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Passivity-based control (PBC) exhibits robustness against parameters shift, providing a substantial level of stability. However, for the LCL-filtered grid-connected inverter (GCI), the conventional PBC (called C-PBC) controller has a narrow control bandwidth due to the control time delay, resulting in poor dynamic performance, especially in the weak grid state. This paper proposes a new PBC (called P-PBC) method to increase the closed-loop bandwidth of the system by setting an appropriate feedback proportional coefficient between the grid-side current and the inverter-side current. By extending the closed-loop bandwidth of the system, the proposed P-PBC method offers improved dynamic performance, particularly in challenging grid conditions. In addition, a state observer is also employed to reduce sensors, which saves costs and enhances the system's reliability. A 110 V/50 Hz/3 kW/3-phase experimental setup has been developed using the dSPACE DS1202 platform to validate the effectiveness of the proposed control method., (© 2024. The Author(s).)

To explore the hub comorbidity genes and potential pathogenic mechanisms of hypopharyngeal carcinoma with esophageal carcinoma, and evaluate their diagnostic value for hypopharyngeal carcinoma with co-morbid esophageal carcinoma. We performed gene sequencing on tumor tissues from 6 patients with hypopharyngeal squamous cell carcinoma with esophageal squamous cell carcinoma (hereafter referred to as "group A") and 6 patients with pure hypopharyngeal squamous cell carcinoma (hereafter referred to as "group B"). We analyzed the mechanism of hub genes in the development and progression of hypopharyngeal squamous cell carcinoma with esophageal squamous cell carcinoma through bioinformatics, and constructed an ROC curve and Nomogram prediction model to analyze the value of hub genes in clinical diagnosis and treatment. 44,876 genes were sequenced in 6 patients with group A and 6 patients with group B. Among them, 76 genes showed significant statistical differences between the group A and the group B.47 genes were expressed lower in the group A than in the group B, and 29 genes were expressed higher. The top five hub genes were GABRG2, CACNA1A, CNTNAP2, NOS1, and SCN4B. GABRG2, CNTNAP2, and SCN4B in the hub genes have high diagnostic value in determining whether hypopharyngeal carcinoma patients have combined esophageal carcinoma (AUC: 0.944, 0.944, 0.972). These genes could possibly be used as potential molecular markers for assessing the risk of co-morbidity of hypopharyngeal carcinoma combined with esophageal carcinoma., (© 2024. The Author(s).)

Late Holocene relative sea-level (RSL) data are important to understand the drivers of RSL change, but there is a lack of precise RSL records from the Sunda Shelf. Here, we produced a Late Holocene RSL reconstruction from coral microatolls in Singapore, demonstrating for the first time the utility of Diploastrea heliopora microatolls as sea-level indicators. We produced 12 sea-level index points and three marine limiting data with a precision of < ± 0.2 m (2σ) and < ± 26 years uncertainties (95% highest density region). The data show a RSL fall of 0.31 ± 0.18 m between 2.8 and 0.6 thousand years before present (kyr BP), at rates between - 0.1 ± 0.3 and - 0.2 ± 0.7 mm/year. Surface profiles of the fossil coral microatolls suggest fluctuations in the rate of RSL fall: (1) stable between 2.8 and 2.5 kyr BP; (2) rising at ~ 1.8 kyr BP; and (3) stable from 0.8 to 0.6 kyr BP. The microatoll record shows general agreement with published, high-quality RSL data within the Sunda Shelf. Comparison to a suite of glacial isostatic adjustment (GIA) models indicate preference for lower viscosities in the mantle. However, more high quality and precise Late Holocene RSL data are needed to further evaluate the drivers of RSL change in the region and better constrain GIA model parameters., (© 2024. The Author(s).)

