De novo diploid genome assembly using long noisy reads.

The high sequencing error rate has impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to generate high-quality phased assemblies using long noisy reads. Here, we present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads. We design a haplotype-aware error correction method that can retain heterozygote alleles while correcting sequencing errors. We combine a corrected read SNP caller and a raw read SNP caller to further improve the identification of inconsistent overlaps in the string graph. We use a grouping method to assign reads to different haplotype groups. PECAT efficiently assembles diploid genomes using Nanopore R9, PacBio CLR or Nanopore R10 reads only. PECAT generates more contiguous haplotype-specific contigs compared to other assemblers. Especially, PECAT achieves nearly haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore R9 reads and phase block NG50 with 59.4/58.0 Mb for HG002 using Nanopore R10 reads.

Causal relationship between the gut microbiome and basal cell carcinoma, melanoma skin cancer, ease of skin tanning: evidence from three two-sample mendelian randomisation studies.

Objectives: The present study used publicly available genome-wide association study (GWAS) summary data to perform three two-sample Mendelian randomization (MR) studies, aiming to examine the causal links between gut microbiome and BCC, melanoma skin cancer, ease of skin tanning. Methods: SNPs associated with exposures to basal cell carcinoma, melanoma skin cancer and ease of skin tanning from the genome-wide association study data of UK Biobank and MRC-IEU (MRC Integrative Epidemiology Unit), and the meta-analysis data from Biobank and MRC-IEU were used as instrumental variables (IVs). The casual estimates were assessed with a two-sample Mendelian randomisation test using the inverse-variance-weighted (IVW) method, Wald ratio, MR-Egger method, maximum likelihood, weighted median, simple mode, and weighted mode. Results: After the application of MR analysis, diffirent effects of multiple groups of gut microbiota was observed for BCC, melanoma skin cancer and ease of skin tanning. The relationships between the gut microbiome and BCC, melanoma skin cancer, ease of skin tanning were supported by a suite of sensitivity analyses, with no statistical evidence of instrument heterogeneity or horizontal pleiotropy. Further investigation is required to explore the relationship between between the gut microbiome and BCC, melanoma skin cancer, ease of skin tanning. Conclusion: Our study initially identified potential causal roles between the gut microbiome and BCC, melanoma skin cancer, ease of skin tanning, and highlighted the role of gut microbiome in the progression of basal cell carcinoma, melanoma skin cancer, ease of skin tanning.

Efficacy of probiotics or synbiotics in critically ill patients: A systematic review and meta-analysis.

BACKGROUND: This latest systematic review and meta-analysis aim to examine the effects of probiotic and synbiotic supplementation in critically ill patients. METHODS: Relevant articles were retrieved from PubMed, Embase, the Cochrane Database, and the Web of Science. The primary output measure was the incident of ventilator-associated pneumonia, and the secondary outputs were diarrhea, Clostridium diffusion infection (CDI), incident of sepsis, incident of hospital acquired pneumonia, duration of mechanical exploitation, ICU mortality rate, length of ICU stay, in hospital mortality, and length of hospital stay. Data were pooled and expressed as Relative Risk(RR) and Standardized Mean Difference (SMD) with a 95 % confidence interval (CI). RESULTS: 33 studies were included in this systematic review and meta-analysis, with 4065 patients who received probiotics or synbiotics (treatment group) and 3821 patients who received standard care or placebo (control group). The pooled data from all included studies demonstrated that the treatment group has significantly reduced incidence of ventilation-associated pneumonia (VAP) (RR = 0.80; 95 % CI: 0.67-0.96; p = 0.021, I2 = 52.5 %) and sepsis (RR = 0.97; 95 % CI: 0.66-1.42; p = 0.032, I2 = 54.4 %), As well as significantly increased duration of mechanical exploitation (SMD = -0.47; 95 % CI: -0.74-0.20, p = 0.012, I2 = 63.4 %), ICU mobility (RR = 0.95; 95 % CI: 0.71-1.27; p = 0.004, I2 = 62.8 %), length of ICU stay (SMD = -0.29; 95 % CI: -0.58-0.01; p = 0.000, I2 = 82.3 %) and length of hospital stay (SMD = -0.33; 95 % CI: -0.57-0.08, p = 0.000, I2 = 74.2 %) than the control group. There were no significant differences in diarrhea, CDI, incidence of hospital acquired pneumonia, and in hospital mortality between the two groups. CONCLUSION: Our meta-analysis showed that probiotic and synbiotic supplements are beneficial for critically ill patients as they significantly reduce the incidence of ventilator associated pneumonia and sepsis, as well as the duration of mechanical exploitation, length of hospital stay, length of ICU stay, and ICU mortality. However, this intervention has minimal impact on diarrhea, CDI, incidence of hospital acquired pneumonia, and in hospital mortality in critically ill patients.

