Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient plant regeneration from cotyledonary explants of Tunisian Cucumis melo L. cv. Maazoun and Beji

A procedure for the regeneration of melon (Cucumis melo L.) cv. Maazoun and Beji via shoot organogenesis from cotyledon explants is described. Cotyledons explants cultivated on the basal Murashige and Skoog (1962) medium, added with combinations of BAP, NAA and 2,4-D developed adventitious shoots after two weeks. The rates of caulogenesis varied according to the medium hormonal composition and the genotype. The best induction medium for a morphogenic response was MS containing 0.5 mgl -1 NAA and 2 mgl -1 BAP. The highest caulogenesis percentages were 79.16% and 58.33% for Maazoun and Beji cultivars respectively. The mean number of buds per callus was 2.92. Development phases were characterized by histological studies. Some phases of shoot organogenesis were observed in Cucumis melo L. Maazoun and Beji cultivars. The shoots were rooted in MS medium without growth regulators or added NAA (0.5 or 1 mgl-1). The highest bud rooting of buds occurred on MS medium added with 1 mg/l NAA. The percentage of rooting varied from 16.66 to 75%. The highest percentage of survival plants after acclimatization were 41.73 and 57.63 for Beji and Maazoun respectively.
Tissue-resident macrophages regulate lymphatic vessel growth and patterning in the developing heart

ABSTRACT Macrophages are components of the innate immune system with key roles in tissue inflammation and repair. It is now evident that macrophages also support organogenesis, but few studies have characterized their identity, ontogeny and function during heart development. Here, we show that the distribution and prevalence of resident macrophages in the subepicardial compartment of the developing heart coincides with the emergence of new lymphatics, and that macrophages interact closely with the nascent lymphatic capillaries. Consequently, global macrophage deficiency led to extensive vessel disruption, with mutant hearts exhibiting shortened and mis-patterned lymphatics. The origin of cardiac macrophages was linked to the yolk sac and foetal liver. Moreover, the Cx3cr1+ myeloid lineage was found to play essential functions in the remodelling of the lymphatic endothelium. Mechanistically, macrophage hyaluronan was required for lymphatic sprouting by mediating direct macrophage-lymphatic endothelial cell interactions. Together, these findings reveal insight into the role of macrophages as indispensable mediators of lymphatic growth during the development of the mammalian cardiac vasculature. Highlighted Article: Tissue-resident macrophages are indispensable mediators of lymphatic vessel formation during heart development, and function to remodel the vascular plexus.
Preparatory Suppression and Facilitation of Voluntary and Involuntary Responses to Loud Acoustic Stimuli in an Anticipatory Timing Task

In this study, we sought to characterise the effects of intense sensory stimulation at different stages of preparation for an anticipated action on voluntary and involuntary behaviours. In our experiment, we presented unexpected loud acoustic stimuli (LAS) at four critical times during movement preparation to probe the state of the nervous system (Baseline, −1192 ms, −392 ms, and 0 ms relative to expected movement onset), and measured their effect on voluntary and involuntary motor actions (finger-press and eye-blink startle reflex, respectively). Voluntary responses were largely facilitated by the LAS, leading to earlier and more forceful responses compared to Control and Baseline conditions. Notably, voluntary responses were significantly facilitated on trials where the LAS was presented early during preparation (−1192 ms). Eye-blink reflexes elicited by the LAS at −392 ms were significantly reduced and delayed compared to other time-points, indicating suppression of sub-cortical excitability. Despite being in a suppressive state, voluntary responses on these trials were still facilitated by the LAS. The results provide insight into the mechanisms involved in preparing anticipatory actions. Induced activation can persist in the nervous system and can modulate subsequent actions for a longer time period than previously thought, highlighting that movement preparation is a continuously evolving process that is susceptible to external influence throughout the preparation period. Suppression of sub-cortical excitability shortly before movement onset is consistent with previous work showing corticospinal suppression which may be a necessary step before the execution of any voluntary response.
Spatial engineering of E. coli with addressable phase-separated RNAs

