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. Current approaches to training these models fit model parameters to a known sequence set, which does not suit pandemic forecasting as future sequences differ from known sequences in some respects. To address this, we develop a novel method, called PandoGen, to train protein language models towards the pandemic protein forecasting task. PandoGen combines techniques such as synthetic data generation, conditional sequence generation, and reward-based learning, enabling the model to forecast future sequences, with a high propensity to spread. Applying our method to modeling the SARS-CoV-2 Spike protein sequence, we find empirically that our model forecasts twice as many novel sequences with five times the case counts compared to a model that is 30× larger. Our method forecasts unseen lineages months in advance, whereas models 4× and 30× larger forecast almost no new lineages. When trained on data available up to a month before the onset of important Variants of Concern, our method consistently forecasts sequences belonging to those variants within tight sequence budgets.

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. In this study, Klotho knockout mice, aged 10 weeks, and wild-type mice, aged 10 and 64 weeks, were used for comparison in indicators of sarcopenia (n = 6 for each group). PCR was performed to confirm the mice genotypes. Skeletal muscle sections were analyzed using hematoxylin and eosin staining as well as immunohistochemistry staining. The skeletal muscle cross-sectional area was significantly reduced in Klotho knockout mice and wild-type mice, aged 64 weeks, when compared with wild-type mice, aged 10 weeks, with a decreased percentage of type IIa and IIb myofibers. Likely impaired regenerative capacity, as reflected by the reduction of paired box 7 (Pax7)- and myogenic differentiation protein 1 (MyoD)-positive cells, was also observed in Klotho knockout mice and aged wild-type mice. 8-Hydroxy-2-deoxyguanosine expression was enhanced with Klotho knockout and aging, indicating higher oxidative stress. Adenosine A2B signaling was impaired, with a lower expression of the A2B receptor and the cAMP-response element binding protein in Klotho knockout and aged mice. The present study provides the novel finding that sarcopenia involves adenosine signaling under the influence of Klotho knockout.

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. However, the role of PCTR1 in the ferroptosis of sepsis-related ALI remains unknown. METHODS: A pulmonary epithelial cell line and a mouse model of ALI stimulated with lipopolysaccharide (LPS) were established in vitro and in vivo. Ferroptosis biomarkers, including ferrous (Fe2+), glutathione (GSH), malondialdehyde (MDA) and 4-Hydroxynonenal (4-HNE), were assessed by relevant assay kits. Glutathione peroxidase 4 (GPX4) and prostaglandin-endoperoxide synthase 2 (PTGS2) protein levels were determined by western blotting. Lipid peroxides were examined by fluorescence microscopy and flow cytometry. Cell viability was determined by a CCK-8 assay kit. The ultrastructure of mitochondria was observed with transmission electron microscopy. Morphology and inflammatory cytokine levels predicted the severity of lung injury. Afterward, related inhibitors were used to explore the potential mechanism by which PCTR1 regulates ferroptosis. RESULTS: PCTR1 treatment protected mice from LPS-induced lung injury, which was consistent with the effect of the ferroptosis inhibitor ferrostatin-1. PCTR1 treatment decreased Fe2+, PTGS2 and lipid reactive oxygen species (ROS) contents, increased GSH and GPX4 levels and ameliorated mitochondrial ultrastructural injury. Administration of LPS or the ferroptosis agonist RSL3 resulted in reduced cell viability, which was rescued by PCTR1. Mechanistically, inhibition of the PCTR1 receptor lipoxin A4 (ALX), protein kinase A (PKA) and transcription factor cAMP-response element binding protein (CREB) partly decreased PCTR1 upregulated GPX4 expression and a CREB inhibitor blocked the effects ofPCTR1 on ferroptosis inhibition and lung protection. CONCLUSION: This study suggests that PCTR1 suppresses LPS-induced ferroptosis via the ALX/PKA/CREB signaling pathway, which may offer promising therapeutic prospects in sepsis-related ALI.