Development and validation of a nomogram to predict hypothermia in adult burn patients during escharectomy under general anesthesia.

BACKGROUND: It is very common for burn patients to have hypothermia during escharectomy under general anesthesia, which increases the blood transfusion demand of burn patients, and may lead to blood coagulation disorder or even increase the mortality of patients. It is important to predict the occurrence of hypothermia in advance, but we lack a prognostic prediction model. Our study aimed to develop a nomogram to predict the incidence of hypothermia in adult burn patients undergoing escharectomy under general anesthesia to intervention the hazards associated with hypothermia early. METHODS: This retrospective study included 978 adult burn patients who underwent simple escharectomy under general anesthesia during hospitalization between January 2017 and December 2022, they were further divided into a training cohort and a validation cohort. The clinical data were recorded in electronic medical record system and a self-made collection table of intraoperative hypothermia. The preliminary predictive factors for hypothermia which undergoing simple escharectomy under general anesthesia in burn patients were determined using least absolute shrinkage and selection operator (LASSO) at first, then the final predictive factors determined using binary logistic regression analyses and a nomogram to predict the occurrence of hypothermia was established. The index of concordance(C-index), calibration curves, receiver operating characteristic (ROC) curve, and decision curve analysis (DCA) were used to evaluate the performance of the model. RESULTS: A total of 211 patients with hypothermia and 767 patients without hypothermia were selected. Least absolute shrinkage and selection operator regression analysis and binary logistic regression results concluded that burn index, urinary volume, blood transfusion volume and irrigation volume were significantly associated with hypothermia in burn patients undergoing escharectomy under general anesthesia. The nomogram based on these four variables had good predictive efficiency for hypothermia in adult burn patients during escharectomy under general anesthesia, the C-index in the training cohort was 0.903, areas under the receiver operating characteristic curves (AUROC) of for the training cohort (95 % CI 0.877-0.920) and 0.875 for the validation cohort (95 % CI 0.852-0.897) indicated satisfactory discriminative ability of the nomogram, and the calibration curves for the training cohort and the validation cohort also fit as well, indicating that the nomogram had good clinical application value. CONCLUSIONS: Hypothermia in burn patients during escharectomy under general anesthesia is associated with burn index, urinary volume, blood transfusion volume and irrigation volume. We successfully developed a practical nomogram to accurately predict hypothermia, which is a practical method helping clinicians rapidly and conveniently diagnose and guide the treatment of hypothermia in burn patients during escharectomy under general anesthesia.

compleasm: a faster and more accurate reimplementation of BUSCO.

MOTIVATION: Evaluating the gene completeness is critical to measuring the quality of a genome assembly. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. Benchmarking Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing the completeness of genome assembly by testing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, BUSCO is slow particularly for large genome assemblies. It is cumbersome to apply BUSCO to a large number of assemblies. RESULTS: Here, we present compleasm, an efficient tool for assessing the completeness of genome assemblies. Compleasm utilizes the miniprot protein-to-genome aligner and the conserved orthologous genes from BUSCO. It is 14 times faster than BUSCO for human assemblies and reports a more accurate completeness of 99.6% than BUSCO's 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13. AVAILABILITY AND IMPLEMENTATION: https://github.com/huangnengCSU/compleasm.

