Miracle-dz/UniFAR-FTUs huggingface dataset:
A Study on Sentiment Analysis Techniques of Twitter Data

The entire world is transforming quickly under the present innovations. The Internet has become a basic requirement for everybody with the Web being utilized in every field. With the rapid increase in social network applications, people are using these platforms to voice them their opinions with regard to daily issues. Gathering and analyzing peoples’ reactions toward buying a product, public services, and so on are vital. Sentiment analysis (or opinion mining) is a common dialogue preparing task that aims to discover the sentiments behind opinions in texts on varying subjects. In recent years, researchers in the field of sentiment analysis have been concerned with analyzing opinions on different topics such as movies, commercial products, and daily societal issues. Twitter is an enormously popular microblog on which clients may voice their opinions. Opinion investigation of Twitter data is a field that has been given much attention over the last decade and involves dissecting “tweets” (comments) and the content of these expressions. As such, this paper explores the various sentiment analysis applied to Twitter data and their outcomes.
SETD2 deficiency impairs β-catenin destruction complex to facilitate renal cell carcinoma formation

Clear cell renal cell carcinoma (ccRCC) is a largely incurable disease that is highly relevant to epigenetic regulation including histone modification and DNA methylation. SET domain–containing 2 (SETD2) is a predominant histone methyltransferase catalyzing the trimethylation of histone H3 Lysine 36 (H3K36me3) and its mutations are highly relevant to clear cell renal cell carcinoma (ccRCC). However, its physiology role in ccRCC remains largely unexplored. Here we report that Setd2 deletion impairs the β-catenin destruction complex to facilitate ccRCC formation in a c-MYC-generated polycystic kidney disease (PKD) model, which can be relieved by an inhibitor of β-catenin-responsive transcription. Clinically, SETD2 loss is widely observed in ccRCC samples, and negatively correlated with expression of some members of β-catenin destruction complex, but positively correlated with the activation of Wnt/β-catenin signaling. Our findings thus highlight a previously unrecognized role of SETD2-mediated H3K36me3 modification in regulation of Wnt/β-catenin pathway in ccRCC. Summary Our findings for the first time reveal a previously unrecognized role of the SETD2-mediated H3K36me3 modification in regulation of the Wnt/β-catenin pathway in ccRCC and shed light on the molecular mechanisms underlying the formation of renal cell carcinoma with epigenetic disorders.
EXTRACTION, FRACTIONATION AND ACTIVITY CHARACTERISTICS OF PROTEASES FROM SHRIMP PROCESSING DISCARDS

Proteases recovered from Northern pink shrimp (NPS) and Southern rough shrimp (SS) processing discards (heads, shells, tails) were characterized. Shrimp processing discards were extracted with water following homogenization and centrifugation in order to obtain the crude extract which was subsequently fractionated with solid ammonium sulfate. Two fractions sedimenting with 30-50% (designated as NPS-I and SS-I), and 50- 70% (designated as NPS-II and SS-II) ammonium sulfate were collected following centrifugation, respectively. Endoprotease activity of the crude extract was 0.02 U/mg for hemoglobin (Hb, pH 3.0), 0.16 U/mg for azocasein (Ac, pH 6.0) and 0.12 U/mg for benzoyl-Arg-β-naphthylamide (BANA, pH 7.0). The exoprotease activity was 0.11-0.17 U/mg for Arg-β-naphthylamide (ArgNA, pH7.0), 0.06-0.11 U/mg for Lys-β-naphthylamide (LysNA, pH 7.0) and 0.08-0.09 U/mg for Leu-β-naphthylamide (LeuNA, pH 7.0). Endoprotease activity increased 5-7.4 fold for NPS-I and SS-I, and 1.9-2. 7 fold for NPS-II and SS-II against crude extract. Meanwhile, exoprotease activity increased 3. 6-4. 8 fold for NPS-I and SS-I, and 5.6-7.2 fold for NPS-II and SS-II. Meat treated with NPS-I and SS-I was tenderized more extensively than that treated with NPS-II and SS-II. The results of this study suggest that proteases recovered from shrimp processing discards may potentially be used as processing aids in formulated foods.
Quantitative proteomics reveals the protective effects of ESD against osteoarthritis via attenuating inflammation and modulating immune response

