Miracle-dz/UniFAR-FTUs huggingface dataset:
The Concept of Transmission Coefficient Among Different Cerebellar Layers: A Computational Tool for Analyzing Motor Learning

High-fidelity regulation of information transmission among cerebellar layers is mainly provided by synaptic plasticity. Therefore, determining the regulatory foundations of synaptic plasticity in the cerebellum and translating them to behavioral output are of great importance. To date, many experimental studies have been carried out in order to clarify the effect of synaptic defects, while targeting a specific signaling pathway in the cerebellar function. However, the contradictory results of these studies at the behavioral level further add to the ambiguity of the problem. Information transmission through firing rate changes in populations of interconnected neurons is one of the most widely accepted principles of neural coding. In this study, while considering the efficacy of synaptic interactions among the cerebellar layers, we propose a firing rate model to realize the concept of transmission coefficient. Thereafter, using a computational approach, we test the effect of different values of transmission coefficient on the gain adaptation of a cerebellar-dependent motor learning task. In conformity with the behavioral data, the proposed model can accurately predict that disruption in different forms of synaptic plasticity does not have the same effect on motor learning. Specifically, impairment in training mechanisms, like in the train-induced LTD in parallel fiber-Purkinje cell synapses, has a significant negative impact on all aspects of learning, including memory formation, transfer, and consolidation, although it does not disrupt basic motor performance. In this regard, the overinduction of parallel fiber-molecular layer interneuron LTP could not prevent motor learning impairment, despite its vital role in preserving the robustness of basic motor performance. In contrast, impairment in plasticity induced by interneurons and background activity of climbing fibers is partly compensable through overinduction of train-induced parallel fiber-Purkinje cell LTD. Additionally, blockade of climbing fiber signaling to the cerebellar cortex, referred to as olivary system lesion, shows the most destructive effect on both motor learning and basic motor performance. Overall, the obtained results from the proposed computational framework are used to provide a map from procedural motor memory formation in the cerebellum. Certainly, the generalization of this concept to other multi-layered networks of the brain requires more physiological and computational researches.
Distribution, habitat profile and genetic variability of Namibian succulent Lithops ruschiorum

Background: The species-rich flora of southern Africa comprises a high number of endemics, including succulents such as the flowering stones in the genus Lithops, but conservation status for these species is not well underpinned because detailed field data and assessments of genetic diversity are lacking.Objectives: We wanted to assess plant abundance and identify factors that may affect survival in Lithops ruschiorum through carefully conducted field surveys, and to determine amount and partitioning of genetic variation by amplified fragment length polymorphism (AFLP) analysis.Method: Field surveys were carried out in nine populations in Namibia. The most meticulously studied population was divided into 51 sites, while another 43 sites were recognised in the remaining eight populations. At each site, occupied area and number of plants were recorded as well as altitude, aspect, slope, soil texture and substrate. Amplified fragment length polymorphism markers were employed to study 52 individuals from seven populations.Results: In total, 8465 individuals were recorded. Plant density and/or plant number was associated with aspect, slope, soil texture, substrate and geographic distance from the coast. Analysis of molecular variation showed that 95% of the variability occurs within populations. Genetic and geographic distances among populations were correlated suggesting an isolation-by-distance pattern.Conclusion: Results are concordant with a strong impact of fog-based precipitation on plant density in the coastal populations, whereas rain probably is more important at one population which is situated further inland. Within-population genetic variation was medium high as usually reported for perennial, outcrossing species, but the low population differentiation implies considerable gene flow and/or population fragmentation.
Effect of Spraying by Some Substances on Low Temperature Stress for Growth and Productivity in Late Peas (Pisum sativum L.) Planting under the Middle Egypt Region Conditions

Two field experiments were carried out at Sids Horticulture Research Station, Beni Sueif Governorate, Agriculture Research Center, Egypt during the two successive winter seasons of 2015/2016 and 2016/2017. To study the effect of foliar spraying with two concentrations from three stimulate substances i.e. Salicylic acid at a rate of 0.5 and 1 g/ L, Selenium at a rate of 5 and 10 mg/ L, Green miracle at a rate of 3 and 6 cm/ L beside the control (spraying with tap water) and their interaction on growth characters, pollen grains viability %, yield and its components as well as some chemical constituents in the leaves and the seeds under low temperature stress in the late peas plantations which prevailing under the middle Egypt region conditions during this period of the year for two peas (Pisum sativum L.) cultivars i.e. Entsar 1 and Master B. The experimental design was split– plot; two pea cultivars were devoted in the main plots and foliar applications of three stimulate substances at the two concentrations of each of them arranged in sub plots. Seeds were sown in the 1 week in December during the two seasons. The results showed that the superiority of Entsar 1 cultivar in the studied characters of growth i.e. plant height, number of branches and dry weight/ plant in addition to the percentage of the vitality of the pollen grains, total pods yield (ton/ fed) and its components as well as the chemical content of leaves and seeds i.e. chlorophyll, total sugars, proline, nitrogen, phosphorus and potassium in leaves as well as total sugars and protein in seeds as compared with Master B cultivar. The results also showed that the foliar spraying with the Green miracle at a concentration of 3 cm/ L which was the best stimulant substance markedly improve most of the studied characters. The results of the interaction between the two factors had a significant effect on the studied characters of growth, pods yield and its components as well as the chemical content of leaves and seeds under these conditions. The best results were obtained from foliar spraying of Entsar 1 cv. by the Green miracle substance at a concentration of 3 cm/ L followed by foliar spraying with the highest concentrations of Selenium and Salicylic acid, respectively.
A microfluidic system integrated one-step PCR and high-resolution melting analysis for rapid rice mutant detection

