Drug Discovery Today March 2017 special issue

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Sean Ekins

A special issue on tuberculosis drug research funded by the EU. With particular focus on MM4TB

Science

Drug Discovery Today March 2017 special issue

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How to Win a small business grant.pptx

Sean Ekins

The presentation was given at SETAC 2022 Nov 16 and describes our work on Evaluating Multiple Machine Learning Models for Biodegradation and Aquatic Toxicity. We generated many models that are available to license in our MegaTox software. We found that the support vector machines performed the best after assessing many algorithms for both classification and regression models. The authors of this work are Thomas R Lane, Fabio Urbina and Sean Ekins. The contact is sean@collaborationspharma.com

Evaluating Multiple Machine Learning Models for Biodegradation and Aquatic To...

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This presentation summarizes some early efforts on an open drug discovery collaboration between scientists in Brazil and the US. The amazing virus images were created by John Liebler and can be licensed from him http://www.artofthecell.com/animation/will-the-real-zika-virus-please-stand-up The homology models were created with Swiss Model by Sean Ekins: Marco Biasini, Stefan Bienert, Andrew Waterhouse, Konstantin Arnold, Gabriel Studer, Tobias Schmidt, Florian Kiefer, Tiziano Gallo Cassarino, Martino Bertoni, Lorenza Bordoli, Torsten Schwede. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research; (1 July 2014) 42 (W1): W252-W258; doi: 10.1093/nar/gku340. Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201. Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009). The SWISS-MODEL Repository and associated resources. Nucleic Acids Research. 37, D387-D392. Guex, N., Peitsch, M.C., Schwede, T. (2009). Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis, 30(S1), S162-S173.

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Cotton crops are vulnerable to a variety of sucking pests, which can severely impact plant health, yield, and fiber quality. These pests primarily feed on plant sap, extracting nutrients directly from the plant's vascular system. Here's a breakdown of some of the most significant sucking pests in cotton cultivation: Aphids: Cotton aphids or melon aphids can cause direct damage by sucking sap and indirect damage by secreting honeydew, which encourages sooty mold growth. This can interfere with photosynthesis and weaken the plant. Aphids can also transmit viral diseases. Whiteflies: Two species, the silverleaf whitefly and the bandedwinged whitefly, are particularly troublesome. They not only suck sap from the underside of leaves, causing yellowing and leaf drop, but their honeydew excretion promotes sooty mold and they can transmit several plant viruses. Thrips: While thrips can chew on plants, their primary damage to cotton is through sucking. They attack the cotton plant during its seedling stage, which can stunt growth and reduce vigor. Thrips are also capable of transmitting the Cotton Bud disease. Spider Mites: These are not insects but arachnids. Spider mites, such as the two-spotted spider mite, suck cell contents from the leaves, leading to speckled discoloration and potentially significant leaf loss if infestations are severe. Leafhoppers: Including various species, leafhoppers can cause direct damage through feeding, which results in leaf curling and stunted growth. They can also be vectors for plant diseases. Mealybugs: These pests are less common but can be problematic, especially in clustered planting conditions. They suck sap and secrete honeydew, which leads to sooty mold. Mealybugs can also spread viruses. Stink Bugs: Although primarily known for their chewing mouthparts, certain stink bugs can cause damage similar to sucking pests by injecting saliva into the plant and sucking out nutrients, leading to boll damage and stained lint. Management Strategies: Cultural Controls: This includes practices such as crop rotation, using resistant varieties, and managing planting and harvesting times to avoid peak pest populations. Biological Controls: Beneficial insects like lady beetles, lacewings, and predatory mites can naturally control sucking pest populations. Parasitic wasps also play a role in controlling aphid and whitefly populations. Chemical Controls: Insecticides may be used but should be chosen carefully to minimize resistance development and preserve beneficial insects. Systemic insecticides can be particularly effective against sucking pests. Integrated Pest Management (IPM): Combining multiple control strategies based on monitoring and thresholds to apply the most effective and environmentally sensitive approach. Effective management of sucking pests in cotton requires a thorough understanding of the pest species present, their life cycles, and the ecological balance of the field environment.

