Miracle-dz/UniFAR-FTUs huggingface dataset:
Intelligent Hybrid Model to Enhance Time Series Models for Predicting Network Traffic

Network traffic analysis and predictions have become vital for monitoring networks. Network prediction is the process of capturing network traffic and examining it deeply to decide what is the occurrence in the network. The accuracy of analysis and estimation of network traffic are increasingly becoming significant in achieving guaranteed Quality of Service (QoS) in the network. The main aim of the presented research is to propose a new methodology to improve network traffic prediction by using sequence mining. The significance of this important topic lies in the urge to contribute to solving the research problem in network traffic prediction intelligently. We propose an integrated model that combines clustering with existing series models to enhance prediction the network traffic. Clustering granules are obtained using fuzzy c-means to analyze the network data for improving the existing time series. The novelty of the proposed research has used the clustering approach to handle the ambiguity from the entire network data for enhancing the existing time series models. Furthermore, we have suggested using the weighted exponential smoothing model as preprocessing stages for increasing the reliability of the proposed model. In this research paper, machine intelligence proposed to predict network traffic. The machine intelligence is working as pre-processing for enhancing the existing time series models. The machine intelligence combines non-crisp Fuzzy-C-Means (FCM) clustering and the weight exponential method for improving deep learning Long Short-Time Memory(LSTM)and Adaptive Neuro-Fuzzy Inference System (ANFIS)time series models. The ANFIS and LSMT time series models are applied to predict network traffic. Two real network traffic traces were conducted to test the proposed time series models. The empirical results of proposed to enhanced LSTM 97.95% and enhanced ANFIS model is R = 96.78% for cellular traffic data, with respect to the correlation indicator. It is observed that the proposed model outperforms alternative time series models. A comparative prediction results between the proposed model and existing time series models are presented. The comparisons indicate that the presented model outperforms the opponent models; the proposed method optimises the deep learning LSTM and ANFIS time series models. The proposed methodology offers more effective approach to the prediction of network traffic.
The influence of glycerol on the binding of methotrexate to Mycobacterium tuberculosis dihydrofolate reductase: a molecular modelling study

The enzyme, dihydrofolate reductase (DHFR), from Mycobacterium tuberculosis (mt-DHFR) is believed to be a potential drug target for the treatment of tuberculosis. The co-crystal structure of mt-DHFR bound with glycerol (GOL), NAPDH and methotrexate (MTX) reveals a GOL binding site on the enzyme. This GOL binding site could be very important for the design of novel, selective mt-DHFR inhibitors, because this binding site is absent on human DHFR (h-DHFR). We have performed molecular dynamic simulations and free energy calculations to evaluate the binding affinity of GOL and its free energy contribution to the binding of MTX to mt-DHFR. The results showed that GOL does not bind tightly to mt-DHFR. Although GOL itself contributed free energy on MTX binding to mt-DHFR, GOL also increased the flexibilities of MTX, so that MTX cannot maintain strong electronic interactions with ARG32 and ARG60, which caused the total binding free energy to decrease. These data suggest that GOL binding is weak and it could be expelled from the binding site, to allow inhibitors containing appropriate side chains to bind. This observation can be used to inform future drug design studies, especially those aimed at improving drug selectivity against h-DHFR.
Effect of sex and season of birth on Gompertz growth curve parameters in “Nero di Parma” pigs

