A deep catalogue of protein-coding variation in 983,578 individuals.

Rare coding variants that substantially affect function provide insights into the biology of a gene1-3. However, ascertaining the frequency of such variants requires large sample sizes4-8. Here we present a catalogue of human protein-coding variation, derived from exome sequencing of 983,578 individuals across diverse populations. In total, 23% of the Regeneron Genetics Center Million Exome (RGC-ME) data come from individuals of African, East Asian, Indigenous American, Middle Eastern and South Asian ancestry. The catalogue includes more than 10.4 million missense and 1.1 million predicted loss-of-function (pLOF) variants. We identify individuals with rare biallelic pLOF variants in 4,848 genes, 1,751 of which have not been previously reported. From precise quantitative estimates of selection against heterozygous loss of function (LOF), we identify 3,988 LOF-intolerant genes, including 86 that were previously assessed as tolerant and 1,153 that lack established disease annotation. We also define regions of missense depletion at high resolution. Notably, 1,482 genes have regions that are depleted of missense variants despite being tolerant of pLOF variants. Finally, we estimate that 3% of individuals have a clinically actionable genetic variant, and that 11,773 variants reported in ClinVar with unknown significance are likely to be deleterious cryptic splice sites. To facilitate variant interpretation and genetics-informed precision medicine, we make this resource of coding variation from the RGC-ME dataset publicly accessible through a variant allele frequency browser.

Spatial Imaging and Control of Dark Excitons in Monolayer Transition Metal Dichalcogenides.

Dark excitons play a vital role in exciton condensation and optical properties of monolayer transition metal dichalcogenides (MTMDs). Previous literature mainly focuses on the detection of the energy of the dark exciton, while spatial detection and control are equally important but are less studied. Here we report that for MTMD embedded in a semiconductor microcavity and under a uniform in-plane magnetic field the spatial distribution of the dark exciton can be probed by measuring that of the cavity photon for small exciton-exciton interaction energy. Further, we propose to realize the anomalous exciton Hall effect by exploiting spatially inhomogeneous coupling of the bright and dark excitons under a Gaussian excitation beam. This effect occurs regardless of the exciton-exciton interaction, which will strengthen the diffusion of excitons in the excitation region. These results provide an improved understanding of the excitons in MTMDs, thereby facilitating their potential practical applications.

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.

Emerging ultra-low coverage single-cell DNA sequencing (scDNA-seq) technologies have enabled high resolution evolutionary studies of copy number aberrations (CNAs) within tumors. While these sequencing technologies are well suited for identifying CNAs due to the uniformity of sequencing coverage, the sparsity of coverage poses challenges for the study of single-nucleotide variants (SNVs). In order to maximize the utility of increasingly available ultra-low coverage scDNA-seq data and obtain a comprehensive understanding of tumor evolution, it is important to also analyze the evolution of SNVs from the same set of tumor cells. We present Phertilizer, a method to infer a clonal tree from ultra-low coverage scDNA-seq data of a tumor. Based on a probabilistic model, our method recursively partitions the data by identifying key evolutionary events in the history of the tumor. We demonstrate the performance of Phertilizer on simulated data as well as on two real datasets, finding that Phertilizer effectively utilizes the copy-number signal inherent in the data to more accurately uncover clonal structure and genotypes compared to previous methods.

Evaluation of breast cancer malignancy, prognostic factors and molecular subtypes using a continuous-time random-walk MR diffusion model.

