Miracle-dz/UniFAR-FTUs huggingface dataset:
Lycopene in Feed as Antioxidant and Immuno-Modulator Improves Broiler Chicken's Performance under Heat-Stress Conditions

Lycopene is a type of carotenoid pigment widely distributed in various plants and fruits, with tomatoes, carrots, and guava being the most abundant sources. Due to its high content of beneficial active components, lycopene has been used in medicine, where it is employed as a dietary additive for cancer therapy, immune modulator, and feed additive to improve livestock productivity. Lycopene is a lipophilic substance that can act as either a prooxidant or a free radical scavenger and is particularly efficient in enhancing broiler performance. Furthermore, lycopene can alleviate heat stress by improving the activity of various antioxidant enzymes such as superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and catalase (CAT), as well as increasing the total antioxidant capacity (T-AOC) and nuclear muscle factor erythroid 2-related factor 2 (Nrf2), while simultaneously reducing the levels of malondialdehyde (MDA) and muscle Keap1 expression. In addition, lycopene can improve broiler fertility by enhancing sperm performance and reducing inflammation by modulating the levels of interleukin 1, 2, and 10 (IL-1, IL-2, and IL-10) in cases of infection. In cases of disease by aflatoxin B1 (AFB1), lycopene can modulate interferon-γ (IFN-γ), IL-1, claudin-1 (CLDN-1), and zonula occludens-1 (ZO-1). Furthermore, under the lipopolysaccharide challenge, lycopene can increase the relative weights of immune organ indices such as the bursal, spleen, and thymus.
Variantes genéticas recurrentes y priorización de variantes de significado clínico desconocido asociadas al síndrome de cáncer de mama y ovario hereditario en familias de la Región de Murcia

Resumen Objetivos El síndrome de cáncer de mama y ovario hereditario (SCMOH) presenta un patrón de herencia autosómica dominante en genes de susceptibilidad al cáncer y su riesgo está principalmente vinculado a mutaciones germinales en BRCA1 y BRCA2. Sin embargo, la implementación de paneles genéticos mediante secuenciación masiva en la práctica asistencial, ha ampliado el espectro mutacional de este síndrome hereditario y el número de variantes de significado clínico desconocido (VUS) detectadas en los estudios genéticos. Métodos El estudio de prevalencia del SCMOH realizado en 2928 familias de la Región de Murcia ha permitido identificar las variantes patogénicas recurrentes y mutaciones fundadoras, principalmente asociadas a genes BRCA1 y BRCA2. En el estudio de VUS destaca la aplicación de un algoritmo de priorización diseñado por nuestro grupo de trabajo. Resultados Las variantes c. 68_69del, c.212+1G>A, y c.5123C>A fueron detectadas en un 30 % de los portadores de BRCA1 mientras que la deleción del exón 2 junto con c.3264dupT, c.3455T>G y c.9117G>A se han encontrado en un 30 % de los portadores de BRCA2. Un total de 16 VUS (15 %) fueron priorizadas. Conclusiones La correlación genotipo-fenotipo resultó compatible con lo reportado previamente en la literatura científica. Además, se ha constatado el efecto fundador de c.1918C>T (BRCA1) y c. 8251_8254del (ATM) en población murciana y la deleción del exon2 (BRCA2) como mutación fundadora española. La implementación del algoritmo ha permitido priorizar aquellas VUS susceptibles de patogenicidad en las que sería recomendable realizar estudios complementarios para así, poder determinar su efecto clínico y su posible implicación en el SCMOH.
When the tap runs dry: The physiological effects of acute experimental dehydration in Peromyscus eremicus

