Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic Observation of Lung Nodules on Chest CT Before Diagnosis of Early Lung Cancer

Objective Early recognition and diagnosis of lung cancer can help improve the prognosis of patients. However, early imaging patterns of malignant lung nodules are not fully clear. To understand the early imaging signs of malignant lung cancer nodules, the changes of the lung nodules before diagnosis were dynamically observed and analyzed. Materials and Methods This retrospective study observed dynamic changes of lung nodules before pathological confirmation with consecutive regular chest CT examination from January 2003 to December 2018. At least 3 follow-up CT scans were performed in all cases, and the interval between each follow-up was about 1 year. The size, density, and morphological signs of the nodules were evaluated based on the CT axial image, and a reverse line chart or scatter plot with the diagnosis time as coordinate origin was constructed. Results A total of 55 lung nodules in 53 patients (mean age, 58.40 years ±11.43 [standard deviation]; 20 women) were accessed. The follow-up time was 5.96 ± 2.68 years. The average diameters in maximum slice of the lesion at baseline and last scan were 6.83 ± 2.92 mm and 16.65 ± 7.34 mm, respectively. According to the reverse line chart, the nodule growth curve segments within 4 years from the last scan showed an ascending shape, and those beyond 4 years showed a flat shape. There are 90.9% (50/55) GGN and 9.1% (5/55) SN when the lesion first appears, and 21.8% (12/55) GGN, 38.2% (21/55) PSN, and 40% (22/55) SN in the last scan. There are 12.7% (7/55) and 98.2% (54/55) nodules with poor morphological signs at baseline and last scan, respectively. Conclusion At the time node close to the diagnosis, the growth curve showed an upward pattern; the proportion of PSN and SN rose as the main density types; and the appearance of poor morphological signs of nodules increased. When a persistent lung nodule starts to show a malignant change, a further diagnostic workup is warranted.
Qu'est-ce que mon GNN capture vraiment ? Exploration des représentations internes d'un GNN

Résumé. Nous considérons l’explication de GNN. Alors que les travaux exis-tants expliquent la décision du modèle en s’appuyant sur la couche de sor-tie, nous cherchons à analyser les couches cachées pour identiﬁer les attributs construits par le GNN. Nous extrayons d’abord des règles d’activation qui iden-tiﬁent des ensembles de neurones co-activés pour une classe. Ces règles déﬁ-nissent des représentations internes ayant un impact fort sur la classiﬁcation. Ensuite, nous associons à celles-ci un graphe dont le plongement produit par le GNN est très proche de celui identiﬁé par la règle. Des expériences sur 6 jeux de données et 3 baselines démontrent que notre méthode génère des graphes réalistes de haute qualité.
The Importance of Social Support, Optimism and Resilience on the Quality of Life of Cancer Patients

Introduction The aim of the present study is to carry out a multidimensional analysis on the relation between satisfaction with social support received, resilience and optimism in cancer patients and their quality of life. Materials and Methods Data were gathered through questionnaires fulfilled by 142 cancer patients. Data relate to sociodemographic, health, quality of life, social support, resilience and optimism. Results Satisfaction with the sources and types of support, resilience and optimism relates positively with quality of life. Predictive models show that informational support from friends is the variable that most increases patients’ general health, while emotional support from the partner is the one that best improves how patients cope with the disease. In the same line, emotional support from the partner, together with informational support from family are the ones that most contribute to reduce patients’ symptoms. Resilience improves general health and functioning, and reduces symptoms. Patients’ optimism and resilience also reduce symptoms. Gender differences were found, with females showing lower quality of life than males, mainly in how they cope with cancer. Patients in the stage of treatment showed lower quality of life and higher symptoms. Such increase was observed in patients who received hormonotherapy or chemotherapy. Discussion Important practical implications can be drawn from results, which could help improve cancer patients’ quality of life through intervention strategies aimed at increasing their resilience, optimism and the social support provided by their closer sources.
Reduced Serum Levels of Soluble Interleukin-15 Receptor α in Schizophrenia and Its Relationship to the Excited Phenotype