Pests of cotton_Sucking_Pests_Dr.UPR.pdf

PirithiRaju

On 26 January 2023, a military pilot reported four potential unidentified anomalous phenomena (UAP) while operating in the Eglin Air Force Base training range off the coast of Florida. Through the onboard radar system, the pilot initially observed that the four objects were aloft between 16,000 – 18,000 feet and appeared to be flying in formation. However the pilot observed only one of the four objects visually and captured two images of the single object via the aircraft’s electro-optical/infrared (EO/IR) sensor (see Figures 1A and 1B). The pilot could not record video of the event because the aircraft’s video recording equipment was inoperable prior to and during the aircraft’s flight. The pilot observed this single object aloft at 16,000 feet. The following case information is based on the pilot’s initial report and a subsequent discussion that AARO held with the pilot to seek additional details about the pilot’s observation of the reported object.

All-domain Anomaly Resolution Office U.S. Department of Defense (U) Case: “Eg...

Sérgio Sacani

HotJupiters are amongthebest-studied exoplanets, but it is still poorly understood how their chemical composition and cloud properties vary with longitude. Theoretical models predict that clouds may condense on the nightside and that molecular abundances can be driven out of equilibrium by zonal winds. Here we report a phase-resolved emission spectrum of the hot Jupiter WASP-43b measured from 5–12µ 5–12µ 5–12µm with JWST’s Mid-Infrared Instrument (MIRI). 1524 ±35 1524 ±35 and 863±23 The spectra reveal a large day–night temperature contrast (with average brightness temperatures of 1524 ± 35 863 ±23 863 ±23Kelvin, respectively) and evidence for water absorption at all orbital phases. Comparisons with three-dimensional atmospheric models show that both the phase curve shape and emission spectra strongly suggest the presence of nightside clouds which become optically thick to thermal emission at pressures greater than ∼100mbar. The dayside is consistent with a cloudless atmosphere above the mid-infrared photosphere. Con3trary to expectations from equilibrium chemistry but consistent with disequilibrium kinetics models, methane is not detected on the nightside (2σ upper limit of 1–6 parts per million, depending on model assumptions).

Nightside clouds and disequilibrium chemistry on the hot Jupiter WASP-43b

Sérgio Sacani

Small size (20-300 nm) / bacteria (size measured in μm) Viral genome – single type of nucleic acid: DNA – dezoxyriboviruses RNA - riboviruses Totally dependant on living cells for all metabolic processes May infect humans, animals, plants, bacteria, fungi,parasites, insects Virion = viral corpuscle = elementary, infectious unit. Only visible by electron microscopy. Laboratory diagnosis of viral infections Methods: • Cytology • Electron microscopy • Cultivation • Detection of viral proteins • Serology • Molecular diagnosis (detection of genetic material i.e. nucleic acids) PPT prepared by Dr. Prince C P

