PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning.

One of the challenges in a viral pandemic is the emergence of novel variants with different phenotypical characteristics. An ability to forecast future viral individuals at the sequence level enables advance preparation by characterizing the sequences and closing vulnerabilities in current preventative and therapeutic methods. In this article, we explore, in the context of a viral pandemic, the problem of generating complete instances of undiscovered viral protein sequences, which have a high likelihood of being discovered in the future using protein language models.

Protectin conjugates in tissue regeneration 1 alleviates sepsis-induced acute lung injury by inhibiting ferroptosis.

Background: Acute lung injury (ALI) is a common and serious complication of sepsis with high mortality. Ferroptosis, categorized as programmed cell death, contributes to the development of lung injury. Protectin conjugates in tissue regeneration 1 (PCTR1) is an endogenous lipid mediator that exerts protective effects against multiorgan injury.

Klotho Null Mutation Involvement in Adenosine A2B Receptor-Related Skeletal Muscle Degeneration.

Klotho is known for its age-suppressing function and has been implicated in sarcopenia pathology. It has recently been proposed that the adenosine A2B receptor plays a crucial role in skeletal muscle energy expenditure. However, the association between Klotho and A2B remains elusive.

Phosphoric acid pretreatment of poplar to optimize fermentable sugars production based on orthogonal experimental design.

The recalcitrant structure of raw poplar limited the production of fermentable sugars when applied as the material in the pretreatment of biochemical conversions. Phosphoric acid pretreatment is an efficient method to destroy the compact lignocellulose matrix presence in the poplar. In this study, phosphoric acid pretreatment of poplar was optimised by an orthogonal experimental design [L(3)] to improve enzymatic digestibility through investigating the effects of reaction temperature, time duration, and phosphoric acid concentration.

Effect of Bacillus subtilis fortified inoculation on the microbial communities in different niches of Daqu.

Daqu is the fermentation starter of Baijiu, which is one of the six most renowned distilled spirits. Studies have found that Bacillus is one of the dominant microbial genera in Daqu, and Bacillus subtilis is known to produce amylase, an important enzyme that influences the quality of Daqu. This study aims to explore the influence of B.

New Poplar-Derived Biocomposites via Single-Step Thermoforming Assisted by Phosphoric Acid Pretreatment.

One-step thermoforming represents an effective approach to preparing glue-free biocomposites. This study aimed to produce glue-free biocomposites with high-temperature resistance and mechanical properties using phosphoric acid pretreatments combined with thermoforming. Due to the hot-moulding process, the cell wall was destroyed, which allowed the fibres to adhere closely together.

Structural Characteristics and Formation Mechanism of Microbiota Related to Fermentation Ability and Alcohol Production Ability in Nongxiang .

Fermentation ability and alcohol production ability are important quality indicators of Chinese liquor , reflecting microbial growth and metabolic capacity and ethanol production capacity of microbiota, respectively. However, information on the microbial community related to the fermentation ability and alcohol production ability is unclear. In this study, fermentation functional microbiota (FFM) and alcohol functional microbiota (AFM) were obtained by correlating fermentation ability and alcohol production ability with microbiota.

HELLO: improved neural network architectures and methodologies for small variant calling.

Background: Modern Next Generation- and Third Generation- Sequencing methods such as Illumina and PacBio Circular Consensus Sequencing platforms provide accurate sequencing data. Parallel developments in Deep Learning have enabled the application of Deep Neural Networks to variant calling, surpassing the accuracy of classical approaches in many settings. DeepVariant, arguably the most popular among such methods, transforms the problem of variant calling into one of image recognition where a Deep Neural Network analyzes sequencing data that is formatted as images, achieving high accuracy.

Acoustic landmarks contain more information about the phone string than other frames for automatic speech recognition with deep neural network acoustic model.

Most mainstream automatic speech recognition (ASR) systems consider all feature frames equally important. However, acoustic landmark theory is based on a contradictory idea that some frames are more important than others. Acoustic landmark theory exploits quantal nonlinearities in the articulatory-acoustic and acoustic-perceptual relations to define landmark times at which the speech spectrum abruptly changes or reaches an extremum; frames overlapping landmarks have been demonstrated to be sufficient for speech perception.