Epimedium, Salvia miltiorrhiza, and Dioscorea nipponica Makino (ESD) have been combined to treat osteoarthritis (OA) for a long time. In this study we used quantitative proteomics to find the protective effects of ESD against OA and possible mechanism. After papain-induced rats’ OA model established ESD was intragastrically administrated to rats for four weeks. Label-free quantitative proteomics was used to screen the comprehensive protein profiling changes in both OA and ESD groups. After stringent filtering, 62 proteins were found to be significantly up-regulated and 208 proteins were down-regulated in OA model compared with sham-operated control. Functional analysis revealed that these OA up-regulated proteins were enriched in the activation of humoral immunity response, complement activation, leukocyte mediated immunity, acute inflammatory, endocytosis regulation, and proteolysis regulation. ESD partially recovered the protein profiling changes in OA model. The effects of ESD were also assessed by measurement of behavioral activity and pathologic changes in the joints. ESD showed protective effects in suppressing inflammation, releasing joint pain, and attenuating cartilage degradation. Our study presented that ESD as a potential candidate to alleviate OA damage by reducing inflammation and modulating of immune system.
The annual cycle of Saharan populations of Locusta migratoria cinerascens (Orthoptera: Acrididae: Oedipodinae) in Algeria

Abstract Until recently, the Algerian populations of Locusta migratoria cinerascens were considered as sedentary and solitarious. In the Central Sahara and bordering areas, the extension of pivot-irrigated areas since 1980, has resulted in the creation of biotopes favourable to the reproduction of this acridid, particularly in the cereal crops of the Adrar and Ouargla regions. From analysis of the archives of the National Institute of plant Protection, and our personal work carried out from 1995 to 2004, we can provide new information on the life cycle of L. m. cinerascens. We show that, in the cereal crops of the regions studied, there are three generations of this acridid per annum: the first one developing on corn in the spring, until the harvest; the second a spring-summer generation in market gardens in the vicinity of wheat stubble, or in early-growth Sorghum crops, and a third, summer-autumn generation, that develops on summer cereal crops and probably over-winters as diapausing adults until the following February.
Sapwood Basal Area and Needle Mass of Scots Pine ( Pinus sylvestris L.) Trees in Central Sweden

Etablissement d'une relation entre la masse de feuillage et la surface basale de l'aubier pour un certain nombre de peuplements de pins sylvestres, test de l'adequation a une agregation des arbres echantillons a une regression avec la surface basale de l'aubier comme unique variable independante, test de la relation de la S.B.A. par unite de masse de feuillage a la largeur moyenne du cerne annuel, test de l'information sur le cerne annuel comme amelioration de la regression
DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation

Deep learning approaches are highly sought after solutions for coping with large amounts of collected datasets and are expected to become an essential part of imaging workflows. However, in most cases, deep learning is still considered as a complex task that only image analysis experts can master. DeepMIB addresses this problem and provides the community with a user-friendly and open-source tool to train convolutional neural networks and apply them to segment 2D and 3D light and electron microscopy datasets.
Graphein - a Python Library for Geometric Deep Learning and Network Analysis on Protein Structures and Interaction Networks