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing.

Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence polymerase-chain-reaction treated and M.SssI-methyltransferase treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10 Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 Area Under the Curve on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5-methylcytosines.

Psychological status on informal carers for stroke survivors at various phases: a cohort study in China.

Background: In China, the risk of stroke is higher than that in developed countries such as Europe and North America. Informal caregivers play a major role in providing support to stroke survivors. Currently, only limited studies on changes in psychological state of the caregivers at different stages of stroke have been published. Purpose: To investigate the stress and psychological state of informal caregivers of stroke patients in different periods and to explore the factors that affect their states. Methods: 202 informal caregivers of stroke patients were selected in a 3a-grade hospital in Chengdu, Sichuan. Follow-up was conducted by face-to-face interviews, telephone calls, or home visits on days 3, 2 months, and 1 year after onset. We investigated the basic information about the caregivers, including their anxiety, depression and social support conditions. We analyzed the pressure and psychological conditions of informal caregivers at different stages of stroke and analyzed its influencing factors. The data were displayed by the number and percentage of the cases; the continuous variables were described by means and standard deviation. In addition, the data were compared by Pearson correlation analysis and logistic regression analysis. Results: (1) Within 3 days after the onset of stroke, the informal caregivers had the highest stress, the most severe anxiety and depression, the heaviest burden, and the lowest score of medical-social support. Over time, the pressure and burden of the caregivers are gradually decreasing, anxiety and depression are increasing, and social support is also increasing. (2) The stress and psychological status of informal stroke caregivers are affected by multiple factors, including the caregiver's age, relationship with the patient, patient's age, and patient's physical conditions. Conclusion: The stress and psychological status of informal caregivers varied in the different stages of stroke, and they were affected by several factors. Medical staff should pay attention to informal caregivers while providing care for patients. Relevant interventions may be developed based on the results to improve the health of informal caregivers and thus to promote the health of patients.

miniBUSCO: a faster and more accurate reimplementation of BUSCO.

Motivation: Assembly completeness evaluation of genome assembly is a critical assessment of the accuracy and reliability of genomic data. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. BUSCO is one of the most widely used tools for assessing the completeness of genome assembly by comparing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, the runtime of BUSCO can be long, particularly for some large genome assemblies. It is a challenge for researchers to quickly iterate the genome assemblies or analyze a large number of assemblies. Results: Here, we present miniBUSCO, an efficient tool for assessing the completeness of genome assemblies. miniBUSCO utilizes the protein-to-genome aligner miniprot and the datasets of conserved orthologous genes from BUSCO. Our evaluation of the real human assembly indicates that miniBUSCO achieves a 14-fold speedup over BUSCO. Furthermore, miniBUSCO reports a more accurate completeness of 99.6% than BUSCO's completeness of 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13. Availability: https://github.com/huangnengCSU/minibusco . Contact: hli@ds.dfci.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online.

NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data.

