Miracle-dz/UniFAR-FTUs huggingface dataset:
ChimericFragments: Computation, analysis, and visualization of global RNA networks

RNA-RNA interactions are key for post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA-RNA interactions on a genome-wide scale, computational methods to analyze the underlying data are lagging behind. Here, we present ChimericFragments, an analysis and visualization framework for RNA-seq experiments producing chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and is compatible with several widely used experimental procedures. We demonstrate that ChimericFragments enables the systematic identification of RNA regulators and RNA-RNA pairs and outperforms existing approaches.
A common regulatory switch controls a suite of C4 traits in multiple cell types

The C4 photosynthetic pathway provided a major advantage to plants growing in hot, dry environments, including the ancestors of our most productive crops. Two traits were essential for the evolution of this pathway: increased vein density and the functionalization of bundle sheath cells for photosynthesis. Although GRAS transcriptional regulators, including SHORT ROOT (SHR), have been implicated in mediating leaf patterning in both C3 and C4 species, little is known about what controls the specialized features of the cells that mediate C4 metabolism and physiology. We show in the model monocot, Setaria viridis, that SHR regulates components of multiple cell identities, including chloroplast biogenesis and photosynthetic gene expression in bundle sheath cells, a central feature of C4 plants. Furthermore, we found that it also contributes to the two-cell compartmentalization of the characteristic four-carbon shuttle pathway. Disruption of SHR function clearly reduced photosynthetic capacity and seed yield in mutant plants under heat stress. Together, these results show how cell identities are remodeled by SHR to host the suite of traits characteristic of C4 regulation, which are a main engineering target in non-C4 crops to improve climate resilience.
Activity of oleo-gum resins of myrrha on the growth of Candidiasis

Aims Medicinal plants have a long and significant history of being used for their healing properties. One famous example is Commiphora, which is mostly found in the southern part of Arabia. The objective of this research was to evaluate the effectiveness of a water-based extract obtained from two different varieties of myrrh in suppressing the proliferation of Candida spp. at different concentrations. The objective of this research is to determine the chemical composition of Commiphora and its capacity to prevent the development of Candida spp. Methodology and Results A plant specimen traditionally used in Saudi Arabia for its possible effectiveness against Candida albicans (ATCC 14053), C. neoformans (ATCC 66031), Candida laurentii (ATCC 18803), Candida guilliermondii (ATCC 6260), and Candida tropicalis (ATCC 66029). The results showed that the aqueous extract of both tested species of Myrrha (Commiphora myrrha and C. molmol) shown inhibitory effects on all tested isolates. Moreover, it was discovered that the inhibitory impact decreased with increasing concentrations of Myrrha. During the chemical examination of the Myrrha, it was noted that the material included 12 components known for their antimicrobial properties. The components described before are as follows: The specified chemical compounds consist of β-Elemene, β-bisabolene, Dihydro butyl bezodoxepin, Tetradecanol, methyl palmitate, Tribenzo-1,2,3,4,5,6 anthracene, 9-Eicosene, 2-bromo-4-fluoro-N-(thiophen-2-ylmethyl) aniline, Octadecenoic acid methyl ester, dehydroabietic acid, and Docosene. Conclusion The antimicrobial activity of five yeasts was assessed using the diffusion technique. The essential oil derived from two varieties of myrrha shown the most significant effects on Candida tropicalis (ATCC 66029), Candida guilliermondii (ATCC 6260), Candida laurentii (ATCC 18803), C. neoformans (ATCC 66031), and Candida albicans (ATCC 14053). Upon conducting a chemical examination of the myrrha, it was shown that it consists of 19 known components, of which 12 compounds have been proven by research to suppress the growth of microorganisms. Further research is needed to fully explore the potential of these water extracts as innovative antifungal medicines, including their effectiveness against various strains of Candida and the processes by which they work, as well as the primary components responsible for their action.
Cyfip2 controls the acoustic startle threshold through FMRP, actin polymerization, and GABAB receptor function

