Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatic Glycerol Metabolism-Related Genes in Carnivorous Rainbow Trout (Oncorhynchus mykiss): Insights Into Molecular Characteristics, Ontogenesis, and Nutritional Regulation

Glycerol metabolism in rainbow trout is poorly studied even though it is at the interface between lipid and glucose metabolism. Moreover, glycerol can be an important ingredient in new aquafeed formulation to decrease the catabolism of dietary amino acids. Thus, the present study aimed to characterize for the first time the different genes coding for key enzymes and proteins involved in hepatic glycerol metabolism. From the trout genomes, all the paralogous genes coding for glycerol transport (aqp9b), glycerol kinase (gk2a and gk5), glycerol-3-phosphate phosphatase (pgp), and glycerol-3-phosphate dehydrogenase (gpd1a, gpd1b, and gpd1c) were identified. The ontogenesis determined that the capacity to metabolize glycerol begins with the apparition of the liver during the development (stage 22) and are more expressed at the endogenous–exogenous feeding period (stage 35). The postprandial regulation of the expression of these genes in juvenile trout showed that the postprandial peak of expression is between 4 and 24 h after the last meal for many of the genes, demonstrating that glycerol metabolism could be nutritionally regulated at a molecular level. However, surprisingly, no regulation of the mRNA abundance for the glycerol metabolism-related genes by different levels of dietary glycerol (0, 2.5, and 5%) have been detected, showing that hepatic glycerol metabolism is poorly regulated at a molecular level by dietary glycerol in rainbow trout juveniles.
Continuous variable response, kinetic gating and connectivity that determine topology of insulin signaling are perturbed in hyper-insulinemic states

Understanding kinetic control of biological processes is as important as identifying components that constitute pathways. Insulin signaling (IS) is central for almost all metazoans and its perturbations are associated with various diseases and aging. While temporal phosphorylation changes and kinetic constants have provided some insights, constant or variable parameters that establish and maintain signal topology are poorly understood. Our iterative experimental and mathematical simulation-based approaches reveal novel kinetic parameters of IS that encode concentration and nutrient dependent information. Further, we find that pulsatile fasting insulin rewires IS akin to memory and in anticipation of a fed response. Importantly, selective kinetic gating of signals and maximum connectivity, between metabolic and growth-factor arms under normo-insulinemic states, maintains network topology. In addition to unraveling kinetic constraints that determine cascade architecture, our findings will help in identifying novel therapeutic strategies that conserve coupling between metabolic and growth-factor arms, which is lost in diseases and conditions of hyperinsulinemia.
Unsupervised analysis of multi-experiment transcriptomic patterns with SegRNA identifies unannotated transcripts

Background Exploratory analysis of complex transcriptomic data presents multiple challenges. Many methods often rely on preexisting gene annotations, impeding identification and characterization of new transcripts. Even for a single cell type, comprehending the diversity of RNA species transcribed at each genomic region requires combining multiple datasets, each enriched for specific types of RNA. Currently, examining combinatorial patterns in these data requires time-consuming visual inspection using a genome browser. Method We developed a new segmentation and genome annotation (SAGA) method, SegRNA, that integrates data from multiple transcriptome profiling assays. SegRNA identifies recurring combinations of signals across multiple datasets measuring the abundance of transcribed RNAs. Using complementary techniques, SegRNA builds on the Segway SAGA framework by learning parameters from both the forward and reverse DNA strands. SegRNA’s unsupervised approach allows exploring patterns in these data without relying on pre-existing transcript models. Results We used SegRNA to generate the first unsupervised transcriptome annotation of the K562 chronic myeloid leukemia cell line, integrating multiple types of RNA data. Combining RNA-seq, CAGE, and PRO-seq experiments together captured a diverse population of RNAs throughout the genome. As expected, SegRNA annotated patterns associated with gene components such as promoters, exons, and introns. Additionally, we identified a pattern enriched for novel small RNAs transcribed within intergenic, intronic, and exonic regions. We applied SegRNA to FANTOM6 CAGE data characterizing 285 lncRNA knockdowns. Overall, SegRNA efficiently summarizes diverse multi-experiment data.
Autismo y cociente intelectual: ¿estabilidad?