Our previous studies documented that interleukin-15 receptor α (IL-15Rα) knockout (KO) mice exhibited hyperactivity, memory impairment, and desperate behavior, which are core features of schizophrenia and depression. Due to the overlapping symptomology and pathogenesis observed for schizophrenia and depression, the present study attempted to determine whether IL-15Rα was associated with the risk of schizophrenia or depression. One hundred fifty-six participants, including 63 schizophrenia patients, 29 depressive patients, and 64 age-matched healthy controls, were enrolled in the study. We investigated the circulating levels of soluble IL-15Rα and analyzed potential links between the IL-15Rα levels and clinical symptoms present in schizophrenia or depressive patients. We observed reduced serum IL-15Rα levels in schizophrenia patients, but not depressive patients compared with controls. Moreover, a significant negative association was observed between the circulating IL-15Rα levels and excited phenotypes in the schizophrenia patients. The IL-15Rα KO mice displayed pronounced pre-pulse inhibition impairment, which was a typical symptom of schizophrenia. Interestingly, the IL-15Rα KO mice exhibited a remarkable elevation in the startle amplitude in the startle reflex test compared to wild type mice. These results demonstrated that serum levels of soluble IL-15Rα were reduced in schizophrenia and highlighted the relationship of IL-15Rα and the excited phenotype in schizophrenia patients and mice.
Modelling Fault Scarp Degradation to Determine Earthquake History on the Muztagh Ata and Tahman Faults in the Chinese Pamir

The frequency of earthquakes on active faults is usually revealed by palaeoseismic trenching and geological dating. Nonetheless, field trenching and sampling are sometimes limited by difficulties in logistics, therefore impeding palaeoseismological studies. As surface rupture earthquakes create fault scarps that evolve with time, they may also provide important information about the timing of earthquakes. In this study, we provide a new approach to determine earthquake history based on the morphology of fault scarps. We select the Muztagh Ata and Tahman normal faults in the Chinese Pamir as a test area, on which fault scarps are well preserved but the earthquake history has not been quantified yet. We first simulate fault scarp degradation using a nonlinear transport model to obtain the empirical relationship between scarp width and its evolution time. We then measure 68 fault scarps from high-resolution topographic data derived from WorldView-2 stereo imagery. The measured fault scarps are clustered in four groups, each group possibly representing one earthquake event. Combining the time-width relationship and scarp width measurements, we infer that four earthquakes occurred at 0.1±0.4 kyrs before the present (BP), 2.1±0.5 kyrs BP, 2.9±0.4 kyrs BP and 4.9±0.5 kyrs BP, respectively. The first event is likely to be the most recent earthquake occurred on the faults, i.e., the 1895 Tashkurgan earthquake ( ∼0.13 kyrs BP). Based on the estimated earthquake recurrence intervals and vertical offsets, we obtain a vertical slip rate of 2.2±0.3 mm/yr on the Muztagh Ata and Tahman faults, conforming to previous geological rate estimates.
Age–Period–Cohort Analysis of Long Trend of Mortality for Stroke and Subtypes Attributed to High SBP in Chinese Adults

Stroke has been found as the leading cause of death in China, and high systolic blood pressure (SBP) has been indicated as a critical risk factor of stroke mortality. Accordingly, in this article, the aims were to investigate the long-term trends of mortality in terms of stroke and subtypes arising from high SBP stratified by age and gender among Chinese adults. The data of this article originated from the global burden of disease (GBD) study database. The age, period, and cohort effects were examined with the age–period–cohort model (APC). The age-standardized mortality of stroke attributed to high SBP in China has been significantly declining from 1990 to 2019. As indicated by the result of APC analysis, substantially rising age effects have been exerted on stroke and subtypes from 25 to 84 years of both genders, whereas the age effect on women increased less rapidly than that on men. As opposed to the above result, the period and cohort effects were reported to show similar monotonous decrease trends, and stroke of women more significantly declined than that of men (significantly with p < 0.05 for all). All types of stroke mortality arising from high SBP were indicated to change. The risk of death was identified to be most remarkably reduced in high SBP-attributable subarachnoid hemorrhage (SAH), whereas intracerebral hemorrhage (ICH) and ischemic stroke (IS) decreased at approximately the same rate. People born in the later birth cohorts or living in recent periods had a lower risk of stroke death, whereas men and elder groups were considered as the high-risk populations for stroke mortality due to high SBP. Although the stroke mortality relating to high SBP in China was declining, ICH and IS would continue to be the first and second lethal subtypes of stroke. In contrast to the above finding, SAH accounted for the minimum proportion of deaths and the maximum reduction in period and cohort effects. Thus, it is of high significance to introduce advanced hypertension control technology and knowledge regarding healthy lifestyles.
T-Cell Responses to Immunodominant Listeria Epitopes Limit Vaccine-Directed Responses to the Colorectal Cancer Antigen, Guanylyl Cyclase C