Abstract Rice is a crucial crop to meet global food demands, therefore, it is necessary to develop rapid, efficient and inexpensive methods for screening mutants of important genes in molecular breeding. In this research, a simple microfluidic chip-integrated one-step polymerase chain reaction (PCR) and high-resolution melting (HRM) analysis were designed for the rapid screening of rice mutants. In order to complete the above processes, we also installed a self-developed functional instrument integrated with a temperature control system and a fluorescence detection department. This microfluidic platform was validated by analysing genes related to insect resistance, phenotype and yield of two important varieties of rice, Oryza sativa L. ssp. japonica. and Oryza sativa L. ssp. indica (93–11). The results showed that the platform could detect single-nucleotide mutations between the wild and the mutant rice plants in 1 h and the accuracy was consistent with gene sequencing regarded as the golden standard of the mutants screening. Compared to the traditional method (requiring approximately 3 h), this platform can distinguish mutants from wild types more rapidly. This system is a simple, integrated, disposable and low-cost tool for high-throughput screening of mutants in molecular breeding. More important, this portable instrument can be used as a point-of-care platform for nucleic acid diagnostics in many scientific fields.
Northern Hemisphere megafossil of Dacrycarpus (Podocarpaceae) from the Miocene of South China and its evolutionary and paleoecological implications

The modern genus Dacrycarpus (Endl.) de Laub. of the family Podocarpaceae, containing nine species, is mainly distributed in tropical mountain rainforests of the southwestern Pacific region, ranging from New Zealand to low‐latitude Asia. This genus has abundant fossil records in both hemispheres, but all the known megafossils were limited to Australasia and South America. Here we report on Dacrycarpus guipingensis sp. nov. from the Miocene Erzitang Formation of Guangxi, South China. This is the first megafossil of Dacrycarpus in the Northern Hemisphere. The new species is represented by mummified dimorphic foliage, ovuliferous shoots, and a male cone with in situ pollen. It resembles the extant Dacrycarpus imbricatus (Blume) de Laub. , which is common in rainforests from southern China and northern Myanmar to Fiji. This paper presents the first data on the anatomical structure of seed cone and exine ultrastructure of Dacrycarpus in situ pollen grains from a fossil material by using computed tomography scanning and ultrathin sectioning. For comparative purpose, data on the pollen morphology and ultrastructure were obtained for modern D. imbricatus for the first time. The D. guipingensis fossils strongly suggest the Miocene arrival of Dacrycarpus in Asia from the Southern Hemisphere. Based on the modern ecological niche and related fossil elements, this fossil locality was probably covered by conifer–broad‐leaved mountain rainforests during the Miocene.
New robust weighted averaging‐ and model‐based methods for assessing trait–environment relationships

Statistical analysis of trait–environment association is challenging owing to the lack of a common observation unit: Community‐weighted mean regression (CWMr) uses site points, multilevel models focus on species points, and the fourth‐corner correlation uses all species‐site combinations. This situation invites the development of new methods capable of using all observation levels. To this end, new multilevel and weighted averaging‐based regression methods are proposed. Compared to existing methods, the new multilevel method, called MLM3, has additional site‐related random effects; they represent the unknowns in the environment that interact with the trait. The new weighted averaging method combines site‐level CWMr with a species‐level regression of Species Niche Centroids on to the trait. Because species can vary enormously in frequency and abundance giving diversity variation among sites, the regressions are weighted by Hill's effective number (N2) of occurrences of each species and the N2‐diversity of a site, and are subsequently combined in a sequential test procedure known as the max test. Using the test statistics of these new methods, the permutation‐based max test provides strong statistical evidence for trait–environment association in a plant community dataset, where existing methods show weak evidence. In simulations, the existing multilevel model showed bias and type I error inflation, whereas MLM3 did not. Out of the weighted averaging‐based regression methods, the N2‐weighted version best controlled the type I error rate. MLM3 was superior to the weighted averaging‐based methods with up to 30% more power. Both methods can be extended (a) to account for phylogeny and spatial autocorrelation and (b) to select functional traits and environmental variables from a greater set of variables.
Seroprevalence and Parasite Rates of Plasmodium malariae in a High Malaria Transmission Setting of Southern Nigeria