RAB3B is essential for the transportation and secretion within cells. Its increased expression is linked to the development and progression of various malignancies. However, understanding of RAB3B's involvement in carcinogenesis is mostly limited to specific cancer subtypes. Hence, exploring RAB3B's regulatory roles and molecular mechanisms through comprehensive cancer datasets might offer innovative approaches for managing clinical cancer. To examine the potential involvement of RAB3B in the development of cancer, we analyzed data from various sources including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), cBioPortal, HPA, UALCAN, and tissue microarray (TAM). Using bioinformatics techniques, we examined the correlation between RAB3B expression and prognosis, tumor heterogeneity, methylation modifications, and immune microenvironment across different cancer types. Our findings indicate that elevated RAB3B expression can independently predict prognosis in many tumors and has moderate accuracy for diagnosing most cancers. In most cancer types, we identified RAB3B mutations that showed a significant correlation with tumor mutational burden (TMB), mutant-allele tumor heterogeneity (MATH), and microsatellite instability (MSI). Abnormal DNA methylation patterns were also observed in most cancers compared to normal tissues. Additionally, we found significant correlations between RAB3B expression, immune cell infiltration, and immune scores across various cancers. Through pan-cancer analysis, we observed significant differences in RAB3B expression levels between tumors and normal tissues, making it a potential primary factor for cancer diagnosis and prognosis. The IHC results revealed that the expression of RAB3B in six types of tumors was consistent with the results of the pan-cancer analysis of the database. Furthermore, RAB3B showed potential associations with tumor heterogeneity and immunity. Thus, RAB3B can be utilized as an auxiliary diagnostic marker for early tumor detection and a prognostic biomarker for various tumor types., (© 2024. The Author(s).)

By collecting a large amount of data from various preloading engineering projects, a settlement prediction database was established including up to 15 feature parameters, such as final measured time, magnitude of surcharge loading, porosity ratio, internal friction angle, and others. Furthermore, a settlement prediction model of soft foundation based on random forest (RF) model was also developed. To enhance the accuracy of settlement prediction, the improved sparrow search algorithm (ISSA), which incorporates several enhancements such as the use of Logistic-tent chaotic mapping, adaptive nonlinear inertia-decreasing weight parameters, and Levy flight strategy, was proposed to optimize the hyperparameters of the RF model. The optimization results of various algorithms on benchmark functions revealed that the ISSA algorithm excelled in terms of accuracy and stability when compared to conventional algorithms such as particle swarm optimization and butterfly optimization. The ISSA-RF settlement prediction model was subsequently constructed and applied to practical projects. The results demonstrated that the ISSA-RF model exhibited superior prediction accuracy and applicability compared to the RF model. It can therefore provide valuable guidance for the planning and implementation of preloading engineering projects., (© 2024. The Author(s).)

In this study, a accurate, rapid quantitative PCR method for the simultaneous detection of 4 kinds of pathogenic bacteria in water was established, and the distribution of pathogenic bacteria in surface waters with different levels of pollution (Yulin region, China) was detected. The results showed that the detection accuracy was 94%; the detection limit was 2.7 in bacterial cells. Salmonella enterica subsp. enterica serovar typhimurium and Salmonella dysenteria were always present in water when the universal primer for pathogenic bacteria abundance detection was greater than 10 4 copies 100 mL -1 . When the detection value is lower than 10 4 copy 100 mL -1 , the bacteria in the water are rarely pathogenic bacteria, so the detection value of 10 4 copy 100 mL -1 can be used as a new indicator of waterborne pathogen pollution., (© 2024. The Author(s).)

Hirudin is a pharmacologically active substance in leeches with potent blood anticoagulation properties. Although recombinant hirudin production isolated from Hirudo medicinalis Linnaeus and Hirudinaria manillensis Lesson is known, to our knowledge, this study is the first to report recombinant hirudin expression and production from Hirudo nipponia Whitman. Thus, the present study aimed to clone and characterize the full-length cDNA of a candidate hirudin gene (c16237&#95;g1), which is localized on the salivary gland transcriptome of H. nipponia, and further evaluate its recombinant production using a eukaryotic expression system. The 489-bp cDNA possessed several properties of the hirudin "core" motifs associated with binding to the thrombin catalytic pocket. A fusion expression vector (pPIC9K-hirudin) was constructed and successfully transformed into Pichia pastoris strain GS115 via electroporation. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis and western blot analysis confirmed hirudin expression. The recombinant protein was expressed with a yield of 6.68 mg/L culture. Mass spectrometry analysis further confirmed target protein expression. The concentration and antithrombin activity of purified hirudin were 1.67 mg/mL and 14,000 ATU/mL, respectively. These findings provide a basis for further elucidating the molecular anticoagulation mechanism of hirudin, and address China's growing market demand for engineered H. nipponia-derived hirudin and hirudin-based drugs., (© 2023. The Author(s).)

