A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer.

While the effect of amplification-induced oncogene expression in cancer is known, the impact of copy-number gains on "bystander" genes is less understood. We create a comprehensive map of dosage compensation in cancer by integrating expression and copy number profiles from over 8000 tumors in The Cancer Genome Atlas and cell lines from the Cancer Cell Line Encyclopedia. Additionally, we analyze 17 cancer open reading frame screens to identify genes toxic to cancer cells when overexpressed.

Artificial Photosynthetic Assemblies Constructed by NH-UiO-66 Decorated with Spatially Separated Dual Cocatalysts for Enhanced Photocatalytic Uranium Reduction.

The phenomenon of rapid migration of photogenerated charges in natural photosynthetic systems has motivated the design of efficient photocatalysts capable of fast charge separation and efficient reaction kinetics for photocatalytically assisted enrichment and separation of uranium U(VI) in uranium wastewater. In this study, we developed a biomimetic photocatalytic system MnO/NH-UiO-66-rGO (M/UiO-rGO) with spatially separated dual cocatalysts. Among them, rGO functions to capture electrons and participates in reduction reactions, while MnO captures holes and participates in oxidation reactions.

Sol-gel transition effect based on konjac glucomannan thermosensitive hydrogel for photo-assisted uranium extraction.

Exploiting the intelligent photocatalysts capable of phase separation provides a promising solution to the removal of uranium, which is expected to solve the difficulty in separation and the poor selectivity of traditional photocatalysts in carbonate-containing uranium wastewater. In this paper, the γ-FeOOH/konjac glucomannan grafted with phenolic hydroxyl groups/poly-N-isopropylacrylamide (γ-FeOOH/KGM(Ga)/PNIPAM) thermosensitive hydrogel is proposed as the photocatalysts for extracting uranium from carbonate-containing uranium wastewater. The dynamic phase transformation is demonstrated to confirm the arbitrary transition of γ-FeOOH/KGM(Ga)/PNIPAM thermosensitive hydrogel from a dispersed state with a high specific surface area at low temperatures to a stable aggregated state at high temperatures.

Endogenous p53 inhibitor TIRR dissociates systemic metabolic health from oncogenic activity.

It is unclear whether metabolic health corresponds to reduced oncogenesis or vice versa. We study Tudor-interacting repair regulator (TIRR), an inhibitor of p53 binding protein 1 (53BP1)-mediated p53 activation, and the physiological consequences of enhancing tumor suppressor activity. Deleting TIRR selectively activates p53, significantly protecting against cancer but leading to a systemic metabolic imbalance in mice.

Motif-Aware miRNA-Disease Association Prediction via Hierarchical Attention Network.

As post-transcriptional regulators of gene expression, micro-ribonucleic acids (miRNAs) are regarded as potential biomarkers for a variety of diseases. Hence, the prediction of miRNA-disease associations (MDAs) is of great significance for an in-depth understanding of disease pathogenesis and progression. Existing prediction models are mainly concentrated on incorporating different sources of biological information to perform the MDA prediction task while failing to consider the fully potential utility of MDA network information at the motif-level.

Enhancing Commercially Iron Powder Electron Transport by Surface Biosulfuration to Achieve Uranium Extraction from Uranium Ore Wastewater.

The zero-valent iron (ZVI) has attracted increasing attention due to the enhanced reactivity of ZVI to uranium wastewater. However, ZVI practical application is hampered due to its susceptibility to oxidation and the formation of passivation layers during storage and in situ restoration. To address these issues, we used a biosulfuration approach to modify ZVI for application in uranium ore wastewater treatment.

Acetylation of xenogeneic silencer H-NS regulates biofilm development through the nitrogen homeostasis regulator in Shewanella.

Adjusting intracellular metabolic pathways and adopting suitable live state such as biofilms, are crucial for bacteria to survive environmental changes. Although substantial progress has been made in understanding how the histone-like nucleoid-structuring (H-NS) protein modulates the expression of the genes involved in biofilm formation, the precise modification that the H-NS protein undergoes to alter its DNA binding activity is still largely uncharacterized. This study revealed that acetylation of H-NS at Lys19 inhibits biofilm development in Shewanella oneidensis MR-1 by downregulating the expression of glutamine synthetase, a critical enzyme in glutamine synthesis.

Biogeochemical cycling in paddy soils controls antimony transformation: Roles of iron (oxyhydr)oxides, organic matter and sulfate.

In paddy fields, periodic flooding and drainage phases can significantly affect the availability of antimony (Sb), but the underlying mechanisms remain unclear. In this study, Sb-contaminated paddy soil was incubated under anaerobic (40 day) and subsequently aerobic (40-55 day) conditions. The Sb fractions was investigated and a kinetic model was established to quantitatively evaluate the main processes controlling Sb transformation.

Dynamics of the DYNLL1-MRE11 complex regulate DNA end resection and recruitment of Shieldin to DSBs.

The extent and efficacy of DNA end resection at DNA double-strand breaks (DSB) determine the repair pathway choice. Here we describe how the 53BP1-associated protein DYNLL1 works in tandem with the Shieldin complex to protect DNA ends. DYNLL1 is recruited to DSBs by 53BP1, where it limits end resection by binding and disrupting the MRE11 dimer.

A Novel Fiber-Optic Ice Sensor to Identify Ice Types Based on Total Reflection.

To address the issues of not accurately identifying ice types and thickness in current fiber-optic ice sensors, in this paper, we design a novel fiber-optic ice sensor based on the reflected light intensity modulation method and total reflection principle. The performance of the fiber-optic ice sensor was simulated by ray tracing. The low-temperature icing tests validated the performance of the fiber-optic ice sensor.