PURPOSE: To assess the continuous-time random-walk (CTRW) model's diagnostic value in breast lesions and to explore the associations between the CTRW parameters and breast cancer pathologic factors. METHOD: This retrospective study included 85 patients (70 malignant and 18 benign lesions) who underwent 3.0T MRI examinations. Diffusion-weighted images (DWI) were acquired with 16b-values to fit the CTRW model. Three parameters (Dm, α, and ß) derived from CTRW and apparent diffusion coefficient (ADC) from DWI were compared among the benign/malignant lesions, molecular prognostic factors, and molecular subtypes by Mann-Whitney U test. Spearman correlation was used to evaluate the associations between the parameters and prognostic factors. The diagnostic performance was assessed by the area under the receiver operating characteristic curve (AUC) based on the diffusion parameters. RESULTS: All parameters, ADC, Dm, α, and ß were significantly lower in the malignant than benign lesions (P < 0.05). The combination of all the CTRW parameters (Dm, α, and ß) provided the highest AUC (0.833) and the best sensitivity (94.3%) in differentiating malignant status. And the positive status of estrogen receptor (ER) and progesterone receptor (PR) showed significantly lower ß compared with the negative counterparts (P < 0.05). The high Ki-67 expression produced significantly lower Dm and ADC values (P < 0.05). Additionally, combining multiple CTRW parameters improved the performance of diagnosing molecular subtypes of breast cancer. Moreover, Spearman correlations analysis showed that ß produced significant correlations with ER, PR and Ki-67 expression (P < 0.05). CONCLUSIONS: The CTRW parameters could be used as non-invasive quantitative imaging markers to evaluate breast lesions.

A deep catalog of protein-coding variation in 985,830 individuals.

Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.

Improved method for benthic ecosystem health assessment by integrating chemical indexes into multiple biological indicator species-A case study of the Baiyangdian Lake, China.

A comprehensive and scientific assessment of benthic ecosystem health is key to the rational selection of endogenous pollution reduction technologies for lakes. However, current assessments are mainly limited to biological indicators and ignore the actual benthic ecosystem situations, such as the impact of eutrophication and heavy metal pollution, which may lead to the one-sidedness of the evaluation results. In this study, taking Baiyangdian Lake, the largest shallow mesotrophic-eutrophic lake in the North China Plain, as an example, the chemical assessment index and biological integrity index were first combined to estimate the biological conditions, nutritional status and heavy metal pollution of lakes. The indicator system incorporated three biological assessments (benthic index of biotic integrity (B-IBI), submerged aquatic vegetation index of biological integrity (SAV-IBI) and microbial index of biological integrity (M-IBI)) and three chemical assessments (dissolved oxygen (DO), comprehensive trophic level index (TLI) and index of geoaccumulation (Igeo)). Twenty-three attributes of B-IBI, fourteen attributes of SAV-IBI and twelve attributes of M-IBI were screened by range, responsiveness, and redundancy tests to keep the core metrics that were significantly correlated with disturbance gradients or showed strong discriminatory power between reference and impaired sites. The assessment results of B-IBI, SAV-IBI, and M-IBI showed significant differences in the response to anthropogenic activities and seasonal change, among which the submerged plants showed more significant seasonal differences. It is difficult to reach a comprehensive conclusion regarding the benthic ecosystem health status based on a single biological community. In comparison with biological indicators, the score of chemical indicators is relatively low. DO, TLI and Igeo provide an essential supplement for the benthic ecosystem health assessment of lakes with eutrophication and heavy metal pollution problems. Using the new integrated assessment method, the benthic ecosystem health of Baiyangdian Lake was rated as fair, especially the northern parts of the lake adjacent to the inflow mouth of the Fu River, which were in poor condition, indicating that the lake has experienced anthropogenic disturbance, resulting in eutrophication, heavy metal pollution and biological community degradation. Whether it's spring or summer, the integrated assessment method provides a more plausible and comprehensive view of benthic ecosystem health under the pressure of increasing human activities and changing habitat and hydrological conditions, overcoming the narrow perspective and uncertainties of the single-index method. Thus, it can assist lake managers in providing technical support for ecological indication and restoration.

[Kirschner wire retractor-assisted reduction and inverted insertion of elastic nail in the treatment of children's irreducible subradial 1/3 fractures].

