Investigating the biological relevance in trained embedding representations of protein sequences

As genome sequencing is becoming faster and cheaper, an abundance of DNA and protein sequence data is available. However, experimental annotation of structural or functional information develops at a much slower pace. Therefore, machine learning techniques have been widely adopted to make accurate predictions on unseen sequence data. In recent years, deep learning has been gaining popularity, as it allows for effective end-to-end learning. One consideration for its application on sequence data is the choice for a suitable and effective sequence representation strategy. In this paper, we investigate the significance of three common encoding schemes on the multi-label prediction problem of Gene Ontology (GO) term annotation, namely a one-hot encoding, an ad-hoc trainable embedding, and pre-trained protein vectors, using different hyper-parameters. We found that traditional unigram one-hot encodings achieved very good results, only slightly outperformed by unigram ad-hoc trainable embeddings and bigram pre-trained embeddings (by at most 3%for the F maxscore), suggesting the exploration of different encoding strategies to be potentially beneficial. Most interestingly, when analyzing and visualizing the trained embeddings, we found that biologically relevant (dis)similarities between amino acid n-grams were implicitly learned, which were consistent with their physiochemical properties

Mechanical rolling formation of interpenetrated lithium metal/lithium tin alloy foil for ultrahigh-rate battery anode

To achieve good rate capability of lithium metal anodes for high-energy-density batteries, one fundamental challenge is the slow lithium diffusion at the interface. Here we report an interpenetrated, three-dimensional lithium metal/lithium tin alloy nanocomposite foil realized by a simple calendering and folding process of lithium and tin foils, and spontaneous alloying reactions. The strong affinity between the metallic lithium and lithium tin alloy as mixed electronic and ionic conducting networks, and their abundant interfaces enable ultrafast charger diffusion across the entire electrode. We demonstrate that a lithium/lithium tin alloy foil electrode sustains stable lithium stripping/plating under 30mAcm(-2) and 5mAhcm(-2) with a very low overpotential of 20mV for 200 cycles in a commercial carbonate electrolyte. Cycled under 6C (6.6mAcm(-2)), a 1.0mAhcm(-2) LiNi0.6Co0.2Mn0.2O2 electrode maintains a substantial 74% of its capacity by pairing with such anode

Thermal Effect of a Revolving Gaussian Beam on Activating Heat-Sensitive Nociceptors in Skin

17 USC 105 interim-entered record; under review.The article of record as published may be found at https://doi.org/10.4236/jamp.2021.91007We consider the problem of inducing withdrawal reflex on a test subject by exposing the subject’s skin to an electromagnetic beam. Heat-sensitive noci ceptors in the skin are activated wherever the temperature is above the activa tion temperature. Withdrawal reflex occurs when the activated volume reaches a threshold. Previously we studied static beams with 3 types of power density distribution: Gaussian, super-Gaussian, and flat-top. We found that the flap top is the best and the Gaussian is the worst in their performance with regard to 1) minimizing the time to withdrawal reflex, 2) minimizing the energy con sumption and 3) minimizing the maximum temperature increase. The less than-desirable performance of Gaussian beams is attributed to the uneven distribution of power density resulting in low energy efficiency: near the beam center the high power density does not contribute proportionally to increas ing the activated volume; outside the beam effective radius the low power density fails to activate nociceptors. To overcome the drawbacks of Gaussian beams, in this study, we revolve a Gaussian beam around a fixed point to make the power density more uniformly distributed. We optimize the performance over two parameters: the spot size of static beam and the radius of beam rev olution. We find that in comparison with a static Gaussian beam, a revolving Gaussian beam can reduce the energy consumption, and at the same time lower the maximum temperature.Joint Intermediate Force Capabilities Office of US Department of DefenseNaval Postgraduate Schoo

A Slurry Consolidation Approach to Reconstitute Low-Plasticity Silt Specimens for Laboratory Triaxial Testing

Silt Specimen Reconstitution using a Slurry Consolidation Approach is Commonly Used for Laboratory Testing. This Paper Presents a New Slurry Consolidation Approach to Reconstitute Silt Specimens for Use in Triaxial Testing. Silt Specimens Were Reconstituted in a Split Vacuum Mold Mounted on a Special Experimental Setup. the Uniformity of the Reconstituted Specimens Was Verified by Measuring the Water Content and Grain Size Distribution throughout the Specimens. the Testing Program Was Expedited using a Special Sample Handling Technique to Move the Specimen from the Special Experimental Setup to the Triaxial Chamber Base Platen. the Handling Process Did Not Disturb the Specimens to a Measurable Degree. Further, the Replicas of the Reconstituted Specimens Were Verified by Submitting Them to Basic Volumetric Measurements Followed by Static and Cyclic Triaxial Tests. the Triaxial Test Results Reported Very Small Differences. Copyright © by ASTM Int\u27l (All Rights Reserved)

