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IntroductionThe work was designed to investigate the effect of continuous positive airway pressure (CPAP) on hypertension in obstructive sleep apnea-hypopnea syndrome (OSAHS) patients and to elucidate the underlying mechanisms.Material and methodsWe examined the effect of CPAP on blood pressure and biomarkers reflecting inflammation and oxidative stress, and investigated the correlation between changes in blood pressure and the biomarkers.ResultsCPAP significantly improved clinic, ambulatory and home blood pressure (p < 0.05). The hypotensive effect of CPAP was positively correlated with the decrease of interleukin-6, C-reactive protein, NADPH oxidase and malonaldehyde.ConclusionsCPAP has a significant antihypertensive effect on OSAHS patients, especially nocturnal hypertension, possibly by counteracting inflammation and oxidative stress.

Background To support the implementation of high-throughput pipelines suitable for SARS-CoV-2 sequencing and analysis in a clinical laboratory, we developed an automated sample preparation and analysis workflow. Methods We used the established ARTIC protocol with approximately 400 bp amplicons sequenced on Oxford Nanopore’s MinION. Sequences were analyzed using Nextclade, assigning both a clade and quality score to each sample. Results A total of 2179 samples on twenty-five 96-well plates were sequenced. Plates of purified RNA were processed within 12 h, sequencing required up to 24 h, and analysis of each pooled plate required 1 h. The use of samples with known threshold cycle (Ct) values enabled normalization, acted as a quality control check, and revealed a strong correlation between sample Ct values and successful analysis, with 85% of samples with Ct 30 samples achieving a “good” classification rising by 60% after addition of a post-ARTIC PCR normalization. Serial dilutions of 3 variant of concern samples, diluted from approximately Ct = 16 to approximately Ct = 50, demonstrated successful sequencing to Ct = 37. The sample set contained a median of 24 mutations per sample and a total of 1281 unique mutations with reduced sequence read coverage noted in some regions of some samples. A total of 10 separate strains were observed in the sample set, including 3 variants of concern prevalent in British Columbia in the spring of 2021. Conclusions We demonstrated a robust automated sequencing pipeline that takes advantage of input Ct values to improve reliability.

Supplemental Data

Purpose: Neuroblastoma (NB) is an aggressive tumor of the developing peripheral nervous system that remains difficult to cure in the advanced stages. The poor prognosis for high-risk NB patients is associated with common disease recurrences that fail to respond to available therapies. NB tumor-initiating cells (TICs), isolated from metastases and primary tumors, may escape treatment and contribute to tumor relapse. New therapies that target the TICs may therefore prevent or treat tumor recurrences.Experimental Design: We undertook a system-level characterization of NB TICs to identify potential drug targets against recurrent NB. We used next-generation RNA sequencing and/or human exon arrays to profile the transcriptomes of 11 NB TIC lines from six NB patients, revealing genes that are highly expressed in the TICs compared with normal neural crest-like cells and unrelated cancer tissues. We used gel-free two-dimensional liquid chromatography coupled to shotgun tandem mass spectrometry to confirm the presence of proteins corresponding to the most abundant TIC-enriched transcripts, thereby providing validation to the gene expression result.Results: Our study revealed that genes in the BRCA1 signaling pathway are frequently misexpressed in NB TICs and implicated Aurora B kinase as a potential drug target for NB therapy. Treatment with a selective AURKB inhibitor was cytotoxic to NB TICs but not to the normal neural crest-like cells.Conclusion: This work provides the first high-resolution system-level analysis of the transcriptomes of 11 primary human NB TICs and identifies a set of candidate NB TIC-enriched transcripts for further development as therapeutic targets. Clin Cancer Res; 16(18); 4572–82. ©2010 AACR.

Supplementary Table S3.

Table S5: Data from this study have been submitted to the European Genome-Phenome Archive (EGA) (www.ebi.ac.uk/ega/home) under the study accession number EGAS00001001159. This table provides the accession numbers for each dataset included in this study.

Supplementary Figures S1-S5. Supplementary Tables S1-S5. Figure S1. Comparison of SNV mutation signatures across histological and molecular subtypes. Figure S2. Treatment timelines and radiographic outcomes. Figure S3. Mutation signature stability metrics and comparisons to known signatures. Figure S4. Structural variant mutation sigantures. Figure S5. Comparison of mutation burden between aging-driven and non-aging-driven breast tumours. Table S1. Kruskal-Wallis tests. Table S2. HRDetect prediction test metrics. Table S3. Area under the curve of HRD signatures in platinum response prediction. Table S4. Logistic regression model odds ratios of clinical improvement on platinum. Table S5. Accession IDs of genome datasets submitted to the European Genome-Phenome Archive.