OBJECTIVE: To explore the clinical effect of Kirschner wire retractor-assisted reduction and inverted insertion of elastic nail in the treatment of children's irreducible subradial 1/3 fractures. METHODS: A total of 34 children with irreducible subradial 1/3 fractures treated by surgery from August 2016 to December 2020 were retrospective analyzed. Among them, 16 cases underwent Kirschner wire retractor-assisted closed reduction and percutaneous elastic intramedullary nailing with inverted insertion(observation group), 10 males and 6 females, aged from 4 to 10 years old with an average of(6.0±0.4)years;18 cases underwent open reduction and plate internal fixation (control group), 11 males and 7 females, the age from 3 to 10 years with an average of(7.0±0.5) years. The operation time, intraoperative blood loss, hospital stay, incision length, fracture healing time and complications of the two groups were observed and the wrist function was evaluated by Cooney wrist joint score. RESULTS: All patients were followed up for 3-12 years old with an average of (11.40±0.48) months in the observation group and 4-13 months with an average of (11.50±0.39) months in the control group. Bone healing was achieved in all patients, and there was no incision infection in both groups. The operation time, intraoperative blood loss, hospital stay and incision length in observation groups were lower than those of control group (P<0.05). There was no significant difference in the fracture healing time between two groups(P>0.05). There was no significant difference in postoperative healing and recovery of wrist function between groups(P>0.05). CONCLUSION: Compared with open reduction and plate internal fixation, Kirschner wire retractor-assisted reduction and percutaneous elastic intramedullary nail fixation for irreducible subradial radial 1/3 fractures has the advantages of less trauma, shorter operation time, less blood loss, and satisfactory short-term clinical results.

Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses.

Transcription regulatory sequences (TRSs), which occur upstream of structural and accessory genes as well as the 5' end of a coronavirus genome, play a critical role in discontinuous transcription in coronaviruses. We introduce two problems collectively aimed at identifying these regulatory sequences as well as their associated genes. First, we formulate the TRS Identification problem of identifying TRS sites in a coronavirus genome sequence with prescribed gene locations. We introduce CORSID-A, an algorithm that solves this problem to optimality in polynomial time. We demonstrate that CORSID-A outperforms existing motif-based methods in identifying TRS sites in coronaviruses. Second, we demonstrate for the first time how TRS sites can be leveraged to identify gene locations in the coronavirus genome. To that end, we formulate the TRS and Gene Identification problem of simultaneously identifying TRS sites and gene locations in unannotated coronavirus genomes. We introduce CORSID to solve this problem, which includes a web-based visualization tool to explore the space of near-optimal solutions. We show that CORSID outperforms state-of-the-art gene finding methods in coronavirus genomes. Furthermore, we demonstrate that CORSID enables de novo identification of TRS sites and genes in previously unannotated coronavirus genomes. CORSID is the first method to perform accurate and simultaneous identification of TRS sites and genes in coronavirus genomes without the use of any prior information.

A Sternoclavicular Joint-Specific Plate for the Displaced Medial-End Clavicle Fracture.

Objectives: This study aimed to introduce a sternoclavicular joint (SCJ)-specific plate for the treatment of medial-end clavicle fracture and evaluate the clinical and radiological results of this method. Methods: From January 2006 to December 2020, 31 patients with displaced medial-end clavicle fractures were included in this study, with 8 patients with accompanying SCJ dislocation. Abduction and forward elevation of the shoulder, the Visual Analogue Scale (VAS), and the American Shoulder and Elbow Surgeons Score (ASES) were used for evaluation before index surgery and at the latest follow-up. Results: After an average of 98.5 (range, 13 to 171) months, the mean VAS significantly decreased from 6.8 ± 1.0 preoperatively to 0.9 ± 0.8 at the latest follow-up (P < 0.001). The mean ASES score significantly increased from 34.3 ± 7.8 preoperatively to 90.2 ± 4.9 at the latest follow-up (P < 0.001). The mean abduction of the shoulder significantly increased from 72.1 ± 6.6 preoperatively to 169.5 ± 8.5 at the latest follow-up (P < 0.001). The mean forward elevation of the shoulder significantly increased from 97.1 ± 11.0 preoperatively to 163.1 ± 11.5 at the latest follow-up (P < 0.001). The union of all fractures was achieved, and all implants were removed. No loose or breakage of implants was observed. No vascular or nerve damage occurred during the operation. Conclusions: This SCJ-specific plate provided excellent long-term results for the treatment of displaced medial-end clavicle fractures and was an alternative implant for medial-end clavicle fractures with or without small or comminuted medial fragments, especially those associated with SCJ dislocation.