Introduccion. El autismo es un trastorno heterogeneo. La posibilidad de determinar sus caracteristicas a lo largo del tiempo tendra una gran repercusion en el pronostico y las predicciones que se puedan hacer. En ese sentido, el cociente intelectual y su posible estabilidad a lo largo del ciclo vital pueden ayudar a definir mejor el fenotipo del trastorno y sus necesidades asociadas. Desarrollo. Los estudios longitudinales muestran cierta estabilidad en las puntuaciones del cociente intelectual, sobre todo a partir de los anos escolares. Antes, en la etapa preescolar, existe mayor variabilidad, especialmente en aquellos ninos que tienen un funcionamiento intelectual limite o discapacidad intelectual moderada. Conclusion. Debe seguirse desarrollando mas investigacion para conocer el perfil cognitivo de las personas con trastorno del espectro autista y poder realizar predicciones a partir de su funcionamiento intelectual.
Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism

Neurological complications are common in patients with COVID-19. While SARS-CoV-2, the causal pathogen of COVID-19, has been detected in some patient brains, its ability to infect brain cells and impact their function are not well understood, and experimental models using human brain cells are urgently needed. Here we investigated the susceptibility of human induced pluripotent stem cell (hiPSC)-derived monolayer brain cells and region-specific brain organoids to SARS-CoV-2 infection. We found modest numbers of infected neurons and astrocytes, but greater infection of choroid plexus epithelial cells. We optimized a protocol to generate choroid plexus organoids from hiPSCs, which revealed productive SARS-CoV-2 infection that leads to increased cell death and transcriptional dysregulation indicative of an inflammatory response and cellular function deficits. Together, our results provide evidence for SARS-CoV-2 neurotropism and support use of hiPSC-derived brain organoids as a platform to investigate the cellular susceptibility, disease mechanisms, and treatment strategies for SARS-CoV-2 infection.
Mutational Pressure Drives Differential Genome Conservation in Two Bacterial Endosymbionts of Sap-Feeding Insects

Compared to free-living bacteria, endosymbionts of sap-feeding insects have tiny and rapidly evolving genomes. Increased genetic drift, high mutation rates, and relaxed selection associated with host control of key cellular functions all likely contribute to genome decay. Phylogenetic comparisons have revealed massive variation in endosymbiont evolutionary rate, but such methods make it difficult to partition the effects of mutation vs. selection. For example, the ancestor of auchenorrhynchan insects contained two obligate endosymbionts, Sulcia and a betaproteobacterium (BetaSymb; called Nasuia in leafhoppers) that exhibit divergent rates of sequence evolution and different propensities for loss and replacement in the ensuing ∼300 Ma. Here, we use the auchenorrhynchan leafhopper Macrosteles sp. nr. severini, which retains both of the ancestral endosymbionts, to test the hypothesis that differences in evolutionary rate are driven by differential mutagenesis. We used a high-fidelity technique known as duplex sequencing to measure and compare low-frequency variants in each endosymbiont. Our direct detection of de novo mutations reveals that the rapidly evolving endosymbiont (Nasuia) has a much higher frequency of single-nucleotide variants than the more stable endosymbiont (Sulcia) and a mutation spectrum that is even more AT-biased than implied by the 83.1% AT content of its genome. We show that indels are common in both endosymbionts but differ substantially in length and distribution around repetitive regions. Our results suggest that differences in long-term rates of sequence evolution in Sulcia vs. BetaSymb, and perhaps the contrasting degrees of stability of their relationships with the host, are driven by differences in mutagenesis. SIGNIFICANCE STATEMENT Two ancient endosymbionts in the same host lineage display stark differences in genome conservation over phylogenetic scales. We show the rapidly evolving endosymbiont has a higher frequency of mutations, as measured with duplex sequencing. Therefore, differential mutagenesis likely drives evolutionary rate variation in these endosymbionts.
The role of alpha oscillations in a premotor-cerebellar loop in modulation of motor learning: insights from transcranial alternating current stimulation

Alpha oscillations (8-13 Hz) have been shown to play an important role in dynamic neural processes underlying learning and memory. The goal of this study was to scrutinize the role of α oscillations in communication within a network implicated in motor sequence learning. To this end, we conducted two experiments using the serial reaction time task. In the first experiment, we explored changes in α power and cross-channel α coherence. We found a gradual decrease in learning-related α power over left premotor cortex (PMC), somatosensory cortex (S1) and tempo-parietal junction (TPJ). Alpha coherence between left PMC/S1 and right cerebellar crus I was reduced for sequence learning, possibly reflecting a functional decoupling in a motor-cerebellar loop during the motor learning process. In the second experiment in a different cohort, we applied 10Hz transcranial alternating current stimulation (tACS), a method shown to entrain local oscillatory activity, to left M1 (lM1) and right cerebellum (rCB) during sequence learning. We observed learning deficits during rCB tACS compared to sham, but not during lM1 tACS. In addition, learning-related α power following rCB tACS was increased in left PMC, possibly reflecting a decrease in neural activity. Importantly, learning-specific coherence between left PMC and right cerebellar lobule VIIb was enhanced following rCB tACS. These findings suggest that interactions within a premotor-cerebellar loop, which are underlying motor sequence learning, are mediated by α oscillations. We show that they can be modulated through external entrainment of cerebellar oscillations, which then modulates motor cortical α and interferes with sequence learning.
A test of the Baldwin Effect: Differences in both constitutive expression and inducible responses to parasites underlie variation in host response to a parasite

