Automated exploitation of deep learning for cancer patient stratification across multiple types.

MOTIVATION: Recent frameworks based on deep learning have been developed to identify cancer subtypes from high-throughput gene expression profiles. Unfortunately, the performance of deep learning is highly dependent on its neural network architectures which are often hand-crafted with expertise in deep neural networks, meanwhile, the optimization and adjustment of the network are usually costly and time consuming. RESULTS: To address such limitations, we proposed a fully automated deep neural architecture search model for diagnosing consensus molecular subtypes from gene expression data (DNAS). The proposed model uses ant colony algorithm, one of the heuristic swarm intelligence algorithms, to search and optimize neural network architecture, and it can automatically find the optimal deep learning model architecture for cancer diagnosis in its search space. We validated DNAS on eight colorectal cancer datasets, achieving the average accuracy of 95.48%, the average specificity of 98.07%, and the average sensitivity of 96.24%, respectively. Without the loss of generality, we investigated the general applicability of DNAS further on other cancer types from different platforms including lung cancer and breast cancer, and DNAS achieved an area under the curve of 95% and 96%, respectively. In addition, we conducted gene ontology enrichment and pathological analysis to reveal interesting insights into cancer subtype identification and characterization across multiple cancer types. AVAILABILITY AND IMPLEMENTATION: The source code and data can be downloaded from https://github.com/userd113/DNAS-main. And the web server of DNAS is publicly accessible at 119.45.145.120:5001.

Accuracy, Linearity and Precision of Spine QCT vBMD Phantom Measurements for Different Brands of CT Scanner: A Multicentre Study.

We describe a multicenter study using the European Spine Phantom (ESP) to compare the accuracy, linearity and precision of QCT measurements of spine vBMD between different brands of scanner, different models of the same brand and identical units of the same model. Ten scans of the same ESP with repositioning were performed on forty CT scanners from five manufacturers in different hospitals across China, all calibrated with the Mindways QCT system. The three ESP vertebral bodies simulating low (L1), medium (L2) and high (L3) vBMD and their average (L1-3 vBMD) were compared with phantom values. Linearity was assessed using the standard error of the estimate derived from linear regression. Precision errors were expressed as the standard deviation of the ten measurements on each scanner. Median (IQR) vBMD over all forty CT scanners compared with phantom values were: L1: 52.2 (49.9-56.4) vs 51.0; L2: 104.4 (101.2-108.6) vs 102.2; L3: 201.4 (195.0-204.9) vs 200.4; L1-3: 119.3 (116.6-123.2) vs 117.9 mg/cm3. Statistically significant differences in L1-3 vBMD were found between different brands (p= 0.005) and between different models of the same brand and identical units of the same model (both p< 0.001). Cross-calibration using linear regression gave a good fit for all forty systems with a median standard error of the estimate of 1.7 mg/cm3. The median precision error for L1-3 vBMD was 0.61 mg/cm3. Statistically significant differences in spine vBMD measurements between different scanners reinforce the importance of cross-calibration in multi-center studies. Cross-calibration can be reliably performed using linear regression equations.

Acyl-CoA synthetase 6 enriches the neuroprotective omega-3 fatty acid DHA in the brain.

Docosahexaenoic acid (DHA) is an omega-3 fatty acid that is highly abundant in the brain and confers protection against numerous neurological diseases, yet the fundamental mechanisms regulating the enrichment of DHA in the brain remain unknown. Here, we have discovered that a member of the long-chain acyl-CoA synthetase family, Acsl6, is required for the enrichment of DHA in the brain by generating an Acsl6-deficient mouse (Acsl6-/-). Acsl6 is highly enriched in the brain and lipid profiling of Acsl6-/- tissues reveals consistent reductions in DHA-containing lipids in tissues highly abundant with Acsl6. Acsl6-/- mice demonstrate motor impairments, altered glutamate metabolism, and increased astrogliosis and microglia activation. In response to a neuroinflammatory lipopolysaccharide injection, Acsl6-/- brains show similar increases in molecular and pathological indices of astrogliosis compared with controls. These data demonstrate that Acsl6 is a key mediator of neuroprotective DHA enrichment in the brain.