Non-invasive prediction for KIT/PDGFRA status in GIST is a challenging problem. This study aims to evaluate whether CT based sarcopenia could differentiate KIT/PDGFRA wild-type gastrointestinal stromal tumor (wt-GIST) from the mutant-type GIST (mu-GIST), and to evaluate genetic features of GIST. A total of 174 patients with GIST (wt-GIST = 52) were retrospectively identified between January 2011 to October 2019. A sarcopenia nomogram was constructed by multivariate logistic regression. The performance of the nomogram was evaluated by discrimination, calibration curve, and decision curve. Genomic data was obtained from our own specimens and also from the open databases cBioPortal. Data was analyzed by R version 3.6.1 and clusterProfiler ( http://cbioportal.org/msk-impact ). There were significantly higher incidence (75.0% vs. 48.4%) and more severe sarcopenia in patients with wt-GIST than in patients with mu-GIST. Multivariate logistic regression analysis showed that sarcopenia score (fitted based on age, gender and skeletal muscle index), and muscle fat index were independent predictors for higher risk of wt-GIST (P < 0.05 for both the training and validation cohorts). Our sarcopenia nomogram achieved a promising efficiency with an AUC of 0.879 for the training cohort, and 0.9099 for the validation cohort with a satisfying consistency in the calibration curve. Favorable clinical usefulness was observed using decision curve analysis. The additional gene sequencing analysis based on both our data and the external data demonstrated aberrant signal pathways being closely associated with sarcopenia in the wt-GIST. Our study supported the use of CT-based assessment of sarcopenia in differentiating the wt-GIST from the mu-GIST preoperatively., (© 2023. The Author(s).)

The difficulty of feature extraction and the small sample size are two challenges in the field of mechanical fault diagnosis for a long time. Here we propose an intelligent mechanical fault diagnosis method for scenario with small sample datasets. This method can not only diagnose bearing faults but also gear faults, and has strong generalization performance. We use convolutional neural network to realize automatic feature extraction. Through sliding window scanning, one sample set is expanded to three sub-sample sets with different scales to meet the needs of deep learning training. Three convolutional networks are used to extract the features of the subsets respectively to ensure that their useful features are fully extracted. After feature extraction, the feature is reconstructed through feature splicing. Because of the unique advantages of SVM in dealing with small sample sets, we use SVM to classify the reconstructed features. We use the bearing data set collected by Case Western Reserve University in the United States, the bearing fault data set collected by Xi'an Jiaotong University in China, and the gearbox fault data collected by the University of Connecticut in the United States to conduct experiments. The experimental results show that the accuracy of training, validation and testing of the proposed method on the three data sets all reach 100%. This proves that our method can not only tackle the two challenges, but also has high fault diagnosis accuracy and strong generalization performance. It is hoped that our proposed method can contribute to the development of mechanical fault diagnosis., (© 2022. The Author(s).)

This paper reports on the development of a magnetically driven high-velocity implosion experiment conducted on the CQ-3 facility, a compact pulsed power generator with a load current of 2.1 MA. The current generates a high Lorentz force between inner and outer liners made from 2024 aluminum. Equally positioned photonic Doppler velocimetry probes record the liner velocities. In experiment CQ3-Shot137, the inner liner imploded with a radial converging velocity of 6.57 km/s while the outer liner expanded at a much lower velocity. One-dimensional magneto-hydrodynamics simulation with proper material models provided curves of velocity versus time that agree well with the experimental measurements. Simulation then shows that the inner liner underwent a shock-less compression to approximately 19 GPa and reached an off-Hugoniot high-pressure state. According to the scaling law that the maximum loading pressure is proportional to the square of the load current amplitude, the results demonstrate that such a compact capacitor bank as CQ-3 has the potential to generate pressure as high as 100 GPa within the inner liner in such an implosion experiment. It is emphasized that the technique described in this paper can be easily replicated at low cost., (© 2021. The Author(s).)