MOTIVATION: Oxford Nanopore sequencing has great potential and advantages in population-scale studies. Due to the cost of sequencing, the depth of whole-genome sequencing for per individual sample must be small. However, the existing single nucleotide polymorphism (SNP) callers are aimed at high-coverage Nanopore sequencing reads. Detecting the SNP variants on low-coverage Nanopore sequencing data is still a challenging problem. RESULTS: We developed a novel deep learning-based SNP calling method, NanoSNP, to identify the SNP sites (excluding short indels) based on low-coverage Nanopore sequencing reads. In this method, we design a multi-step, multi-scale and haplotype-aware SNP detection pipeline. First, the pileup model in NanoSNP utilizes the naive pileup feature to predict a subset of SNP sites with a Bi-long short-term memory (LSTM) network. These SNP sites are phased and used to divide the low-coverage Nanopore reads into different haplotypes. Finally, the long-range haplotype feature and short-range pileup feature are extracted from each haplotype. The haplotype model combines two features and predicts the genotype for the candidate site using a Bi-LSTM network. To evaluate the performance of NanoSNP, we compared NanoSNP with Clair, Clair3, Pepper-DeepVariant and NanoCaller on the low-coverage (∼16×) Nanopore sequencing reads. We also performed cross-genome testing on six human genomes HG002-HG007, respectively. Comprehensive experiments demonstrate that NanoSNP outperforms Clair, Pepper-DeepVariant and NanoCaller in identifying SNPs on low-coverage Nanopore sequencing data, including the difficult-to-map regions and major histocompatibility complex regions in the human genome. NanoSNP is comparable to Clair3 when the coverage exceeds 16×. AVAILABILITY AND IMPLEMENTATION: https://github.com/huangnengCSU/NanoSNP.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Use of Composite Acellular Dermal Matrix-Ultrathin Split-Thickness Skin in Hand Hot-Crush Injuries: A One-Step Grafting Procedure.

Background: Hot-crush injuries to the hands can be devastating, and early debridement and coverage with skin autograft remains the golden standard of wound treatment. However, this type of treatment is not feasible or unlikely to succeed due to limited donor sites and wound characteristics of hot-crush injuries on hands. Thus, the composite grafting of acellular dermal matrix (ADM) and split-thickness skin graft (STSG) as a novel alternative method has been attempted. In this series, the results are presented to demonstrate the feasibility and effectiveness of the use of one-stage procedure for early reconstruction in hand hot-crush injuries. Methods: All consecutive patients with hand hot-crush injuries, who underwent one-stage procedure of ADM and ultrathin STSG for soft tissue coverage at our institution from December 2018 to November 2019, were retrospectively analyzed. Wound dressings were opened on 7 days after operation to examine graft survival and complications. Patients were followed up for at least 9 months to evaluate their hand profiles. Results: Samples of 14 patients with a total of 23 wounds were involved in the study. Thirteen of the 23 third-fourth-degree wounds had varying degrees of tendon exposure. On 7 days postoperation, the composite grafts survived in 12 patients with minimal focal graft losses and liquefaction and necrosis in 2 patients, which achieved successful healing following new coverage of ultrathin STSG. All the wounds healed with hospital stays ranging from 9 days to 32 days (median: 24.5 days). At the final follow-up (from 9 months to 20 months), all patients achieved excellent or good total active motion grade and good scar quality (Vancouver scar scale scored 1-3) with no revision surgery. Conclusions: One-stage composite grafting of ADM and ultrathin STSG is a reliable alternative for early reconstruction in hand hot-crush injuries, which delivers good functional outcomes and a good cosmetic appearance.

Fec: a fast error correction method based on two-rounds overlapping and caching.

The third-generation sequencing technology has advanced genome analysis with long-read length, but the reads need error correction due to the high error rate. Error correction is a time-consuming process especially when the sequencing coverage is high. Generally, for a pair of overlapping reads A and B, the existing error correction methods perform a base-level alignment from B to A when correcting the read A. And another base-level alignment from A to B is performed when correcting the read B. However, based on our observation, the base-level alignment information can be reused. In this article, we present a fast error correction tool Fec, using two-rounds overlapping and caching. Fec can be used independently or as an error correction step in an assembly pipeline. In the first round, Fec uses a large window size (20) to quickly find enough overlaps to correct most of the reads. In the second round, a small window size (5) is used to find more overlaps for the reads with insufficient overlaps in the first round. When performing base-level alignment, Fec searches the cache first. If the alignment exists in the cache, Fec takes this alignment out and deduces the second alignment from it. Otherwise, Fec performs base-level alignment and stores the alignment in the cache. We test Fec on nine datasets, and the results show that Fec has 1.24-38.56 times speed-up compared to MECAT, CANU and MINICNS on five PacBio datasets and 1.16-27.8 times speed-up compared to NECAT and CANU on four nanopore datasets. AVAILABILITY AND IMPLEMENTATION: Fec is available at https://github.com/zhangjuncsu/Fec. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The Trend of Burn Injury Patients in Ningbo between 2012 and 2021: A Clinical Study.