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 [L9(33)] to improve enzymatic digestibility through investigating the effects of reaction temperature, time duration, and phosphoric acid concentration. The optimal conditions were selected based on the variance of chemical compositions, hemicellulose removal ratio, and delignification of the woody material after pretreatment. The optimum enzymatic hydrolysis yield of up to 73.44% was obtained when the phosphoric acid pretreatment performed at 190°C for 150 min under 1.5% of v/v 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. subtilis inoculation on the microbial community structure in different niches of Daqu. We studied the microbial community structure of the natural inoculated Daqu (i.e., control Daqu) and the fortified Daqu (i.e., B. subtilis-inoculated Daqu) by amplicon sequencing. Our results showed that compared with the control Daqu rind microbial community, the relative abundance of Bacillus, Aspergillus, Thermomyces, and Rasamsonia in the fortified Daqu rind microbial community increased, and the relative abundance of Weissella, Lactobacillus, Leuconostoc, and Pichia decreased. Compared with the control Daqu core microbial community, the relative abundance of Bacillus in the fortified Daqu core microbial community also increased, but the relative abundance of Pseudomonas and Paecilomyces decreased. The effect of B. subtilis inoculation on the rind microbial community of Daqu was more significant. In addition, the bacterial community of Daqu was more susceptible to the effect of the B. subtilis inoculation than was the fungal community of Daqu. The correlation between the bacterial community of Daqu and the fungal community of Daqu increased significantly after the B. subtilis inoculation. These results provide an important theoretical basis for the production of fortified Daqu.

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

Fermentation ability and alcohol production ability are important quality indicators of Chinese liquor Daqu, reflecting microbial growth and metabolic capacity and ethanol production capacity of Daqu 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 Daqu microbiota. FFM and AFM consisted of 50 and 49 genera, respectively, which were basically the same at the phylum level but differed at the genus level. Correlation analysis showed that FFM and AFM were mainly affected by moisture, acidity, and humidity in the early stage of Daqu fermentation, and oxygen content was a critical factor for microbial succession in the middle stage of fermentation. FFM and AFM had commensal or synergistic interactions with multiple microbes. Function predictions indicated that fermentation functional bacterial microbiota was active in product synthesis and transport-related metabolic functions, and alcohol functional bacterial microbiota was very active in raw material utilization and its own metabolic synthesis. This study reveals the structural characteristics and formation mechanism of FFM and AFM, which is important for control of Daqu quality.

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. Most hemicelluloses were hydrolysed through pretreatment with phosphoric acid, and the contact area between the cellulose and lignin was significantly increased. The biocomposites prepared by ball milling demonstrated remarkable flexural strength (49.03 MPa) and tensile strength (148.23 MPa). Moreover, they had excellent thermal stability, with the maximum temperature for pyrolysis rate at 374 °C, which was much higher than that of poplar (337 °C). In addition, the material released no formaldehyde during the preparation process, which is in line with the concept of green production.

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. In this paper, we explore an alternative approach to designing Deep Neural Networks for variant calling, where we use meticulously designed Deep Neural Network architectures and customized variant inference functions that account for the underlying nature of sequencing data instead of converting the problem to one of image recognition. RESULTS: Results from 27 whole-genome variant calling experiments spanning Illumina, PacBio and hybrid Illumina-PacBio settings suggest that our method allows vastly smaller Deep Neural Networks to outperform the Inception-v3 architecture used in DeepVariant for indel and substitution-type variant calls. For example, our method reduces the number of indel call errors by up to 18%, 55% and 65% for Illumina, PacBio and hybrid Illumina-PacBio variant calling respectively, compared to a similarly trained DeepVariant pipeline. In these cases, our models are between 7 and 14 times smaller. CONCLUSIONS: We believe that the improved accuracy and problem-specific customization of our models will enable more accurate pipelines and further method development in the field. HELLO is available at https://github.com/anands-repo/hello.

