaging in Intervertebral Disc Disease

Imaging is integral in the diagnosis of canine intervertebral disc disease (IVDD) and in differentiating subtypes of intervertebral disc herniation (IVDH). These include intervertebral disc extrusion (IVDE), intervertebral disc protrusion (IVDP) and more recently recognized forms such as acute non-compressive nucleus pulposus extrusion (ANNPE), hydrated nucleus pulposus extrusion (HNPE), and intradural/intramedullary intervertebral disc extrusion (IIVDE). Many imaging techniques have been described in dogs with roles for survey radiographs, myelography, computed tomography (CT), and magnetic resonance imaging (MRI). Given how common IVDH is in dogs, a thorough understanding of the indications and limitations for each imaging modality to aid in diagnosis, treatment planning and prognosis is essential to successful case management. While radiographs can provide useful information, especially for identifying intervertebral disc degeneration or calcification, there are notable limitations. Myelography addresses some of the constraints of survey radiographs but has largely been supplanted by cross-sectional imaging. Computed tomography with or without myelography and MRI is currently utilized most widely and have become the focus of most contemporary studies on this subject. Novel advanced imaging applications are being explored in dogs but are not yet routinely performed in clinical patients. The following review will provide a comprehensive overview on common imaging modalities reported to aid in the diagnosis of IVDH including IVDE, IVDP, ANNPE, HNPE, and IIVDE. The review focuses primarily on canine IVDH due to its frequency and vast literature as opposed to feline IVDH.
Forensic application of EST-derived STR markers in opium poppy

Abstract Discrimination study in opium poppy (Papaver somniferum L.) genotypes has been performed by short tandem repeat (STR) markers derived from expressed sequence tags (ESTs) retrieved from the opium poppy DNA. Some of STRs originate from the gene sequences involved in the biosynthesis of morphine. Eight of twelve tested EST-derived STR markers generated polymorphism, 2-4 alleles were identified per locus, and the mean polymorphic information content value was 0.338. Seven cultivars developed in Slovakia, registered and released at present time for commercial cultivation were discriminated mutually. All the Slovak and Czech cultivars were also different from each other. EST-derived STR markers have shown a potential for discrimination of opium poppy genotypes cultivated for commercial production of either edible seeds or pharmacologically active alkaloids and could be applicable for the PCR-based forensic analyses.
Detection of Micro-expression Recognition Based on Spatio-Temporal Modelling and Spatial Attention

My PhD project aims to make contributions in the affective computing application to assist in the depression diagnosis by micro-expression recognition. My motivation is the similarities of the low-intensity facial expressions in micro-expressions and the low-intensity facial expressions (`frozen face? ) in people with psycho-motor retardation caused by depression. It will focus on, firstly, investigating spatio-temporal modelling and attention systems for micro-expression recognition (MER) and, secondly, exploring the role of micro-expressions in automated depression analysis by improving deep learning architectures to detect low-intensity facial expressions. This work will investigate different deep learning architectures (e.g. Temporal Convolutional Networks (TCNN) or Gate Recurrent Unit (GRU)) and validate the results on publicly available micro-expression benchmark datasets to quantitatively analyse the robustness and accuracy of MER's contribution to improving automatic depression analysis. Moreover, video magnification as a way to enhance small movements will be combined with the deep learning methods to address the low-intensity issues in MER.