Counterion Control of t-BuO-Mediated Single Electron Transfer to Nitrostilbenes to Construct N-Hydroxyindoles or Oxindoles.

tert-Butoxide unlocks new reactivity patterns embedded in nitroarenes. Exposure of nitrostilbenes to sodium tert-butoxide was found to produce N-hydroxyindoles at room temperature without an additive. Changing the counterion to potassium changed the reaction outcome to yield solely oxindoles through an unprecedented dioxygen-transfer reaction followed by a 1,2-phenyl migration. Mechanistic experiments established that these reactions proceed via radical intermediates and suggest that counterion coordination controls whether an oxindole or N-hydroxyindole product is formed.

Multicomponent Synthesis of Iminocoumarins via Rhodium-Catalyzed C-H Bond Activation.

We herein establish a multicomponent annulation method for the synthesis of valuable iminocoumarins using aryl thiocarbamates, internal alkynes, and sulfonamides as starting materials, which are safe and readily available. The key step is a Rh-catalyzed and sulfur-directed C-H bond activation. Preliminary mechanistic investigations suggested that the nucleophilic attack of the sulfonamide on an active iminium cation finally completes the imine segment.

An Analysis of the Attitude Estimation Errors Caused by the Deflections of Vertical in the Integration of Rotational INS and GNSS.

This paper investigates the attitude estimation errors caused by the deflections of vertical (DOV) in the case of a rotational inertial navigation system (INS) integrated with a global satellite navigation system (GNSS). It has been proved theoretically and experimentally that the DOV can introduce a tilt error to the INS/GNSS integration, whereas less attention has been given to its effect to the heading estimation. In fact, due to the intercoupling characteristic of attitude errors, the heading estimation of an INS/GNSS integrated navigation system can also be affected. In this paper, first, the attitude estimation errors caused by DOV were deduced based on the INS's error propagation functions. Then, the corresponding simulations were conducted and the results were well consistent with the theoretical analysis. Finally, a real shipborne marine test was organized with the aimed to verify the effect of DOV on attitude estimation in the rotational INS/GNSS integration, whereas the global gravity model was used for DOV compensation. The results with DOV compensation were compared with the corresponding results where the compensation was not used and showed that the heading estimation errors caused by DOV could exceed 20 arcsecs, which must be considered in high-precision application cases.

Time series modeling of the ring laser gyroscope's bias considering the temperature delay effect.

Due to the temperature delay effect, the coefficients of the traditional ring laser gyroscope's (RLG) bias temperature model usually change with environmental temperature. In order to improve the applicability of the temperature model in complex temperature-varying environments, a modified RLG bias modeling method based on the temperature delay effect is proposed. The time series model (TSM), whose coefficients are independent of the environmental temperature variation, is established through theoretical analysis according to the temperature delay effect. The forecasting accuracy of the proposed method is compared with the conventional stepwise regression model (SRM) when both the temperature and temperature-varying rate exceed their boundaries. The experimental results indicate that the proposed TSM can overcome the defect that the compensation accuracy will decline or even diverge when outside the boundaries of temperature and temperature-varying rate. Therefore, the TSM is more suitable for the RLG bias temperature modeling in complex temperature-varying environments.

Chemoselective acylation of benzimidazoles with phenylacetic acids under different Cu catalysts to give fused five-membered N-heterocycles or tertiary amides.

C-N bond formation via a copper-catalyzed aerobic oxidative decarboxylative tandem protocol was realized. The phenylacetic acids which contain ortho-X (X = F or Br) on the aromatic ring will render a fused five-membered heterocycle via a tandem aromatic nucleophilic substitution and aerobic oxidative decarboxylative acylation at the C(sp(2))-H bond of benzimidazoles under the Cu(OAc)2/K2CO3/BF3·Et2O catalytic system, while with CuBr as the catalyst and pyridine as the base, N-acylation occurred and tertiary amides were obtained.

Oxygen-sulfur rearrangement in the reaction of thiocarbamate imidazolium ylide with arylaldehyde.

The nucleophilic addition of thiocarbamate imidazolium ylide to aldehyde triggered sequential intramolecular N to O migration of thiocarbonyl amide group and reversible oxygen-sulfur rearrangement to afford 2-imidazolium alkylcarbamothioate. The ortho group on phenyl of aldehyde strongly affects the balance of the O- to S-rearrangement.

Optimization of pulsed-field gel electrophoresis protocols for Salmonella Paratyphi A subtyping.