Both histologic subtypes and tumor mutation burden (TMB) represent important biomarkers in lung cancer, with implications for patient prognosis and treatment decisions. Typically, TMB is evaluated by comprehensive genomic profiling but this requires use of finite tissue specimens and costly, time-consuming laboratory processes. Histologic subtype classification represents an established component of lung adenocarcinoma histopathology, but can be challenging and is associated with substantial inter-pathologist variability. Here we developed a deep learning system to both classify histologic patterns in lung adenocarcinoma and predict TMB status using de-identified Hematoxylin and Eosin (H&E) stained whole slide images. We first trained a convolutional neural network to map histologic features across whole slide images of lung cancer resection specimens. On evaluation using an external data source, this model achieved patch-level area under the receiver operating characteristic curve (AUC) of 0.78-0.98 across nine histologic features. We then integrated the output of this model with clinico-demographic data to develop an interpretable model for TMB classification. The resulting end-to-end system was evaluated on 172 held out cases from TCGA, achieving an AUC of 0.71 (95% CI 0.63-0.80). The benefit of using histologic features in predicting TMB is highlighted by the significant improvement this approach offers over using the clinical features alone (AUC of 0.63 [95% CI 0.53-0.72], p = 0.002). Furthermore, we found that our histologic subtype-based approach achieved performance similar to that of a weakly supervised approach (AUC of 0.72 [95% CI 0.64-0.80]). Together these results underscore that incorporating histologic patterns in biomarker prediction for lung cancer provides informative signals, and that interpretable approaches utilizing these patterns perform comparably with less interpretable, weakly supervised approaches., (© 2021. The Author(s).)

The ligation site of the inferior mesenteric artery (IMA) during laparoscopic radical resection for rectal cancer has been controversial. Consecutive patients (n = 205) with rectal cancer who underwent laparoscopic-assisted low anterior resection from January 2009 to December 2015 were retrospectively analyzed. The patients were divided into high ligation (n = 126) and improved low ligation groups (n = 79). A total of 205 rectal cancer patients underwent laparoscopic assisted anterior resection: 126 patients in the high ligation group and 79 patients in the improved low ligation group. The improved low ligation group was better than the high ligation group in terms of postoperative flatus time and postoperative defecation time. There were no differences between the groups in terms of blood loss, operation time, total number of lymph nodes, anastomotic leakage, postoperative time to first liquid diet and postoperative hospital stay. There were also no differences in 5-year overall survival (OS). Compared to high ligation, the improved low ligation ensures the extent of lymph node dissection, and promotes the early recovery of postoperative gastrointestinal function, but does not increase the operation time, bleeding risk, or anastomotic leakage. A ligation site of the IMA in laparoscopic rectal cancer surgery may not influence oncological outcomes.

One of the main culprits of Alzheimer's disease (AD) is the formation of toxic amyloid-β (Aβ) peptide polymers and the aggregation of Aβ to form plaques in the brain. We have developed techniques to purify the catalytic domain of plasmin, micro-plasmin (µPlm), which can be used for an Aβ-clearance based AD therapy. However, in serum, µPlm is irreversibly inhibited by its principal inhibitor α2-antiplasmin (α2-AP). In this study, we engineered and selected mutant forms of µPlm that are both catalytically active and insensitive to α2-AP inhibition. We identified surface residues of μPlm that might interact and bind α2-AP, and used an alanine-scanning mutagenesis method to select residues having higher activity but lower α2-AP inhibition. Then we employed saturation mutagenesis for further optimize both properties. Modeled complex structure of µPlm/α2-AP shows that F587 is a critical contact residue, which can be used as a starting position for further investigation.

