Miracle-dz/UniFAR-FTUs huggingface dataset:
presentee en vu d'obtenir le grade de Docteur, specialite « Physique » par

Recent advances in the fields of computational biology and molecular biology techniques have led to the emerging discipline of population genomics, whose main objective is the study of the spatial structure of genetic diversity. This structure is determined by both neutral forces, like migration and drift, and adaptive forces, like natural selection, and has important applications in many fields like medical genetics or conservation biology. Here, we develop new statistical methods to evaluate the role of natural selection and environment in this spatial structure. All these methods are based on the Bayesian Dirichlet-multinomial model of genetic differentiation. First, we propose to include environmental variables in the estimation process, in order to identify the biotic and abiotic factors that determine the genetic structure. Then, we study the possibility of extending the Dirichlet-multinomial model to dominant markers, which have become very popular in the last few years, but which are affected by various ascertainment biases. Finally, we try to separate neutral effects from adaptive effects on the genetic structure, in order to identify regions of the genome influenced by natural selection. Three databases have been analyzed as illustrations of the use of these new methods : human data, data of argan tree in Morocco, and data of periwinkle. Finally, we developed three softwares implementing these various models.
Hotspots: Adherence in home foot temperature monitoring interventions for at‐risk feet with diabetes—A narrative review

Home foot temperature monitoring (HFTM) is recommended for those at moderate to high ulcer risk. Where a > 2.2°C difference in temperature between feet (hotspot) is detected, it is suggested that individuals (1) notify a healthcare professional (HCP); (2) reduce daily steps by 50%. We assess adherence to this and HFTM upon detecting a recurrent hotspot.
Körperliche Krankheit bei älteren PatientInnen in der Psychosomatischen Klinik

Zusammenfassung Bisher ist wenig über das Ausmaß körperlicher Krankheiten bei älteren PatientInnen in psychosomatischen Kliniken bekannt. In der vorliegenden Studie wurde an einer Gruppe von 150 PatientInnen in der zweiten Lebenshälfte (jeweils 50 der Altersgruppen 40–54, 55–69 und≥70) Häufigkeit und Anzahl körperlicher Krankheiten sowie deren Zusammenhang mit der psychischen Symptomatik untersucht. Methode: Zur Erfassung der körperlichen Erkrankungen wurde die CIRS (Cumulative Illness Rating Scale) eingesetzt, ein etabliertes Fremdeinschätzungsverfahren für körperliche Krankheiten auf 14 Skalen. Die Ergebnisse zeigen die größte Häufigkeit sowie die größere Schwere körperlicher Krankheiten in der ältesten Gruppe. Zudem erwies sich, dass körperliche Erkrankungen mit ansteigendem Alter stärker mit psychischen Erkrankungen zusammenhängen. Es wird ein mentaler Bedeutungszuwachs körperlicher Krankheit mit ansteigendem Alter postuliert. In der Diskussion werden versorgungspolitische und therapeutische Aspekte aufgegriffen.
Dealing with systematic laser scanner errors due to misalignment at area-based deformation analyses

Abstract The ability to acquire rapid, dense and high quality 3D data has made terrestrial laser scanners (TLS) a desirable instrument for tasks demanding a high geometrical accuracy, such as geodetic deformation analyses. However, TLS measurements are influenced by systematic errors due to internal misalignments of the instrument. The resulting errors in the point cloud might exceed the magnitude of random errors. Hence, it is important to assure that the deformation analysis is not biased by these influences. In this study, we propose and evaluate several strategies for reducing the effect of TLS misalignments on deformation analyses. The strategies are based on the bundled in-situ self-calibration and on the exploitation of two-face measurements. The strategies are verified analyzing the deformation of the Onsala Space Observatory’s radio telescope’s main reflector. It is demonstrated that either two-face measurements as well as the in-situ calibration of the laser scanner in a bundle adjustment improve the results of deformation analysis. The best solution is gained by a combination of both strategies.
Non‐compartmental and population pharmacokinetic analysis of dapsone in healthy NIGERIANS: A pilot study