Despite the significant effect of host-parasite interactions on both ecological systems and organism health, there is still limited understanding of the mechanisms driving evolution of host resistance to parasites. One model of rapid evolution, the Baldwin Effect, describes the role of plasticity in adaptation to novel conditions, and subsequent canalization of associated traits. While mostly applied in the context of environmental conditions, this theory may be relevant to the evolution of host resistance to novel parasites. Here we test the applicability of the Baldwin Effect to the evolution of resistance in a natural system using threespine stickleback fish (Gasterosteus aculeatus) and their cestode parasite Schistochephalus solidus. We leverage a large transcriptomic data set to describe the response to S. solidus infection by three different genetic crosses of stickleback, from a resistant and a tolerant population. Hosts mount a multigenic response to the parasite that is similar among host genotypes. In addition, we document extensive constitutive variation in gene expression among host genotypes. However, although many genes are both infection-induced and differentially expressed between genotypes, this overlap is not more extensive than expected by chance. We also see little evidence of canalization of infection-induced gene expression in the derived resistant population. These patterns do not support the Baldwin Effect, though they illustrate the importance of variation in both constitutive expression and induced responses to parasites. Finally, our results improve understanding of the cellular mechanisms underlying a putative resistance phenotype (fibrosis). Combined, our results highlight the importance of both constitutive and inducible variation in the evolution of resistance to parasites, and identify new target genes contributing to fibrosis. These findings advance understanding of host-parasite interactions and co-evolutionary relationships in natural systems.
Biomarkers of memory variability in traumatic brain injury

Traumatic brain injury (TBI) is a leading cause of cognitive disability and is often associated with significant impairment in episodic memory. In TBI survivors, as in healthy controls, there is marked variability between individuals in memory ability. Using recordings from indwelling electrodes, we characterized and compared the oscillatory biomarkers of mnemonic variability in two cohorts of epilepsy patients: a group with a history of moderate-to-severe TBI (n = 37) and a group of non-TBI controls (n = 111) closely matched for demographics and electrode coverage. Analysis of these recordings demonstrated that increased high frequency power and decreased theta power across a broad set of brain regions mark periods of successful memory formation in both groups. As features in a logistic-regression classifier, spectral power biomarkers effectively predicted recall probability, with little difference between TBI and non-TBI controls. The two groups also displayed similar patterns of theta-frequency connectivity during successful encoding periods. These biomarkers of successful memory, highly conserved between TBI patients and controls, could serve as the basis for novel therapies that target disordered memory across diverse forms of neurological disease.
Hyperspectral Image Recovery Using Non-Convex Low-Rank Tensor Approximation

Low-rank tensors have received more attention in hyperspectral image (HSI) recovery. Minimizing the tensor nuclear norm, as a low-rank approximation method, often leads to modeling bias. To achieve an unbiased approximation and improve the robustness, this paper develops a non-convex relaxation approach for low-rank tensor approximation. Firstly, a non-convex approximation of tensor nuclear norm (NCTNN) is introduced to the low-rank tensor completion. Secondly, a non-convex tensor robust principal component analysis (NCTRPCA) method is proposed, which aims at exactly recovering a low-rank tensor corrupted by mixed-noise. The two proposed models are solved efficiently by the alternating direction method of multipliers (ADMM). Three HSI datasets are employed to exhibit the superiority of the proposed model over the low rank penalization method in terms of accuracy and robustness.
INVESTIGATING MOBILE TRAFFIC VIOLATION TICKETING SERVICE IN EGYPT: THE PROVIDER AND USER PERSPECTIVES

The advances in information and communication technology are affecting many aspects of the economy in developed and developing nations. The Internet and the World Wide Web innovations are increasingly promising to provide various tools to increase business and economic developmental processes for developing nations. Egypt in specific is one of the major countries in the region, especially with its very high population, around 94 million. This high population has in turn led to many challenges, on top of which is the transportation traffic, especially in the two main cities, Cairo and Alexandria. The Information and Communication Technology development in Egypt, together with the very high mobile adoption rate, reaching over 116% subscribers in a country with such a high population brings a calling need to adopt a mobile application as a partial solution to the traffic problem in Egypt. However, adopting a new technology is not primarily a technical problem but is rather a social problem, where customers acceptance plays an important role. Accordingly, a structured questionnaire will be designed in English and Translated to Arabic. Then, questionnaires will be distributed over a sufficient number of Egyptian car drivers. Also Semi-structured face to face interviews were selected with decision makers. Both questionnaires and interviews inquire on how do both parties perceive the current traffic and ticketing system in Egypt, and what are the main factors that affect the driver intention to adopt an m-traffic in Egypt. Data collected will be analyzed. Finally, conclusions will be drawn and recommendations will be proposed.
Protein Synthesis, Cell Division and the Cell Cycle in Saccharomyces cerevisiae following a Shift to a Richer Medium