Disruption of re-endothelialization and haemodynamic balance remains a critical side effect of drug-eluting stents (DES) for preventing intimal hyperplasia. Previously, we found that 5-aminolevulinic acid-mediated sonodynamic therapy (ALA-SDT) suppressed macrophage-mediated inflammation in atherosclerotic plaques. However, the effects on intimal hyperplasia and re-endothelialization remain unknown. In this study, 56 rabbits were randomly assigned to control, ultrasound, ALA and ALA-SDT groups, and each group was divided into two subgroups (n = 7) on day 3 after right femoral artery balloon denudation combined with a hypercholesterolemic diet. Histopathological analysis revealed that ALA-SDT enhanced macrophage apoptosis and ameliorated inflammation from day 1. ALA-SDT inhibited neointima formation without affecting re-endothelialization, increased blood perfusion, decreased the content of macrophages, proliferating smooth muscle cells (SMCs) and collagen but increased elastin by day 28. In vitro, ALA-SDT induced macrophage apoptosis and reduced TNF-α, IL-6 and IL-1β via the ROS-PPARγ-NF-κB signalling pathway, which indirectly inhibited human umbilical artery smooth muscle cell (HUASMC) proliferation, migration and IL-6 production. ALA-SDT effectively inhibits intimal hyperplasia without affecting re-endothelialization. Hence, its clinical application combined with bare-metal stent (BMS) implantation presents a potential strategy to decrease bleeding risk caused by prolonged dual-antiplatelet regimen after DES deployment.

High temperature studies of spin Hall effect have often been neglected despite its profound significance in real-world devices. In this work, high temperature spin torque ferromagnetic resonance measurement was performed to evaluate the effects of temperature on the Gilbert damping and spin Hall efficiency of Pt x Cu 1-x . When the temperature was varied from 300 K to 407 K, the Gilbert damping was relatively stable with a change of 4% at composition x = 66%. Alloying Pt and Cu improved the spin Hall efficiency of Pt 75 Cu 25 /Co/Ta by 29% to a value of 0.31 ± 0.03 at 407 K. However, the critical switching current density is dependent on the ratio between the Gilbert damping and spin Hall efficiency and the smallest value was observed when x = 47%. It was found that at this concentration, the spin transparency was at its highest at 0.85 ± 0.09 hence indicating the importance of interfacial transparency for energy efficient devices at elevated temperature.

The spin-orbit torque (SOT) effective fields, namely field-like and damping-like terms, depend on the thicknesses of heavy metal (HM) and ferromagnetic metal (FM) layers, in a stack comprising of HM/FM/HM or oxide. In this work, we report on the dependence of the SOT effective fields on the magnetization uniformity in the wires comprising of Ta/Co/Pt layer structure. SOT dependence on magnetization uniformity dependence was investigated by concurrent variation of the magnetization uniformity in Co layer and characterization of the SOT effective fields in each wire which excludes the layer thickness dependence influences. Our experimental results reveal that the field-like term decreases while the damping-like term increases with increasing Co magnetization uniformity. The magnetization uniformity influence on the effective fields is attributed to the spin Hall effect, which contributes to the SOT.

Identifying the occurrence mechanism of drug-induced side effects (SEs) is critical for design of drug target and new drug development. The expression of genes in biological processes is regulated by transcription factors(TFs) and/or microRNAs. Most of previous studies were focused on a single level of gene or gene sets, while studies about regulatory relationships of TFs, miRNAs and biological processes are very rare. Discovering the complex regulating relations among TFs, gene sets and miRNAs will be helpful for researchers to get a more comprehensive understanding about the mechanism of side reaction. In this study, a framework was proposed to construct the relationship network of gene sets, miRNAs and TFs involved in side effects. Through the construction of this network, the potential complex regulatory relationship in the occurrence process of the side effects was reproduced. The SE-gene set network was employed to characterize the significant regulatory SE-gene set interaction and molecular basis of accompanied side effects. A total of 117 side effects complex modules including four types of regulating patterns were obtained from the SE-gene sets-miRNA/TF complex regulatory network. In addition, two cases were used to validate the complex regulatory modules which could more comprehensively interpret occurrence mechanism of side effects.