Biochemical processes often require spatial regulation and specific microenvironments. The general lack of organelles in bacteria limits the potential of bioengineering complex intracellular reactions. Here we demonstrate Transcriptionally Engineered Addressable RNA Solvent droplets (TEARS) as synthetic microdomains within the Escherichia coli. TEARS are assembled from RNA-binding protein recruitment domains fused to poly-CAG repeats that spontaneously drive liquid-liquid phase separation from the bulk cytoplasm. Targeting TEARS with fluorescent proteins revealed multilayered structures and a non-equilibrium mechanism controlling their composition and reaction robustness. We show that TEARS provide organelle-like bioprocess isolation for sequestering biochemical pathways, controlling metabolic branch points, buffering mRNA translation rates and scaffolding protein-protein interactions. TEARS are a simple and versatile tool for spatially controlling E. coli biochemistry.
The structure of enteric human adenovirus 41 - a leading cause of diarrhea in children

Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ strikingly in tissue tropism and pathogenicity from respiratory and ocular adenoviruses, but the structural basis for this divergence has been unknown. Here we present the first structure of an enteric HAdV - HAdV-F41 - determined by cryo-EM to a resolution of 3. 8Å. The structure reveals extensive alterations to the virion exterior as compared to non-enteric HAdVs, including a unique arrangement of capsid protein IX. The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Our findings provide the structural basis for adaptation to a fundamentally different tissue tropism of enteric HAdVs.
Immunocytochemical analysis of the process of keratinization of the epidermis of snakes

The epidermis of snakes produces two types of keratinocytes containing an alpha (soft) and a beta (hard) form of keratin. During epidermal renewal, which allows body growth, six types of epidermal layers are produced before moulting: oberhautchen, beta-, mesos, alpha-, lacunar, and clear. The precise layers in which beta-keratin, alpha-keratin and matrix proteins (loricrin and filaggrin) are produced, have been studied by light and ultrastructural immunocytochemistry. An antibody against chick scale beta-keratin recognizes also snake beta-keratin only in the oberhautchen and beta-layer. This confirms the phylogenetic relationships between avian and reptilian hard (beta) keratins. Beta-keratin rapidly disappears in mesos-cells, where little beta-keratin is present. Antibodies that recognize alpha-keratins (AE1, AE2, AE3) show that acidic keratins (AE1 positive) mainly localize in the most basal layers and basic keratins (AE3 positive) in all layers but disappear in those layers that are keratinized, especially in the beta-layer. The AE2 immunolabelling (a marker of keratinization in mammalian epidermis) is localized in the compact alpha-layer. This pattern is similar to that for loricrin and filaggrin, although in the latter the reaction is less intense and located mainly in the hinge regions among scales. Alpha-keratins and associated proteins disappear in the oberhautchen and beta-cells where beta-keratin is produced instead. This study suggests that the shedding mechanism in snakes evolved after the hard beta-keratin was compartmentalized beneath the soft alpha-keratin to create an intra-epidermal weakness region. The study also suggests that some common mechanism of alpha-keratinization is present in snakes, and the other amniotes in general.
Hyperosmotic stress induces downstream-of-gene transcription and alters the RNA Polymerase II interactome despite widespread transcriptional repression

Stress-induced readthrough transcription results in the synthesis of thousands of downstream-of-gene (DoG) containing transcripts. The mechanisms underlying DoG formation during cellular stress remain unknown. Nascent transcription profiles during DoG induction in human cell lines using TT-TimeLapse-seq revealed that hyperosmotic stress induces widespread transcriptional repression. Yet, DoGs are produced regardless of the transcriptional level of their upstream genes. ChIP-seq confirmed that the stress-induced redistribution of RNA Polymerase (Pol) II correlates with the transcriptional output of genes. Stress-induced alterations in the Pol II interactome are observed by mass spectrometry. While subunits of the cleavage and polyadenylation machinery remained Pol II-associated, Integrator complex subunits dissociated from Pol II under stress conditions. Depleting the catalytic subunit of the Integrator complex, Int11, using siRNAs induces hundreds of readthrough transcripts, whose parental genes partially overlap those of stress-induced DoGs. Our results provide insights into the mechanisms underlying DoG production and how Integrator activity influences DoG transcription. In brief Rosa-Mercado et al. report that hyperosmotic stress causes widespread transcriptional repression in human cells, yet DoGs arise regardless of the transcriptional response of their upstream genes. They find that the interaction between Pol II and Integrator is disrupted by hypertonicity and that knocking down the Integrator nuclease leads to DoG production. Highlights Hyperosmotic stress triggers transcriptional repression of many genes. DoG RNAs arise independent of the transcriptional level of their upstream gene. The interaction between Pol II and Integrator subunits decreases after salt stress. Depletion of the Int11 nuclease subunit induces the production of hundreds of DoGs.
Role of PARylation and PTEN Mutation on PARP and PARG Inhibitor Efficacy on Glioblastoma