Objective: This study was designed to understand the local changes of burn injuries in recent 10 years, so as to provide reliable reference data and viewpoints for prevention and vigilance of local burn injuries. Methods: In this study, 184 patients with a burn injury admitted to our hospital from 2012 to 2021 were enrolled and analyzed retrospectively. According to their information in the electronic database, the number of patients with burn injuries and the location of each disaster each year were analyzed, and the age, sex, hospital stay and hospitalization expense of each patient were collected. With 5 years as the boundary, the patients were divided into a 2012-2016 group and a 2017-2021 group and the differences of the two groups in the abovementioned aspects were compared. Results: During 2012-2021, the incidence rate of burn injuries in men was higher than that in women and workplaces had a higher burn injury rate than residents' homes. Compared with the period of 2012-2016, the number of fires or explosions and the number of patients with a burn injury during 2017-2028 both increased, but there was no significant change in disaster location, male-female ratio, age, average hospital stay, and average hospitalization expense. Conclusion: In the face of the increasing prevalence of burn injuries, we should strengthen fire-fighting knowledge-related education and fire prevention management and actively explore post-burn injury treatment strategies and potential treatment targets to promote the development of burn injury management and treatment strategies.

SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism.

Highly portable Oxford Nanopore sequencer producing long reads in real-time at low cost has made many breakthroughs in genomics studies. However, a major limitation of nanopore sequencing is its high errors when deciphering DNA sequences from noisy and complex raw data. In this paper, we developed an end-to-end basecaller, SACall, based on convolution layers, transformer self-attention layers and a CTC decoder. In SACall, the convolution layers are used to downsample the signals and capture the local patterns. To achieve the contextual relevance of signals, self-attention layers are adopted to calculate the similarity of the signals at any two positions in the raw signal sequence. Finally, the CTC decoder generates the DNA sequence by a beam search algorithm. We use a benchmark consisting of nine isolated genomes to test the quality of different basecallers including SACall, Albacore, and Guppy. The performances of basecallers are evaluated from the perspective of read accuracy, assembly quality, and consensus accuracy. Among most of the genomes in the test benchmark, the reads basecalled by SACall have fewer errors than the reads basecalled by other basecallers. When assembling the basecalled reads of each genome, the assembly from SACall basecalled reads achieves a higher assembly identity. In addition, there are fewer errors in the polished assembly from reads basecalled by SACall compared to those basecalled by Albacore and Guppy. In general, SACall outperforms the Nanopore official basecallers Albacore and Guppy in the benchmark. Moreover, SACall is an open-source and freely available basecaller, which gives a chance for researchers to train their own basecalling models on specific data and basecall Nanopore reads.

BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer.

Long-read sequencing technology enables significant progress in de novo genome assembly. However, the high error rate and the wide error distribution of raw reads result in a large number of errors in the assembly. Polishing is a procedure to fix errors in the draft assembly and improve the reliability of genomic analysis. However, existing methods treat all the regions of the assembly equally while there are fundamental differences between the error distributions of these regions. How to achieve very high accuracy in genome assembly is still a challenging problem. Motivated by the uneven errors in different regions of the assembly, we propose a novel polishing workflow named BlockPolish. In this method, we divide contigs into blocks with low complexity and high complexity according to statistics of aligned nucleotide bases. Multiple sequence alignment is applied to realign raw reads in complex blocks and optimize the alignment result. Due to the different distributions of error rates in trivial and complex blocks, two multitask bidirectional Long short-term memory (LSTM) networks are proposed to predict the consensus sequences. In the whole-genome assemblies of NA12878 assembled by Wtdbg2 and Flye using Nanopore data, BlockPolish has a higher polishing accuracy than other state-of-the-arts including Racon, Medaka and MarginPolish & HELEN. In all assemblies, errors are predominantly indels and BlockPolish has a good performance in correcting them. In addition to the Nanopore assemblies, we further demonstrate that BlockPolish can also reduce the errors in the PacBio assemblies. The source code of BlockPolish is freely available on Github (https://github.com/huangnengCSU/BlockPolish).

Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning.

In plants, cytosine DNA methylations (5mCs) can happen in three sequence contexts as CpG, CHG, and CHH (where H = A, C, or T), which play different roles in the regulation of biological processes. Although long Nanopore reads are advantageous in the detection of 5mCs comparing to short-read bisulfite sequencing, existing methods can only detect 5mCs in the CpG context, which limits their application in plants. Here, we develop DeepSignal-plant, a deep learning tool to detect genome-wide 5mCs of all three contexts in plants from Nanopore reads. We sequence Arabidopsis thaliana and Oryza sativa using both Nanopore and bisulfite sequencing. We develop a denoising process for training models, which enables DeepSignal-plant to achieve high correlations with bisulfite sequencing for 5mC detection in all three contexts. Furthermore, DeepSignal-plant can profile more 5mC sites, which will help to provide a more complete understanding of epigenetic mechanisms of different biological processes.

NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks.

MOTIVATION: Oxford Nanopore sequencing producing long reads at low cost has made many breakthroughs in genomics studies. However, the large number of errors in Nanopore genome assembly affect the accuracy of genome analysis. Polishing is a procedure to correct the errors in genome assembly and can improve the reliability of the downstream analysis. However, the performances of the existing polishing methods are still not satisfactory. RESULTS: We developed a novel polishing method, NeuralPolish, to correct the errors in assemblies based on alignment matrix construction and orthogonal Bi-GRU networks. In this method, we designed an alignment feature matrix for representing read-to-assembly alignment. Each row of the matrix represents a read, and each column represents the aligned bases at each position of the contig. In the network architecture, a bi-directional GRU network is used to extract the sequence information inside each read by processing the alignment matrix row by row. After that, the feature matrix is processed by another bi-directional GRU network column by column to calculate the probability distribution. Finally, a CTC decoder generates a polished sequence with a greedy algorithm. We used five real datasets and three assembly tools including Wtdbg2, Flye and Canu for testing, and compared the results of different polishing methods including NeuralPolish, Racon, MarginPolish, HELEN and Medaka. Comprehensive experiments demonstrate that NeuralPolish achieves more accurate assembly with fewer errors than other polishing methods and can improve the accuracy of assembly obtained by different assemblers. AVAILABILITY AND IMPLEMENTATION: https://github.com/huangnengCSU/NeuralPolish.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MultiNanopolish: refined grouping method for reducing redundant calculations in Nanopolish.

MOTIVATION: Compared with the second-generation sequencing technologies, the third-generation sequencing technologies allows us to obtain longer reads (average ∼10 kbps, maximum 900 kbps), but brings a higher error rate (∼15% error rate). Nanopolish is a variant and methylation detection tool based on hidden Markov model, which uses Oxford Nanopore sequencing data for signal-level analysis. Nanopolish can greatly improve the accuracy of assembly, whereas it is limited by long running time since most executive parts of Nanopolish is a serial and computationally expensive process. RESULTS: In this paper, we present an effective polishing tool, Multithreading Nanopolish (MultiNanopolish), which decomposes the whole process of iterative calculation in Nanopolish into small independent calculation tasks, making it possible to run this process in the parallel mode. Experimental results show that MultiNanopolish reduces running time by 50% with read-uncorrected assembler (Miniasm) and 20% with read-corrected assembler (Canu and Flye) based on 40 threads mode compared to the original Nanopolish. AVAILABILITY AND IMPLEMENTATION: MultiNanopolish is available at GitHub: https://github.com/BioinformaticsCSU/MultiNanopolish. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

CLPred: a sequence-based protein crystallization predictor using BLSTM neural network.