Animals process a constant stream of sensory input, and to survive they must detect and respond to dangerous stimuli while ignoring innocuous or irrelevant ones. Behavioral responses are elicited when certain properties of a stimulus such as its intensity or size reach a critical value, and such behavioral thresholds can be a simple and effective mechanism to filter sensory information. For example, the acoustic startle response is a conserved and stereotyped defensive behavior induced by sudden loud sounds, but dysregulation of the threshold to initiate this behavior can result in startle hypersensitivity that is associated with sensory processing disorders including schizophrenia and autism. Through a previous forward genetic screen for regulators of the startle threshold a nonsense mutation in Cytoplasmic Fragile X Messenger Ribonucleoprotein (FMRP)-interacting protein 2 (cyfip2) was found that causes startle hypersensitivity in zebrafish larvae, but the molecular mechanisms by which Cyfip2 establishes the acoustic startle threshold are unknown. Here we used conditional transgenic rescue and CRISPR/Cas9 to determine that Cyfip2 acts though both Rac1 and FMRP pathways, but not the closely related FXR1 or FXR2, to establish the acoustic startle threshold during early neurodevelopment. To identify proteins and pathways that may be downstream effectors of Rac1 and FMRP, we performed a candidate-based drug screen that indicated that Cyfip2 can also act acutely to maintain the startle threshold branched actin polymerization and N-methyl D-aspartate receptors (NMDARs). To complement this approach, we used unbiased discovery proteomics to determine that loss of Cyfip2 alters cytoskeletal and extracellular matrix components while also disrupting oxidative phosphorylation and GABA receptor signaling. Finally, we functionally validated our proteomics findings by showing that activating GABAB receptors, which like NMDARs are also FMRP targets, restores normal startle sensitivity in cyfip2 mutants. Together, these data reveal multiple mechanisms by which Cyfip2 regulates excitatory/inhibitory balance in the startle circuit to control the processing of acoustic information.
Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants

The evolution of SARS-CoV-2 variants with increased fitness has been accompanied by structural changes in the spike (S) proteins that are the major target for the adaptive immune response. Single-particle cryo-EM analysis of soluble S from SARS-CoV-2 variants has revealed this structural adaptation at high-resolution. The analysis of S trimers in situ on intact virions has the potential to provide more functionally relevant insights into S structure and virion morphology. Here, we characterized B.1, Alpha, Beta, Gamma, Delta, Kappa, and Mu variants by cryo-electron microscopy and tomography, assessing S cleavage, virion morphology, S incorporation, “in-situ” high-resolution S structures and the range of S conformational states. We found no evidence for adaptive changes in virion morphology, but describe multiple different positions in the S protein where amino acid changes alter local protein structure. Considered together, our data is consistent with a model where amino acid changes at multiple positions from the top to the base of the spike cause structural changes that can modulate the conformational dynamics of S.
Variation in echolocation call emission of Neotropical insect-eating bats in response to shifting ambient temperatures

The sensory systems of animals are essential for them to respond to environmental cues and signals. However, their functionality might be altered by climate change. Most bats, for example, rely on acoustic signal emission for acquiring food, but their high-frequency echolocation calls are strongly attenuated in the air. Attenuation in air changes with changing weather conditions, which can lead to shifts in echo-based prey detection distance. However, bats adjust call parameters to the task and environment, and this behavioural plasticity may also help them to counteract potential increases in sound attenuation to keep echo detectability constant. We explored this ability in a community of insectivorous bats in a montane forest of Costa Rica. We recorded bat echolocation calls in response to experimentally increased temperatures, simulating intermediate and arguably realistic projected climate change scenarios. We calculated atmospheric attenuation and detection distance for each temperature and echolocation call. We found some changes in source level and call duration, yet not in peak frequency, and responses were not consistent across species with increasing atmospheric attenuation. This might be explained by several non-mutually exclusive reasons, including that the experimental increase in temperature and change of atmospheric attenuation were not sufficient to affect close-range prey detection. Ultimately, this study contributes to our understanding of sensory system adaptation under the pressure imposed by climate change. SUMMARY STATEMENT Studying adjustments in bats’ call parameters can reveal responses to the pressure imposed by climate change.
Cryo-EM structure of the bacterial effector protein SipA bound to F-actin reveals a unique mechanism for filament stabilization