Glioblastoma (GBM) is the most aggressive primary adult brain tumor, with a median survival of approximately 15 months. Despite novel therapeutic approaches, median survival has remained largely unchanged since the standard of care therapy for GBM was established nearly 15 years ago. Phosphatase and tensin homolog (PTEN) is a prognostic biomarker of GBM. PTEN mutation is associated with defects in homologous recombination (HR), making it a candidate for targeted therapy by synthetic lethality (SL). The SL concept has been clinically validated in HR-deficient breast and ovarian cancers upon treatment with poly(ADP-ribose) polymerase (PARP 1) inhibitors (PARPi). This inhibitor, as well as poly(ADP-ribose) glycohydrolase (PARG) inhibitors (PARGi), dysregulate PARylation post-translational modification, which plays a major role in DNA repair and genomic stability. To determine whether PARPi/PARGi promotes SL in GBM, this study investigated the effects of PARPi (veliparib and olaparib) and PARGi in GBM cells with wildtype versus mutant PTEN. Sensitivity to these drugs was analyzed in function of PTEN status. Specifically, PTEN-wildtype cells displayed higher levels of DNA damage after PARPi treatment compared to PTEN-mutant cells. However, focusing on DNA double-strand break (DSB) repair, there was no indication of efficient activation of non-homologous end joining (NHEJ) or homologous recombination (HR). These findings highlight the complex relationship between PARylation and PTEN. Thus, our results do not support the SL between PARP/PARG inhibition and PTEN mutations in GBM cells in absence of other DNA damaging agents.
An approach to analyse and Forecast Social media data using Machine Learning and Data Analysis

Twitter is one of the most used social network platforms with more than 321 million active users, sending a daily average of 500 million Tweets. Twitter basically reaches a broad audience, connects many users, and also provides a useful point of view on an ongoing topic based on their interests. This research paper includes works of Machine Learning, NLP, and sentiment analysis on twitter data which is related to Goods and Service Tax (GST) collected from twitter by web scraping technology. Basically here we have found out how many people are against or for about the GST.Here we calculated the sentiments of positive, negative and neutral according to the twitter user. Here Data visualization also used to visualize the data can include cleaning checking transforming and finding the pattern. Machine learning and NLP are used on the data-driven model from the prediction purpose. Machine learning techniques applied to corresponding twitter dataset that contain reviews of GST users to find out the relevant information and inference. Machine learning used to extract the sentiments of the user and find future trends based on current uses.
Cooperative Spectrum Sensing in Cognitive Radio Networks with Rayleigh Fadings

Spectral sensing in "white space frequencies is important feature for cognitive radio networks. Performances of detection of licensed users by individual secondary users (SU) degraded under the influence of the fading in radio channel, both in the sensing channel and in the reporting channels. Reliable detection of licensed primary users (PU) is implemented on the basis of cooperation of SU (CSS). Two solutions to improve the performances of the CSS are introduced in this paper. First, in the sensing channel, instead of single-threshold detectors scheme, a four-threshold scheme with an "erasure" zone is applied. Only "significant" local decisions from SU that do not fall within "erasure" zone are sent to the central station of CSS,while reducing the average number of messages sent via the reporting channel using QPSK-HM twobit symbols. The highest bit in the hierarchy of the symbol shows the local decision of the VP, and the lowest bit shows the likelyhood level of this decision. This solution does not lead to an increase in traffic over the reporting channel while improve the performances CSS.
Speech Recognition to Build Context: A Survey