The efficacy and safety of anterior versus posterior approach for the treatment of thoracolumbar burst fractures: a systematic review and meta-analysis.

Background: There has always been controversy about the choice of anterior approach or posterior approach for the surgical approach of thoracolumbar burst fractures (TBFs). The aim of this study was to systematically evaluate the efficacy and safety of anterior and posterior approaches in the treatment of TBFs. Methods: Multiple databases including PubMed, Excerpt Medica Database (Embase), Cochrane Library, and Web of Science (WOS) were used to search for relevant studies, namely full-text articles comparing the anterior versus posterior approach for the treatment of TBFs, which based on population, intervention, control, outcome, and study (PICOS) framework. Review Manager 5.4 was used to assess the effects of the results among selected studies. The risk of bias of the trials was assessed using the Newcastle Ottawa scale (NOS) and the Cochrane Collaboration's tool. Forest plots and funnel plots were also generated for the included articles. Results: Finally, 723 patients were included in 13 studies which satisfied the eligibility criteria, funnel plots and Egger's test showed that there was no significant bias in the publications. There were no differences in terms of length of stay [mean difference (MD): -1.31, (-5.31, 2.69); P=0.52], hospitalization expenses [standardized mean difference (SMD): 1.26, (-0.38, 2.89); P=0.13], and return to work between the anterior approach and posterior approach. However, the posterior approach had the advantages of better Cobb angle correction [MD: 2.06, (0.17, 3.94); P=0.03], shorter operation time [MD: 58.29, (35.39, 81.18); P<0.00001], and lower estimated blood loss [MD: 185.92, (131.76, 240.07); P<0.00001]. Discussion: The posterior approach appeared to be superior to the anterior approach in the treatment of TBFs. However, more high-quality randomized controlled trials should be conducted to confirm the conclusions of this study and guide clinical decision-making.

Jumper enables discontinuous transcript assembly in coronaviruses.

Genes in SARS-CoV-2 and other viruses in the order of Nidovirales are expressed by a process of discontinuous transcription which is distinct from alternative splicing in eukaryotes and is mediated by the viral RNA-dependent RNA polymerase. Here, we introduce the DISCONTINUOUS TRANSCRIPT ASSEMBLYproblem of finding transcripts and their abundances given an alignment of paired-end short reads under a maximum likelihood model that accounts for varying transcript lengths. We show, using simulations, that our method, JUMPER, outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1, SARS-CoV-2 and MERS-CoV samples, we find that JUMPER not only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are supported by subsequent orthogonal analyses. Moreover, application of JUMPER on samples with and without treatment reveals viral drug response at the transcript level. As such, JUMPER enables detailed analyses of Nidovirales transcriptomes under varying conditions.

Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples.