The bacterial pathogen Salmonella spp. modulates cellular processes by delivering effector proteins through its type III secretion systems. Among these effectors, SipA facilitates bacterial invasion and promotes intestinal inflammation. The mechanisms by which this effector carries out these functions are incompletely understood, although SipA’s ability to modulate actin dynamics is central to some of these activities. Here, we report the cryo-EM structure of SipA bound to filamentous actin. The structure shows that this effector stabilizes actin filaments through unique interactions of its carboxy-terminal domain with four actin subunits. Furthermore, our structure-function studies revealed that SipA’s actin-binding activity is independent of its ability to stimulate intestinal inflammation. Overall, these studies illuminate critical aspects of Salmonella pathogenesis and provide unique insight into the mechanisms by which a bacterial effector modulates actin dynamics.
Rab3 mediates cyclic AMP-dependent presynaptic plasticity and olfactory learning

Presynaptic forms of plasticity occur throughout the nervous system and play an important role in learning and memory but the underlying molecular mechanisms are insufficiently understood. Here we show that the small GTPase Rab3 is a key mediator of cyclic AMP (cAMP)-induced presynaptic plasticity in Drosophila. Pharmacological and optogenetic cAMP production triggered concentration-dependent alterations of synaptic transmission, including potentiation and depression of evoked neurotransmitter release, as well as strongly facilitated spontaneous release. These changes correlated with a nanoscopic rearrangement of the active zone protein Unc13A and required Rab3. To link these results to animal behaviour, we turned to the established role of cAMP signalling in memory formation and demonstrate that Rab3 is necessary for olfactory learning. As Rab3 is dispensable for basal synaptic transmission, these findings highlight a molecular pathway specifically dedicated to tuning neuronal communication and adaptive behaviour.
An Endogenous Aryl Hydrocarbon Receptor Ligand Induces Preeclampsia-like Phenotypes: Transcriptome, Phosphoproteome, and Cell Functions

Background Preeclampsia (PE) is one hypertensive disorder and a leading cause of maternal and fetal mortality and morbidity during human pregnancy. Aryl hydrocarbon receptor (AhR) is a transcription factor, which regulates vascular functions. Exogenous and endogenous AhR ligands can induce hypertension in animals. However, if dysregulation of endogenous AhR ligands contributes to the pathophysiology of PE remains elusive. Methods We measured AhR activities in human maternal and umbilical vein sera. We also applied physiological, cellular, and molecular approaches to dissect the role of endogenous AhR ligands in vascular functions during pregnancy using pregnant rats and primary human umbilical vein endothelial cells (HUVECs) as models. Results PE elevated AhR activities in human umbilical vein sera. Exposure of pregnant rats to an endogenous AhR ligand, 2-(1’H-indole-3’-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE) increased blood pressure and proteinuria, while decreased uteroplacental blood flow and reduced fetal and placental weights, all of which are hallmarks of PE. ITE dampened vascular growth and fetal sex-specifically altered immune cell infiltration in rat placentas. ITE also decreased cell proliferation and cell monolayer integrity in HUVECs in vitro. RNA sequencing analysis revealed that ITE dysregulated transcriptome in rat placentas and HUVECs in a fetal sex-specific manner. Bottom-up phosphoproteomics showed that ITE disrupted phosphoproteome in HUVECs. These ITE-dysregulated genes and phosphoproteins were enriched in biological functions and pathways which are highly relevant to diseases of heart, liver, and kidney, vascular functions, inflammation responses, cell death, and kinase inhibition. Conclusions Dysregulation of endogenous AhR ligands during pregnancy may lead to the development of PE with underlying impaired vascular functions, fetal sex-specific immune cell infiltration and transcriptome, and phosphoproteome. Thus, this study has provided a novel mechanism for the development of PE and potentially other forms of hypertensive pregnancies. These AhR ligand-activated genes and phosphoproteins might represent promising therapeutic and fetal sex-specific targets for PE-impaired vascular functions.
Monitoring weediness and persistence of genetically modified oilseed rape (Brassica napus) in the UK