Abstract The growth curves of “Nero di Parma” pigs were studied by applying the Gompertz equation to 1069 body weight (BW) records from 285 pigs (156 females, 129 castrated males) born in 11 outdoor and 5 indoor herds; pigs were fed commercial complete feeds offered ad libitum and, on a limited basis in the outdoor system, diets were integrated with pasture. The parameters of the Gompertz equation were compared with reference to sex and season of birth. Mature BW for castrated males (229.0 kg) was 3.5% greater than that for females (221.3 kg) (P<0.05), but growth rate was 7.6% lower (7.38*10-3 vs 7.99*10-3, respectively) (P<0.05) and age at maturity (205.7 vs 189.6 d, respectively) was 16.1 d greater (P<0.05). Summer and winter born pigs showed a lower mature BW (P<0.05) than those born in other seasons. Summer born pigs grew slower than those born in spring (9.57%), winter (9.58%) and autumn (21.47%) (P<0.05). Earlier maturing pigs were those born in autumn, followed by those born in winter, spring and summer, respectively. Regardless of sex and season of birth, pigs showed their maximum ADG (ADGmax) of 635 g/d at 82.6 kg BW. Castrated males have a lower ADGmax than females (622 vs 650 g/d) at a heavier weight (84.2 vs 81.4 kg). Autumn born pigs showed the highest ADGmax (695 g/d), reached at 84.9 kg BW. The growth performance of “Nero di Parma” pigs is greater than those reported for Italian domestic pig breeds. The significant effect of the studied environmental factors on the growth curve in this genetic type will make it possible to choose the best rearing conditions in relation to its usual weight at slaughter (>180 kg).
The use of iStar in Situational Method Engineering: An Ongoing Study

Context. Situational Method Engineering (SME) is the discipline that aims at the systematic definition of methods adapted to specific contexts of use (situations). The use of goal-oriented methods for supporting SME is an active research line where the iStar 2.0 language is applied. Objective. We plan to conduct an experiment to investigate some designated pragmatic qualities, namely the perceived usefulness, ease of use and accuracy of iStar 2.0 when used in the SME context. Method. This paper presents our current work on designing an empirical study for the use of iStar 2.0 in SME. Next steps . We plan to refine our current study and run pilots until our measurement tools and sample population are ready for experimental execution.
A Review of Gait Phase Detection Algorithms for Lower Limb Prostheses

Fast and accurate gait phase detection is essential to achieve effective powered lower-limb prostheses and exoskeletons. As the versatility but also the complexity of these robotic devices increases, the research on how to make gait detection algorithms more performant and their sensing devices smaller and more wearable gains interest. A functional gait detection algorithm will improve the precision, stability, and safety of prostheses, and other rehabilitation devices. In the past years the state-of-the-art has advanced significantly in terms of sensors, signal processing, and gait detection algorithms. In this review, we investigate studies and developments in the field of gait event detection methods, more precisely applied to prosthetic devices. We compared advantages and limitations between all the proposed methods and extracted the relevant questions and recommendations about gait detection methods for future developments.
Differences in morphological and physiological leaf characteristics between Tabebuia aurea and T. impetiginosa is related to their typical habitats of occurrence

The genus Tabebuia is representative of the Cerrado biome, occurring in savanna and forest formations. These vegetation types are associated with distinct environmental conditions in terms of water availability, microclimate and soil properties. We compared morphological and physiological traits between Tabebuia aurea (Silva Manso) Benth. & Hook. f. ex S. Moore, which is typical of the savanna vegetation, and T. impetiginosa (Mart. ex DC.) Standl, which is commonly found in the gallery forests that occur along streams and rivers. Both were sampled in savanna conditions under full sun. The savanna species had higher values of leaf and petiole thickness, specific leaf mass, maximum CO2 assimilation on a leaf area basis, stomatal conductance, transpiration and in leaf concentration of carotenoids. The forest species stood out by higher values of specific leaf area, petiole length and of CO2 assimilation on a mass basis, parameters related to shade tolerance and higher growth rates. This functional distinction in a range of leaf traits that was maintained when both were naturally growing under similar environmental conditions, suggests that these are probably the result of differences in the evolutionary history of the two species in response to the contrasting environmental conditions in the typical habitats where they occur.
Molecular Species Delimitation of the Genus Reishia (Mollusca: Gastropoda) along the Coasts of China and Korea