Salmonella enterica serovar Paratyphi A infection has caused public health problems in some countries in recent years. Pulsed-field gel electrophoresis (PFGE) has been used for the subtyping and epidemiological investigations of some serotypes of Salmonella, mainly in outbreaks caused by non-typhoidal Salmonella. In this study, different restriction endonucleases and electrophoresis parameters were compared for the PFGE subtyping by using Salmonella Paratyphi A strain panels. Two protocols for the enzymes SpeI and XbaI showed higher discriminatory power, which may facilitate epidemiological analysis for more accurate case definition, and clonality study of Salmonella Paratyphi A.

[The study of inter-simple sequences repeat genotyping based on one pentanucleotide repeat sequences in mycobacteria].

OBJECTIVE: To establish inter-simple sequences repeat (ISSR) molecular makers based on (CAGCG)n repeat sequence in mycobacteria. METHODS: The distribution of pentanucleotide repeat sequence (CAGCG)n in mycobacterial genomes was analyzed by MICdb 2.0 software in the microsatellite database. ISSR primer MISP6 based on (CAGCG)n sequences was designed and tested in mycobacterial strains, which included 17 mycobacterial strains and 41 Mycobacterium tuberculosis clinical strains. RESULTS: The abundances of pentanucleotide repeat sequences (CAGCG)n were high in most of the mycobacterial genomes and they were mainly located in the coding regions. The results of ISSR analysis in mycobacteria showed that 15 reference strains from mycobacteria were clustered into 2 major clusters. The first cluster contained 2 subtypes and the second cluster contained 4 subtypes. Forty-one clinical strains from Mycobacterium tuberculosis were divided into 2 major clusters by the analysis of MISP6 primer, and each cluster had 2 subtypes. CONCLUSION: ISSR primer MISP6 based on (CAGCG)n sequences can be used as a genetic marker to genotype mycobacterial strains.

[Identification and evaluation of a new nucleic acid amplification test target for specific detection of Mycobacterium tuberculosis complex].

OBJECTIVE: To identify and evaluate a new nucleic acid amplification (NAA) test target for specific detection of Mycobacterium tuberculosis (MTB) complex (MTC). METHODS: MTC-specific fragment was obtained by ISSR genotyping technology. Primer pairs were designed based on the sequences of MTC-specific fragment and tested in 211 mycobacterial strains including 107 MTC strains and 104 nontuberculous mycobacteria (NTM) strains. IS6110 element (specific identification of MTC strains) and 16s rRNA gene (specific identification of Mycobacterium) amplification were used as a control to evaluate the efficacy of the NAA test target in the detection of MTC strains. RESULTS: One MTC-specific fragment with the length of 588 bp, located in 315947 - 316534 of the genome from MTB reference strain H(37) Rv, were obtained, cloned and sequenced. MTC-specific primer pairs MTCF/R were designed based on these sequences. All 211 mycobacterial strains accurately produced the genus-specific 16s rRNA amplicon. All MTC strains were positive in the MTCF/R PCR amplification while 99% MTC strains (106/107) were positive in the amplification of IS6110 sequences. All NTM strains were negative in both IS6110 and MTCF/R PCR amplification. CONCLUSIONS: The MTC-specific fragment developed in this study can be used as a new NAA test target to correctly distinguish MTC from NTM.

Genome-wide characterization and analysis of Golden 2-Like transcription factors related to leaf chlorophyll synthesis in diploid and triploid Eucalyptus urophylla.

Golden 2-Like (GLK) transcription factors play a crucial role in chloroplast development and chlorophyll synthesis in many plant taxa. To date, no systematic analysis of GLK transcription factors in tree species has been conducted. In this study, 40 EgrGLK genes in the Eucalyptus grandis genome were identified and divided into seven groups based on the gene structure and motif composition. The EgrGLK genes were mapped to 11 chromosomes and the distribution of genes on chromosome was uneven. Phylogenetic analysis of GLK proteins between E. grandis and other species provided information for the high evolutionary conservation of GLK genes among different species. Prediction of cis-regulatory elements indicated that the EgrGLK genes were involved in development, light response, and hormone response. Based on the finding that the content of chlorophyll in mature leaves was the highest, and leaf chlorophyll content of triploid Eucalyptus urophylla was higher than that of the diploid control, EgrGLK expression pattern in leaves of triploid and diploid E. urophylla was examined by means of transcriptome analysis. Differential expression of EgrGLK genes in leaves of E. urophylla of different ploidies was consistent with the trend in chlorophyll content. To further explore the relationship between EgrGLK expression and chlorophyll synthesis, co-expression networks were generated, which indicated that EgrGLK genes may have a positive regulatory relationship with chlorophyll synthesis. In addition, three EgrGLK genes that may play an important role in chlorophyll synthesis were identified in the co-expression networks. And the prediction of miRNAs targeting EgrGLK genes showed that miRNAs might play an important role in the regulation of EgrGLK gene expression. This research provides valuable information for further functional characterization of GLK genes in Eucalyptus.