Dynamics of the DYNLL1/MRE11 complex regulates DNA end resection and recruitment of the Shieldin complex to DSBs.

Extent and efficacy of DNA end resection at DNA double strand break (DSB)s determines the choice of repair pathway. Here we describe how the 53BP1 associated protein DYNLL1 works in tandem with Shieldin and the CST complex to protect DNA ends. DYNLL1 is recruited to DSBs by 53BP1 where it limits end resection by binding and disrupting the MRE11 dimer.

sp. nov., a novel carotenoid-producing bacterium isolated from coastal sediment.

A Gram-stain-negative, aerobic, non-motile and pleomorphic bacterium designated as YG55 was isolated from a coastal sediment sample. Growth was found to occur at 10-37 °C (optimum, 28 °C), at pH 6-9 (optimum, pH 8) and in 0-6 % NaCl (optimum, 1 %). The results of 16S rRNA gene-based analysis showed that strain YG55 was related to the members of the genus and shared the highest identity of 99.

Non-targeted metabolomics and 16s rDNA reveal the impact of uranium stress on rhizosphere and non-rhizosphere soil of ryegrass.

As a radioactive heavy metal element with a long half-life, uranium causes environmental pollution when it enters the surrounding soil. This study analyzed the changes about soil enzyme activity, non-targeted metabolomics, microbial community structure and function microbial community structure and function to assess the differences in the effects of uranium stress on rhizosphere and non-rhizosphere soil. Results showed that uranium stress significantly inhibited the activities of urease and sucrase in rhizosphere and non-rhizosphere, which had less effect on rhizosphere.

Incorporating higher order network structures to improve miRNA-disease association prediction based on functional modularity.

As microRNAs (miRNAs) are involved in many essential biological processes, their abnormal expressions can serve as biomarkers and prognostic indicators to prevent the development of complex diseases, thus providing accurate early detection and prognostic evaluation. Although a number of computational methods have been proposed to predict miRNA-disease associations (MDAs) for further experimental verification, their performance is limited primarily by the inadequacy of exploiting lower order patterns characterizing known MDAs to identify missing ones from MDA networks. Hence, in this work, we present a novel prediction model, namely HiSCMDA, by incorporating higher order network structures for improved performance of MDA prediction.

RLFDDA: a meta-path based graph representation learning model for drug-disease association prediction.

Background: Drug repositioning is a very important task that provides critical information for exploring the potential efficacy of drugs. Yet developing computational models that can effectively predict drug-disease associations (DDAs) is still a challenging task. Previous studies suggest that the accuracy of DDA prediction can be improved by integrating different types of biological features.

CCAR2 functions downstream of the Shieldin complex to promote double-strand break end-joining.

The 53BP1-RIF1 pathway restricts the resection of DNA double-strand breaks (DSBs) and promotes blunt end-ligation by non-homologous end joining (NHEJ) repair. The Shieldin complex is a downstream effector of the 53BP1-RIF1 pathway. Here, we identify a component of this pathway, CCAR2/DBC1, which is also required for restriction of DNA end-resection.

Analysis of Tissue-Specific Defense Responses to in .

Sclerotinia stem rot (SSR) caused by () is the main disease threat of oilseed rape (), resulting in huge economic losses every year. SSR resistance manifests as quantitative disease resistance (QDR), and no gene with complete SSR resistance has been cloned or reported so far. Transcriptome analysis has revealed a large number of defense-related genes and response processes.

PPISB: A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel.

Protein-protein interactions (PPIs) play an essential role for most of biological processes in cells. Many computational algorithms have thus been proposed to predict PPIs. However, most of them heavily rest on the biological information of proteins while ignoring the latent structural features of proteins presented in a PPI network.

Feasibility and discriminatory value of tissue motion annular displacement in sepsis-induced cardiomyopathy: a single-center retrospective observational study.

Background: There is no formal diagnostic criterion for sepsis-induced cardiomyopathy (SICM), but left ventricular ejection fraction (LVEF) < 50% was the most commonly used standard. Tissue motion annular displacement (TMAD) is a novel speckle tracking indicator to quickly assess LV longitudinal systolic function. This study aimed to evaluate the feasibility and discriminatory value of TMAD for predicting SICM, as well as prognostic value of TMAD for mortality.

Comparison of past and current dental school curricula for dental students of National Taiwan University.

Background/purpose: The complete curriculum schedule of the School of Dentistry, National Taiwan University (NTU) appeared in 1960. This study aimed to understand the development of dental education in Taiwan by comparing the past and current dental school curricula of NTU.

Materials And Methods: This study collected the 1960, 1990 and 2020 dental school curriculum schedules for dental students of NTU from the related websites and used the documentary and secondary data analyses to further compare the obtained data.

OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice.

As a multigenic trait, rice tillering can optimize plant architecture for the maximum agronomic yield. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE14 (OsSPL14) has been demonstrated to be necessary and sufficient to inhibit rice branching, but the underlying mechanism remains largely unclear. Here, we demonstrated that OsSPL14, which is cleaved by miR529 and miR156, inhibits tillering by fine-tuning auxin transport in rice.

Contrast-Enhanced Ultrasonography Value for Early Prediction of Delayed Graft Function in Renal Transplantation Patients.

Objectives: Delayed graft function (DGF) is a common early complication after kidney transplantation. The aim of the present study was to evaluate the value of contrast-enhanced ultrasonography (CEUS) in the early prediction of DGF after kidney transplantation.

Methods: A total of 89 renal transplant recipients were retrospectively enrolled and divided into DGF group or normal graft function (NGF) group according to the allograft function.