Geometric deep learning has well-motivated applications in the context of biology, a domain where relational structure in datasets can be meaningfully leveraged. Currently, efforts in both geometric deep learning and, more broadly, deep learning applied to biomolecular tasks have been hampered by a scarcity of appropriate datasets accessible to domain specialists and machine learning researchers alike. However, there has been little exploration of how to best to integrate and construct geometric representations of these datatypes. To address this, we introduce Graphein as a turn-key tool for transforming raw data from widely-used bioinformatics databases into machine learning-ready datasets in a high-throughput and flexible manner. Graphein is a Python library for constructing graph and surface-mesh representations of protein structures and biological interaction networks for computational analysis. Graphein provides utilities for data retrieval from widely-used bioinformatics databases for structural data, including the Protein Data Bank, the recently-released AlphaFold Structure Database, and for biomolecular interaction networks from STRINGdb, BioGrid, TRRUST and RegNetwork. The library interfaces with popular geometric deep learning libraries: DGL, PyTorch Geometric and PyTorch3D though remains framework agnostic as it is built on top of the PyData ecosystem to enable inter-operability with scientific computing tools and libraries. Graphein is designed to be highly flexible, allowing the user to specify each step of the data preparation, scalable to facilitate working with large protein complexes and interaction graphs, and contains useful pre-processing tools for preparing experimental files. Graphein facilitates network-based, graph-theoretic and topological analyses of structural and interaction datasets in a high-throughput manner. As example workflows, we make available two new protein structure-related datasets, previously unused by the geometric deep learning community. We envision that Graphein will facilitate developments in computational biology, graph representation learning and drug discovery. Availability and implementation Graphein is written in Python. Source code, example usage and tutorials, datasets, and documentation are made freely available under the MIT License at the following URL: graphein.ai
A LOW-SPRAY APPLE-PEST-MANAGEMENT PROGRAM FOR SMALL ORCHARDS

Abstract From 1981 to 1984, a low-spray management program was employed against injurious arthropods on the 40 disease-resistant apple trees in my experimental orchard in Massachusetts. The program consisted of an annual early-season application of petroleum oil followed by 2 applications of phosmet (1 at petal fall and another 10–14 days later). Visual traps were used to suppress Rhagoletis pomonella flies. For all years combined, a mean of 89.7% of fruit sampled at harvest in this orchard was free of insect injury compared with 0% uninjured fruit on neighboring unsprayed trees. Populations of foliar-feeding pests never reached injurious levels. Résumé De 1981 à 1984, on a appliqué un programme de régie basé sur un minimum d'arrosage contre les arthropodes nuisibles à 40 pommiers résistants aux maladies dans mon verger expérimental au Massachusetts. Le programme comprenait une application annuelle hâtive d'huile suivie de 2 applications de phosmet (l'une à la chute des pétales et l'autre 10–14 jours plus tard). Des pièges visuels ont servi à supprimer les mouches de Rhagoletis pomonella. Sur l'ensemble des années, on a observé une moyenne de 89,7% de fruits exempts de dommages dus aux insectes lors de la récolte, comparé à 0% sur des arbres avoisinants non arrosés. Les populations de défoliateurs n'ont jamais atteint de niveaux dommageables.
Cellular Communications Systems in Congested Environments: Resource Allocation and End-to-End Quality of Service Solutions with MATLAB

This book presents a mathematical treatment of the radio resource allocation of modern cellular communications systems in contested environments. It focuses on fulfilling the quality of service requirements of the living applications on the user devices, which leverage the cellular system, and with attention to elevating the users quality of experience. The authors also address the congestion of the spectrum by allowing sharing with the band incumbents while providing with a quality-of-service-minded resource allocation in the network. The content is of particular interest to telecommunications scheduler experts in industry, communications applications academia, and graduate students whose paramount research deals with resource allocation and quality of service.
Roles of motor on-rate and cargo mobility in intracellular transport