In era Computer evolution many problems can be solved using computer vision and signal processing. These domains are typically Digitized in binary files like Images, Audio, and Videos. The translation, recognition and synthesis are required while understating the meaning of the binary content. The recognition process is also having many problems in case of audio processing. The missing context is the major reason in pattern-based matching. This is due to unclear or low-quality input, as well as training model on different frequencies but by using context some of the accuracy may improve. Context finding from binary files is a challenge as it works in temporal and space domain. Binary data like images contain special information, while audio files contain temporal information. Video files have both time and space domains. Updating context in the temporal domain, to find proper context from the audio corpus, speech recognition is applied. Over the time period, there are different models adapted like Hidden Markov Model (HMM), Rule Based models with fuzzy support, pattern-based models including machine learning techniques K-nearest neighbor, Support Vector Machine, also latest techniques like Artificial Neural Network (ANN). These technologies are typically included in Automatic Speech Recognition (ASR). ASR uses Language resources with any one of the above models. Here, an in-depth survey on ASR and available APIs. Technologies used to build APIs also discussed.
Deep Learning of Attitude in Children’s Emotional Speech

Attitude comprises a paralinguistic information associated to affective states without the explicit connection to either positive nor negative valence. As such, its automatic recognition plays an integral role in all speech-based systems. This work focuses on classifying attitude in children’s emotional speech into four classes, i.e. confident, uncertain, apathetic, and enthusiastic. We present a flexible classification scheme based on a directed acyclic graph able to easily incorporate heterogeneous feature sets and classifiers according to the necessities of each task. More precisely, this work employs features coming from both frequency and wavelet domains combined with convolutional and recurrent neural networks. The obtained results confirm the efficacy of such a classification graph outperforming traditional neural network schemes.
Drosophila USP22/non-stop regulates the Hippo pathway to polarise the actin cytoskeleton during collective border cell migration

Polarisation of the actin cytoskeleton is vital for the collective migration of cells in vivo. During invasive border cell migration in Drosophila, actin polarisation is directly controlled by Hippo pathway components, which reside at contacts between border cells in the cluster. Here we identify, in a genetic screen for deubiquitinating enzymes involved in border cell migration, an essential role for non-stop/USP22 in the expression of Hippo pathway components expanded and merlin; loss of non-stop function consequently leads to a redistribution of F-actin and the polarity determinant Crumbs, loss of polarised actin protrusions and premature tumbling of the border cell cluster. Non-stop is a component of the Spt-Ada-Gcn5-acetyltransferase (SAGA) transcriptional coactivator complex, but SAGA’s histone acetyltransferase module, which does not bind to expanded or merlin, is dispensable for migration. Taken together, our results uncover novel roles for SAGA-independent non-stop/USP22 in Hippo-mediated collective cell migration, which may help guide studies in other systems where USP22 is necessary for cell motility and invasion.
Antagonistic roles for Ataxin-2 structured and disordered domains in RNP condensation

Ataxin-2 is a conserved translational control protein associated with spinocerebellar ataxia type II (SCA2) and amyotrophic lateral sclerosis (ALS) as well as an important target for ALS therapeutics under development. Despite its clinical and biological significance, Ataxin-2’s activities, mechanisms and functions are not well understood. While Drosophila Ataxin-2 (Atx2) mediates mRNP condensation via a C-terminal intrinsically disordered domain (cIDR), how Ataxin-2 IDRs work with structured (Lsm, Lsm-AD and PAM2) domains to enable positive and negative regulation of target mRNAs remains unclear. Using TRIBE (Targets of RNA-Binding Proteins Identified by Editing) technology, we identified and analysed Atx-2 target mRNAs in the Drosophila brain. We show that Atx2 preferentially interacts with AU-rich elements (AREs) in 3’UTRs and plays a broad role in stabilization of identified target mRNAs. Strikingly, Atx2 interaction with its targets is dependent on the cIDR domain required for neuronal-granule formation. In contrast, Atx2 lacking its Lsm domain not only interacts more efficiently with the target mRNA identified, but also forms larger RNP granules. Providing an extensive dataset of Atx2-interacting brain mRNAs, our results demonstrate that Atx2: (a) interacts with target mRNAs within RNP granules; (b) modulates the turnover of these target mRNAs; (c) has an additional essential role outside of mRNP granules; and (d) contains distinct protein domains that drive or oppose RNP-granule assembly. These findings increase understanding of neuronal translational control mechanisms and inform Ataxin-2-based interventions in development for SCA2 and ALS.
Optimization for Multi-Join Queries on the GPU