Desert organisms have evolved physiological, biochemical, and genomic mechanisms to survive the extreme aridity of desert environments. Studying desert-adapted species provides a unique opportunity to investigate the survival strategies employed by organisms in some of the harshest habitats on Earth. Two of the primary challenges faced in desert environments are maintaining water balance and thermoregulation. We collected data in a simulated desert environment and a captive colony of cactus mice (Peromyscus eremicus) and used lab-based experiments with real time physiological measurements to characterize the response to water-deprivation. Mice without access to water had significantly lower energy expenditures and in turn, reduced water loss compared to mice with access to water after the first 24 hours of the experiment. Additionally, we observed significant weight loss likely related to dehydration-associated anorexia a response to limit fluid loss by reducing waste and the solute load as well as allowing water reabsorption from the kidneys and gastrointestinal tract. Finally, we observed body temperature correlated with sex, with males without access to water maintaining body temperature when compared to hydrated males while body temperature decreased for females without access to water compared to hydrated, suggesting daily torpor in females.
Exposure to constant artificial light alters honey bee sleep rhythms and disrupts sleep

Artificial light at night (ALAN) is known to create changes in animal behavior in some invertebrates and vertebrates and can result in decreased fitness. ALAN effects have not been studied in European honey bees (Apis mellifera), an important pollinator. Colonies can be exposed to ALAN in swarm clusters, when bees cluster outside the nest on hot days and evenings, and, in limited cases, when they build nests in the open. Forager bees maintained in incubated cages were subjected to constant light or dark and observed with infrared cameras. The bees maintained a regular sleep pattern for three days but showed a shift on the fourth day in the presence of continuous light. Bees under constant light demonstrated a 24.05-hour rhythm, compared to a 23.12-hour rhythm in the dark. After 95 hours, the light-exposed bees slept significantly less and experienced significantly more disturbances from their peers. They also preferred to sleep in the lower portion of the cages, which had lower light intensity. These findings suggest that ALAN can disrupt honey bees’ sleep patterns, which may have implications for their behavior and overall colony health.
Identifying conceptual neural responses to symbolic numerals

Neural processing of numerical concepts may be measured in humans automatically, without a related numerical task. However, the extent to which neural responses to symbolic numbers are due to physical stimulus confounds independently of conceptual representations remains unknown. Here, we targeted conceptual responses to parity (even vs. odd), using an electroencephalographic (EEG) frequency-tagging approach with a symmetry/asymmetry paradigm. Fifty second sequences of Arabic numerals (2–9) were presented at 7.5 Hz; odd and even numbers were alternated, so that differential responses to parity would be captured at 3.75 Hz (7.5 Hz/2). Parity responses were probed with four different stimulus sets, increasing in intra-numeral stimulus variability. Moreover, two control conditions were tested for each stimulus set, comprised of non-conceptual numeral alternations (strong control, for small inter-group physical differences: 2,3,6,7 vs. 4,5,8 and 9; weak control, for large physical differences: 2,4,5,7 vs. 3,6,8,9). Significant asymmetrical responses at 3.75 Hz were found over the occipitotemporal cortex to all conditions, thus even for arbitrary numeral groups. The weak control condition elicited the largest response in the stimulus set with the lowest level of variability (1 font). Only in the stimulus set with the highest level of variability (20 hand-drawn, colored exemplars per numeral) did the response to parity surpass both control conditions. These findings show that physical differences across small sets of Arabic numerals can strongly influence, and even account for, automatic brain responses. However, carefully designed control conditions and highly variable stimulus sets may be used towards identifying truly conceptual neural responses.
Ym1 protein crystals promote type 2 immunity

Spontaneous protein crystallization is a rare event, yet protein crystals are frequently found in eosinophil-rich inflammation. In humans, Charcot-Leyden crystals (CLCs) are made from galectin-10 (Gal10) protein, an abundant protein in eosinophils. Whereas mice do not encode Gal10 in their genome, they do form pseudo-CLCs, made from the chitinase-like proteins Ym1 and/or Ym2, encoded by Chil3 and Chil4 and made by myeloid and epithelial cells respectively. Here, we investigated the biological effects of pseudo-CLCs since their function is currently unknown. We produced recombinant Ym1 crystals which were shown to have identical crystal packing and structure by X-ray crystallography as in vivo native crystals derived from murine lung. When administered to the airways of mice, crystalline but not soluble Ym1 stimulated innate and adaptive immunity and acted as a type 2 immune adjuvant for eosinophilic inflammation via triggering of dendritic cells (DCs). Murine Ym1 protein crystals found at sites of eosinophilic inflammation reinforce type 2 immunity and could serve as a surrogate model for studying the biology of human CLCs.
Disregarding multimappers leads to biases in the functional assessment of NGS data

