Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictive Model for Network Intrusion Detection System Using Deep Learning

Given the recent COVID-19 situation, many organizations and companies have asked their employees to work from home by connecting to their on-premises servers This situation may continue a much more extended period in the future, thereby opening more threats to confidentiality and security to the information available in the organizations It becomes of hell of a task for network administrators to counter the threats Intrusion Detection Systems are deployed in firewalls to identify attacks or threats In preset modern technologies, Network Intrusion Detection System plays a significant role in defense of the network threat Statistical or pattern-based algorithms are used in NIDS to detect the benign activities that are taking place in the network In this work, deep learning algorithms have developed in NIDS predictive models to detect anomalies and threats automatically Performance of the proposed model assessed on the NSL-KDD dataset in the view of metrics such as accuracy, recall, precision, and F1-score The experimental results show that the proposed deep learning model outperforms when compared with existing shallow models © 2020 Lavoisier All rights reserved
CREB mediates the C. elegans dauer polyphenism through direct and cell-autonomous regulation of TGF-β expression

Animals can adapt to dynamic environmental conditions by modulating their developmental programs. Understanding the genetic architecture and molecular mechanisms underlying developmental plasticity in response to changing environments is an important and emerging area of research. Here, we show a novel role of cAMP response element binding protein (CREB)-encoding crh-1 gene in developmental polyphenism of C. elegans. Under conditions that promote normal development in wild-type animals, crh-1 mutants inappropriately form transient pre-dauer (L2d) larva and express the L2d marker gene. L2d formation in crh-1 mutants is specifically induced by the ascaroside pheromone ascr#5 (asc-ωC3; C3), and crh-1 functions autonomously in the ascr#5-sensing ASI neurons to inhibit L2d formation. Moreover, we find that CRH-1 directly binds upstream of the daf-7 TGF-β locus and promotes its expression in the ASI neurons. Taken together, these results provide new insight into how animals alter their developmental programs in response to environmental changes.
Réviser les tarifs de cubage pour mieux gérer les forêts du Cameroun

Volume tables are routinely used by for- est planners and managers, but generally with no regard for the conditions in which they are applied (geographical zone, diameter range), which can cause errors in estimations of timber volumes. The aim of this study is to test the validity of currently available volume tables, includ- ing those used by the government, for three commercial tree species in the forests of south-eastern Cameroon, and if required to propose tables suited to the study zone. The three species con- cerned are sapelli, Entandrophragma cylindricum , tali, Erythrophleum suaveolens , and assamela Pericopsis elata . Dendrometric data were collected by destructive sampling of 43 trees that were evenly distributed across the diameter range. Stemwood volume was calculated through successive butt-log measurements and linear and non-linear vol- ume tables were adjusted by means of the weighted least-squares method. The results show that the best volume tables for all three species are non-linear. The equations used by the forests authority until now significantly under-estimate standing timber volumes and the estimation errors increase with the size of the trees. The proposed volume tables, once validated, should in future produce more accurate estimations of standing timber in the study zone. Given the international challenges involving Cameroon (FLEGT and REDD+), it is essential that it should have effective tools for estimating stand- ing timber volumes. It is therefore impor- tant for Cameroon’s forests authority to conduct a large-scale programme to revise its volume tables.
Q-SNARE Syntaxin 7 confers actin-dependent rapidly replenishing synaptic vesicles upon high activity

Replenishment of readily releasable synaptic vesicles (SVs) with vesicles in the recycling pool is important for sustained transmitter release during repetitive stimulation. Kinetics of replenishment and available pool size define synaptic performance. However, whether all SVs in the recycling pool are recruited for release with equal probability is unknown. Here, using comprehensive optical imaging for various presynaptic endosomal SNARE proteins in cultured hippocampal neurons, we demonstrate that part of the recycling pool bearing the endosomal Q–SNARE Syntaxin 7 (Stx7) is preferentially mobilized for release during high–frequency repetitive stimulation. Recruitment of the SV pool marked with the Stx7–reporter requires high intra–terminal Ca2+ concentrations and actin polymerization. Furthermore, disruption of Stx7 function by overexpressing the N–terminal domain selectively abolished this pool. Thus, our data indicate that endosomal membrane fusion involving Stx7 is essential for adaptation of synapses to respond high-frequency repetitive stimulation.
Maternal schistosomiasis impairs offspring IL-4 production and B cell expansion