[Expression of estrogen receptor alpha in the testis of infertile men with spermatogenic arrest].

OBJECTIVE: To explore the association of spermatogenic arrest with the expression of estrogen receptor alpha (ERalpha) in human testes. METHODS: We examined the testicular biopsy specimens of 120 infertile men by HE staining, detected the expression of ERalpha in the specimens of those with spermatogenic arrest by the two-step immunohistochemical method, and compared the results with those of 10 healthy men. RESULTS: Of the 120 specimens from the infertile men, 31 (25.8%) met the diagnostic criteria of spermatogenic arrest. In the testis tissue of normal men, ERalpha expressed in Sertoli, myoid and Leydig cells, but not in spermatogenic cells, while in the testis tissues of those with spermatogenic arrest, ERalpha expressed lowly in Sertoli, myoid and Leydig cells, with statistically significant differences in immunostaining intensity between the two groups (P < 0.05). CONCLUSION: Androgen receptor (AR) and ERalpha may play a coordinating role in facilitating spermatogenesis. Spermatogenic arrest may be related to a complex series of disorders in cell signal transduction involving AR, ERalpha and HSP90.

[Comparison of the promoter activity of metabolism-related pabB and lpdA genes between Mycobacterium tuberculosis strains H37Rv and H37Ra].

OBJECTIVE: Comparative genomic study revealed mutations at the promoter regions of pabB and lpdA in avirulent Mycobacterium tuberculosis strain H37Ra compared to its virulent counterpart strain H37Rv. We used LacZ reporter system to test whether those mutations will affect promoter activity and its potential relationship to virulence attenuation of H37Ra. METHODS: Promoter regions of pabB and lpdA were predicted by the "Neural Network Promoter Prediction" method (http://www. fruitfly. org/seq_tools/promoter. html). Promoter sequences were PCR amplified and cloned into mycobacterial promoterless probe vector pMC210. Resultant recombinant plasmids were transformed into M. smegmatis by electroporation. The transcription activity of lacZ under the control of cloned promoters were monitored by Quantitative Real-Time RT-PCR. RESULTS: Quantitative Real Time PCR results showed that the promoter activity of H37Ra pabB was six times more than that of H37Rv pabB (p < 0.05), while the promoter activity of the H37Rv lpdA was two fold of that of H37Ra lpdA (p < 0.05). CONCLUSION: The mutations in pabB and lpdA promoters affect its expression activity. The T-A mutation in lpdA promoter may be related to virulence attenuation of H37Ra.

Molecular Evolution of Maize Ascorbate Peroxidase Genes and Their Functional Divergence.

Ascorbate peroxidase (APX) is an important antioxidant enzyme. APXs in maize are encoded by multiple genes and exist as isoenzymes. The evolutionary history and functional divergence of the maize APX gene family were analyzed through comparative genomic and experimental data on the Internet in this paper. APX genes in higher plants were divided into classes A, B, and C. Each type of APX gene in angiosperms only had one ancestral gene that was duplicated along with the genome duplication or local (or tandem) duplication of the angiosperm. A total of eight genes were retained in maize and named APXa1, APXa2, APXa3, APXb1, APXb2, APXc1.1, APXc1.2, and APXc2. The APX genes of class A were located in the chloroplasts or mitochondria, and the class B and C genes were localized in the peroxisomes and cytoplasm, respectively. The expression patterns of eight APXs were different in vegetative and reproductive organs at different growth and development stages. APXa1 and APXb1 of maize may participate in the antioxidant metabolism of vegetative organs under normal conditions. APXa2, APXb2, APXc1.1, and APXc1.2 may be involved in the stress response, and APXb2 and APXc2 may participate in the senescence response. These results provide a basis for cultivating high-yield and resistant maize varieties.