Abstract. Although Plasmodium falciparum continues to be the main target for malaria elimination, other Plasmodium species persist in Africa. Their clinical diagnosis is uncommon, whereas rapid diagnostic tests (RDTs), the most widely used malaria diagnostic tools, are only able to distinguish between P. falciparum and non-falciparum species, the latter as “pan-species. ” Blood samples from health facilities were collected in southern Nigeria (Lagos and Calabar) in 2017 (October–December) and Calabar only in 2018 (October–November), and analyzed by several methods, namely, microscopy, quantitative real-time PCR (qPCR), and peptide serology targeting candidate antigens (Plasmodium malariae apical membrane antigen, P. malariae lactose dehydrogenase, and P. malariae circumsporozoite surface protein). Both microscopy and qPCR diagnostic approaches detected comparable proportions (∼80%) of all RDT-positive samples infected with the dominant P. falciparum malaria parasite. However, higher proportions of non-falciparum species were detected by qPCR than microscopy, 10% against 3% infections for P. malariae and 3% against 0% for Plasmodium ovale, respectively. No Plasmodium vivax infection was detected. Infection rates for P. malariae varied between age-groups, with the highest rates in individuals aged > 5 years. Plasmodium malariae–specific seroprevalence rates fluctuated in those aged < 10 years but generally reached the peak around 20 years of age for all peptides. The heterogeneity and rates of these non-falciparum species call for increased specific diagnosis and targeting by elimination strategies.
Disease Exposure and Antifungal Bacteria on Skin of Invasive Cane Toads, Australia

Cane toads, an invasive species in Australia, are resistant to fungal pathogens affecting frogs worldwide (Batrachochytrium dendrobatidis). From toad skin swabs, we detected higher proportions of bacteria with antifungal properties in Queensland, where toad and pathogen distributions overlap, than in other sites. This finding suggests that site-specific pathogen pressures help shape skin microbial communities.
A numerical code for the simulation of non-equilibrium chemically reacting flows on hybrid CPU-GPU clusters

In the present work a computer code RCFS for numerical simulation of chemically reacting compressible flows on hybrid CPU/GPU supercomputers is developed. It solves 3D unsteady Euler equations for multispecies chemically reacting flows in general curvilinear coordinates using shock-capturing TVD schemes. Time advancement is carried out using the explicit Runge-Kutta TVD schemes. Program implementation uses CUDA application programming interface to perform GPU computations. Data between GPUs is distributed via domain decomposition technique. The developed code is verified on the number of test cases including supersonic flow over a cylinder.
Acoustic accelerometry reveals diel activity patterns in premigratory Port Jackson sharks

Abstract Distinguishing the factors that influence activity within a species advances understanding of their behavior and ecology. Continuous observation in the marine environment is not feasible but biotelemetry devices provide an opportunity for detailed analysis of movements and activity patterns. This study investigated the detail that calibration of accelerometers measuring root mean square (RMS) acceleration with video footage can add to understanding the activity patterns of male and female Port Jackson sharks (Heterodontus portusjacksoni) in a captive environment. Linear regression was used to relate RMS acceleration output to time‐matched behavior captured on video to quantify diel activity patterns. To validate captive data, diel patterns from captive sharks were compared with diel movement data from free‐ranging sharks using passive acoustic tracking. The RMS acceleration data showed captive sharks exhibited nocturnal diel patterns peaking during the late evening before midnight and decreasing before sunrise. Correlation analysis revealed that captive animals displayed similar activity patterns to free‐ranging sharks. The timing of wild shark departures for migration in the late breeding season corresponded with elevated diel activity at night within the captive individuals, suggesting a form of migratory restlessness in captivity. By directly relating RMS acceleration output to activity level, we show that sex, time of day, and sex‐specific seasonal behavior all influenced activity levels. This study contributes to a growing body of evidence that RMS acceleration data are a promising method to determine activity patterns of cryptic marine animals and can provide more detailed information when validated in captivity.
Using high-definition transcranial direct current stimulation to investigate the role of the dorsolateral prefrontal cortex in explicit sequence learning