Standard ChIP-seq and RNA-seq processing pipelines typically disregard sequencing reads whose origin is ambiguous (“multimappers”). This usual practice has potentially important consequences for the functional interpretation of the data: genomic elements belonging to clusters composed of highly similar members are left unexplored. In particular, disregarding multimappers leads to the systematic underrepresentation in epigenetic studies of recently active transposons, such as AluYa5 and L1HS. Furthermore, this common strategy also has implications for transcriptomic analysis: members of repetitive gene families, such the ones including major histocompatibility complex (MHC) class I and II genes, are systematically underquantified. Based on these findings, we strongly advocate for the implementation of multimapper-aware bioinformatic genomic analyses.
New variants in the Chloroplast Genome Sequence of two Colombian individuals of the Cedar timber species (Cedrela odorata L.), using long read Oxford Nanopore Technology

The plant species Cedrela odorata has been largely exploited in the timber industry due to the high demand of its wood. Therefore, C. odorata, has been considered as a vulnerable species since 1994, with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). C. odorata is one of the key timber species included in the management and conservation plans in Colombia. These plans include the study of local populations by developing genetic resources for the species. In this study, two novel chloroplast (cp) genomes have been generated using the MinION long read sequencing technology. The new cp assemblies were compared with other cp genomes for the species, supporting previous hypothesis of intraspecific diversity associated to their place of origin. Furthermore, the cp genomes were screened for sequence variants (SV) and a total of 16 SNPs were identified, presumably unique to populations of the amazon region in Colombia. Here, the first cp genome sequences of C. odorata from Colombian individuals represent novel and valuable genomic resources for the species suitable for DNA fingerprinting and DNA barcoding applications.
Et si on comprenait la structure de graphes de connaissances comme Wikidata ?

Résumé La production participative de graphes de connaissances comme Wikidata a permis l’émergence de vastes bases de connaissances agglomérant des expertises et des opinions variées. Fortement dépendant de sa communauté, ce pro-cessus décentralisé interroge sur sa capacité à faire émer-ger un graphe de connaissances représentatif et cohérent. Dans cet article, nous affirmons que la représentation des connaissances gagnerait à modéliser la manière dont les faits s’organisent dans la partie assertionnelle. L’objectif serait de définir et étudier des processus permettant de gé-nérer des données synthétiques qui ressemblent étroitement aux graphes de connaissances réels. Nous indiquons des retombées possibles de ces modèles en optimisation et en analyse de données. Enfin, nous envisageons les principaux verrous scientifiques à lever pour parvenir à modéliser la structure des graphes de connaissances.
Des données tabulaires aux graphes de connaissances : état de l'art des méthodes d'interprétations sémantique de tables

Résumé Les données tabulaires sont omniprésentes sur le Web et dans les entrepôts de données des entreprises. Ces tableaux contiennent des informations pouvant potentiellement de-venir des connaissances après une étape d’interprétation sémantique de tables se basant sur un graphe de connais-sances. Ce papier propose un état de l’art des différentes tâches et méthodes existantes pour mener à bien cette in-terprétation. Dans un premier temps, nous proposons une nouvelle classification des tableaux reflétant la diversité et la complexité de ces structures. Nous décomposons ensuite le problème de l’interprétation sémantique en cinq sous-tâches et passons en revue trois familles d’approches au travers du prisme des corpus d’évaluation proposés par la communauté.
Nouveaux réseaux neuronaux profonds pour l'alignement d'ontologies

Résumé L’alignement d’ontologies s’appuie souvent sur des ap-proches lexicales. Cependant, avec le développement des modèles de langage basés sur les transformeurs, il est dé-sormais possible de comparer des textes en se basant sur le contexte plutôt que sur les caractéristiques lexicales. Dans ce travail, nous proposons de nouveaux modèles neu-ronaux siamois qui optimisent une fonction d’apprentis-sage contrastif auto-supervisé sur des articles de la lit-térature scientifique. Les résultats obtenus sur plusieurs benchmarks montrent que les modèles proposés permettent d’améliorer différentes tâches biomédicales. Ensuite, nous exploitons ces modèles dans la tâche d’alignement d’onto-logies biomédicales.
MODELING AND FABRICATING ION TRAPS FOR QUANTUM COMPUTING