MOTIVATION: Determining the structures of proteins is a critical step to understand their biological functions. Crystallography-based X-ray diffraction technique is the main method for experimental protein structure determination. However, the underlying crystallization process, which needs multiple time-consuming and costly experimental steps, has a high attrition rate. To overcome this issue, a series of in silico methods have been developed with the primary aim of selecting the protein sequences that are promising to be crystallized. However, the predictive performance of the current methods is modest. RESULTS: We propose a deep learning model, so-called CLPred, which uses a bidirectional recurrent neural network with long short-term memory (BLSTM) to capture the long-range interaction patterns between k-mers amino acids to predict protein crystallizability. Using sequence only information, CLPred outperforms the existing deep-learning predictors and a vast majority of sequence-based diffraction-quality crystals predictors on three independent test sets. The results highlight the effectiveness of BLSTM in capturing non-local, long-range inter-peptide interaction patterns to distinguish proteins that can result in diffraction-quality crystals from those that cannot. CLPred has been steadily improved over the previous window-based neural networks, which is able to predict crystallization propensity with high accuracy. CLPred can also be improved significantly if it incorporates additional features from pre-extracted evolutional, structural and physicochemical characteristics. The correctness of CLPred predictions is further validated by the case studies of Sox transcription factor family member proteins and Zika virus non-structural proteins. AVAILABILITY AND IMPLEMENTATION: https://github.com/xuanwenjing/CLPred.

Loss-of-Function NUBPL Mutation May Link Parkinson's Disease to Recessive Complex I Deficiency.

In an unbiased genome-wide screen for copy number variants (CNVs) on a cohort of Parkinson's disease (PD) patients, we identified in one patient a complex chromosomal rearrangement involving the nucleotide binding protein-like (NUBPL) gene on chromosome 14q12. We noted that mutations in the NUBPL gene had been reported as causing autosomal recessive (AR) mitochondrial Complex I (CI) deficiency in children. The precise breakpoints of the rearrangement in our PD case were found to be identical to those described in a patient with AR CI deficiency who also harbored a second pathogenic mutation in NUBPL. Mitochondrial dysfunction has long been considered a strong contributor to PD, and there is substantial evidence that decreased CI activity plays a central role in PD pathogenesis. We hypothesize that pathogenic NUBPL variants may increase the risk for PD analogous to variants in the glucosylceramidase beta (GBA) gene that increase the risk of developing PD in heterozygous carriers.

Effects of epinephrine on heart rate variability and cytokines in a rat sepsis model.

Catecholamines have both anti-inflammatory and vasoactive properties. A decreased cardiac response to catecholamines has been associated with a high risk of death in sepsis and septic shock. The aim of this study was to investigate the effects of epinephrine (EPI) on heart rate variability (HRV) and autonomic balance, as well as cytokine levels, in a rat sepsis model. Thirty-six male Sprague-Dawley rats were assigned to 4 experimental groups and 2 control groups of 6 rats each. The rats in the experimental groups were inoculated with a lipopolysaccharide (LPS, endotoxin) to establish a sepsis model. Group A received only LPS; group B received LPS, antecedent EPI and the nonselective ß-blocker propranolol; group C received LPS and antecedent EPI; and group D received LPS, antecedent EPI and the selective ß1-blocker esmolol. One control group received EPI and the other received saline placebo. Heart rate variability (HRV) was analyzed and tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and interleukin-1ß (IL-1ß) levels were measured. Measurements were carried out at baseline, at 0 hour after EPI infusion, and at 0.5, 2, and 4 hours after LPS inoculation. There were significant differences in HRV and cytokine levels between the groups, indicating that LPS infusion caused autonomic imbalance. Antecedent EPI significantly decreased the level of TNF-α in group C compared with group A in which TNF-α level peaked at 2 hours and then declined. Propranolol (group B) but not esmolol (group D) administration resulted in elevated TNF-α levels, comparable to those observed in group A. In conclusion, antecedent administration of EPI in a rat sepsis model inhibits the production of TNF-α possibly via the ß2-adrenoceptor.