Miracle-dz/UniFAR-FTUs huggingface dataset:
The Impact of the Gut Microbiome on Colorectal Cancer

Colorectal cancer (CRC) represents one of the leading causes of morbidity and cancer-related mortality in the world. While the etiology of CRC is believed to arise from genetic mutations, alterations in the gut microbiota composition also influence cancer incidence and progression. This review focuses on how gut microbiota and their relationship with the innate immune system link inflammation to genotoxicity and carcinogenesis.
Effect of L-carnitine enrichment on the rotifer and influences on clownfish larvae

Enrichment has shown considerable influence on the population growth, reproduction and individual growth of rotifer (Brachionus plicatilis Müller, 1786) and its utility on the clownfish larvae (Amphiprion ocellaris Cuvier 1830). Using the culture medium of microalgae (Nannochloropsis salina D.J. Hibberd 1981) as the control, rotifers were enriched by dissolving in S-presso (for short term enrichment) or L-carnitine supplements. The study was conducted in three replicates for five and 10 days of batch culture. On day-4, the population density of rotifers exposed to 1, 10 and 100 mg l -1 L-carnitine was significantly increased (p<0.001) by 43, 39 and 54%, respectively, compared to the control. The population density in these three treatments also increased on day-2, day-3 and day-5 compared to the 1000 mg L treatment (p<0.05) and control (p<0.05). The body length (p<0.001) and width (p<0.05) were significantly reduced in the 1000 mgL treatment compared to the control. The mean values of total unsaturated fatty acids (PUFA's, HUFA's and n-3 fatty acids) and the ratio of n-3/n-6, DHA/EPA, EPA/AA were significantly higher (p<0.05) in the rotifers enriched with L-carnitine compared to S-presso and algae. Larvae fed using rotifer enriched with Lcarnitine gained the maximum growth (65.7±1 mg), followed by those enriched with S-presso (42.2±0 mg). In L-carnitine treatment, metamorphosis took only 9 days, followed by the control. In L-carnitine and S-presso units, the clownfish larvae took only three days for the first pigmentation compared to four days in N. salina (control) and 10 days with S-presso. Rotifers enriched with L-carnitine showed the highest survival rate (70 %) of the clownfish followed by the control (68%) and S-presso (52%). The results suggested that L-carnitine could be a positive factor to enhance the rotifer production and also its utilization in clownfish larval culture.
Phenolic constituents, anti-radicals, and enzymes inhibitory potentials of Brachystegia eurycoma seeds: Effects of processing methods

ABSTRACT Impact of roasting and boiling on the phenolic constituents, anti-radicals, xanthine oxidase (XO), and angiotensin 1-converting enzyme (ACE) inhibitory potentials of Brachystegia eurycoma seeds (BES) was evaluated. Raw BES contained caffeic acid, ellagic acid, rutin, and quercetin as the predominant phenolics, and strongly scavenged DPPH* and ABTS*+, and inhibited XO and ACE. Both roasting and boiling resulted in decrease in the levels of phenolics and bioactivities of the seeds, but roasted seeds retained higher levels of the phenolics and the bioactivities than the boiled seeds. Roasting could be recommended as a valuable processing method for the retention of the phenolics and bioactivities of BES.
Simultaneous Selection of the Wild‐type Genotypes of the G894T and 4B/ 4A Polymorphisms of NOS3 Associate with High‐altitude Adaptation