The Gram-positive bacterium Listeria monocytogenes (Lm) is an emerging platform for cancer immunotherapy. To date, over 30 clinical trials have been initiated testing Lm cancer vaccines across a wide variety of cancers, including lung, cervical, colorectal, and pancreatic. Here, we assessed the immunogenicity of an Lm vaccine against the colorectal tumor antigen GUCY2C (Lm-GUCY2C). Surprisingly, Lm-GUCY2C vaccination did not prime naïve GUCY2C-specific CD8+ T-cell responses towards the dominant H-2Kd-restricted epitope, GUCY2C254-262. However, Lm-GUCY2C produced robust CD8+ T-cell responses towards Lm-derived peptides suggesting that GUCY2C254-262 peptide may be subdominant to Lm-derived peptides. Indeed, incorporating immunogenic Lm peptides into an adenovirus-based GUCY2C vaccine previously shown to induce robust GUCY2C254-262 immunity completely suppressed GUCY2C254-262 responses. Comparison of immunogenic Lm-derived peptides to GUCY2C254-262 revealed that Lm-derived peptides form highly stable peptide-MHC complexes with H-2Kd compared to GUCY2C254-262 peptide. Moreover, amino acid substitution at a critical anchoring residue for H-2Kd binding, producing GUCY2CF255Y, significantly improved stability with H-2Kd and rescued GUCY2C254-262 immunogenicity in the context of Lm vaccination. Collectively, these studies suggest that Lm antigens may compete with and suppress the immunogenicity of target vaccine antigens and that use of altered peptide ligands with enhanced peptide-MHC stability may be necessary to elicit robust immune responses. These studies suggest that optimizing target antigen competitiveness with Lm antigens or alternative immunization regimen strategies, such as prime-boost, may be required to maximize the clinical utility of Lm-based vaccines.
PENDUGAAN AREA KECIL MENGGUNAKAN PENDEKATAN PENALIZED SPLINE PADA PENDUGAAN PENGELUARAN PERKAPITA TINGKAT KECAMATAN DI KABUPATEN SUMENEP

Pendugaan pada subpopulasi berdasarkan hasil survei pada populasi kemungkinan akan menghasilkan pendugaan yang bias dan varians yang besar yang disebabkan oleh jumlah sampel yang kurang representatif untuk mewakili data (subpopulasi). Salah satu cara untuk menduga subpopulasi tersebut adalah dengan small area estimation (SAE). SAE umumnya menggunakan pemodelan parametik untuk menghubungkan statistik area kecil dengan variabel-variabel pendukungnya. Pemodelan ini kurang fleksibel dalam menyesuaikan dengan pola data hasil survei yang mungkin saja tidak mirip sama sekali dengan distribusi formal yang ada. Sehingga pendekatan nonparametrik menjadi alternatif pilihan. Pada laporan ini peneliti akan mencoba menggunakan pemodelan nonparametrik untuk mengatasi masalah ini yaitu dengan menggunakan metode nonparametrik P-Spline. Pendugaan dengan menggunakan pendekatan P-Spline ini kemudian digunakan untuk menduga pengeluaran perkapita pada masing-masing kecamatan di Kabupaten Sumenep. Evaluasi hasil pendugaan dilakukan melihat nilai MSE (Mean Square Error) hasil pendugaan dengan menggunakan metode resampling jackknife.
Snrpb, the CCMS gene, is required in neural crest cells for proper splicing of genes essential for craniofacial morphogenesis

Heterozygous mutations in SNRPB, an essential core component of the five small ribonucleoprotein particles of the spliceosome, are responsible for Cerebrocostomandibular Syndrome (CCMS). We show that Snrpb heterozygous embryos arrest shortly after implantation. Additionally, heterozygous deletion of Snrpb in the developing brain and neural crest cells models craniofacial malformations found in CCMS, and results in death shortly after birth. RNAseq analysis of mutant heads prior to morphological defects revealed increased exon-skipping and intron-retention in association with increased 5’ splice site strength. We found increased exon-skipping in negative regulators of the P53-pathway, increased levels of nuclear P53, P53-target genes. However, removing TrP53 in Snrpb heterozygous mutant neural crest cells did not completely rescue craniofacial development. We also found a small but significant increase in exon-skipping of several transcripts required for head and midface development, including Smad2 and Rere. Furthermore, mutant embryos exhibited ectopic or missing expression of Fgf8 and Shh, which are required to coordinate face and brain development. Thus, we propose that mis-splicing of transcripts that regulate P53-activity and craniofacial-specific genes both contribute to craniofacial malformations.
Rapport à vague de Xavier Caruso Période : décembre 2015 — décembre 2020 A . Rapport d ’ activités 1 C