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Supplementary Table S2.

Supplemental Table 1

Purpose:Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions.Experimental Design:Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches.Results:In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1).Conclusions:Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.

Purpose: Recent studies have identified mutation signatures of homologous recombination deficiency (HRD) in over 20% of breast cancers, as well as pancreatic, ovarian, and gastric cancers. There is an urgent need to understand the clinical implications of HRD signatures. Whereas BRCA1/2 mutations confer sensitivity to platinum-based chemotherapies, it is not yet clear whether mutation signatures can independently predict platinum response.Experimental Design: In this observational study, we sequenced tumor whole genomes (100× depth) and matched normals (60×) of 93 advanced-stage breast cancers (33 platinum-treated). We computed a published metric called HRDetect, independently trained to predict BRCA1/2 status, and assessed its capacity to predict outcomes on platinum-based chemotherapies. Clinical endpoints were overall survival (OS), total duration on platinum-based therapy (TDT), and radiographic evidence of clinical improvement (CI).Results: HRDetect predicted BRCA1/2 status with an area under the curve (AUC) of 0.94 and optimal threshold of 0.7. Elevated HRDetect was also significantly associated with CI on platinum-based therapy (AUC = 0.89; P = 0.006) with the same optimal threshold, even after adjusting for BRCA1/2 mutation status and treatment timing. HRDetect scores over 0.7 were associated with a 3-month extended median TDT (P = 0.0003) and 1.3-year extended median OS (P = 0.04).Conclusions: Our findings not only independently validate HRDetect, but also provide the first evidence of its association with platinum response in advanced breast cancer. We demonstrate that HRD mutation signatures may offer clinically relevant information independently of BRCA1/2 mutation status and hope this work will guide the development of clinical trials. Clin Cancer Res; 23(24); 7521–30. ©2017 AACR.

Supplementary Figure 3 from [18F]Fluoromethyl-[1,2-2H4]-Choline: A Novel Radiotracer for Imaging Choline Metabolism in Tumors by Positron Emission Tomography

Supplementary Figure 1 from [18F]Fluoromethyl-[1,2-2H4]-Choline: A Novel Radiotracer for Imaging Choline Metabolism in Tumors by Positron Emission Tomography

Supplementary Figure 2 from [18F]Fluoromethyl-[1,2-2H4]-Choline: A Novel Radiotracer for Imaging Choline Metabolism in Tumors by Positron Emission Tomography

Current radiotracers for positron emission tomography imaging of choline metabolism have poor systemic metabolic stability in vivo. We describe a novel radiotracer, [18F]fluoromethyl-[1,2-2H4]-choline (D4-FCH), that employs deuterium isotope effect to improve metabolic stability. D4-FCH proved more resistant to oxidation than its nondeuterated analogue, [18F]fluoromethylcholine, in plasma, kidneys, liver, and tumor, while retaining phosphorylation potential. Tumor radiotracer levels, a determinant of sensitivity in imaging studies, were improved by deuterium substitution; tumor uptake values expressed as percent injected dose per voxel at 60 min were 7.43 ± 0.47 and 5.50 ± 0.49 for D4-FCH and [18F]fluoromethylcholine, respectively (P = 0.04). D4-FCH was also found to be a useful response biomarker. Treatment with the mitogenic extracellular kinase inhibitor PD0325901 resulted in a reduction in tumor radiotracer uptake that occurred in parallel with reductions in choline kinase A expression. In conclusion, D4-FCH is a very promising metabolically stable radiotracer for imaging choline metabolism in tumors. [Cancer Res 2009;69(19):7721–8]