Dapsone is employed for both non‐dermatological and dermatological indications but with non‐existent population pharmacokinetics (popPK) data in Nigerians. This study was therefore designed to develop a popPK model in Nigerians. Non‐compartmental analysis and nonlinear mixed effects modelling were utilized for data analysis. Eleven participants administered 50 mg dapsone tablet were included in the analysis. Derived pharmacokinetic parameters were: Cmax = 1.16 ± 0.32 μg/mL, Tmax = 3.77 ± 2.40 h, and t1/2z = 30.23 ± 11.76 h. PopPK model parameter estimates with inter‐individual variability were Tlag = 0.40 h (10.0%, fixed); ka = 1.78 h−1 (75.9%); V/F = 89.25 L (21.6%); and Cl/F = 1.32 Lh−1 (27.7%). Sex was significantly associated with Cl/F, and body weight with V/F. Best popPK model was one‐compartment with lag time, and first‐order absorption and elimination. Sex and body weight significantly influenced the clearance and distribution volume of dapsone respectively.
Trends in incidence and overdiagnosis of thyroid cancer in China, Japan, and South Korea

We used data from 13 cancer registries in China, Japan, and South Korea to analyze time trends in overdiagnosis of thyroid cancer between 1998 and 2012. Age‐standardized and age‐specific incidence and annual percentage changes were calculated. The number of thyroid cancers diagnosed and the proportion attributable to overdiagnosis were estimated, with calculations stratified by sex and age group. The Spearman method was used to analyze the correlation between thyroid cancer incidence and overdiagnosis. From 1998 to 2012, both the incidence and proportions of overdiagnoses of thyroid cancer in China, Japan, and South Korea showed an increasing trend, with higher rates in women than men. South Korea had both the highest incidence for men (10.1/105) and women (46.7/105) and the highest proportions of overdiagnosis (men, 90.3%; women, 94.9%). The fastest growth in overdiagnosis was in Chinese men and women (annual percentage changes 6.1 and 4.6, respectively). We found significant positive correlations between age‐standardized incidence and proportions of overdiagnosis for both men (Spearman r = 0.98, p < 0.05) and women (Spearman r = 0.99, p < 0.05) in the three countries. Age‐specific incidence curves in Chinese and South Korean individuals were of an inverted U‐shape. Overdiagnosis of thyroid cancer in Japan was mainly concentrated in middle‐aged and older patients, whereas in China and South Korea, it occurred primarily in the middle‐aged. The incidence and overdiagnosis of thyroid cancer in China, Japan, and South Korea are increasing, necessitating the implementation of comprehensive measures to reduce these overdiagnoses.
What We Know About Intracranial Hypertension in Children With Syndromic Craniosynostosis

Objective: A scoping review of literature about mechanisms leading to intracranial hypertension (ICH) in syndromic craniosynostosis (sCS) patients, followed by a narrative synopsis of whether cognitive and behavioral outcome in sCS is more related to genetic origins, rather than the result of ICH. Methods: The scoping review comprised of a search of keywords in EMBASE, MEDLINE, Web of science, Cochrane Central Register of Trials, and Google scholar databases. Abstracts were read and clinical articles were selected for full-text review and data were extracted using a structured template. A priori, the authors planned to analyze mechanistic questions about ICH in sCS by focusing on 2 key aspects, including (1) the criteria for determining ICH and (2) the role of component factors in the Monro-Kellie hypothesis/doctrine leading to ICH, that is, cerebral blood volume, cerebrospinal fluid (CSF), and the intracranial volume. Results: Of 1893 search results, 90 full-text articles met criteria for further analysis. (1) Invasive intracranial pressure measurements are the gold standard for determining ICH. Of noninvasive alternatives to determine ICH, ophthalmologic ones like fundoscopy and retinal thickness scans are the most researched. (2) The narrative review shows how the findings relate to ICH using the Monro-Kellie doctrine. Conclusions: Development of ICH is influenced by different aspects of sCS: deflection of skull growth, obstructive sleep apnea, venous hypertension, obstruction of CSF flow, and possibly reduced CSF absorption. Problems in cognition and behavior are more likely because of genetic origin. Cortical thinning and problems in visual function are likely the result of ICH.
Exploring mechanisms and contexts in a Peer Education Project to improve mental health literacy in schools in England: a qualitative realist evaluation