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. In this work, experiments are conducted on the TIMIT corpus, with both Gaussian mixture model (GMM) and deep neural network (DNN)-based ASR systems, and it is found that frames containing landmarks are more informative for ASR than others. It is discovered that altering the level of emphasis on landmarks by re-weighting acoustic likelihood tends to reduce the phone error rate (PER). Furthermore, by leveraging the landmark as a heuristic, one of the hybrid DNN frame dropping strategies maintained a PER within 0.44% of optimal when scoring less than half (45.8% to be precise) of the frames. This hybrid strategy outperforms other non-heuristic-based methods and demonstrate the potential of landmarks for reducing computation.

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. Despite a similarity in the primary sequence of NbMnSOD1 and NbMnSOD2, the latter shows a remarkable degree of amino acid sequence difference on the protein's surface and in the active site, where there is a substitution of a phenylalanine for a histidine in NbMnSOD2. Immuno-electron microscopy demonstrates that NbMnSOD1 is present in the cytosol of mature spores, whereas NbMnSOD2 is localized on the polar tube and the spore wall. Immunofluorescence confirms the localization of NbMnSOD2 on the polar tube of the germinated spore. Quantitative measurement of gene expression (qRT-PCR) demonstrates production of both alleles during the first day of infection followed by a dramatic decrease during the second to fourth day of infection. From the fifth day onward, the two alleles show a complementary pattern of expression. The qRT-PCR of the host manganese superoxide dismutase (BmMnSOD) shows a notable increase in transcription upon infection, leading to a three-fold spike by the first day of infection, followed by a decrease in transcription. Measurement of overall MnSOD activity shows a similar peak at day 1 followed by a decrease to a constant rate of enzyme activity. The differences in cellular localization and pattern of gene expression of NbMnSOD2 compared to NbMnSOD1, as well as the differences in protein structure seen for NbMnSOD2 compared to other microsporidial MnSODs, strongly suggest a unique, recently evolved role for NbMnSOD2.

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. In our study, the reduction of WNT5A in MTB-treated mice lung tissues or MTB-infected mice bone marrow-derived macrophages (BM-Mø) was in a dose- and time-dependent manner. Then, WNT5A-silenced mice, secreted frizzled-related protein 1 (SFRP1)-overexpressed or -silenced mice BM-Mø, were constructed to regulate Wnt5a levels. When Wnt5a is deficient, MTB-induced increases of pro-inflammatory cytokines (TNF-α, IL-1ß, IL-12, and IL-6) can be markedly attenuated in mice lung tissues or BM-Mø. Besides, external disturbance triggered that Wnt5a lower expression can induce Mø to be M2 phenotype and enhance cell apoptosis of MTB-infected mice BM-Mø. Hence, the reduction of Wnt5a is a tactful strategy adopted by Mø to resistant MTB-induced immune responses and to enhance MTB-induced Mø apoptosis in mice. Our study revealed a new style for Mø to manipulate themselves against MTB infection. Our research identifies that Wnt5a deficiency can regulate inflammatory cytokine secretion, polarization, and apoptosis in MTB-infected Mø.

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. The new version, called BLESS 2, has an error correction algorithm that is more accurate than BLESS, and the algorithm has been parallelized using hybrid MPI and OpenMP programming. BLESS 2 was compared with five top-performing tools, and it was found to be the fastest when it was executed on two computing nodes using MPI, with each node containing twelve cores. Also, BLESS 2 showed at least 11% higher gain while retaining the memory efficiency of the previous version for large genomes. AVAILABILITY AND IMPLEMENTATION: Freely available at https://sourceforge.net/projects/bless-ec CONTACT: dchen@illinois.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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. The carbon nanotube films also serve as the sulfur entrapment layer in the Li-S battery. The foldable battery showed <12% loss in specific capacity over 100 continuous folding and unfolding cycles. Such shape-conformable Li-S batteries with significantly greater energy density than traditional lithium-ion batteries could power the flexible and foldable devices of the future including laptops, cell phones, tablet computers, surgical tools, and implantable biomedical devices.