This study aimed to determine the best fungi to form the algal-bacterial-fungi symbiotic system and identify the optimal conditions for the synchronous processing of biogas slurry and biogas. Chlorella vulgaris (C. vulgaris) and endophytic bacteria (S395-2) isolated from it and four different fungi (Ganoderma lucidum, Pleurotus ostreatus, Pleurotus geesteranus, and Pleurotus corucopiae) were used to form different symbiotic systems. Four different concentrations of GR24 were added to systems to examine the growth characteristics, the content of chlorophyll a (CHL-a), the activity of carbonic anhydrase (CA), the photosynthetic performance, the removal of nutrients, and the biogas purification performance. The results suggested that the growth rate, CA, CHL-a content, and photosynthetic performance of the C. vulgaris-endophytic bacteria-Ganoderma lucidum symbiosis were higher than the other three symbiotic systems when 10-9 M GR24 was added. The highest nutrients/CO2 removal efficiency 78.36 ± 6.98% for chemical oxygen demand (COD), 81.63 ± 7.35% for total nitrogen (TN), 84.05 ± 7.16% for total phosphorus (TP) and 65.18 ± 6.12% for CO2 was obtained under the above optimal conditions. This approach will provide a theoretical basis for the selection and optimization of an algal-bacterial-fungi symbiotic system for biogas slurry and biogas purification.

This paper deals with the problem of determining the position of a single target from time difference of arrival (TDOA) and angle of arrival (AOA) measurements using multitransmitter multireceiver passive radar system with widely separated antennas. A practically motivating scenario where the transmitter and receiver positions are contaminated by errors is addressed. First, the reduction in localization accuracy due to the presence of transmitter and receiver position errors is derived through the Cramér-Rao lower bound (CRLB) analysis. Then, a novel algebraic localization algorithm based on weighted least squares minimization is proposed that takes the transmitter and receiver position errors into consideration to reduce the estimation error. The proposed solution is shown theoretically to reach the CRLB even when the transmitter and receiver positions have errors. Simulation results also verify the theoretical developments and the performance improvement of the proposed solution over existing algorithms.

Natural products are a major source of anticancer agents and play critical roles in anticancer drug development. Inspired by the complexity-to-diversity strategy, novel deoxypodophyllotoxin (DPT) analogues were designed and synthesized. Among them, compound

This letter proposes the use of neural networks to realize the passive localization by signal time difference of arrival (TDOA). In the face of multiple complex targets with radiation sources in a specific area, real-time localization is an urgent problem. In this letter, positions of the known targets from the prior data are obtained and their time difference is calculated, which will be connected as data pairs and input to the neural network trained to obtain a corresponding model. Subsequently, unknown targets can be localized by this network. It is verified that the localization accuracy of the algorithm is reliable and its robustness is higher than that of traditional algorithms. The proposed method also shows that great reduction of operation time depending on the previous network training can complete real-time goals.

In this study, biogas and biogas slurry were simultaneously treated using two symbiotic systems: Chlorella vulgaris-Ganoderma lucidum-S395-2 (endophytic bacteria) and Scenedesmus obliquus-G. lucidum-S395-2. The influence of different mixed illumination (red and blue) intensity ratios on the algal symbionts' extracellular carbonic anhydrase activities was investigated, as well as the rates of microalgal growth and photosynthesis. The treatment performance was simultaneously assessed in terms of the efficiency of organic matter or nutrient removal and the level of CO

In this study, Chlorella vulgaris, Ganoderma lucidum, and endophytic bacteria were co-cultivated with the stimulation of strigolactone analogs GR24 to prepare pellets. During the purification of biogas slurry and biogas, multi-walled carbon nanotubes (MWCNTs) were introduced to enhance the removal efficiencies of nutrients and CO

Photosynthetic and metabolomic performance of Euglena gracilis was examined and compared under autotrophic and mixotrophic conditions. Autotrophic protozoa (AP) obtained greater biomass (about 33% higher) than the mixotrophic protozoa (MP) after 12 days of growth. AP maintained steady photosynthesis, while MP showed a remarkable decrease in photosynthetic efficiency and dropped to an extremely low level at day 12. In MP, low light absorption and photosynthetic electron transport efficiency, and high energy dissipation were reflected by the chlorophyll (chl a) fluorescence (OJIP) of the protozoa. The values of Ψ

Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.