Species of the predatory gastropod genus Reishia Kuroda and Habe, 1971 (Muricidae) inhabit intertidal rocky shores in East Asia. Due to their highly variable external shell morphology, the taxonomy of this genus at species-level is still in need of re-evaluation. Using DNA-based delimitation methods, we aimed to ascertain the number of species of Reishia along the coasts of China and adjacent Asian areas. Also, we looked for diagnostic traits using morphology-based statistical approaches. Our genetic data suggest that the studied individuals comprised two separate species of a Reishia complex in this region, in contrast to the previously proposed four or more taxa. This conclusion is further supported by statistical analyses of shell morphological characteristics. The morphospecies R. bronni (Dunker, 1860), R. jubilaea (Tan and Sigurdsson, 1990), and R. luteostoma (Holten, 1803) were assigned to a single taxon, indicating that they might be synonyms of the same species. The morphospecies R. clavigera (Küster, 1860) singly formed one group, suggesting that it is likely a valid name. The estimated divergence time of the two identified taxa indicates that speciation might have been associated with the sea level and temperature fluctuations during the Plio-Pleistocene period. Our study on Reishia species provides crucial information for further research on the ecology, evolutionary biology, and conservation of this genus.
Spatiotemporal dynamics between interictal epileptiform discharges and ripples during associative memory processing

We describe the spatiotemporal course of cortical high-gamma activity (HGA), hippocampal ripple activity and interictal epileptiform discharges (IEDs) during an associative memory task in 15 epilepsy patients undergoing invasive electroencephalography (iEEG). Successful encoding trials were significantly greater HGA in hippocampus and frontal regions. Successful recall trials manifested sustained HGA in occipital pole and hippocampus compared to failed responses. Hippocampal ripple rates were greater during successful encoding and retrieval trials. IEDs during encoding were associated with decreased odds of remembering in hippocampus (−19%), temporal pole (−18%) or middle temporal gyrus (−15%). Hippocampal IEDs during retrieval predicted 33% decreased odds of remembering. Odds of remembering were further reduced if IEDs occurred during the 500-2000 ms window of encoding or retrieval. Hippocampal IEDs were followed by a transient decrease in ripple rate. We hypothesize that IEDs impair associative memory in a regionally and temporally specific manner by decreasing physiologic hippocampal ripples necessary for effective encoding and recall. Because dynamic memory impairment arises from pathological IED events competing with physiological ripples, IEDs represent a promising therapeutic target for memory remediation in patients with epilepsy.
Characterization of two novel proteins involved in mitochondrial DNA anchoring

Trypanosoma brucei is a single celled eukaryotic parasite in the group of the Excavates. T. brucei cells harbor a single mitochondrion with a singular mitochondrial genome, that consists of a unique network of thousands of interwoven circular DNA molecule copies and is termed the kinetoplast DNA (kDNA). To ensure proper inheritance of the kDNA to the daughter cells the genome is linked to the basal body, the master organizer of the cell cycle in trypanosomes. The structure connecting the basal body and kDNA is termed the tripartite attachment complex (TAC). Using a combination of proteomics and RNAi (depletomics) we test the current model of hierarchical TAC assembly and identify TbmtHMG44 and Tb927.11. 16120 as novel candidates of a structure that connects the TAC to the kDNA. Both proteins localize in the region of the unilateral filaments between TAC102 and the kDNA and depletion of each leads to a strong kDNA loss phenotype. TbmtHMG44 and Tb927.11. 16120 stably associate with extracted flagella, even after DNase treatment however they do require the kDNA for initial assembly. Furthermore we demonstrate that recombinant Tb927.11. 16120 is a DNA binding protein and thus a promising candidate to link the TAC to the kDNA.
Soluble corn fiber reduces ovalbumin-induced sinonasal inflammation via the gut microbiota-airway axis