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Context. WASP-76 b has been a recurrent subject of study since the detection of a signature in high-resolution transit spectroscopy data indicating an asymmetry between the two limbs of the planet. The existence of this asymmetric signature has been confirmed by multiple studies, but its physical origin is still under debate. In addition, it contrasts with the absence of asymmetry reported in the infrared (IR) phase curve. Aims. We provide a more comprehensive dataset of WASP-76 b with the goal of drawing a complete view of the physical processes at work in this atmosphere. In particular, we attempt to reconcile visible high-resolution transit spectroscopy data and IR broadband phase curves. Methods. We gathered 3 phase curves, 20 occultations, and 6 transits for WASP-76 b in the visible with the CHEOPS space telescope. We also report the analysis of three unpublished sectors observed by the TESS space telescope (also in the visible), which represents 34 phase curves. Results. WASP-76 b displays an occultation of 260±11 and 152±10 ppm in TESS and CHEOPS bandpasses respectively. Depending on the composition assumed for the atmosphere and the data reduction used for the IR data, we derived geometric albedo estimates that range from 0.05 ± 0.023 to 0.146 ± 0.013 and from <0.13 to 0.189 ± 0.017 in the CHEOPS and TESS bandpasses, respectively. As expected from the IR phase curves, a low-order model of the phase curves does not yield any detectable asymmetry in the visible either. However, an empirical model allowing for sharper phase curve variations offers a hint of a flux excess before the occultation, with an amplitude of ∼40 ppm, an orbital offset of ∼−30◦ , and a width of ∼20◦ . We also constrained the orbital eccentricity of WASP-76 b to a value lower than 0.0067, with a 99.7% confidence level. This result contradicts earlier proposed scenarios aimed at explaining the asymmetry observed in high-resolution transit spectroscopy. Conclusions. In light of these findings, we hypothesise that WASP-76 b could have night-side clouds that extend predominantly towards its eastern limb. At this limb, the clouds would be associated with spherical droplets or spherically shaped aerosols of an unknown species, which would be responsible for a glory effect in the visible phase curves.

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Bollworms are among the most damaging pests in cotton cultivation, affecting the bolls where the cotton fibers are formed. There are several species of bollworms, each capable of causing significant yield loss and quality degradation if not effectively managed. Here’s a detailed look at the primary bollworm species affecting cotton: Cotton Bollworm (Helicoverpa armigera): Also known as the corn earworm or the Old World bollworm, this pest is found in many regions around the world. It is highly polyphagous (feeds on many different plants) and poses a threat not only to cotton but also to maize, tomatoes, and legumes. The larvae bore into the cotton bolls, feeding on the developing seeds and fibers, which can lead to boll rot. Pink Bollworm (Pectinophora gossypiella): A significant pest of cotton, the pink bollworm larvae infest the cotton bolls, feeding on the seeds and lint. This can severely damage or destroy the bolls. In regions where pink bollworms are prevalent, they have been a major driver for the adoption of genetically engineered Bt cotton, which expresses a bacterium gene toxic to certain insects. Tobacco Budworm (Heliothis virescens): Closely related to the cotton bollworm, the tobacco budworm primarily attacks tobacco but is also a common pest in cotton. It primarily damages the flowers and bolls of the cotton plant. Differentiating between the tobacco budworm and the cotton bollworm based on appearance can be challenging, but it is crucial for effective management. American Bollworm (Helicoverpa zea): Known in some regions as the corn earworm, it is similar in behavior to Helicoverpa armigera and poses a threat to a variety of crops, including cotton. The larvae attack the cotton bolls, leading to direct damage to the cotton lint and seeds. Management Strategies: Cultural Controls: Crop rotation, destruction of crop residues, and deep plowing can help break the pest’s life cycle. Timing of planting can also be adjusted to avoid peak pest infestation. Biological Controls: Natural enemies like Trichogramma wasps, which parasitize bollworm eggs, and predators such as lacewings and ladybugs can be encouraged. Bacillus thuringiensis (Bt) products can also be sprayed, which are particularly effective against young larvae. Chemical Controls: Insecticides may be required when infestation levels exceed economic thresholds. However, resistance management must be considered, alternating modes of action to avoid developing resistance. Genetic Approaches: Bt cotton, genetically modified to express Bacillus thuringiensis toxin, has been highly effective in controlling bollworms and has dramatically reduced the reliance on chemical insecticides. Monitoring and Scouting: Regular field scouting and using pheromone traps to monitor adult populations can help in timely and targeted application of control measures. The effective management of bollworms often requires an integrated approach

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Botany is the branch of biology that deals with the scientific study of plants, including their structure, growth, reproduction, metabolism, development, and classification. It encompasses a wide range of topics, from the molecular biology of plant cells to the ecological relationships between plants and their environments. Botany is essential for understanding plant diversity, ecology, evolution, and the roles plants play in ecosystems and human societies.