Deep learning unlocks applications with societal impacts, e.g., detecting child exploitation imagery and genomic analy sis of rare diseases. Deployment, however, needs compliance with stringent privacy regulations. Training algorithms that preserve the privacy of training data are in pressing need. Purely cryptographic approaches can protect privacy, but they are still costly, even when they rely on two or more non colluding servers. Seemingly-“trivial” operations in plain text quickly become prohibitively inefficient when a series of them are “crypto-processed,” e.g., (dynamic) quantization for ensuring the intermediate values would not overflow. Slalom, recently proposed by Tramer and Boneh, is the first ` solution that leverages both GPU (for efficient batch compu tation) and a trusted execution environment (TEE) (for min imizing the use of cryptography). Roughly, it works by a lot of pre-computation over known and fixed weights, and hence it only supports private inference. Five related problems for private training are left unaddressed. Goten, our privacy-preserving training and prediction frame work, tackles all five problems simultaneously via our care ful design over the “mismatched” cryptographic and GPU data types (due to the tension between precision and ef ficiency) and our round-optimal GPU-outsourcing protocol (hence minimizing the communication cost between servers). It 1) stochastically trains a low-bitwidth yet accurate model, 2) supports dynamic quantization (a challenge left by Slalom), 3) minimizes the memory-swapping overhead of the memory-limited TEE and its communication with GPU, 4) crypto-protects the (dynamic) model weight from untrusted GPU, and 5) outperforms a pure-TEE system, even without pre-computation (needed by Slalom). As a baseline, we build CaffeScone that secures Caffe using TEE but not GPU; Goten shows a 6.84× speed-up of the whole VGG-11. Goten also outperforms Falcon proposed by Wagh et al., the latest se cure multi-server cryptographic solution, by 132.64× using VGG-11. Lastly, we demonstrate Goten’s efficacy in training models for breast cancer diagnosis over sensitive images. Info-communications Media Development Authority (IMDA) National Research Foundation (NRF) Submitted/Accepted version This research is supported by the National Research Foundation, Singapore under its Strategic Capability Research Centres Funding Initiative.

We present a genome assembly of Caretta caretta (the Loggerhead sea turtle; Chordata, Testudines, Cheloniidae), generated from genomic data from two unrelated females. The genome sequence is 2.13 gigabases in size. The majority of the assembly is scaffolded into 28 chromosomal representations with a remaining 2% of the assembly being excluded from these.

Purpose:Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions.Experimental Design:Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches.Results:In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1).Conclusions:Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.

The practical application of genome-scale technologies to precision oncology research requires flexible tissue processing strategies that can be used to differentially select both tumour and normal cell populations from formalin-fixed, paraffin-embedded tissues. As tumour sequencing scales towards clinical implementation, practical difficulties in scheduling and obtaining fresh tissue biopsies at scale, including blood samples as surrogates for matched 'normal' DNA, have focused attention on the use of formalin-preserved clinical samples collected routinely for diagnostic purposes. In practice, such samples often contain both tumour and normal cells which, if correctly partitioned, could be used to profile both tumour and normal genomes, thus identifying somatic alterations. Here we report a semi-automated method for laser microdissecting entire slide-mounted tissue sections to enrich for cells of interest with sufficient yield for whole genome and transcriptome sequencing. Using this method, we demonstrated enrichment of tumour material from mixed tumour-normal samples by up to 67%. Leveraging new methods that allow for the extraction of high-quality nucleic acids from small amounts of formalin-fixed tissues, we further showed that the method was successful in yielding sequence data of sufficient quality for use in BC Cancer's Personalized OncoGenomics (POG) program. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Vegetation restoration is considered a potentially useful strategy for controlling soil erosion and improving soil organic carbon (SOC) in arid and semiarid ecosystems. However, there is still debate regarding which vegetation restoration type is the best choice. In this study, four vegetation restoration types (i.e., grasslands, shrubs, forests and mixed forests) converted from sloping farmlands were selected to explore the SOC variation among the four types and to investigate which soil factors had the greatest effect on SOC. The results showed while the magnitude of effect differed between vegetation restoration type, all studied systems significantly increased SOC and labile organic carbon contents (p < 0.01), soil nutrients such as total nitrogen (TN) (p < 0.01), available nitrogen (AN) (p < 0.01), total phosphorus (TP) (p < 0.05) and available phosphorus (AP) (p < 0.05), soil enzyme activities such as phosphatase (p < 0.01), soil microbial biomass carbon (MBC) (p < 0.05), and basal respiration (BR) (p < 0.05), but had significant negative correlationswith polyphenol oxidase (p < 0.05). However, the effects of vegetation restoration of farmland converted to natural grasslands, shrubs, forests and mixed forests varied. Among the types studied, the mixed forests had the largest overall positive effects on SOC overall, followed by the natural grasslands. Soil nutrients such as N and P and soil microbial activities were the main factors that affected SOC after vegetation restoration. Mixed forests such as Robinia pseudoacacia and Caragana korshinskii are the best choice for farmland conversion on the central of the Loess Plateau.