Asthma is a chronic airway inflammatory disease that affects approximately 300 million people worldwide, causing a substantial healthcare burden. Although there is a large degree of heterogeneity in the inflammatory response of asthmatics, a subset of patients are characterized by type-2 inflammation, which is in part mediated by TH2 cells in both the upper and lower airways. Asthma prevalence is increased in low-socioeconomic-status populations, where disparities in health behavior exist, including a shift toward a western diet characterized by low dietary fiber. Gut microbes metabolize fiber into short chain fatty acids that can reduce type-2 inflammation in peripheral organs, such as the airways. We hypothesized that soluble fiber can reduce ovalbumin (OVA)-induced upper airway inflammation in the context of the unified airway hypothesis, in mice maintained on ingredient-matched western (WD) and control diets (CD) through production of short chain fatty acids. Our results show that soluble fiber reduces IL-4 and IL-13 gene expression (p<0.05, Mann Whitney) in the sinonasal cavity of CD-fed mice, but this effect was lost in WD-fed mice. This loss of protection in WD-fed mice parallels compositional changes of the cecal and fecal microbiota. Mice fed a soluble fiber supplement while being maintained on a WD had altered microbial communities characterized by lower abundance of fiber fermentering bacteria. This work can be used to develop effective microbiome-based therapeutics as a low-cost method to reduce asthma morbidity. IMPORTANCE Previous research has supported that western-style diets, typically high-fat and low-fiber, are associated with changes in the gut microbiome and increased inflammation. Western diets are accessible and prominent in low-socioeconomic-status populations, where asthma rates are highest; however, there has yet to be a low-cost asthma therapeutic. For the first time, we investigated whether supplementation with a physiologically relevant quantity of soluble corn fiber can reduce allergic airway inflammation. Our study supports that soluble corn fiber supplementation is associated with compositional shifts of the gut microbiota and reduced airway inflammation, promoting the use of fiber as a low-cost microbiome modifying therapy to reduce asthma-associated inflammation. However, soluble corn fiber in conjunction with a western diet resulted in an alternate gut microbiome composition and loss of protection against allergic airway inflammation. These findings further support the importance of the gut microbiota in host health.
The essential role of Dnmt1 in gametogenesis in the large milkweed bug Oncopeltus fasciatus

Given the importance of DNA methylation in protection of the genome against transposable elements and transcriptional regulation in other taxonomic groups, the diversity in both levels and patterns of DNA methylation in the insects raises questions about its function and evolution. We show that the maintenance DNA methyltransferase, DNMT1, affects meiosis and is essential to fertility in milkweed bugs, Oncopeltus fasciatus, while DNA methylation is not required in somatic cells. Our results support the hypothesis that Dnmt1 is required for the transition of germ cells to gametes in O. fasciatus and that this function is conserved in male and female gametogenesis. They further suggest that DNMT1 has a function independent of DNA methylation in germ cells. Our results raise the question of how a gene so critical in fitness across multiple insect species can have diverged widely across the insect tree of life.
DLX5/6 GABAergic Expression Affects Social Vocalization: Implications for Human Evolution

DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated to neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioural and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present an hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1400 calls/10min with longer, uninterrupted, call sequences and a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time they spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. We then compared the DLX5/6 genomic regions from Neanderthal and modern humans to examine if DLX5/6 GABAergic expression could have been involved in human social evolution. We identify an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype is not significantly associated to Autism Spectrum Disorders (ASDs) but includes the binding site for GTF2I, a gene associated to Williams-Beuren syndrome, a neurodevelopmental disorder characterized by hyper-sociability and hyper-vocalization. Interestingly, the DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105y of age), a well-established human model of healthy ageing and longevity, suggesting its potential involvement in the co-evolution of longevity, sociability and speech.
Survival rates of radio-collared female polar bears and their dependent young