Summary: When both haploid and diploid cells of the yeast Saccharomyces cerevisiae were shifted to media supporting faster growth rates, rate maintenance of cell division was observed. Both protein synthesis and cell division displayed a variable period of rate maintenance prior to achieving new rates after shift-up; however, the interval between the increase in rate of protein synthesis and the increase in rate of cell division remained constant. These results are consistent with a model of the cell division cycle in which there is an expandable G1 phase during which growth to some critical size must be attained. Once cell division cycle events are initiated they proceed at a constant rate regardless of the overall population growth rate.
Histone Tails and the H3 αN Helix Regulate Nucleosome Mobility and Stability

ABSTRACT Nucleosomes fulfill the apparently conflicting roles of compacting DNA within eukaryotic genomes while permitting access to regulatory factors. Central to this is their ability to stably associate with DNA while retaining the ability to undergo rearrangements that increase access to the underlying DNA. Here, we have studied different aspects of nucleosome dynamics including nucleosome sliding, histone dimer exchange, and DNA wrapping within nucleosomes. We find that alterations to histone proteins, especially the histone tails and vicinity of the histone H3 αN helix, can affect these processes differently, suggesting that they are mechanistically distinct. This raises the possibility that modifications to histone proteins may provide a means of fine-tuning specific aspects of the dynamic properties of nucleosomes to the context in which they are located.
Psychological Trends in the Achievement Goals of College and University Athletes

Objectives: This study aimed to validate the application of the 3 × 2 achievement goal model in sports. Motivations: In order to offer new perspectives on achievement goals, this study explores 3 × 2 achievement goals used in competitive sports, and the prediction of passion and psychological well-being for sports. Methods: The study sample consists of 406 college and university athletes, including 230 males and 176 females. Average age of the subjects was 20.34 years. Average length of years of sports participation was 8.23 years. Data were collected with a questionnaire that incorporated a 3 × 2 achievement goal scale, a sports passion scale, and the Psychological Well-Being Scale. Statistical Methods: Data were analyzed using descriptive statistics for fuzzy data, fuzzy correlation coefficients, and fuzzy regression models. Finding: 1. There was a correlation between every two of task-approach, task-avoidance, self-approach, self-avoidance, other-approach, other-avoidance, harmonious passion, obsessive passion, and psychological well-being. 2. Among college and university athletes, task-approach and self-approach positively influence harmonious passion; task-approach, self-approach, other-approach, and other-avoidance positively influence obsessive passion; task-avoidance negatively influences obsessive passion; task-approach and self-approach positively influence psychological well-being, and task-avoidance negatively influences psychological well-being. Innovations: Use of the 3 × 2 achievement goal scale is applicable to college sportsmen in Taiwan, and the research method uses fuzzy statistical analysis, which breaks through the barriers of traditional psychological survey methods, and will improve the research quality of the sample survey. This study provides new techniques for research on psychological trends in sports. Value: In the future, coaches and athletes should focus on task-approach and self-approach goals in order to enhance the college or university athletes’ harmonious passion for a positive impact on their psychological well-being when they engage in sports through their own free will.
Plant and fungal identity determines pathogen protection of plant roots by arbuscular mycorrhizas

1. A major benefit of the mycorrhizal symbiosis is that it can protect plants from below‐ground enemies, such as pathogens. Previous studies have indicated that plant identity (particularly plants that differ in root system architecture) or fungal identity (fungi from different families within the Glomeromycota) can determine the degree of protection from infection by pathogens. Here, we test the combined effects of plant and fungal identity to assess if there is a strong interaction between these two factors.
Communication Performance of a Real-Life Wide-Area Low-Power Network Based on Sigfox Technology

In this paper, we study real-world performance of Sigfox, which is one of the most mature Low-Power Wide-Area Network (LPWAN) technologies that operate in unlicensed frequency bands. During an extensive measurement campaign conducted over three months in the city of Brno, Czech Republic, we assessed the communication performance and the radio channel properties in 311 different test locations. We observed that despite the challenging natural landscape and urban environment of the test area, more than 94% of the packets sent were received successfully, with at least one packet delivered from 297 out of 311 tested locations. Our results also reported experiment-based radio channel and signal-to-noise characterization as well as provided insights into the efficiency of two crucial mechanisms used by Sigfox to improve the packet delivery - packet repetition and multi-gateway reception. Finally, we employed our experimental data to understand the efficiency of two non-fingerprint localization methods based on received signal strength indicator in a practical Sigfox network.