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. RESULTS: The lesions were mainly located at lower lobes and dorsal of lungs, involving multiple lobes and segments. Ground-glass opacities and/or pulmonary opacities were the more often imaging manifestations of severe pneumonia caused by human infected avian influenza (H7N9) in early and evolving phases (19/19,100%). By biopsy following percutaneous lung puncture, exudation of slurry, cellulose, RBC and neutrophils, formation of hyaline membrane, squamous metaplasia and organizing exudates were observable at the alveolar space. Some of alveoli collapsed, and some responded to show compensatory emphysema. CONCLUSION: The imaging features of severe pneumonia caused by human infected avian influenza (H7N9) include obvious ground-glass opacity and pulmonary consolidation, mainly at lower lobes and dorsal of lungs, with rapid changes. The cross-analysis of imaging and pathology preliminary can elucidate the pathological mechanisms of ground-glass opacities and pulmonary consolidation of severe pneumonia. Such an intensive study is beneficial to prompt clinicians to observe and evaluate the progress of the disease. In addition, it is also in favor of managing the symptoms and reducing the mortality rate.

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. RESULTS: We present a novel algorithm that produces accurate correction results with much less memory compared with previous solutions. The algorithm, named BLoom-filter-based Error correction Solution for high-throughput Sequencing reads (BLESS), uses a single minimum-sized Bloom filter, and is also able to tolerate a higher false-positive rate, thus allowing us to correct errors with a 40× memory usage reduction on average compared with previous methods. Meanwhile, BLESS can extend reads like DNA assemblers to correct errors at the end of reads. Evaluations using real and simulated reads showed that BLESS could generate more accurate results than existing solutions. After errors were corrected using BLESS, 69% of initially unaligned reads could be aligned correctly. Additionally, de novo assembly results became 50% longer with 66% fewer assembly errors. AVAILABILITY AND IMPLEMENTATION: Freely available at http://sourceforge.net/p/bless-ec CONTACT: dchen@illinois.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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. RESULTS: We have developed a novel de novo assembly framework, called Tiger, which adapts to available computing resources by iteratively decomposing the assembly problem into sub-problems. Our method is also flexible to embed different assemblers for various types of target genomes. Using the sequence data from a human chromosome, our results show that Tiger can achieve much better NG50s, better genome coverage, and slightly higher errors, as compared to Velvet and SOAPdenovo, using modest amount of memory that are available in commodity computers today. CONCLUSIONS: Most state-of-the-art assemblers that can achieve relatively high assembly quality need excessive amount of computing resource (in particular, memory) that is not available to most researchers to achieve high quality results. Tiger provides the only known viable path to utilize NGS de novo assemblers that require more memory than that is present in available computers. Evaluation results demonstrate the feasibility of getting better quality results with low memory footprint and the scalability of using distributed commodity computers.

[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. One group of animals were killed randomly at 1, 3 and 6 months after operation to evaluate the material biological compatibility using anatomic, X-ray examination, histological and ECT methods. RESULTS: The histological photographs showed that Sr-HA caused little infection around implanted area and, almost was not repulsed by hosts. With the degradation of biomaterial, there was more apparent new bone growth in the area around Sr-HA than that around HA and some ossification can be found in soft tissue nearby. Also a tight osteointegrity was gradually got after the operation, according to the results of X-ray and, the border between Sr-HA and bone was hardly discovered at the 6th month after the operation. A more obvious nuclide assembling was observed at the side of Sr-HA by ECT images. With the biodegradation of Sr-HA, more new bone was intruded into the spare space of the biomaterial. CONCLUSION: Sr-HA has better biocompatibility and higher biodegradation than that of pure HA. It holds an excellent osteoinductivity and fair osteoconductivity to some degree too. So a more satisfying effect of bone defect rehabilitation was gained with the increasing new bone depositing in the free space of the material, when it degraded gradually.