Abstract Poor adolescent mental health calls for universal prevention. The Mental Health Foundation’s ‘Peer Education Project’ equips older students (‘peer educators’) to teach younger students (‘peer learners’) about mental health. The peer-led lessons cover defining good and bad mental health, risk and protective factors, self-care, help-seeking and looking after one another. While previous pre-post evaluations have suggested effectiveness, the mechanisms through which the intervention improves mental health literacy remain unclear. We purposively recruited seven secondary schools across England from 2020 to 2022 and collected data through five observations, 12 staff interviews and 15 student focus groups (totalling 134 students; 46 peer educators aged 14–18 years and 88 peer learners aged 11–13 years). Our realist analysis adopted retroductive logic, intertwining deductive and inductive approaches to test the initial programme theory against insights arising from the data. We developed Context–Mechanisms–Outcome configurations related to four themes: (i) modelling behaviours and forming supportive relationships, (ii) relevant and appropriate content, (iii) peer educators feeling empowered and (iV) a school culture that prioritises mental health support. Our refined programme theory highlights key mechanisms, contexts conducive to achieving the outcomes and ways to improve training, recruitment and delivery to maximise effectiveness for similar peer-led initiatives.
Nsp3-N interactions are critical for SARS-CoV-2 fitness and virulence

Significance SARS-CoV-2, the causative agent of COVID-19, encodes several proteins not present in other coronaviruses. SARS-Unique Domain (SUD), a domain in the nonstructural protein 3 (nsp3) of coronavirus, is present only in Sarbecovirus, a subgenus of Betacoronavirus, including two highly pathogenic human coronaviruses, SARS-CoV and SARS-CoV-2. We report that nsp3-S676T, a single mutation in the SUD, causes SARS-CoV-2 fitness loss through dysregulation of its translational enhancement ability. N-S194L, a compensatory mutation identified in the nucleocapsid (N) protein, reverts viral virulence. Our study reveals a mechanism by which N-nsp3 interactions contribute to SARS-CoV-2 replication and pathogenesis but also identifies an effective antiviral therapeutic target for COVID-19.
Effects of multiple stressors on pancreatic human islets proteome reveal new insights into the pathways involved

Pancreatic β‐cell dysfunction is an early hallmark of type 1 diabetes mellitus. Among the potentially critical factors that cause β‐cell dysfunction are cytokine attack, glucotoxicity, induction of endoplasmic reticulum (ER) or mitochondria stress. However, the exact molecular mechanism underlying β‐cell's inability to maintain glucose homeostasis under severe stresses is unknown. This study used proinflammatory cytokines, thapsigargin, and rotenone in the presence of high concentration glucose to mimicking the conditions experienced by dysfunctional β‐cells in human pancreatic islets, and profiled the alterations to the islet proteome with TMT‐based proteomics. The results were further verified with label‐free quantitative proteomics. The differentially expressed proteins under stress conditions reveal that immune related pathways are mostly perturbed by cytokines, while the respiratory electron transport chains and protein processing in ER pathways by rotenone. Thapsigargin together with high glucose induces dramatic increases of proteins in lipid synthesis and peroxisomal protein import pathways, with energy metabolism and vesicle secretion related pathways downregulated. High concentration glucose, on the other hand, alleviated complex I inhibition induced by rotenone. Our results contribute to a more comprehensive understanding of the molecular events involved in β‐cell dysfunction.
RNA Secondary Structure Analysis Using RNAstructure

RNAstructure is a user‐friendly program for the prediction and analysis of RNA secondary structure. It is available as a web server, a program with a graphical user interface, or a set of command line tools. The programs are available for Microsoft Windows, macOS, or Linux. This article provides protocols for prediction of RNA secondary structure (using the web server, the graphical user interface, or the command line) and high‐affinity oligonucleotide binding sites to a structured RNA target (using the graphical user interface). © 2023 Wiley Periodicals LLC.
A duality for finite lattices