Multi-join queries are important operations in data management systems and data integration systems, and their efficiency has attracted the attention of researchers. In recent years, graphics processing units (GPUs) have developed rapidly and become a powerful tool for parallel computing, providing a new idea for multi-join query optimization. This paper studies the use of GPU technology to optimize multi-join queries and focuses on two points: 1) a multi-phase optimization strategy and 2) optimization methods of each stage. For the first point, we discuss a two-phase optimization strategy on the GPU and prove the effectiveness of this strategy. For the second point, we provide an establishment method of a minimum cost join tree on the GPU, the parallel execution methods of intra-join and inter-join on the GPU, and a strategy of scheduling multiple joins to execute in parallel on the GPU. Experimental results show that the multi-join query optimization proposed in this paper improves the efficiency of multi-join queries, especially in the case of high load and complex join queries, achieving higher throughput than that of previous optimization algorithms.
Leptin suppresses development of GLP-1 inputs to the paraventricular nucleus of the hypothalamus

The nucleus of the solitary tract is critical for the central integration of signals from visceral organs and contains preproglucagon (PPG) neurons, which express leptin receptors and send direct projections to the paraventricular nucleus of the hypothalamus (PVH). Here, we visualized neuronal projections of PPG neurons in leptin-deficient Lepob/ob mice and found that projections from PPG neurons are elevated compared with controls, and PPG projections were normalized by targeted rescue of leptin receptors in LepRbTB/TB mice, which lack functional neuronal leptin receptors. Moreover, Lepob/ob and LepRbTB/TB mice displayed increased levels of neuronal activation in the PVH following vagal stimulation, and whole-cell patch recordings of GLP-1 receptor-expressing PVH neurons revealed enhanced excitatory neurotransmission, suggesting that leptin acts cell autonomously to suppress representation of excitatory afferents from PPG neurons, thereby diminishing the impact of visceral sensory information on GLP-1 receptor neurons in the PVH.
Antimicrobial peptides signal need for sleep from peripheral wounds to the nervous system

Wounding triggers a protective innate immune response that includes the production of antimicrobial peptides and increased sleep. Little is known, however, about how peripheral wounds signal need for sleep to the nervous system. We found that during C. elegans larval molting, a tolloid/BMP-1-like protein promotes sleep through an epidermal innate immune pathway and the expression of more than a dozen antimicrobial peptide (AMP) genes. In the adult, epidermal injury activates innate immunity and turns up AMP production to trigger sleep. We show for one AMP, NLP-29, that it acts through the neuropeptide receptor NPR-12 in neurons that depolarize the sleep-active RIS neuron to induce sleep. Sleep in turn increases the chance of surviving injury. Thus, we found a novel mechanism by which peripheral wounds signal to the nervous system to increase protective sleep. Such a long-range somnogen signaling function of AMPs might also boost sleep in other animals including humans. Highlights - Gain-of-function mutation in the tolloid/BMP-1-like NAS-38 protein increases sleep - NAS-38 activates innate immunity pathways to ramp up STAT-dependent antimicrobial peptide (AMP) expression - Wounding increases sleep through the innate immune response and AMPs - Antimicrobial peptides are long-range somnogens that act through neuronal neuropeptide receptors to depolarize a sleep-active neuron - Sleep increases the chance to survive injury Graphical Abstract