The routine performance of high‐altitude (HA) natives in the hypoxic environment of HA exemplifies the process of adaptation mainly through natural selection. The recent therapeutic application of nitric oxide (NO) in HA disorders, for the improvement of oxygenation and vasodilation, ushered us to investigate the endothelial nitric oxide synthase gene (NOS3) with respect to HA adaptation. The study subjects, 131 HA monks (HAM), 136 HA controls (HAC), and 170 lowlanders (LLs) were screened for NOS3 G894T (Glu298Asp) and 4B/4A polymorphisms. The NO levels were estimated, for a correlation with the polymorphisms. The three groups were in Hardy‐Weinberg equilibrium for the polymorphisms. The overall genotype distributions for the G894T and 4B/4A polymorphisms were significant (P = 0.01 and 0.02, respectively) in the three groups. Wild‐type alleles G and 4B were significantly over‐represented in the HA groups as compared to the LLs (P = 0.006 and P = 0.02, respectively). The NO levels were in the order of HAM>HAC>LLs (P < 0.0001). Furthermore, combinations of the GG and BB genotypes were distributed significantly more frequently in the HAM (P < 0.0001) and HAC (P = 0.0005) than in LLs. The NO levels contributed by the wild‐type genotype combination GG, BB were significantly elevated when compared with the remaining eight genotype combinations together in the HAM, HAC and LLs (P = 0.003, P = 0.0006 and P < 0.0001, respectively). To conclude, the genotype combination of NOS3 wild‐type homozygotes (GG, BB) was found significantly more frequently in HA groups than in LLs, by contributing to higher NO levels associated with HA adaptation.
Regeneration of native Mariana Island forest in disturbed habitats

The present vegetation of a habitat disturbed ca. 45 years ago on Saipan, Mariana Islands, was studied to determine the extent to which native trees have become reestablished, to gain insights into the mechanisms involved in natural reforestation, and to determine if natural reforestation offers any management lessons. In ten 10 X 5 m plots, all tree species present were enumerated and their basal areas measured in 4 vertical strata (canopy, sapling, shrub, seedling). Introduced species, particularly Leucaena leucocephala and Carica papaya, were proportionately most dense in the canopy and seedling layers, whereas native species, particularly Melanolepis multiglandulosa and Aidia cochinchinensis, reached their highest proportionate density in the shrub and sapling layers. Moreover, introduced species increased and native species declined in proportionate basal area from the shrub layer to the canopy. The great majority of native trees present were characterized by having small fleshy fruits, and were probably dispersed into the area by indigenous forest birds. Native tree species appear to be successfully recolonizing this site, and may eventually come to predominate if no additional human disturbance occurs. However, temporal shifts in vegetation composition seem likely to involve a complex interplay of seed dispersal agents, evolving microenvironments, plant competitive interactions, and external events such as typhoons. Several potential management strategies are described.
The Role of SAP97 Isoforms in Regulating Synaptic Function in Hippocampal Neurons

i Acknowledgements . ii List of Figures. vi List of Tables. viii Abbreviations and definitions . viii Chapter 1. General Introduction. 1 1.1. Overview . 1 1.2. The Hippocampus . 1 1.3. Glutamatergic Synapses . 3 1.3. 1. AMPA receptors . 4 1.3. 2. NMDA receptors.6 1.4. LTP and LTD . 7 1.4. 1. NMDAR-Dependent LTP . 7 1.4. 2. LTD.10 1.5. Postsynaptic density (PSD) and MAGUKs.11 1.5. 1. PSD-95 . 12 1.5. 2. SAP102 . 12 1.5. 3. PSD-93 . 13 1.6. SAP97.13 1.6. 1. The Structure of SAP97 . 14 1.6. 2. SAP97 Binding partners.16 1.6. 3. Functions of SAP97 . 17 1.6. 4. SAP97 and AMPARs.18 1.6. 5. SAP97 and NMDARs . 19 1.7. The aims of the study.20 Chapter 2. Methods. 22 2.1. Primary hippocampal neuron culture . 22 2.2. Molecular Biology . 23 2.2.1. Expression constructs.23 2.2.2. Transformation.24 2.2.3. Mini-Plasmid Preparation . 24 2.2.4. Maxi Plasmid Preparation.25 2.2. 5. Enzymatic Digestion . 26 2.3. Calcium Phosphate Transfection . 27 2.4. Immunocytochemistry.28 2.4. 1. Fixation . 28
Enquête sérologique sur la maladie de Newcastle et la maladie de Gumboro chez les canards et les pintades indigènes de Jos, dans l’Etat du Plateau au Nigeria