Parcours scolaire et professionnel 2018– Directeur de recherche au CNRS, affecté à l’IMB (Bordeaux) 2017–2021 Titulaire de la prime d’encadrement doctoral et de recherche (PEDR) 2011 Habilitation à diriger les recherches soutenue le 3 juin à l’université de Rennes 1 durant le jury composé de Laurent Berger, Christophe Breuil, Pierre Colmez, Jean-Marc Fontaine et Michael Rapoport. 2009–2010 Mobilité d’une année au laboratoire Poncelet à l’Université Indépendante de Moscou 2006–2018 Chargé de recherche au CNRS, affecté à l’IRMAR (Rennes) 2005 Thèse sous la direction de Christophe Breuil intitulée Conjecture de l’inertie modérée de Serre et soutenue le 7 décembre devant le jury composé de Ahmed Abbes, Pierre Berthelot (rapporteur), Lawrence Breen, Christophe Breuil (directeur de thèse), Michel Raynaud. Autre rapporteur : Mark Kisin. 2003–2006 Moniteur à l’université Paris 13. 1999–2003 Élève de de l’École normale supérieure de Paris
Representation learning of scene images for task and motion planning

This thesis investigates two different methods to learn a state representation from only image observations for task and motion planning (TAMP) problems. Our first method integrates a multimodal learning formulation to optimize an autoencoder not only on a regular image reconstruction but also jointly on a natural language processing (NLP) task. Therefore, a discrete, spatially meaningful latent representation is obtained that enables effective autonomous planning for sequential decisionmaking problems only using visual sensory data. We integrate our method into a full planning framework and verify its feasibility on the classic blocks world domain [26]. Our experiments show that using auxiliary linguistic data leads to better representations, thus improves planning capability. However, since the representation is not interpretable, learning an accurate action model is extremely challenging, rendering the method still inapplicable to TAMP problems. Therefore, to address the necessity of learning an explainable representation, we present a self-supervised learning method to learn scene graphs that represent objects (“red box”) and their spatial relationships (“yellow cylinder on red box”). Such a scene graph representation provides spatial relations in the form of symbolic logical predicates, thus eliminates the need of pre-defining these symbolic rules. Finally, we unify the proposed representation with a non-linear optimization method for robot motion planning and verify its feasibility on the classic blocks-world domain. Our proposed framework successfully finds the sequence of actions and enables the robot to execute feasible motion plans to realize the given tasks.
Thora: Atomic and Privacy-Preserving Multi-Channel Updates

Most blockchain-based cryptocurrencies suffer from a heavily limited transaction throughput, which is a barrier to their growing adoption. Payment channel networks (PCNs) are one of the promising solutions to this problem. PCNs reduce the on-chain load of transactions and increase the throughput by processing many payments off-chain. In fact, any two users connected via a path of payment channels (i.e., joint addresses between the two channel end-points) can perform payments, and the underlying blockchain is used only when there is a dispute between users. Unfortunately, payments in PCNs can only be conducted securely along a path, which prevents the design of many interesting applications. Moreover, the most widely used implementation, the Lightning Network in Bitcoin, suffers from a collateral lock time linear in the path length, it is affected by security issues, and it relies on specific scripting features called Hash Timelock Contracts that hinders the applicability of the underlying protocol in other blockchains. In this work, we present Thora, the first Bitcoin-compatible off-chain protocol that enables the atomic update of arbitrary channels (i.e., not necessarily forming a path). This enables the design of a number of new off-chain applications, such as payments across different PCNs sharing the same blockchain, secure and trustless crowdfunding, and channel rebalancing. Our construction requires no specific scripting functionalities other than digital signatures and timelocks, thereby being applicable to a wider range of blockchains. We formally define security and privacy in the Universal Composability framework and show that our cryptographic protocol is a realization thereof. In our performance evaluation, we show that our construction requires only constant collateral, independently from the number of channels, and has only a moderate off-chain communication as well as computation overhead.
Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications

Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU–atpA and atpH–atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.
Predictors of frailty in older people users of Primary Health Care.

OBJECTIVE to identify the prevalence and predictors of frailty in older people in Primary Health Care. METHOD this is a descriptive and correlational study, carried out in a convenience sample of 136 older people in the community. Data were collected through a sociodemographic and clinical questionnaire and frailty phenotype. Student's t test or U-Mann-Whitney test, chi-square and binary logistic regression were used for data analysis. RESULTS the prevalence of frailty was 26.5% (n=36). Frail individuals had older age (p=0.011), worse self-rated health (p=0.001) and lower physical capacity (p<0.001). In the multivariable regression, it was observed that frail individuals had older age (Odds Ratio=1.111; 95% confidence interval=1.026-1.203) and worse physical capacity (Odds Ratio=0.673; 95% confidence interval=0.508-0.893). CONCLUSIONS the prevalence of frailty in older people in Primary Health Care was considerable. Advanced age and worse physical capacity were the most relevant predictors of frailty in the elderly.