Maternal helminth infections are a global public health concern and correlate with altered infant immune responses to some childhood immunizations, but a mechanistic understanding of how maternal helminth infection alters the cellular immune responses of offspring is lacking. Here we establish a model of maternal Schistosoma mansoni infection in dual IL-4 reporter mice. We find that offspring born to mothers infected with S. mansoni have impaired production of IL-4 during homoeostasis, and following immunization with a Tetanus-Diphtheria vaccine. We identified that iNKT cells are the dominant source of IL-4 during early life homeostasis, and that diminished IL-4 production was associated with both reduced B cell and follicular dendritic cell responses. These defects were maintained long-term, affecting memory B and T cell responses. Single-cell RNASeq analysis of immunized offspring identified egg antigen-dependent reductions in B-cell cell cycle and proliferation-related genes. These data reveal that maternal infection leads to long-lasting defects in the cellular responses to heterologous antigens and provide vital insight into the influence of maternal infection on offspring immunity.
Genetic and Physiological Characterization of the Antibacterial Activity of Bacillus subtilis subsp. inaquosorum Strain T1 Effective Against pirABVp-Bearing Vibrio parahaemolyticus

Acute hepatopancreatic necrosis disease (AHPND) is caused by PirAB toxin-producing Vibrio parahaemolyticus and has devastated the global shrimp aquaculture industry. One approach for preventing growth of AHPND-producing Vibrio spp. is through the application of beneficial bacteria capable of inhibiting these pathogens. In this study we focus on the inhibitory activity of Bacillus subtilis subsp. inaquosorum strain T1, which hinders V. parahaemolyticus growth in co-culture experiments in a density-dependent manner; inhibition was also obtained using cell-free supernatants from T1 stationary phase cultures. Using a mariner-based transposon mutagenesis, 17 mutants were identified having complete or partial loss of inhibitory activity. Of those having total activity loss, 13 had insertions within a 42.6 kb DNA region comprising 15 genes whose deduced products were homologous to non-ribosomal polypeptide synthetases (NRPSs), polyketide synthases (PKSs) and related activities, which were mapped as one transcriptional unit. Mutants with partial activity contained insertions in spo0A and oppA, indicating stationary phase control. Expression of lacZ transcriptional fusions to NRPS and PKS genes was negligible during growth and at their highest during early stationary phase. Inactivation of sigH resulted in loss of inhibitor activity, indicating a role for σH in transcription. Disruption of abrB resulted in NRPS and PKS gene overexpression during growth as well as enhanced growth inhibition. This is the first study examining expression and control of an NRPS-PKS region unique to the inaquosorum subspecies of B. subtilis and an understanding of factors involved in T1 inhibitor production will enable its development for use as a potential tool against AHPND Vibrio pathogens in shrimp aquaculture. IMPORTANCE The shrimp aquaculture industry has been impacted by the rise of acute hepatopancreatic necrosis disease (AHPND), resulting in significant financial losses annually. Caused by strains of the bacterial pathogen, Vibrio parahaemolyticus, treatment of AHPND involves the use of antibiotics, which leads to a rise in antibiotic resistant strains. An alternative approach is through the application of beneficial microorganisms having inhibitory activities against AHPND-generating pathogens. In this study, we examine the genetic basis for the ability of Bacillus subtilis strain T1 to inhibit growth of an AHPND Vibrio strain and show that activity is associated with genes having the potential for synthesizing antibacterial compounds. We found that expression of these genes is under stationary phase control and showed that inactivation of a global transition state regulator results in enhancement of inhibitory activity against the AHPND Vibrio. Our approach for understanding the factors involved in production B. subtilis strain T1 inhibitory activity may allow for development of this strain for use as a potential tool for the prevention of AHPND outbreaks.
A multi-hierarchical approach reveals D-serine as a hidden substrate of sodium-coupled monocarboxylate transporters

Transporter research primarily relies on the canonical substrates of well-established transporters. This approach has limitations when studying transporters for the low-abundant micromolecules, such as micronutrients, and may not reveal physiological functions of the transporters. While D-serine, a trace enantiomer of serine in the circulation, was discovered as an emerging biomarker of kidney function, its transport mechanisms in the periphery remain unknown. Here, using a multi-hierarchical approach from body fluids to molecules, combining multi-omics, cell-free synthetic biochemistry, and ex vivo transport analyses, we have identified two types of renal D-serine transport systems. We revealed that the small amino acid transporter ASCT2 serves as a D-serine transporter previously uncharacterized in the kidney and discovered D-serine as a noncanonical substrate of the sodium-coupled monocarboxylate transporters (SMCTs). These two systems are physiologically complementary, but ASCT2 dominates the role in the pathological condition. Our findings not only shed light on renal D-serine transport, but also clarify the importance of non-canonical substrate transport. This study provides a framework for investigating multiple transport systems of various trace micromolecules under physiological conditions and in multifactorial diseases.
Early classification of motor tasks using dynamic functional connectivity graphs from EEG