Results from monitoring the incidence and persistence of genetically modified (GM) oilseed rape volunteers at National List sites and at eight large scale release sites throughout the UK show that volunteer numbers in subsequent crops can vary considerably from site to site. At some sites volunteers were fully controlled in subsequent crops. At other sites viable GM seeds persisted in the soil, producing volunteer populations for up to three years after the release. Where GM and non GM varieties were grown together, the proportion of transgenic volunteers in subsequent crops appears to be lower than the original percentage grown. Initial results from this study suggest that weediness and invasiveness of oilseed rape volunteers is not enhanced by the specific genetic modifications studied.
AND ATHEROSCLEROTIC CARDIOVASCULAR DISEASE IN TYPE 2 DIABETES (NARRATIVE REVIEW)

This narrative review was aimed to analyze the current views on the biochemical and molecular mechanisms of ω - 3 polyunsaturated fatty acids (ω -3 PUFAs), in particular icosapent ethyl (IPE), in atherosclerotic cardiovascular disease (ASCVD) and type 2 diabetes mellitus (T2D). The results of experimental, cohort, prospective, randomized clinical trials confirm the prospects of using IPE to prevent and treat ASCVD in T2D. Search Techniques. Databases from Scopus, Science Direct (from Elsevier), EBSCO, PubMed, and Medline were all searched. To find trials that were missed by the web search, a manual search of the publishing bibliographies was conducted.
Language Teaching Research Quarterly

This longitudinal case study from a Complex Dynamic Systems Theory (CDST) perspective touches upon an under-researched issue: L1 development over the lifespan. Levinson (1978) predicts three stages in adulthood: early, mid and late, with a decline in late adulthood. We examine Diane Larsen-Freeman’s publications over a period of 50 years (from age 27 to 77) and trace seven complexity measures--three lexical (density, sophistication and diversity) and four syntactic (mean length of sentence, finite verb ratio, dependent clause per T-unit and complex nominals per clause)--to investigate whether early, middle, and late stages in adulthood occur as predicted. After employing common CDST methods to find out if there are significant peaks or interactions among the variables over time, we used a Hidden Markov time-series analysis to locate moments of self-organization, suggesting a new stage of development. The HMM shows a clear phase shift between middle and late adulthood when the writer was 63. Her vocabulary became more diversified, but her sentences were shorter, but not less complex. Therefore, we argue that this shift should not be seen as a decline in complexity but a shift in style as more precise words may lessen the need for more words.
HotTiles: Accelerating SpMM with Heterogeneous Accelerator Architectures

—Sparse Matrix Dense Matrix Multiplication (SpMM) is an important kernel with application across a wide range of domains, including machine learning and linear algebra solvers. In many sparse matrices, the pattern of nonzeros is nonuniform: nonzeros form dense and sparse regions, rather than being uniformly distributed across the whole matrix. We refer to this property as Intra-Matrix Heterogeneity ( IMH ). Currently, SpMM accelerator designs do not leverage this heterogeneity. They employ the same processing elements (PEs) for all the regions of a sparse matrix, resulting in suboptimal acceleration. To address this limitation, we utilize heterogeneous SpMM accelerator architectures, which include different types of PEs to exploit IMH. We develop an analytical modeling framework to predict the performance of different types of accelerator PEs taking into account IMH. Furthermore, we present a heuristic for partitioning sparse matrices among heterogeneous PEs. We call our matrix modeling and partitioning method HotTiles . To evaluate HotTiles , we simulate three different heterogeneous architectures. Each one consists of two types of workers (i.e., PEs): one suited for compute-bound denser regions ( Hot Worker ) and one for memory-bound sparser regions ( Cold Worker ). Our results show that exploiting IMH with HotTiles is very effective. Depending on the architecture, heterogeneous execution with HotTiles outperforms homogeneous execution using only hot or only cold workers by 9.2-16.8 × and 1.4-3.7 × , respectively. In addition, HotTiles outperforms the best worker type used on a per-matrix basis by 1.3-2.5 × . Finally, HotTiles outperforms an
Initial Estimates from an Integrated Study Examining the Residence Period and Migration Timing of Juvenile Sockeye Salmon from the Fraser River through Coastal Waters of British Columbia