Though we have a general understanding of the brain areas involved in motor sequence learning, there is more to discover about the neural mechanisms underlying skill acquisition. Skill acquisition may be subserved, in part, by interactions between the cerebellum and prefrontal cortex through a cerebello-thalamo-prefrontal network. In prior work, we investigated this network by targeting the cerebellum; here, we explored the consequence of stimulating the dorsolateral prefrontal cortex using high-definition transcranial direct current stimulation (HD-tDCS) before administering an explicit motor sequence learning paradigm. Using a mixed within- and between-subjects design, we employed anodal (n = 24) and cathodal (n = 25) HD-tDCS (relative to sham) to temporarily alter brain function and examine effects on skill acquisition. The results indicate that both anodal and cathodal prefrontal stimulation impedes motor sequence learning, relative to sham. These findings suggest an overall negative influence of active prefrontal stimulation on the acquisition of a sequential pattern of finger movements. Collectively, this provides novel insight on the role of the dorsolateral prefrontal cortex in initial skill acquisition, when cognitive processes such as working memory are used. Exploring methods that may improve motor learning is important in developing therapeutic strategies for motor-related diseases and rehabilitation.
Deep neural networks for analysis of fisheries surveillance video and automated monitoring of fish discards

We report on the development of a computer vision system that analyses video from CCTV systems installed on fishing trawlers for the purpose of monitoring and quantifying discarded fish catch. Our system is designed to operate in spite of the challenging computer vision problem posed by conditions on-board fishing trawlers. We describe the approaches developed for isolating and segmenting individual fish and for species classification. We present an analysis of the variability of manual species identification performed by expert human observers and contrast the performance of our species classifier against this benchmark. We also quantify the effect of the domain gap on the performance of modern deep neural network-based computer vision systems.
Elucidating the Gene Regulatory Network of the Sonic Hedgehog Subgroup of Medulloblastoma

Sonic Hedgehog subgroup medulloblastoma (SHH MB) is classified by the molecular signature of overactive Hedgehog (Hh) signaling pathway. GLI2, the major transcriptional activator of Hh pathway, is often amplified or overexpressed in SHH MB. My project examines two molecular components of Hh signaling pathway in SHH MB. The first part focuses on SUFU, a key regulator of GLI2. SUFU mutations are commonly found in SHH MB patients, however the molecular actions of SUFU are poorly characterized. Through CRISPR/Cas9-mediated knockout of SUFU, I unveiled that SUFU is required for stabilization of GLI2 in human SHH MB. The second part focuses on a candidate GLI2 partner, OLIG2. My results suggested that OLIG2 has a tumor-promoting role in SHH MB, and it possesses the ability to transcriptionally repress as well as activate GLI2 target genes. Together, my study allowed the elucidation of the molecular actions of human SUFU, and unveiled a novel player, OLIG2, in SHH MB.
Epitranscriptomic regulation of the response to the air pollutant naphthalene in mouse lungs: from the perspectives of specialized translation and tolerance linked to the writer ALKBH8

Background The epitranscriptomic writer Alkylation Repair Homolog 8 (ALKBH8) is a tRNA methyltransferase that modifies the wobble uridine of selenocysteine tRNA to promote the specialized translation, via stop codon recoding, of proteins that contain selenocysteine. Corresponding selenoproteins play critical roles in protecting against reactive oxygen species and environmental stress. Using a novel animal model deficient in Alkbh8, we have investigated the importance of epitranscriptomic systems in the response to naphthalene (NA), an abundant polycyclic aromatic hydrocarbon, glutathione depleter and lung toxicant found in tobacco smoke, gasoline and mothballs. Objectives Our goal was to define the molecular reprogramming of Alkbh8 deficient (Alkbh8def) mice and evaluate the roles that the epitranscriptomic writer ALKBH8 and selenoproteins play in mitigating NA-induced toxicity and lung dysfunction. Methods We performed basal lung analysis and NA exposure studies using WT, Alkbh8def and Cyp2abfgs-null mice, the latter of which lack the cytochrome P450 enzymes required for NA bioactivation. We characterized gene expression, molecular markers of damage, viability and tolerance to NA. Results Under basal conditions, lungs from Alkbh8def mice have increased oxidation-reduction potential (ORP) and 8-isoprostane levels, and have reprogrammed at the molecular level to display increased stress response transcripts. In addition, the ALKBH8 writer deficient lungs have a decreased GSH/GSSG ratio. Alkbh8def mice are more sensitive to NA than WT, showing higher susceptibility to lung damage both at the cellular and molecular levels. WT mice develop a tolerance to NA after 3 days, defined as resistance to a high challenging dose after repeated exposures, which is absent in Alkbh8def mice, with writer deficient not surviving NA exposure. Discussion We conclude that the epitranscriptomic writer ALKBH8 plays a protective role against NA-induced lung dysfunction and promotes NA tolerance. Our work provides an early example of how epitranscriptomic systems can regulate the response to environmental stress in vivo.
On the lempel-ziv parsing algorithm and its digital tree representation

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. On the lempel-ziv parsing algorithm and its digital tree representation Philippe Jacquet, Wojciec Szpankowski