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Past civilisations have nurtured small populations of those trying to understand and manipulate nature to some advantage in materials, tools, weapons, food, and wealth. However, they never formed communities and lacked the means of recording, communicating, and sharing successes and failures. They also lacked a common framework/philosophy to qualify them as scientists, but that all began to change in the 16th Century. In this lecture we consider the progression to a philosophy of science, and the underlying principles and assumptions that now guide scientific inquiry.We also examines the nature of scientific knowledge, the methods of acquisition, evolution, and significance over past centuries, and reflect on the value to society. In the struggle to solve problems, deliver understanding, and reveal the truth about our universe, science had to suffer and survive: ignorance, bigotry, established superstitions, and the ‘diktats’ of religions and politics, and latterly, falling education standards mired by social media. We chart that ‘scientific’ journey emphasising the importance of observation, experimentation, and the search for universal laws. Ultimately, this essentially Aristotelian perspective was challenged and overtaken by the rise of empiricism, which emphasised the importance of sensory experience and the limitations of human knowledge. Science continues to evolve and provide us with the best truths attainable with our leading edge technologies of observation and experimentation. Today, it stands as the greatest and richest contributor to human knowledge, understanding, progress, and wellbeing. In turn, debates and controversies are ongoing, shaping the field and philosophy which remains essential for understanding the nature of scientific knowledge and the models it creates. But unlike any belief system, the answers and models furnishers by science are not certain and invariant, they tend to be stochastic and incomplete - ‘the best we can do’ at a given time.

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Understanding circumstellar disks is of prime importance in astrophysics, however, their birth process remains poorly constrained due to observational and numerical challenges. Recent numerical works have shown that the small-scale physics, often wrapped into a sub-grid model, play a crucial role in disk formation and evolution. This calls for a combined approach in which both the protostar and circumstellar disk are studied in concert. Aims. We aim to elucidate the small scale physics and constrain sub-grid parameters commonly chosen in the literature by resolving the star-disk interaction. Methods. We carry out a set of very high resolution 3D radiative-hydrodynamics simulations that self-consistently describe the collapse of a turbulent dense molecular cloud core to stellar densities. We study the birth of the protostar, the circumstellar disk, and its early evolution (< 6 yr after protostellar formation). Results. Following the second gravitational collapse, the nascent protostar quickly reaches breakup velocity and sheds its surface material, thus forming a hot (∼ 103 K), dense, and highly flared circumstellar disk. The protostar is embedded within the disk, such that material can flow without crossing any shock fronts. The circumstellar disk mass quickly exceeds that of the protostar, and its kinematics are dominated by self-gravity. Accretion onto the disk is highly anisotropic, and accretion onto the protostar mainly occurs through material that slides on the disk surface. The polar mass flux is negligible in comparison. The radiative behavior also displays a strong anisotropy, as the polar accretion shock is shown to be supercritical whereas its equatorial counterpart is subcritical. We also f ind a remarkable convergence of our results with respect to initial conditions. Conclusions. These results reveal the structure and kinematics in the smallest spatial scales relevant to protostellar and circumstellar disk evolution. They can be used to describe accretion onto regions commonly described by sub-grid models in simulations studying larger scale physics.

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The presentation first gives the brief introduction about the animal communication covering the reasons for communication. It then describes the important types of animal communication emphasizing the important points regarding auditory and visual communication. With respect to auditory communication, it covers the uses of it and mechanisms of auditory communication along with examples. Later the presentation discusses the various forms of visual communication such as gestures, postures, facial expressions, color changes , bioluminescent communication. It then describes the visual communication in bees in the form of bee dance . In bee dance it gives a brief overview of round dance , sickle dance and waggle dance .

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