A long-time coherent integration could effectively improve the detection ability of radar for maneuvering targets. Nevertheless, the Doppler ambiguity and frequency migration caused by the high speed and acceleration severely degrade the detection performance. In this regard, a novel coherent integration algorithm is proposed, particularly for maneuvering targets with Doppler ambiguity. Specifically, the acceleration is firstly estimated by scaled non-uniform fast Fourier transform (SNuFFT). Then, the scaled periodic discrete Fourier transform (SPDFT), which periodically extends the observable Doppler scope of discrete Fourier transform (DFT), is proposed to estimate the unambiguous Doppler frequency. Finally, the grating lobes are significantly suppressed via product operation, and coherent integration is achieved after phase compensation. To alleviate the computational burden and eliminate the brute force searching procedure, an efficient implementation based on chirp-z transform (CZT) is also derived. Analysis shows that the proposed algorithm achieves a good balance between computational complexity and anti-noise performance. Extensive simulations and real measured radar data are conducted to verify the proposed algorithm.

Long-term coherent integration can remarkably improve the ability of detection and motion parameter estimation of radar for maneuvering targets. However, the linear range migration, quadratic range migration (QRM), and Doppler frequency migration within the coherent processing interval seriously degrade the detection and estimation performance. Therefore, an efficient and noise-resistant coherent integration method based on location rotation transform (LRT) and non-uniform fast Fourier transform (NuFFT) is proposed. QRM is corrected by the second-order keystone transform. Using the relationship between the rotation angle and Doppler frequency, a novel phase compensation function is constructed. Motion parameters can be rapidly estimated by LRT and NuFFT. Compared with several representative algorithms, the proposed method achieves a nearly ideal detection performance with low computational cost. Finally, experiments based on measured radar data are conducted to verify the proposed algorithm.

Recent research interest has focused on microalgae cultivation for biogas slurry purification and biogas upgrading due to the requirement of high efficiency for nutrient uptake and CO2 capture, with economic feasibility and environmental benefits. Numerous studies have suggested that biogas slurry purification and biogas upgrading can occur simultaneously via microalgae-based technology. However, there is no comprehensive review on this technology with respect to the nutrient removal from biogas slurry and biogas upgrading. This article summarizes microalgal cultivation with biogas slurry and biogas from anaerobic digestion. The parameters, techniques, and modes of microalgae cultivation have been discussed in detail to achieve high efficiency in biogas slurry purification and biogas upgrading. In addition, the evaluation of energy efficiency and safety has also been explored. Compared with mono-cultivation of microalgae and co-cultivation of microalgae and bacteria, microalgae-fungi symbiosis has demonstrated greater development prospect and higher energy efficiency and the energy consumption for pollutants and CO2 removal were 14.2-39.0% · USD-1 and 19.9-23.3% · USD-1, respectively. Further, a sustainable recycling scheme is proposed for the purification of biogas slurry from anaerobic digestion process and biogas upgrading via microalgae-based technology.

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

Advanced and metastatic tumors with complex treatment histories drive cancer mortality. Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and clinical dataset, amenable for exploration of the impacts of therapies on genomic landscapes. Previous exposure to DNA-damaging chemotherapies and mutations affecting DNA repair genes, including POLQ and genes encoding Polζ, were associated with genome-wide, therapy-induced mutagenesis. Exposure to platinum therapies coincided with signatures SBS31 and DSB5 and, when combined with DNA synthesis inhibitors, signature SBS17b. Alterations in ESR1, EGFR, CTNNB1, FGFR1, VEGFA and DPYD were consistent with drug resistance and sensitivity. Recurrent noncoding events were found in regulatory region hotspots of genes including TERT, PLEKHS1, AP2A1 and ADGRG6. Mutation burden and immune signatures corresponded with overall survival and response to immunotherapy. Our data offer a rich resource for investigation of advanced cancers and interpretation of whole-genome and transcriptome sequencing in the context of a cancer clinic. Marra and colleagues describe POG570, a pan-cancer, whole-genome, transcriptome and clinical dataset stressing the molecular interactions in advanced and post-therapy cancer patients.