Intra-tumor heterogeneity renders the identification of somatic single-nucleotide variants (SNVs) a challenging problem. In particular, low-frequency SNVs are hard to distinguish from sequencing artifacts. While the increasing availability of multi-sample tumor DNA sequencing data holds the potential for more accurate variant calling, there is a lack of high-sensitivity multi-sample SNV callers that utilize these data. Here we report Moss, a method to identify low-frequency SNVs that recur in multiple sequencing samples from the same tumor. Moss provides any existing single-sample SNV caller the ability to support multiple samples with little additional time overhead. We demonstrate that Moss improves recall while maintaining high precision in a simulated dataset. On multi-sample hepatocellular carcinoma, acute myeloid leukemia and colorectal cancer datasets, Moss identifies new low-frequency variants that meet manual review criteria and are consistent with the tumor's mutational signature profile. In addition, Moss detects the presence of variants in more samples of the same tumor than reported by the single-sample caller. Moss' improved sensitivity in SNV calling will enable more detailed downstream analyses in cancer genomics.

Long-term results for traumatic sternoclavicular joint dislocation treated with a sternoclavicular joint-specific plate.

BACKGROUND: The treatment of traumatic sternoclavicular joint (SCJ) dislocation (SCJD) with internal fixation has been reported with good short-term results, but data on its long-term results are scarce. METHODS: Patients with traumatic SCJD treated with an SCJ-specific plate between January 2003 and January 2018 were evaluated retrospectively. All implants were routinely removed. Data from radiography, the American Shoulder and Elbow Surgeons score, the visual analogue scale and abduction and forward elevation of the shoulder were collected and evaluated before the index surgery, at implant removal and at the latest follow-up. RESULTS: A total of 22 patients were included in this study with a mean follow-up period of 94.8 months. All patients maintained good reduction after the index surgery and implant removal. The visual analogue scale significantly improved from 7.1 ± 1.3 before the index surgery to 0.9 ± 1.0 at implant removal (P < 0.001) and to 1.0 ± 1.1 at the latest follow-up (P < 0.001); the American Shoulder and Elbow Surgeons score significantly improved from 37.9 ± 10.1 to 90.8 ± 7.8 (P < 0.001) and to 86.7 ± 8.6; and both abduction and forward elevation of the shoulder significantly improved at the latest follow-up (P < 0.001). There was no significant difference in the clinical results after implant removal. CONCLUSION: Traumatic SCJD treated with an SCJ-specific plate appeared to be efficient, with satisfactory clinical and radiological results at long-term follow-up.

Fast start-up of PN/A process in a single-stage packed bed and mechanism of nitrogen removal.

The single-stage partial nitritation-anammox (PN/A) process is severely limited by a long start-up time and unstable removal efficiency. In this study, PN/A was developed in 67 days in a novel packed bed equipped with porous bio-carriers by gradually increasing the influent nitrogen loading rate (0.15-0.73 kg-N m-3·d-1) and controlling the dissolved oxygen (< 1.2 mg L-1). An average ammonium nitrogen removal efficiency (ARE) and total nitrogen removal efficiency (TNR) of 87.01 and 72.41%, respectively, were obtained. This represents a reliable alternative method of achieving rapid PN/A start-up. The results of 16S rRNA sequencing showed that Proteobacteria and Planctomycetes, with which ammonia-oxidizing bacteria and anammox bacteria were affiliated, accounted for 38.8%, representing the dominant phylum in the system after acclimation. The abundance of Nitrosomonas and Candidatus Brocadia increased by 16 and 1.79%, respectively. The results of metagenomics and metatranscriptomics revealed that the nitrite oxidation process was blocked by the transcriptional suppression of nitrite oxidoreductase and the entire nitrogen metabolism process was dominated by the partial nitritation and anammox process. Moreover, a high abundance of heterotrophic bacteria with potential for nitrogen removal was detected. In the nitrogen cycle, a widespread nitrite-accumulated denitrification helps to form a nitrite loop, which promotes the efficiency of total nitrogen removal. This is crucial for further improving the nitrogen removal mechanism in the PN/A system.

A lectin-based glycomic approach identifies FUT8 as a driver of radioresistance in oesophageal squamous cell carcinoma.