Molecular motors like kinesin are critical for cellular organization and biological function including in neurons. There is detailed understanding of how they move and how factors such as applied force and the presence of microtubule-associated proteins can alter this single-motor travel. In order to walk, the cargo-motor complex must first attach to a microtubule. This attachment process is less studied. Here, we use a combination of single-molecule bead experiments, modeling, and simulation to examine how cargos with kinesin-1 bind to microtubules. In experiment, we find that increasing cargo size and environment viscosity both signficantly slow cargo binding time. We use modeling and simulation to examine how the single motor on rate translates to the on rate of the cargo. Combining experiment and modeling allows us to estimate the single motor on rate as 100 s−1. This is a much higher value than previous estimates. We attribute the difference between our measurements and previous estimates to two factors: first, we are directly measuring initial motor attachment (as opposed to re-binding of a second motor) and second, the theoretical framework allows us to account for missed events (i.e. binding events not detected by the experiments due to their short duration). This indicates that the mobility of the cargo itself, determined by its size and interaction with the cytoplasmic environment, play a previously underestimated role in determining intracellular transport kinetics.
HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball

Knowledge manipulation of gene ontology (GO) and gene ontology annotation (GOA) can be done primarily by using vector representation of GO terms and genes for versatile applications such as deep learning. Previous studies have represented GO terms and genes or gene products to measure their semantic similarity using the Word2Vec-based method, which is an embedding method to represent entities as numeric vectors in Euclidean space. However, this method has the limitation that embedding large graph-structured data in the Euclidean space cannot prevent a loss of information of latent hierarchies, thus precluding the semantics of GO and GOA from being captured optimally. In this paper, we propose hierarchical representations of GO and genes (HiG2Vec) that apply Poincaré embedding specialized in the representation of hierarchy through a two-step procedure: GO embedding and gene embedding. Through experiments, we show that our model represents the hierarchical structure better than other approaches and predicts the interaction of genes or gene products similar to or better than previous studies. The results indicate that HiG2Vec is superior to other methods in capturing the GO and gene semantics and in data utilization as well. It can be robustly applied to manipulate various biological knowledge. Availability https://github.com/JaesikKim/HiG2Vec Contact kasohn@ajou.ac. kr, Dokyoon.Kim@pennmedicine.upenn. edu
In Vitro Antibacterial Potential of Some Medicinal Plants Against Human Enteric Pathogens

To investigate in vitro antibacterial potentials of five different medicinal plant leaf extracts against enteric pathogens. Five solvent were used Viz., hexane, chloroform, ethyl acetate, acetone and methanol extracts. Leaf extracts were evaluated against enteric bacterial pathogens by using standard disc diffusion, determination of minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC). Methanol extract of Vitex negundo leaves showed potent antibacterial activity (inhibition zone: 7.8-20.7 mm, MIC: 15.62 - 31.25 µg/mL, MBC: 31.25 -62.5 µg/mL) against all the pathogenic enteric bacteria (Escherichia coli, Salmonella typhi, Vibrio cholera, Vibrio fluvialis, Shigella flexneri, Proteus vulgaris and Proteus mirabilis) tested. For the first time it was observed that methanol extract of V. negundo leaves exhibited strong vibriocidal activity in vitro conditions. Therefore, it will be useful to identify and isolate the active compounds of this extract that could be a good alternative medicine to treat cholera.
Pikeperch habitat use within a canal network in spring

Thirteen pikeperch Sander lucioperca were implanted with acoustic transmitters and 10 were successfully tracked twice a week from March to early July in a drainage canal connected to a brackish lagoon located in the Rhone delta. Pikeperch was found in the main canal and in narrow tributaries, but never in the lagoon. Pikeperch avoided shallow parts of the canal and selected areas with high riparian vegetation (mainly trees). No between sexes differences occurred in habitat selection. At the basin scale, while both sexes remained in the upstream part of the canal during the spawning period, after spawning, females migrated downstream and also into the tributaries. This migration may have been induced by the movement of prey while males remained guarding the nests.
Prophylactic and Therapeutic Inhibition of In Vitro SARS-CoV-2 Replication by Oleandrin