Divergence of a Tandem Duplication of Manganese Superoxide Dismutase in Nosema bombycis.

Manganese superoxide dismutase (MnSOD) is a key enzyme in the protection of cells from oxidative stress. A tandem duplication of the MnSOD gene (NbMnSOD1 and NbMnSOD2) in the genome of Nosema bombycis, a parasite of the silkworm Bombyx mori, was previously identified. Here, we compare the protein structures of NbMnSOD1 and NbMnSOD2 and characterize these two proteins in terms of cellular localization, timing of transcription, protein structure, and enzyme activity.

Wnt5a Deficiency Regulates Inflammatory Cytokine Secretion, Polarization, and Apoptosis in Mycobacterium tuberculosis-Infected Macrophages.

Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis (MTB), is one of the global public health catastrophes. Wnt signaling has recently been identified to exert immunoregulatory functions in a variety of inflammatory and infectious diseases, including tuberculosis. The opposite expression of Wnt5a in human and mice during MTB infection drives us to explore the roles and biological significances of reduced Wnt5a for MTB-treated mice.

BLESS 2: accurate, memory-efficient and fast error correction method.

Unlabelled: The most important features of error correction tools for sequencing data are accuracy, memory efficiency and fast runtime. The previous version of BLESS was highly memory-efficient and accurate, but it was too slow to handle reads from large genomes. We have developed a new version of BLESS to improve runtime and accuracy while maintaining a small memory usage.

A Foldable Lithium-Sulfur Battery.

The next generation of deformable and shape-conformable electronics devices will need to be powered by batteries that are not only flexible but also foldable. Here we report a foldable lithium-sulfur (Li-S) rechargeable battery, with the highest areal capacity (∼3 mAh cm(-2)) reported to date among all types of foldable energy-storage devices. The key to this result lies in the use of fully foldable and superelastic carbon nanotube current-collector films and impregnation of the active materials (S and Li) into the current-collectors in a checkerboard pattern, enabling the battery to be folded along two mutually orthogonal directions.

Imaging manifestations and pathological analysis of severe pneumonia caused by human infected avian influenza (H7N9).

Objective: To investigate the imaging and pathological findings of severe pneumonia caused by human infected avian influenza (H7N9), and therefore to further understand and improve diagnostic accuracy of severe pneumonia caused by human infected avian influenza (H7N9).

Methods: The relevant clinical and imaging data of 19 cases, including 10 males and 9 females, with pneumonia caused by human infected avian influenza (H7N9) was retrospectively analyzed. One of the cases had received percutaneous lung biopsy, with the clinical, imaging and pathological changes possible to be analyzed.

BLESS: bloom filter-based error correction solution for high-throughput sequencing reads.

Motivation: Rapid advances in next-generation sequencing (NGS) technology have led to exponential increase in the amount of genomic information. However, NGS reads contain far more errors than data from traditional sequencing methods, and downstream genomic analysis results can be improved by correcting the errors. Unfortunately, all the previous error correction methods required a large amount of memory, making it unsuitable to process reads from large genomes with commodity computers.

TIGER: tiled iterative genome assembler.

Background: With the cost reduction of the next-generation sequencing (NGS) technologies, genomics has provided us with an unprecedented opportunity to understand fundamental questions in biology and elucidate human diseases. De novo genome assembly is one of the most important steps to reconstruct the sequenced genome. However, most de novo assemblers require enormous amount of computational resource, which is not accessible for most research groups and medical personnel.

[A fundamental study on bioreactions of Sr-HA].

Objective: Sr-HA, a new type of hydroxyapatite biomaterial, was implanted into animals to study the bioreaction and character, which would be helpful for the further clinical applications in the future.

Methods: Totally 24 rabbits were divided into 3 groups. The bone defect of 6 mm x 12 mm x 4 mm was made at both mandibular angles of rabbits and Sr-HA of different proportion (10%, 5%, 0) was applied to reform the defects.