Polar bears (Ursus maritimus) are hunted throughout most of their range. In addition to hunting, polar bears of the Beaufort Sea region are exposed to mineral and hydrocarbon extraction and related human activities such as shipping, road building, and seismic testing. As human populations increase and demands for polar bears and other arctic resources escalate, reliable estimates of survivorship of polar bears are needed to predict and manage the impacts of those activities. We used the Kaplan–Meier model to estimate annual survival (with 95% confidence intervals) for radio-collared female polar bears and their dependent young that were followed during a 12-year study in the Alaskan Beaufort Sea. Survival of adult female polar bears was higher than had been previously thought: Ŝ = 0.969 (range 0.952–0.983). If human-caused mortalities were deleted, the computed survival rate was 0.996 (0.990–1.002). Survival of young from den exit to weaning was 0.676 (0.634–0.701). Survival during the second year of life.
SMAP – A Modular Superresolution Microscopy Analysis Platform for SMLM Data

Reconstruction of superresolved images from the raw data of blinking fluorophores in single-molecule localization microscopy (SMLM) requires extensive data analysis. Current software solutions often lack functionality, continuous development and cannot easily be extended with own algorithms. Here we release as open source a comprehensive Superresolution Microscopy Analysis Platform (SMAP) for SMLM. Its modular architecture makes it easy for anyone with basic programming experience to add own plugins, limiting development effort to implementing algorithms. It has a freely configurable graphical user interface (GUI) and currently contains more than 200 plugins spanning all steps of data analysis from single molecule fitting to post-processing, rendering and advanced quantitative analyses. SMAP is a powerful, ready-to-use software package for all steps of SMLM data analysis, that enables anyone to use state-of-the art algorithms and complex analysis workflows and that provides a versatile platform for developers to share and publish new SMLM algorithms.
Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations

Background The wheat leaf rust fungus, Puccinia triticina Erikss. is a worldwide pathogen of tetraploid durum and hexaploid wheat. Many races of P. triticina differ for virulence to specific leaf rust resistance genes and are found in most wheat-growing regions of the world. Wheat cultivars with effective leaf rust resistance exert selection pressure on P. triticina populations for virulent race types. The objectives of this study were to examine whole-genome sequence data of 121 P. triticina isolates and to gain insight into race evolution. The collection included isolates comprising many different race phenotypes collected worldwide from common wheat in the U.S. and the European Union together with isolates from durum wheat. One isolate from the wild wheat relative Aegilops speltoides, and two from Ae. cylindrica were also included for comparison. Results Based on 121,907 variants identified relative to the reference race 1-1 genome, the isolates were clustered into 11 major lineages with 100% bootstrap support. The isolates were also grouped based on variation in approximately 1400 secreted resistance interactor candidate proteins. In gene-coding regions, all groups had high ratios of non-synonymous to synonymous mutations and nonsense to readthrough mutations. Conclusions Based on total variation or variation in the secreted protein genes, isolates grouped the same indicating that variants were distributed across the entire genome. Our results suggest that recurrent mutation and selection play a major role in differentiation within the clonal lineages.
Brain geometry matters in Alzheimer’s disease progression: a simulation study

The Amyloid cascade hypothesis (ACH) for Alzheimer’s disease (AD) is modeled over the whole brain tissue with a set of partial differential equations. Our results show that the amyloid plaque formation is critically dependent on the secretion rate of amyloid β (Aβ), which is proportional to the product of neural density and neural activity. Neural atrophy is similarly related to the secretion rate of Aβ. Due to a heterogeneous distribution of neural density and brain activity throughout the brain, amyloid plaque formation and neural death occurs heterogeneously in the brain. The geometry of the brain and microglia migration in the parenchyma bring more complexity into the system and result in a diverse amyloidosis and dementia pattern of different brain regions. Although the pattern of amyloidosis in the brain cortex from in-silico results is similar to experimental autopsy findings, they mismatch at the central regions of the brain, suggesting that ACH is not able to explain the whole course of AD without considering other factors, such as tau-protein aggregation or neuroinflammation.