A serological survey was conducted to determine the prevalence of Newcastle disease (ND) and infectious bursal disease (IBD) antibodies in local ducks and local guinea fowls brought from different locations within Plateau State and neighboring areas to be sold at Yankaji, a poultry market in Jos. The hemagglutination inhibition test and agar gel immunodiffusion test were used to diagnose ND and IBD, respectively. Results indicated that out of the 165 serum samples collected from ducks, 11 (6.7%) had antibodies against the ND virus. Similarly, out of the 205 serum samples collected from guinea fowls, 28 (13.6%) had antibodies against the ND virus. All sera from ducks and guinea fowls were negative for IBD antibodies. It was concluded that both local ducks and guinea fowls had been exposed to the Newcastle disease virus but not to the infectious bursal disease virus.
Neuro-Insular Complexes in the Human Pancreas

It is well known that pancreatic islets are complex structures composed of endodermally derived endocrine cells, integrated with endothelial cells and other cells, originating from the mesoderm, and innervated by nerve fibers that have a neuroectodermal origin. In our studies, we focused on the interactions between the structures of the nervous system and endocrine cells, the so-called neuro-insular complexes, in the human pancreas. In this chapter, we present our results and literature data concerning the morphological organization of neuro-insular complexes in humans and other mam- mals. We also discuss the possible functional role of neuro-insular complexes, such as the involvement of the nervous system in the regulation and synchronization of islet hormone secretion and the morphogenetic plasticity of the endocrine pancreas in adults, as well as in the regulation of endocrine cell proliferation and maturation during prenatal development of the pancreas.
LFMM 2.0: Latent factor models for confounder adjustment in genome and epigenome-wide association studies

Motivation Genome-wide, epigenome-wide and gene-environment association studies are plagued with the problems of confounding and causality. Although those problems have received considerable attention in each application field, no consensus have emerged on which approaches are the most appropriate to solve this problem. Current methods use approximate heuristics for estimating confounders, and often ignore correlation between confounders and primary variables, resulting in suboptimal power and precision. Results In this study, we developed a least-squares estimation theory of confounder estimation using latent factor models, providing a unique framework for several categories of genomic data. Based on statistical learning methods, the proposed algorithms are fast and efficient, and can be proven to provide optimal solutions mathematically. In simulations, the algorithms outperformed commonly used methods based on principal components and surrogate variable analysis. In analysis of methylation profiles and genotypic data, they provided new insights on the molecular basis of diseases and adaptation of humans to their environment. Availability and implementation Software is available in the R package lfmm at https://bcm-uga.github. io/lfmm/.
Production of moss‐dominated biocrusts to enhance the stability and function of the margins of artificial water bodies

Margins of water reservoirs associated with dams can have high‐frequency tides, promoting soil erosion and nutrient leaching. We propose the use of biocrusts for restoration and ecological engineering purposes, due to their poikilohydric character, to stabilize reservoir margins. We promoted biocrust growth under controlled conditions, testing two types of substrate: native sand and organic substrate. After 2 months, biocrusts grew on organic substrate covering almost all the area, but not on native sand. This fast and easy nature‐based solution for soil stabilization can be used as an environmental engineering tool in highly degraded sites.
Maternal rearing condition and age affect progeny fitness in the parasitoid wasp Lysiphlebus fabarum

Maternal rearing conditions are expected to affect fitness components of progeny so that maternal effects effectively protect offspring from environmental stressors. The objective of this study was to elucidate the interaction between maternal rearing condition, age, and offspring rearing condition in the parasitoid wasp Lysiphlebus fabarum (Marshall) (Hymenoptera: Braconidae, Aphidiinae). The effects of maternal age, body size, and host instar used for development on fitness components of progeny were evaluated. Host was the black bean aphid, Aphis fabae Scopoli (Hemiptera: Aphididae). Results indicated that small and young mothers (developing in first‐instar hosts) produced progeny with a longer developmental time compared to large and old mothers (developing in second‐instar hosts). Progeny that hatched from larger eggs also had a larger body size. There were, however, no significant differences in the size of progeny that developed in different host instars. Progeny that hatched from large eggs had a higher initial egg load, and progeny produced by younger mothers had larger eggs. These differences were significant only when progeny developed in the first host instar, whereas in the second and fourth instar no differences were observed. Our findings indicate that progeny with larger size at the egg stage had superior fitness. Age‐specific maternal effects were not as strong as the effect of the mother's body size. Although the interaction between host instar of progeny development and maternal rearing condition was not statistically significant, developing in suboptimal instars led to trade‐offs between fitness components in progeny. The ecological significance of these findings is discussed.
Diferencia en la reacción a Pyricularia oryzae de materiales de trigo en los estadios vegetativo y reproductivo