Antibiotics in water have recently caused increasing concerns for public health and ecological environments. In this work, we demonstrated polydopamine-coated graphene oxide/Fe 3 O 4 (PDA@GO/Fe 3 O 4 ) imprinted nanoparticles coupled with magnetic separation for fast and selective removal of fluoroquinolone antibiotics in water. The nanoparticles were prepared by the self-polymerization of dopamine using sarafloxacin as a template. The imprinted PDA film of 10~20 nm uniformly covered the surface of GO/Fe 3 O 4 providing selective binding sites. The nanoparticles showed rapid binding and a large capacity (70.9 mg/g). The adsorption data fitted well the Langmuir and pseudo-second order kinetic equations. The nanoparticles could be easily separated by a magnet following the adsorption and then regenerated by simple washing for repetitive adsorptions. The nanoparticles were successfully used for the removal of fluoroquinolone antibiotics in seawater, with removal efficiencies of more than 95%. The proposed strategy has potentials for efficient removal of antibiotics in environmental water.

Excitatory amino acid transporter 2 (EAAT2), also known as glial glutamate transporter type 1 (GLT-1), plays an important role in maintaining the extracellular glutamate concentrations below neurotoxic levels. The highly conserved TM2 transmembrane domain of GLT-1 maintains a stable position during the transport cycle; however, the effect of the transport cycle on the topology of TM4 in not well established. To further reveal the function of TM4, two cysteine pairs between TM2 and TM4 were introduced using site-directed mutagenesis. A significant decrease of transport activity was observed in the I93C/V241C and I97C/V241C mutants upon application of the oxidative cross-linking reagent, copper (II) (1,10-phenanthroline) 3 (CuPh), which suggests that a conformational shift is essential for transporter activity. Furthermore, the decrease in activity by CuPh crosslinking was enhanced in external media with glutamate or potassium, which suggests that TM2 and TM4 assume closer proximity in the inward-facing conformation of the transporter. Our results suggest that the TM4 domain of GLT-1, and potentially other glutamate transporters, undergoes a complex conformational shift during substrate translocation, which involves an increase in the proximity of the TM2 and TM4 domains in the inward-facing conformation.

Recent years have witnessed an increasing interest in highly-efficient absorbers of visible light for the conversion of solar energy into electrochemical energy. This study presents a TiO2-Au bilayer that consists of a rough Au film under a TiO2 film, which aims to enhance the photocurrent of TiO2 over the whole visible region and may be the first attempt to use rough Au films to sensitize TiO2. Experiments show that the bilayer structure gives the optimal optical and photoelectrochemical performance when the TiO2 layer is 30 nm thick and the Au film is 100 nm, measuring the absorption 80-90% over 400-800 nm and the photocurrent intensity of 15 μA·cm(-2), much better than those of the TiO2-AuNP hybrid (i.e., Au nanoparticle covered by the TiO2 film) and the bare TiO2 film. The superior properties of the TiO2-Au bilayer can be attributed to the rough Au film as the plasmonic visible-light sensitizer and the photoactive TiO2 film as the electron accepter. As the Au film is fully covered by the TiO2 film, the TiO2-Au bilayer avoids the photocorrosion and leakage of Au materials and is expected to be stable for long-term operation, making it an excellent photoelectrode for the conversion of solar energy into electrochemical energy in the applications of water splitting, photocatalysis and photosynthesis.