PURPOSE: Radio-resistance is recognized as a main factor in the failure of radiotherapy in oesophageal squamous cell carcinoma (ESCC). Aberrant cell surface glycosylation has been reported to correlate with radio-resistance in different kinds of tumours. However, glycomic alterations and the corresponding enzymes associated with ESCC radio-resistance have not yet been defined. METHODS: Two radioresistant cell lines, EC109R and TE-1R, were established from parental ESCC cell lines EC109 and TE-1 by fractionated irradiation. A lectin microarray was used to screen for altered glycan patterns. RNA-sequencing (RNA-seq) was employed to identify differentially expressed glycosyltransferases. Cell Counting Kit-8, colony formation and flow cytometry assays were used to measure cell viability and radiosensitivity. Expression of glycosyltransferase in ESCC tissues was assessed by immunohistochemistry. In vivo radiosensitivity was analysed using a nude mouse xenograft model. Downstream effectors of the enzyme were verified using a lectin-based pull-down assay combined with mass spectrometry. RESULTS: We found that EC109R and TE-1R cells were more resistant to irradiation than the parental EC109 and TE-1 cells. Using lectin microarrays combined with RNA sequencing, we found that α1, 6-fucosyltransferase (FUT8) was overexpressed in the radioresistant ESCC cell lines. Both gain- and loss-of-function studies confirmed that FUT8 regulates the sensitivity of ESCC cells to irradiation. Importantly, we found that high FUT8 expression was positively linked to radio-resistance and a poor prognosis in ESCC patients who received radiation therapy. Moreover, FUT8 inhibition suppressed the growth and formation of xenograft tumours in nude mice after irradiation. Using a lectin-based pull-down assay and mass spectrometry, we found that CD147 could be glycosylated by FUT8. As expected, inhibition of CD147 partly reversed FUT8-induced radio-resistance in ESCC cells. CONCLUSIONS: Our results indicate that FUT8 functions as a driver of radio-resistance in ESCC by targeting CD147. Therefore, FUT8 may serve as a marker for predicting the response to radiation therapy in patients with ESCC.

Spinless Fulde-Ferrell superfluid in Haldane model with nearest-neighbor interaction.

Fulde-Ferrell (FF) state is an exotic superconducting or superfluid state, characterized by Cooper pairs with a finite center-of-mass momentum, and it has been intensively investigated in spinful systems, but the spin population imbalance is usually necessary. Here we propose a model to realize and modulate the spinless FF superfluid, namely, Haldane model with nearest-neighbor interaction. The FF state appears when the space-inversion and time-reversal symmetries are broken simultaneously, and there exists the first order phase transition. A higher Berezinskii-Kosterlitz-Thouless transition temperature is obtained at larger absolute value of Peierls phase and smaller energy offset of the sublattices. Our proposal provides a feasible option for experimental researchers to detect the FF superfluid.

Improved membrane sequencing batch reactor: effect of carbon and nitrogen volumetric loading rate on dephosphatation.