--The purpose of this project was to design, model, and fabricate the fundamental element for a 2D Quantum Computer. My aim was to design a 2D Quantum Computer based on trapped ions. Using a Paul Trap concept, I designed a surface electrode ion trap in order to trap an ion qubit. Using the COMSOL Multiphysics software, I modeled and tested various parameters, drive frequency, RF amplitude, and materials to produce an ideal scenario for fabrication. I then use the fabrication equipment available to me to create a physical representation of the model created in COMSOL.
No Free Lunch: On the Increased Code Reuse Attack Surface of Obfuscated Programs

Obfuscation has been widely employed to protect software from the malicious reverse analysis. However, its security risks have not previously been studied in detail. For example, most obfuscation methods introduce large blocks of opaque code that are black boxes to normal users. In this paper, we show that, indeed, obfuscation can increase the attack risk. Existing gadget search tools, while able to find more gadgets in obfuscated code, do not succeed in assembling them into more exploits. However, these tools use strict pattern matching, greedy searching strategies, and only very simple gadgets. We develop Gadget-Planner, a more flexible approach to building code-reuse attacks that overcomes previous limitations via symbolic execution and automated planning. In a study across both benchmark and real-world programs, this approach finds many more exploit payloads on obfuscated programs, both in terms of number and diversity.
The Complexity of the Matroid Homomorphism Problem

We show that for every binary matroid $N$ there is a graph $H_*$ such that for the graphic matroid $M_G$ of a graph $G$, there is a matroid-homomorphism from $M_G$ to $N$ if and only if there is a graph-homomorphism from $G$ to $H_*$. With this we prove a complexity dichotomy for the problem $\rm{Hom}_\mathbb{M}(N)$ of deciding if a binary matroid $M$ admits a homomorphism to $N$. The problem is polynomial time solvable if $N$ has a loop or has no circuits of odd length, and is otherwise $\rm{NP}$-complete. We also get dichotomies for the list, extension, and retraction versions of the problem.
Interaction Fields: Sketching Collective Behaviours

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Interaction Fields: Sketching Collective Behaviours Adèle Colas, Wouter van Toll, Ludovic Hoyet, Claudio Pacchierotti, Marc Christie, Katja Zibrek, Anne-Hélène Olivier, Julien Pettré
Analyzing Domain of Convergence for Broyden’s Method

Analyzing Domain of Convergence for Broyden’s Method Broyden’s method is a quasi-Newton iterative method used to find roots of non-linear systems of equations. Research has shown and improved the rate of convergence for special cases and specific applications of the method. However, there is limited literature regarding the well-posedness of the method. In practice, a numerical method must reliably converge to the appropriate root. This paper will discuss the domain of attraction for the roots of a system found by using Broyden’s method. A method of approximating the radius of convergence of a root will be described which considers the largest disk centered at the root such that all values within the disk converge to the root. Literature on Broyden’s method has conflicting claims about the initial approximation of the Jacobian. Plots will demonstrate the effect of the initial guess of the Jacobian for the iterative scheme. In this paper, the importance of using a finite difference approximation for the initial guess of the Jacobian will be shown through examples of 2× 2 systems of equations.
(2015). Ultrastructural Correlates of Enhanced Norepinephrine and Neuropeptide Y Cotransmission in the Spontaneously Hypertensive Rat Brain. ASN NEURO, 7(5), 1-19.