Saline stress has been identified as the primary factor inhibiting rice seedling growth, which represents a complex abiotic stress process. Most plant hormones have been shown to alleviate the plant damage caused by salt stress. The effects of synthetic strigolactone (GR24) on Jinongda 667 rice seedlings treated with 200 mM NaCl were studied. Photosynthesis and its related physiological characteristics were analyzed in salt-stressed rice seedlings treated with GR24. NaCL stress inhibited the growth of the rice, including plant height and root length, by approximately 14% and 40%, respectively. Compared to the control check group (CK), the adverse effects of salt stress on the growth status, leaf photosynthesis, and physiological/biochemical indices in the rice seedlings were alleviated in the GR24 treatment group. With increases in the GR24 concentration, the plant height and root length of the seedlings increased. The plant height in the groups treated with 1/2 Hoagland’s complete nutrient solution + 200 mM NaCl +1 μM GR24 (T4) and 1/2 Hoagland’s complete nutrient solution + 200 mM NaCl +5 μM GR24 (T5) were significantly different than the 1/2 Hoagland’s complete nutrient solution + 200 mM NaCl group (T1) (P 0.05). The transpiration rate, stomatal conductance, and intercellular CO2 concentrations showed the same trends as the net photosynthetic rate. The MAD, POD, and SOD activities were significantly increased by 68%, 60%, 14%, respectively, compared to the CK group (P

Nanofluid minimum quantity lubrication (NMQL) is an emerging cleaner and sustainable technique. However, the effective immersion of nanofluids in the grinding zone in NMQL grinding limits the extensive application of this technique. Ultrasonic vibration can exert a pumping effect that injects nanofluids into the interface between the grinding wheel and workpiece. Furthermore, technique integration benefits the infiltration state transition of micro-droplets. However, evaluation of the coupling effect and surface morphology of multi-angle 2D ultrasonic vibration integrated with NMQL has rarely been performed. This study aims to address these research limitations. A kinematics model was developed, and the grain and workpiece relative motion trails in 2D ultrasonic vibration-assisted grinding (UVAG) were simulated at different resultant vibration angles (θ). The grain’s cutting characteristics were then analyzed and found to be conducive to the full infiltration of nanofluids into the grinding zone. Moreover, the surface characterization of multi-angle 2D UVAG coupled with NMQL was evaluated experimentally. Results showed that the optimal θ was achieved at 45° due to the differential cutting action of the follow-up grain. NMQL obtained a better result than flooding at the same θ. When the gain effect of the coupling techniques was reflected in surface roughness, the Ra value decreased by 19.5 % (compared with UVAG) and 39.9 % (compared with NMQL). The autocorrelation function curves presented periodic and continuous local oscillations under the grinding conditions of 2D UVAG with θ = 45° and θ = 135°.

Accurate and fast identification of vibration signals detected based on the phase-sensitive optical time-domain reflectometer (Φ-OTDR) is crucial in reducing the false-alarm rate of the long-distance distributed vibration warning system. This study proposes a computer vision-based Φ-OTDR multi-vibration events detection method in real-time, which can effectively detect perimeter intrusion events and reduce personnel patrol costs. Pulse accumulation, pulse cancellers, median filter, and pseudo-color processing are employed for vibration signal feature enhancement to generate vibration spatio-temporal images and form a customized dataset. This dataset is used to train and evaluate an improved YOLO-A30 based on the YOLO target detection meta-architecture to improve system performance. Experiments show that using this method to process 8069 vibration data images generated from 5 abnormal vibration activities for two types of fiber optic laying scenarios, buried underground or hung on razor barbed wire at the perimeter of high-speed rail, the system mAP@.5 is 99.5%, 555 frames per second (FPS), and can detect a theoretical maximum distance of 135.1 km per second. It can quickly and effectively identify abnormal vibration activities, reduce the false-alarm rate of the system for long-distance multi-vibration along high-speed rail lines, and significantly reduce the computational cost while maintaining accuracy.

A biogas slurry composed of carbon, nitrogen, phosphorus, and antibiotics was generated. Investigations into the nutrient and tetracycline removal performance of four microalgae-based contaminant removal technologies, including Chlorella vulgaris, C. vulgaris co-cultured with endophytic bacteria, C. vulgaris co-cultured with Ganoderma lucidum, and C. vulgaris co-cultured with G. lucidum and endophytic bacteria, were conducted. The algal-bacterial-fungal consortium with 10