[Comparison of the transcriptional levels of mannitol PTS operon between epidemic and non-epidemic strains of Vibrio cholerae].

OBJECTIVE: To compare the transcription difference of the mannitol PTS genes between epidemic and non-epidemic strains of Vibrio cholerae El Tor in mannitol ferment tests. METHODS: Growth curves of 10 epidemic strains (slow-ferment) and 10 non-epidemic strains (rapid-ferment) of Vibrio cholerae were detected in the process of fermentation test, and the transcriptional level of mannitol PTS operon of these strains were determined with quantitative reverse-transcriptional PCR. RESULTS: After 4 hours of test, the non-epidemic strains became positive and the average growth density of the non-epidemic strains was higher than that of the epidemic strains; however, some were still lower than the epidemic strains. In contrast, at the eighth hour of test, when epidemic strains got positive, they showed higher average growth density. Compared to the epidemic strains, the transcription of mannitol PTS genes of the non-epidemic strains were much more active at the 1st and 2nd hour and were lower at the 4th and 8th hour. CONCLUSIONS: The difference of mannitol PTS operon transcription level should be an important feature to identify the epidemic and non-epidemic strains of Vibrio cholerae, which directly influences the mannitol fermentation rate during the test. The growth rate is not a key factor that affect such difference.

Palladium-catalyzed Suzuki-Miyaura coupling of thioureas or thioamides.

Cross-coupling reactions involving metal carbene intermediates play an increasingly important role in C-C bond formation. Expanding the carbene precursors to a broader range of starting materials and more diverse products is an ongoing challenge in synthetic organic chemistry. Herein, we report a Suzuki-Miyaura coupling reaction of in situ-generated Pd-carbene complexes via desulfurization of thioureas or thioamides. This strategy enables the preparation of a broad array of substituted amidinium salts and unsymmetrical diaryl ketones. The reaction is readily scalable, compatible with bromo groups on aromatic rings, tolerant to moisture and air and has a broad substrate scope. Furthermore, a single crystal structure of Pd-diaminocarbene complex is obtained and proven to be the key intermediate in both catalytic and stoichiometric reactions. Preliminary mechanistic studies demonstrate the dual role of the silver salt as a desulfurating reagent assisting the elimination of sulfur and as oxidant facilitating the PdII/Pd0/PdII catalytic cycle.

Controlling the Selectivity Patterns of Au-Catalyzed Cyclization-Migration Reactions.

As little as 2 mol % of (XPhos)AuNTf2 catalyzes the transformation of a broad range of o-acetylene-substituted styrenes into 1,2-dihydronaphthalenes. Our data suggests that this transformation occurs via a gold-stabilized cyclopropyl carbinyl cation, which triggers either a [1,2] carboxylate shift or a less favorable [1,2] aryl shift. The relative rates of these migrations can be controlled by the identity of the ligand or by stabilizing the mesomeric cation.

Nicotine exerts neuroprotective effects by attenuating local inflammatory cytokine production following crush injury to rat sciatic nerves.

Recent studies have demonstrated that nicotine exhibited anti-inflammatory and neuroprotective properties by interacting with the alpha 7 nicotinic acetylcholine receptor (α7nAChR). However, the role of nicotine in regeneration during peripheral nerve injury has not been elucidated. The aim of this study was to investigate whether nicotine down-regulated production of proinflammatory cytokines and promoted peripheral nerve regeneration in rats. Rats challenged with sciatic nerve crush injury were treated with nicotine (1.5 mg/kg), three times per day. The expression of the proinflammatory cytokines tumor necrosis factor alpha (TNF-α) and interleukin (IL-1ß), pinch test results, growth-associated protein 43 (GAP-43) expression, morphometric analyses, and the sciatic functional indexes were determined in sciatic nerves. Treatment with nicotine decreased local levels of TNF-α and IL-1ß, and increased the expression of GAP-43. Nicotine also improved nerve regeneration and functional recovery. The overall protective effects of nicotine were reversed by concomitant treatment with α7nACHR antagonist methyllycaconitine, indicating that nicotine exerted its specific anti-inflammatory and neuroprotective effects through the α7nAChR. These findings show that nicotine administration can provide a potential therapeutic pathway for the treatment of peripheral nerve injury, by a direct protective effect through the α7nAChR-mediated cholinergic anti-inflammatory pathway.