With continued expansion of the COVID-19 pandemic, antiviral drugs are desperately needed to treat patients at high risk of life-threatening disease and even to limit spread if administered early during infection. Typically, the fastest route to identifying and licensing a safe and effective antiviral drug is to test those already shown safe in early clinical trials for other infections or diseases. Here, we tested in vitro oleandrin, derived from the Nerium oleander plant and shown previously to have inhibitory activity against several viruses. Using Vero cells, we found that prophylactic oleandrin administration at concentrations down to 0.05 μg/ml exhibited potent antiviral activity against SARS-CoV-2, with an 800-fold reduction in virus production, and a 0.1 μg/ml dose resulted in a greater than 3,000-fold reduction in infectious virus production. The EC50 values were 11.98ng/ml when virus output was measured at 24 hours post-infection, and 7.07ng/ml measured at 48 hours post-infection. Therapeutic (post-infection) treatment up to 24 hours after infection of Vero cells also reduced viral titers, with the 0.1 μg/ml dose causing greater than 100-fold reductions as measured at 48 hours, and the 0.05 μg/ml dose resulting in a 78-fold reduction. The potent prophylactic and therapeutic antiviral activities demonstrated here strongly support the further development of oleandrin to reduce the severity of COVID-19 and potentially also to reduce spread by persons diagnosed early after infection. IMPORTANCE COVID-19, a pandemic disease caused by infection with SARS-CoV-2, has swept around the world to cause millions of infections and hundreds-of-thousands of deaths due to the lack of vaccines and effective therapeutics. We tested oleandrin, derived from the Nerium oleander plant and shown previously to reduce the replication of several viruses, against SARS-CoV-2 infection of Vero cells. When administered both before and after virus infection, nanogram doses of oleandrin significantly inhibited replication by up to 3,000-fold, indicating the potential to prevent disease and virus spread in persons recently exposed to SARS-CoV-2, as well as to prevent severe disease in persons at high risk. These results indicate that oleandrin should be tested in animal models and in humans exposed to infection to determine its medical usefulness in controlling the pandemic.
Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon

A major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report a cis-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factor vestigial-like 3 (vgll3) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (Salmo salar). Using a common-garden experiment, we first show that vgll3 genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling of vgll3 expression in ten tissues across the first year of salmon development, we identify a pubertal transition in vgll3 expression where maturation coincided with a 66% reduction in testicular vgll3 expression. The late maturation allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform of vgll3 pre-puberty. By comparing absolute vgll3 mRNA copies in heterozygotes we show that the expression difference between the early and late maturity alleles is largely cis-regulatory. We propose a model whereby expression of a rare isoform from the late allele shifts the liability of its carriers towards delaying puberty. These results exemplify the potential importance of regulatory differences as a mechanism for the evolution of life history traits.
Optogenetic control of small GTPases reveals RhoA-mediated intracellular calcium signaling

Rho/Ras family small GTPases are known to regulate numerous cellular processes, including cytoskeletal reorganization, cell proliferation, and cell differentiation. These processes are also controlled by Ca2+, and consequently, crosstalk between these signals is considered likely. However, systematic quantitative evaluation is not yet reported. Thus, we developed optogenetic tools to control the activity of small GTPases (RhoA, Rac1, Cdc42, Ras, Rap, and Ral) using an improved light-inducible dimer system (iLID). Using these optogenetic tools, we investigated calcium mobilization immediately after small GTPase activation. Unexpectedly, we found that only RhoA activation induced a transient intracellular calcium elevation in RPE1 and HeLa cells. Transients were also observed in MDCK and HEK293T cells by RhoA activation, but interestingly, molecular mechanisms were identified to be different among cell types. In RPE1 and HeLa cells, RhoA directly activated phospholipase C (PLC)ε at the plasma membrane, which in turn induced Ca2+ release from the endoplasmic reticulum (ER). The RhoA-PLCε axis induced calcium-dependent NFAT nuclear translocation, suggesting it does activate intracellular calcium signaling.