Many stocks of Pacifi c salmon enter into and transit through the Strait of Georgia during their migration to off shore waters. Knowledge of the duration of juvenile sockeye salmon residency in the Strait of Georgia and when they migrate out of the strait is essential to understand both natural and anthropogenic factors that may be regulating their early marine survival. We present results from the fi rst year of a multi-year integrated study that demonstrates stock-specifi c diff erences in the migration timing of juvenile Fraser River sockeye salmon over the fi rst eight to 12 weeks of their marine life. The geography of the study region provides a unique opportunity to sample virtually the entire population as they migrate down the Fraser River and as they leave the Strait of Georgia through the Discovery Islands and lower Johnstone Strait. This analysis indicated that juvenile 1-year-old sockeye salmon were resident in the Strait of Georgia for seven to eight weeks in 2014. The catch rates in the Discovery Islands indicated that, in 2014, the peak migration period for Fraser River sockeye salmon occurred over approximately two weeks, with about 80% of all sockeye salmon caught between June 12 and June 19. The results suggest that the Strait of Georgia and the Discovery Islands/Johnstone Strait regions function in a similar manner as the nursery lakes and main river ways in the Fraser River watershed. The Strait of Georgia provides abundant food in a relatively protected habitat similar to their rearing lakes in the watershed. The Discovery Islands and Johnstone Strait, an area of lower food availability, is similar to the river, where fi sh move in concentrated numbers through high current fl ow areas over a relatively short period of time.
IMPACT ANALYSIS OF INFERENCE TIME ATTACK OF PERCEPTION SENSORS ON 1 AUTONOMOUS VEHICLES 2

1 As a safety-critical cyber-physical system, cybersecurity and related safety issues for Autonomous 2 Vehicles (AVs) have been important research topics for a while. Among all the modules on AVs, 3 perception is one of the most accessible attack surfaces, as drivers and AVs have no control over 4 the outside environment. Most current work targeting perception security for AVs focuses on 5 perception correctness. In this work, we propose an impact analysis based on inference time attacks 6 for autonomous vehicles. We demonstrate in a simulation system that such inference time attacks 7 can also threaten the safety of both the ego vehicle and other traffic participants. 8
Averaged Nystr¨om interpolants for the solution of Fredholm integral equations of the second kind

Fredholm integral equations of the second kind that are defined on a finite or infinite interval arise in many applications. This paper discusses Nystr¨om methods based on Gauss quadrature rules for the solution of such integral equations. It is important to be able to estimate the error in the computed solution, because this allows the choice of an appropriate number of nodes in the Gauss quadrature rule used. This paper explores the application of averaged and weighted averaged Gauss quadrature rules for this purpose
Al-Azhar University Journal for Virus Research and Studies Comparison of Two Nd:YAG Laser Posterior Capsulotomy: Cruciate Pattern vs Circular Pattern

Cataract is the principal cause of visual impairment worldwide. Despite improvements in cataract surgery techniques, years after surgery, lens epithelial cells can colonize causing development of posterior capsule opacification (PCO). Neodymium Yttrium Aluminum Garnet (Nd: YAG) laser capsulotomy is an effective technique in treating visually significant PCO. The aim of the work is to compare circular and cruciate methods of YAG laser capsulotomy. This study included 30 eyes of 30 patients with PCO underwent YAG laser capsulotomy. They were divided into two groups: Group 1 (G1): undergo cruciate pattern, Group (G2): undergo circular pattern with vitreous strand cutting. We examined all patients whome ages were above 25 years old and had posterior capsule opacification affecting the vision and had no previous ocular disease or ocular surgery other than cataract. Nd:YAG laser significantly improved visual functions (P>0.05). There is a slight increase in ocular tension post laser which returned to normal values within 1 week which were insignificant (P>0.05). Group 2 needed a little bit higher energy which were with non-significant difference between both groups. (Nd: YAG) laser is an effective technique in treating visually significant PCO Cruciate method proved to be more popular as it uses less energy and subsequent less possible complications.