Humans benefit from extensive cooperation; however, the existence of free-riders may cause cooperation to collapse. This is called the social dilemma. It has been shown that punishing free-riders is an effective way of resolving this problem. Because punishment is costly, this gives rise to the second-order social dilemma. Without exception, existing solutions rely on some stringent assumptions. This paper proposes, under very mild conditions, a simple model of a public goods game featuring increasing returns to scale. We find that punishers stand out and even dominate the population provided that the degree of increasing returns to scale is large enough; consequently, the second-order social dilemma dissipates. Historical evidence shows that people are more willing to cooperate with others and punish defectors when they suffer from either internal or external menaces. During the prehistoric age, the abundance of contributors was decisive in joint endeavours such as fighting floods, defending territory, and hunting. These situations serve as favourable examples of public goods games in which the degrees of increasing returns to scale are undoubtedly very large. Our findings show that natural selection has endowed human kind with a tendency to pursue justice and punish defection that deviates from social norms.

On-chip integration of optical detection units into the microfluidic systems for online monitoring is highly desirable for many applications and is also well in line with the spirit of optofluidics technology-fusion of optics and microfluidics for advanced functionalities. This paper reports the construction of a UV-Vis spectrophotometer on a microreactor, and demonstrates the online monitoring of the photocatalytic degradations of methylene blue and methyl orange under different flow rates and different pH values by detecting the intensity change and/or the peak shift. The integrated device consists of a TiO2-coated glass substrate, a PDMS micro-sized reaction chamber and two flow cells. By comparing with the results of commercial equipment, we have found that the measuring range and the sensitivity are acceptable, especially when the transmittance is in the range of 0.01-0.9. This integrated optofluidic device can significantly cut down the test time and the sample volume, and would provide a versatile platform for real-time characterization of photochemical performance. Moreover, its online monitoring capability may enable to access the usually hidden information in biochemical reactions like intermediate products, time-dependent processes and reaction kinetics.

Infectious agents are the third highest human cancer risk factor and may have a greater role in the origin and/or progression of cancers, and related pathogenesis. Thus, knowing the specific viruses and microbial agents associated with a cancer type may provide insights into cause, diagnosis and treatment. We utilized a pan-pathogen array technology to identify the microbial signatures associated with triple negative breast cancer (TNBC). This technology detects low copy number and fragmented genomes extracted from formalin-fixed paraffin embedded archival tissues. The results, validated by PCR and sequencing, define a microbial signature present in TNBC tissue which was underrepresented in normal tissue. Hierarchical clustering analysis displayed two broad microbial signatures, one prevalent in bacteria and parasites and one prevalent in viruses. These signatures demonstrate a new paradigm in our understanding of the link between microorganisms and cancer, as causative or commensal in the tumor microenvironment and provide new diagnostic potential.

Reaching a comprehensive understanding of how nature solves the problem of degrading recalcitrant biomass may eventually allow development of more efficient biorefining processes. Here we interpret genomic and proteomic information generated from a cellulolytic microbial consortium (termed F1RT) enriched from soil. Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in F1RT indicate that its constituent microbes cooperate in both cellulose-degrading and other important metabolic processes. Support for cellulolytic inter-species cooperation came from the discovery of F1RT microbes that encode and express complimentary enzymatic inventories that include both extracellular cellulosomes and secreted free-enzyme systems. Metabolic reconstruction of the seven F1RT phylotypes predicted a wider genomic rationale as to how this particular community functions as well as possible reasons as to why biomass conversion in nature relies on a structured and cooperative microbial community.

Adverse drug reactions (ADRs) are caused by interactions between drugs or their metabolites and specific proteins. Knowledge of these proteins is important for facilitating mechanistic research of ADRs and new drug discovery. Here, we identified 41 network modules from an ADR-protein network; analysed the function of each module; revealed the potential accompanying actions of the ADRs and the new ADR-related proteins (ADRPs) to a unique ADR and studied the characteristics of composition, subcellular location and tissue distribution of these ADRPs by comparing them with drug-related proteins (DRPs). The results indicated that ADRs are mainly caused by risk drug-related proteins (RDRPs) and that drug off-target effects are a secondary cause. Biological processes that enzymes involve are the main reason for the occurrence of ADRs. However, drug-related transporters have a higher risk of inducing ADRs than drug-related enzymes do, and ADRPs locating in the cell membrane tend to induce multiple ADRs.