La Piricularia o brusone causada por Magnaporthe oryzae B. C. Couch and L. M. Kohn (sin. Pyricularia oryzae), es actualmente considerada una de las mas importantes enfermedades del trigo en Sudamerica, considerando las pocas fuentes de resistencia reportadas en el mundo, el objetivo del trabajo fue relacionar la resistencia a Pyricularia oryzae en hojas con la resistencia en espigas, en base a la inoculacion de 61 materiales de trigo, pertenecientes al Programa Nacional de Trigo, del Instituto Paraguayo de Tecnologia Agraria. Estos fueron seleccionados en base a su amplia variabilidad genetica de progenitores para resistencia al patogeno. Las inoculaciones se realizaron en invernadero, cuando las plantas presentaban cuatro hojas para el estadio vegetativo y en espigazon para el estadio reproductivo, utilizando una suspension de 2 105 conidios/mL de un aislado del hongo seleccionado por su alta virulencia en ensayos previos. De los 61 materiales evaluados, solo cuatro presentaron resistencia tanto en hoja como en espiga, y tres fueron resistentes a nivel foliar y moderadamente resistentes en espigas, demostrando la estrechez en la base de germoplasma resistente para las infecciones de brusone en las espigas. En base al bajo numero de lineas consideradas resistentes a Pyricularia en este estudio, se enfatiza la necesidad de ampliar la resistencia genetica en el germoplasma de trigo de manera urgente.
She talks to me as if she were alive: Assessing the social reactions and perceptions of children toward voice assistants and their appraisal of the appropriateness of these reactions

It has long been observed that people treat technical entities like computers as social actors. Numerous studies have been conducted on media equation theory, which describes users' social reactions toward devices to be unconscious. These users consider this inappropriate when thought about consciously. However, both long-term trends as well as the reactions of children have been neglected - although children might indeed differ in their reactions, as they are especially prone to the tendency to humanize and anthropomorphize. This study examined the social behavior of 20 children aged six to twelve toward a voice assistant during a five-week field study. In the course of three sessions, interviews were conducted to assess the children's tendency to socially react to the devices and to what extent they perceive such reactions as appropriate. Additionally, the tendency to anthropomorphize was assessed together with qualitative data to gain insight into cues that would trigger anthropomorphization. Results indicate that age and duration have an effect on the tendency to anthropomorphize. However, age and duration have only a partial effect on social reactions and the evaluation of their appropriateness. Furthermore, natural speech appeared to be a rather strong cue in triggering tendencies to anthropomorphize in the children.
Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

A central quantity of interest in molecular biology and medicine is the free energy of binding of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding affinity had been widely regarded as out of reach of theoretical methods owing to the lack of reproducibility of the available methods, not to mention their complexity, computational cost and time-consuming procedures. The lack of reproducibility stems primarily from the chaotic nature of classical molecular dynamics (MD) and the associated extreme sensitivity of trajectories to their initial conditions. Here, we review computational approaches for both relative and absolute binding free energy calculations, and illustrate their application to a diverse set of ligands bound to a range of proteins with immediate relevance in a number of medical domains. We focus on ensemble-based methods which are essential in order to compute statistically robust results, including two we have recently developed, namely thermodynamic integration with enhanced sampling and enhanced sampling of MD with an approximation of continuum solvent. Together, these form a set of rapid, accurate, precise and reproducible free energy methods. They can be used in real-world problems such as hit-to-lead and lead optimization stages in drug discovery, and in personalized medicine. These applications show that individual binding affinities equipped with uncertainty quantification may be computed in a few hours on a massive scale given access to suitable high-end computing resources and workflow automation. A high level of accuracy can be achieved using these approaches.
Gender Stereotypes in Virtual Agents