A presentation is a triple $\leangle X,\leq,M\rangle$ with $\langle X,\leq\rangle$ a finite poset and $M : X \rTo \P(\P(X))$ -- these data being subject to additional constraints. Given a presentation we can define closed subsets of $X$, whence a finite lattice. Given a finite lattice $L$, we can define its presentation: $X$ is the set of join-irreducible elements of $L$, $\leq$ is the restriction of the order to join-irreducible elements, and $M(x)$ is the set of minimal join-covers of $x$. Morphisms of presentations can be defined as some zig-zag relations. Our main result is: \emph{the category of presentations is dually equivalent to the category of finite lattice}. The two constructions described above are the object part of contravariant functors giving rise to the duality. We think of presentations as semantic domains for lattice terms and formulas of substructural logics. Relying on previous work by Nation and Semenova, we show that some equational properties of finite lattices correspond to first order properties of presentations. Namely, for each finite tree $T$, we construct an equation $e_{T}$ that holds in a finite lattice if and only its presentation does not have some a shape from $T$. We illustrate further use of these semantics within the theory of fixed points over finite lattices: we generalize, in a non-trivial way, the well known fact that least fixed points on distributive lattice terms can be eliminated.
Sur l'analyse et la synchronisation de systèmes chaotiques Chen

Apres la caracterisation du chaos par le diagramme de bifurcations, l’exposant de Lyapunov et l’espace des phases, une commande par retour d’etat est proposee et appliquee avec succes a la synchronisation de deux systemes chaotiques. Les resultats obtenus pour deux systemes Chen identiques ont montre l’efﬁcacite de l’approche proposee.
Rubus chingii Hu relieved the polycystic ovary syndrome with enhanced insulin sensitivity through inhibiting TXNIP/NLRP3 inflammasome signaling

Abstract Background Polycystic ovary syndrome (PCOS) is one of the most prevalent endocrine disorders in gynecology with severe metabolic abnormalities. Therefore, identifying effective treatments and drugs for PCOS is important. We aimed to investigate effect of the traditional Chinese medicine (TCM) Rubus chingii Hu (R. chingii) on ovarian function and insulin resistance (IR) of PCOS rat models, and to explore the underlying mechanisms Methods A PCOS rat model was established by subcutaneous injection of dehydroepiandrosterone (DHEA) solution for 20 days. PCOS rats were randomly divided into a control group (CON), model group (MOD), metformin group (MET), TCM R. chingii group (RCG), and RCG + Ad-TXNIP groups. After 28 days of treatment, the samples were collected for subsequent experiments. Results R. chingii treatment alleviated hormone imbalance and IR while improving ovarian pathology in the PCOS model. R. chingi inhibited the activation of the thioredoxin-interacting protein (TXNIP)/NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome in the ovarian tissue of PCOS rats. Furthermore, TXNIP overexpression hindered the protective effect of R. chingii intervention in PCOS rats, as evidenced by the increase of homeostasis model assessment of insulin resistance (HOMA-IR), luteinizing hormone (LH), testosterone (T), C-reactive protein (CRP) levels, and atretic follicles. Conclusion R. chingii intervention improved ovarian polycystic development by suppressing the TXNIP/NLRP3 inflammasome, which may be an effective treatment for PCOS.
High-resolution mapping reveals the mechanism and contribution of genome insertions and deletions to RNA virus evolution

Significance RNA viruses are masters at rapid adaptation to adverse conditions. One important and poorly understood viral adaptation strategy is the use of genome insertions and deletions (indels) as a source of variation and evolutionary novelty. This study presents a hybrid experimental-bioinformatic approach to comprehensively characterize the broad indel landscape of adapting RNA virus populations, from extremely low-frequency to high-frequency variants. Using this approach, we identify mechanisms of indel generation and define the selection forces that shape indel diversity and accumulation. Our analyses establish the kinetic and mechanistic tradeoffs between Indel generation and fitness and reveal functional principles defining the central role of Indels in virus evolution, emergence, and the regulation of viral infection.
Bayesian Non-stationary Linear Bandits for Large-Scale Recommender Systems