Tsetse fly (Glossina pallidipes) midgut responses to Trypanosoma brucei challenge

Abstract Background Tsetse flies (Glossina spp.) are the prominent vector of African trypanosome parasites (Trypanosoma spp.) in sub-Saharan Africa, and Glossina pallidipes is the most widely distributed species in Kenya. This species displays strong resistance to infection by parasites, which are typically eliminated in the midgut shortly after acquisition from the mammalian host. Although extensive molecular information on immunity for the related species Glossina morsitans morsitans exists, similar information is scarce for G. pallidipes. Methods To determine temporal transcriptional responses of G. pallidipes to Trypanosoma brucei brucei challenge, we conducted Illumina based RNA-seq on midgut organ and carcass from teneral females G. pallidipes at 24 and 48 h post-challenge (hpc) with T. b. brucei relative to their respective controls that received normal blood meals (without the parasite). We used a suite of bioinformatics tools to determine differentially expressed and enriched transcripts between and among tissues, and to identify expanded transcripts in G. pallidipes relative to their orthologs G. m. morsitans. Results Midgut transcripts induced at 24 hpc encoded proteins were associated with lipid remodelling, proteolysis, collagen metabolism, apoptosis, and cell growth. Midgut transcripts induced at 48 hpc encoded proteins linked to embryonic growth and development, serine endopeptidases and proteosomal degradation of the target protein, mRNA translation and neuronal development. Temporal expression of immune responsive transcripts at 48 relative to 24 hpc was pronounced, indicative of a gradual induction of host immune responses the following challenge. We also searched for G. m. morsitans orthologous groups that may have experienced expansions in the G. pallidipes genome. We identified ten expanded groups in G. pallidipes with putative immunity-related functions, which may play a role in the higher refractoriness exhibited by this species. Conclusions There appears to be a lack of strong immune responses elicited by gut epithelia of teneral adults. This in combination with a compromised peritrophic matrix at this stage during the initial phase of T. b. brucei challenge may facilitate the increased parasite infection establishment noted in teneral flies relative to older adults. Although teneral flies are more susceptible than older adults, the majority of tenerals are still able to eliminate parasite infections. Hence, robust responses elicited at a later time point, such as 72 hpc, may clear parasite infections from the majority of flies. The expanded G. m. morsitans orthologous groups in G. pallidipes may also be functionally associated with the enhanced refractoriness to trypanosome infections reported in G. pallidipes relative to G. m. morsitans

How to turn a brand's friends (and detractors) into evangelists: The case of Canadian wine

With conversion rituals, cool-climate wineries in Ontario managed to overcome a reputation for low quality, write Felipe G. Massa, Wesley Helms, Maxim Voronov and Liang Wan

Ultra-intensified intermittent-perfusion fed-batch (UIIPFB) process quadrupled productivity of a bispecific antibody

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Surface acoustic waves induced micropatterning of cells in gelatin methacryloyl (GelMA) hydrogels

Acoustic force patterning is an emerging technology that provides a platform to control the spatial location of cells in a rapid, accurate, yet contactless manner. However, very few studies have been reported on the usage of acoustic force patterning for the rapid arrangement of biological objects, such as cells, in a three-dimensional (3D) environment. In this study, we report on a bio-acoustic force patterning technique, which uses surface acoustic waves (SAWs) for the rapid arrangement of cells within an extracellular matrix-based hydrogel such as gelatin methacryloyl (GelMA). A proof-of-principle was achieved through both simulations and experiments based on the in-house fabricated piezoelectric SAW transducers, which enabled us to explore the effects of various parameters on the performance of the built construct. The SAWs were applied in a fashion that generated standing SAWs (SSAWs) on the substrate, the energy of which subsequently was transferred into the gel, creating a rapid, and contactless alignment of the cells (<10 s, based on the experimental conditions). Following ultraviolet radiation induced photo-crosslinking of the cell encapsulated GelMA pre-polymer solution, the patterned cardiac cells readily spread after alignment in the GelMA hydrogel and demonstrated beating activity in 5–7 days. The described acoustic force assembly method can be utilized not only to control the spatial distribution of the cells inside a 3D construct, but can also preserve the viability and functionality of the patterned cells (e.g. beating rates of cardiac cells). This platform can be potentially employed in a diverse range of applications, whether it is for tissue engineering, in vitro cell studies, or creating 3D biomimetic tissue structures