Visual, behavioral and verbal cues for gender are often used in designing virtual agents to take advantage of their stereotypical effects on the users. However, recent studies point towards a more gender-balanced view of stereotypical traits and roles in our society. This paper is intended as an effort towards a progressive and inclusive approach for gender representations in virtual agents. Our contributions are two-fold. First, in an iterative design process, we created representative male, female and androgynous agents with few differences in their visual attributes. Second, we used these agents to evaluate the stereotypical assumptions of gendered traits and roles in virtual agents. Our results showed that, indeed, gender stereotypes are not as effective as previously assumed, and androgynous agents could represent a middle-ground between gendered stereotypes. We present our findings in the hope to foster discussions in virtual agent research and the frequent stereotypical use of gender representations.
Effect of Surface Treatment and Cutting Orientation to the Changes in Stents Surface Roughness

During the implantation process, an expandable balloon stent undergoes a change in mesh shape with a high strain rate. Permanent mesh shape changes to the stents indicate plastic deformation has occurred. On a micro-scale, plastic deformation has significant influence when interacting with the soft tissue of human blood vessels. This experimental study aims to investigate the effect of surface treatment and cutting orientation on the changes in surface roughness that definitely occurs when a stent deployed. To study the effect of surface treatment, two types of surface treatment were applied after surface polishing, i.e. etching and electropolishing. Surface polishing is carried out to enable microscopic observation. As for examining the effect of cutting orientation, the plate is cut in lateral and longitudinal orientation against the predicted-rolling direction of 316L sheet-type of stainless steel. An intermittent tensile test is conducted to obtain information about the changes in surface roughness. The surface observation is carried out three times on a similar surface of testpiece after reaching plastic deformation. The experimental study shows that the orientation of raw material has an insignificant effect on the changes in stent surface roughness. As for the surface treatments, electropolishing tended to decrease the tensile property of material.
Hybridization and Asymmetric Introgression after Secondary Contact in Two Tropical African Climber Species, Haumania danckelmaniana and Haumania liebrechtsiana (Marantaceae)

Premise of research. Interspecific hybridization is frequently observed between closely related plant species with overlapping distribution ranges, especially in zones of secondary contact after isolation in different refugia. Although well studied in temperate regions, interspecific hybridization is little documented in tropical regions, where it may be frequent in areas with high species diversity. To bridge this gap, we investigate hybridization in two closely related climber species from the genus Haumania (Haumania danckelmaniana and Haumania liebrechtsiana) originating from Gabon/Cameroon and the Democratic Republic of Congo, respectively, and co-occurring in Northern Gabon. The aim of this study was to genetically quantify and qualify the degree of hybridization between these species in their area of distributional overlap by including for the first time morphological intermediates. Methodology. We investigated 265 individuals from nine sites (seven sites containing both species) by genotyping seven microsatellites and sequencing one chloroplastic region (trnC-petN1r). Bayesian clustering analysis and simulated genotypes allowed the assignment of sampled genotypes to one or the other species or their intermediates (first-generation hybrid or backcrosses). Pivotal results. We found 13% and 41% of intermediates on the basis of morphological versus genetic data, respectively, indicating only a partial congruence. There was an equal amount of backcrosses to both parental species (15%). However, a comparison at the local scale of microsatellites and cpDNA sequence data revealed a unidirectional introgression from H. liebrechtsiana into H. danckelmaniana. At the scale of the nine sites, genetic differentiation was much lower among H. liebrechtsiana than among H. danckelmaniana populations. Conclusions. These results are in line with the previously proposed phylogeographic scenario for the genus Haumania and the theoretical expectation of chloroplast capture when an expanding species (here H. liebrechtsiana) invades the range of a local species (here H. danckelmaniana). Because the forest flora of Central Africa has undergone repeated cycles of fragmentation and expansion following past climate changes, we expect that similar scenarios of hybridization after secondary contact may be common.