Objective. Classification of electroencephalography (EEG) signals with high accuracy using short recording intervals has been a challenging problem in developing brain computer interfaces (BCIs). This paper presents a novel feature extraction method for EEG recordings to tackle this problem. Approach. The proposed approach is based on the concept that the brain functions in a dynamic manner, and utilizes dynamic functional connectivity graphs. The EEG data is first segmented into intervals during which functional networks sustain their connectivity. Functional connectivity networks for each identified segment are then localized, and graphs are constructed, which will be used as features. To take advantage of the dynamic nature of the generated graphs, a long short term memory classifier is employed for classification. Main results. Features extracted from various durations of post-stimulus EEG data associated with motor execution and imagery tasks are used to test the performance of the classifier. Results show an average accuracy of 85.32% about only 500 ms after stimulus presentation. Significance. Our results demonstrate, for the first time, that using the proposed feature extraction method, it is possible to classify motor tasks from EEG recordings using a short interval of the data in the order of hundreds of milliseconds (e.g. 500 ms). This duration is considerably shorter than what has been reported before. These results will have significant implications for improving the effectiveness and the speed of BCIs, particularly for those used in assistive technologies.
Spatial regulation of clathrin-mediated endocytosis through position-dependent site maturation

During clathrin-mediated endocytosis (CME), over 50 different proteins assemble on the plasma membrane to reshape it into a cargo-laden vesicle. It has long been assumed that cargo triggers local CME site assembly in Saccharomyces cerevisiae based on the discovery that cortical actin patches clustered near exocytic sites are CME sites. Quantitative imaging data reported here lead to a radically different view of which CME steps are regulated and which steps are deterministic. We quantitatively and spatially describe progression through the CME pathway and pinpoint a cargo-sensitive regulatory transition point that governs progression from the initiation phase of CME to the internalization phase. Thus, site maturation, rather than site initiation, accounts for the previously observed polarized distribution of actin patches in this organism. While previous studies suggested that cargo ensures its own internalization by regulating either CME initiation rates or frequency of abortive events, our data instead identify maturation through a checkpoint in the pathway as the cargo-sensitive step. Summary Pedersen, Hassinger, et al. investigate steps of the clathrin-mediated endocytosis pathway that are subject to regulation. They report position-dependent differences in endocytic site maturation rates in polarized cells and suggest that cargo controls endocytic internalization through tuning site maturation rather than site initiation.
Wavelet coherence phases decode the universal switching mechanism of Ras GTPase superfamily

Ras superfamily GTPases are molecular switches which regulate critical cellular processes. Extensive structural and computational studies on this G protein family have tried to establish a general framework for their switching mechanism. The current understanding of the mechanism is that two loops, Switch I and Switch II, undergo conformational changes upon GTP binding and hydrolysis, which results in alteration of their functional state. However, because of variation in the extent of conformational changes seen across the members of the Ras superfamily, there is no generic modus operandi defining their switching mechanism, in terms of loop conformation. Here, we have developed a novel method employing wavelet transformation to dissect the structures of these molecular switches to explore indices that defines the unified principle of working. Our analysis shows that the structural coupling between the Switch I and Switch II regions is manifested in terms of wavelet coherence phases. The resultant phase pertaining to these regions serve as a functional identity of the GTPases. The coupling defined in terms of wavelet coherence phases is conserved across the Ras superfamily. In oncogenic mutants of the GTPases the phase coupling gets disentangled, this perhaps provides an alternative explanation for their aberrant function. Although similar observations were made using MD simulations, there was no structural parameter to define the coupling, as delineated here. Furthermore, the technique reported here is computationally inexpensive and can provide significant functional insights on the GTPases by analyzing as few as two structures. Significance Protein-nucleotide interaction induced structural changes are the reflections of functional states of small GTPases. However, from conventional comparison of protein structures these conformational changes cannot be parameterized to directly correlate them with functional states. The wavelet transformation based technique developed here fills this lacuna and provides a novel means to define the universal switching mechanism, with quantifiable indices. The technique gives an alternate prospective on the functional modulations of the GTPase due to oncogenic mutations. The methodology is generic in nature and can be extended to other class of proteins, like kinases.
Gene expression associated with disease resistance and long-term growth in a reef-building coral

Rampant coral disease, exacerbated by climate change and other anthropogenic stressors, threatens reefs worldwide, especially in the Caribbean. Physically isolated yet genetically connected reefs such as Flower Garden Banks National Marine Sanctuary (FGBNMS) may serve as potential refugia for degraded Caribbean reefs. However, little is known about the mechanisms and trade-offs of pathogen resistance in reef-building corals. Here we measure pathogen resistance in Montastraea cavernosa from FGBNMS. We identified individual colonies that demonstrated resistance or susceptibility to Vibrio spp. in a controlled laboratory environment. Long-term growth patterns suggest no trade-off between disease resistance and calcification. Predictive (pre-exposure) gene expression highlights subtle differences between resistant and susceptible genets, encouraging future coral disease studies to investigate associations between resistance and replicative age and immune cell populations. Predictive gene expression associated with long-term growth underscores the role of cation transporters and extracellular matrix remodelers, contributing to the growing body of knowledge surrounding genes that influence calcification in reef-building corals. Together these results demonstrate that coral genets from isolated sanctuaries such as FGBNMS can withstand pathogen challenges and potentially aid restoration efforts in degraded reefs. Furthermore, gene expression signatures associated with resistance and long-term growth help inform strategic assessment of coral health parameters.
DIAPH3 deficiency links microtubules to mitotic errors, defective neurogenesis, and brain dysfunction