Taking advantage of contextual information can potentially boost the performance of recommender systems. In the era of big data, such side information often has several dimensions. Thus, developing decision-making algorithms to cope with such a high-dimensional context in real time is essential. That is specifically challenging when the decision-maker has a variety of items to recommend. In addition, changes in items' popularity or users' preferences can hinder the performance of the deployed recommender system due to a lack of robustness to distribution shifts in the environment. In this paper, we build upon the linear contextual multi-armed bandit framework to address this problem. We develop a decision-making policy for a linear bandit problem with high-dimensional feature vectors, a large set of arms, and non-stationary reward-generating processes. Our Thompson sampling-based policy reduces the dimension of feature vectors using random projection and uses exponentially increasing weights to decrease the influence of past observations with time. Our proposed recommender system employs this policy to learn the users' item preferences online while minimizing runtime. We prove a regret bound that scales as a factor of the reduced dimension instead of the original one. To evaluate our proposed recommender system numerically, we apply it to three real-world datasets. The theoretical and numerical results demonstrate the effectiveness of our proposed algorithm in making a trade-off between computational complexity and regret performance compared to the state-of-the-art.
"Being Simple on Complex Issues" - Accounts on Visual Data Communication about Climate Change.

Data visualizations play a critical role in both communicating scientific evidence about climate change and in stimulating engagement and action. To investigate how visualizations can be better utilized to communicate the complexities of climate change to different audiences, we conducted interviews with 17 experts in the fields of climate change, data visualization, and science communication, as well as with 12 laypersons. Besides questions about climate change communication and various aspects of data visualizations, we also asked participants to share what they think is the main takeaway message for two exemplary climate change data visualizations. Through a thematic analysis, we observe differences regarding the included contents, the length and abstraction of messages, and the sensemaking process between and among the participant groups. On average, experts formulated shorter and more abstract messages, often referring to higher-level conclusions rather than specific details. We use our findings to reflect on design decisions for creating more effective visualizations, particularly in news media sources geared toward lay audiences. We hereby discuss the adaption of contents according to the needs of the audience, the trade-off between simplification and accuracy, as well as techniques to make a visualization attractive.
External version of Laplace method

The aim of this paper is to use some concepts of nonstandard analysis introduced by Robinson A. and axiomatized by Nelson E. to give an external method of Laplace. More precisely under certain conditions we get the following result. 1 Γ 1 1 Where , , , are standard constants and ≃ 0 , .
Investigation of combining dipole antennas with three dimensional photonic crystals

The combination of dipole antennas and 3D diamond-structure photonic crystals is investigated by simulating method in this paper. The radiation frequency point of dipole antennas was selected to correspond to the reflection frequency point of the strongest energy in band gap. The results show that there is a good resonance performance in the range of band gap, which also indicate that in all direction the surface waves which propagate along the surface of the photonic crystals substrate can be suppressed because of the reflection the band gap. Moreover, coupling antenna has low return loss and improves the directionality compared to common dipole antenna. The EM waves are reflected and a high gain is attained, improving from 2.76 dB to 7.14 dB. Due to these merits of photonic crystals substrate, coupling antennas exhibit the excellent radiation performance, which will be widely utilized in communication field.
Effect of strength of gravitational field on electrode processes

Relativistic transformation of electrode potential has been derived to explain time dilation in electrode processes. The newly formulated Lorentz transformation of the electrode potential is explained in terms of the generation of spin 2-boson gravitons from the fusion of spin-1 boson virtual-photons followed by their eventual escape in higher dimensions. Gravitational transformations of electrode potential have also been derived that explains decrease in the cell potential at the lower gravitational field. The dropping of electrode potential at the lower gravitational field is also explained in terms of the greater flux of gravitons escaping into higher dimensions at lower gravitational fields than at higher gravitational fields. Similarly potential energy associated with the spin of magnetically active nuclei in applied magnetic field within NMR spectrometer has been shown to be Lorentz variant that mathematically proves Hamiltonian describing the energy of magnetically active nuclei to be Lorentz variant. Relativistic and gravitational transformations of electrode potential and potential energy of magnetically active nuclei under applied magnetic field are shown analogous to one another.