The spontaneously hypertensive rat (SHR) replicates many clinically relevant features of human essential hypertension and also exhibits behavioral symptoms of attention-deficit/hyperactivity disorder and dementia. The SHR phenotype is highly complex and cannot be explained by a single genetic or physiological mechanism. Nevertheless, numerous studies including our own work have revealed striking differences in central catecholaminergic transmission in SHR such as increased vesicular catecholamine content in the ventral brainstem. Here, we used immunolabeling followed by confocal microscopy and electron microscopy to quantify vesicle sizes and populations across three catecholaminergic brain areas—nucleus tractus solitarius and rostral ventrolateral medulla, both key regions for cardiovascular control, and the locus coeruleus. We also studied colocalization of neuropeptide Y (NPY) in norepinephrine and epinephrine-containing neurons as NPY is a common cotransmitter with central and peripheral catecholamines. We found significantly increased expression and coexpression of NPY in norepinephrine and epinephrine-positive neurons of locus coeruleus in SHR compared with Wistar rats. Ultrastructural analysis revealed immunolabeled vesicles of 150 to 650 nm in diameter (means ranging from 250 to 300 nm), which is much larger than previously reported. In locus coeruleus and rostral ventrolateral medulla, but not in nucleus tractus solitarius, of SHR, noradrenergic and adrenergic vesicles were significantly larger and showed increased NPY colocalization when compared with Wistar rats. Our morphological evidence underpins the hypothesis of hyperactivity of the noradrenergic and adrenergic system and increased norepinephrine and epinephrine and NPY cotransmission in specific brain areas in SHR. It further strengthens the argument for a prohypertensive role of C1 neurons in the rostral ventrolateral medulla as a potential causative factor for essential hypertension
A trophic state index for lakes

A numerical trophic state index for lakes has been developed that incorporates most lakes in a scale of 0 to 100. Each major division (10, 20, 30, etc.) represents a doubling in algal biomass. The index number can be calculated from any of several parameters, including Secchi disk transparency, chlorophyll, and total phosphorus.
Adaptive Quasi-Newton Algorithm for Remote Sensing

Recurrent neural networks (RNNs) have been widely applied to model time series and temporal data due to inherent memory storing past information. However, the optimization algorithms for RNNs either only exploit the first-order information with low computational complexity or gain the second-order information with heavy per-iteration cost. In this paper, an adaptive quasi-Newton algorithm (ADA-L-BFGS) is proposed on the basis of limited-memory BFGS algorithm whose memory size can be determined adaptively during the process of iteration and used to train deep neural networks for extracting deep features of hyperspectral data. Our algorithm can retain low per-iteration cost and ensure fast convergence. It is emphasized that ADA-L-BFGS has two appealing features. One is that multiple memory sizes are selected to construct hybrid search direction for strengthening the usage of recent curvature information. Another is that a promising calculation criterion for step size is introduced to achieve efficient training of deep neural networks for hyperspectral images classification. Experimental results clearly illustrate that the proposed ADA-L-BFGS can achieve faster convergence and better performance than previous methods.
Optimal Primary Tone Levels in Distortion Product Otoacoustic Emissions and the Role of Middle Ear Transmission

Distortion product otoacoustic emissions (DPOAEs) provide objective data on the integrity of active cochlear mechanics and are evoked in response to stimulation with two sinusoids. In part due to ear-specific middle ear energy transmission characteristics, optimal stimulus levels are difficult to predict. In this dissertation, a formula for the prediction of optimal stimulus levels is developed, which accounts for effects of energy absorbance into the middle ear. Additionally, a DPOAE-based method for the quantification of conductive hearing loss is presented.
Resident Load Disaggregation Based on Dilated Causal Convolution and Variational Autoencoder

In smart grids, knowing the usage of individual appliances in a resident house plays a key role in improving energy savings and demand side management. The electrical power of individual devices can be obtained from aggregated power signals via non-intrusive load monitoring (NILM) methods. Deep learning is widely used for NILM due to its strong nonlinear mapping ability. This paper proposes a new NILM method based on variational autoencoder (VAE), which combines the causal convolutional neural network and Instance-Batch Normalization Net (IBN-Net). The proposed model can accurately capture the various features of the time sequence data so as to improve the accuracy of load disaggregation. Experiments are all conducted on UK-DALE. The results show that the proposed model achieves good results in the NILM problem and outperforms the current state-of-the-art methods.