Diaphanous (DIAPH) 3 is a member of the formin proteins that have the capacity to nucleate and elongate actin filaments and therefore, to remodel the cytoskeleton. DIAPH3 is essential for cytokinesis as its dysfunction impairs the contractile ring and produces multinucleated cells. Here, we report that DIAPH3 localizes at the centrosome during mitosis and regulates the assembly and polarity of the mitotic spindle. DIAPH3-deficient cells display disorganized cytoskeleton, multipolar spindles, and supernumerary centrosomes. DIAPH3-deficiency disrupts the expression and/or stability of microtubule-associated proteins SPAG5 and KNSTRN. SPAG5 and DIAPH3 have similar expression patterns in the developing brain and overlapping subcellular localization during mitosis. Knockdown of SPAG5 phenocopies the DIAPH3 deficiency, whereas its overexpression rescues the DIAH3 phenotype. Conditional inactivation of Diaph3 in the cerebral cortex profoundly disrupts neurogenesis depleting cortical progenitors and neurons; and leading to cortical malformation and autistic-like behavior. Our data uncover uncharacterized functions of DIAPH3 and provide evidence that this protein belongs to a molecular toolbox that links microtubule dynamics during mitosis to aneuploidy, cell death, fate determination defects, and cortical malformation.
The tiny Cretaceous stem-bird Oculudentavis revealed as a bizarre lizard

Oculudentavis khaungraae was described based on a tiny skull trapped in amber. The slender tapering rostrum with retracted osseous nares, large eyes, and short vaulted braincase led to its identification as the smallest avian dinosaur on record, comparable to the smallest living hummingbirds. Despite its bird-like appearance, Oculudentavis showed several features inconsistent with its original phylogenetic placement. Here we describe a more complete, specimen that demonstrates Oculudentavis is actually a bizarre lizard of uncertain position. The new interpretation and phylogenetic placement highlights a rare case of convergent evolution rarely seen among reptiles. Our results re-affirm the importance of Myanmar amber in yielding unusual taxa from a forest ecosystem rarely represented in the fossil record.
Chemical-Genetic Interactions with the Proline Analog L-Azetidine-2-Carboxylic Acid in Saccharomyces cerevisiae

Non-proteinogenic amino acids, such as the proline analog L-azetidine-2-carboxylic acid (AZC), are detrimental to cells because they are mis-incorporated into proteins and lead to proteotoxic stress. Our goal was to identify genes that show chemical-genetic interactions with AZC in Saccharomyces cerevisiae and thus also potentially define the pathways cells use to cope with amino acid mis-incorporation. Screening the yeast deletion and temperature sensitive collections, we found 72 alleles with negative synthetic interactions with AZC treatment and 12 alleles that suppress AZC toxicity. Many of the genes with negative synthetic interactions are involved in protein quality control pathways through the proteasome. Genes involved in actin cytoskeleton organization and endocytosis also had negative synthetic interactions with AZC. Related to this, the number of actin patches per cell increases upon AZC treatment. Many of the same cellular processes were identified to have interactions with proteotoxic stress caused by two other amino acid analogs, canavanine and thialysine, or a mistranslating tRNA variant that mis-incorporates serine at proline codons. Alleles that suppressed AZC-induced toxicity functioned through the amino acid sensing TOR pathway or controlled amino acid permeases required for AZC uptake.
Stage-mediated priority effects and season lengths shape long-term competition dynamics

The relative arrival time of species can affect their interactions and thus determine which species persist in a community. Although this phenomenon, called priority effect, is widespread in natural communities, it is unclear how it depends on the length of growing season. Using a seasonal stage-structured model, we show that differences in stages of interacting species could generate priority effects by altering the strength of stabilizing and equalizing coexistence mechanisms, changing outcomes between exclusion, coexistence, and positive frequency dependence. However, these priority effects are strongest in systems with just one or a few generations per season and diminish in systems where many overlapping generations per season dilute the importance of stage-specific interactions. Our model reveals a novel link between the number of generations in a season and the consequences of priority effects, suggesting that consequences of phenological shifts driven by climate change should depend on specific life histories of organisms.