A lab-scale anaerobic-anoxic-aerobic membrane bioreactor (A2NO-MBR) fed with synthetic wastewater was operated to investigate the impact of influent carbon and nitrogen volumetric loading rate (VLR) on dephosphatation, and the corresponding influent concentration was 100-300 mg L-1 (COD), 24-50 mg L-1 (NH4+-N) and 4.8-6.0 mg L-1 (TP), respectively. The results demonstrated that carbon VLR had a negligible effect on the COD removal with effluent below 50 mg L-1, and high and stable removal capacity for phosphorus were also obtained, regardless of carbon VLR change. Whereas TN removal efficiency was positively correlated with carbon VLR reduction, and lower carbon VLR produced a negative effect on TN removal. In addition, since nitrate served as an electron acceptor for denitrifying phosphorus removal (DPR), a significant effect on nitrogen and phosphorus removal was observed with different nitrogen VLR. The TN and TP removal efficiency was 68.30 ± 1.36%, 70.70 ± 1.23%, 45.19 ± 1.72% and 41.63 ± 3.09%, 98.14 ± 0.53%, 53.34 ± 2.68% with influent nitrogen VLR of 0.024 ± 0.001, 0.034 ± 0.001 and 0.045 ± 0.001 kg-N/(m3 d), respectively. Moreover, bacterial community structure of sludge samples in Run I and V from anaerobic-anoxic-aerobic-SBR (named A2OSBR_1 and A2OSBR_2) and membrane bioreactor (named N-MBR_1 and N-MBR_2) revealed that Candidatus_Accumulibacter was the most dominant genus in A2OSBR_1 (21.50%) and A2OSBR_2 (18.98%). The relative lower carbon VLR favoured the enrichment of Saprospiraceae, which was related with DPR, with the proportion of 9.31% and 14.61% in A2OSBR_1 and A2OSBR_2. Besides, Nitrospira and Nitrosomonas with proportions of 11.14%, 5.38% in N-MBR_1 and 10.72%, 6.77% in N-MBR_2 were observed, which were likely responsible for the nearly complete nitrification.

VEF: a variant filtering tool based on ensemble methods.

MOTIVATION: Variants identified by current genomic analysis pipelines contain many incorrectly called variants. These can be potentially eliminated by applying state-of-the-art filtering tools, such as Variant Quality Score Recalibration (VQSR) or Hard Filtering (HF). However, these methods are very user-dependent and fail to run in some cases. We propose VEF, a variant filtering tool based on decision tree ensemble methods that overcomes the main drawbacks of VQSR and HF. Contrary to these methods, we treat filtering as a supervised learning problem, using variant call data with known 'true' variants, i.e. gold standard, for training. Once trained, VEF can be directly applied to filter the variants contained in a given Variants Call Format (VCF) file (we consider training and testing VCF files generated with the same tools, as we assume they will share feature characteristics). RESULTS: For the analysis, we used whole genome sequencing (WGS) Human datasets for which the gold standards are available. We show on these data that the proposed filtering tool VEF consistently outperforms VQSR and HF. In addition, we show that VEF generalizes well even when some features have missing values, when the training and testing datasets differ in coverage, and when sequencing pipelines other than GATK are used. Finally, since the training needs to be performed only once, there is a significant saving in running time when compared with VQSR (4 versus 50 min approximately for filtering the single nucleotide polymorphisms of a WGS Human sample). AVAILABILITY AND IMPLEMENTATION: Code and scripts available at: github.com/ChuanyiZ/vef. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Performance enhancement by adding ferrous to a combined modified University of Cape Town and post-anoxic/aerobic-membrane bioreactor.

The removal of nutrients in a combined modified University of Cape Town and post-anoxic/aerobic-membrane bioreactor (UCT-A/MBR) was investigated. Denitrifying phosphorus removal (DPR) and nitrate-dependent anaerobic ferrous oxidation (NAFO) were applied to enhance the nutrient removal performances. The results showed that NAFO with the addition of Fe(II) and DPR could promote nitrogen and phosphorus removal. The total nitrogen removal efficiency gradually increased from 71.05 ±â€¯2.00% to 73.84 ±â€¯1.74% and 75.70 ±â€¯1.47% with no Fe(II) addition, addition to the post-anoxic tank, and addition to the anoxic tank, and the total phosphorus removal efficiency increased from 89.37 ±â€¯1.91% to 95.21 ±â€¯0.85% and 96.01 ±â€¯1.10%, respectively. Gene sequencing was conducted, and Saprospiraceae was determined to be the dominant DPR-related bacteria, with its abundance increasing from 16.31% to 22.45% after Fe(II) addition. Additionally, the proportion of the NAFO-related bacteria Azospira increased from 0.58% to 1.91% after Fe(II) addition. The microbial succession caused by the addition of Fe(II) may have resulted in the enhanced removal performance.