Evaluation of automated cell disruptor methods for oomycetous and ascomycetous model organisms

Two automated cell disruptor-based methods for RNA extraction, disruption of thawed cells submerged in TRIzol Reagent (method QP), and direct disruption of frozen cells on dry ice (method CP), were optimized for a model oomycete, Phytophthora capsici, and a model filamentous ascomycete, Neurospora crassa. The results were compared with more conventional methods of manual grinding in a mortar and pestle under liquid nitrogen (method M&P) and those using lyophilized samples. A chip-based electrophoresis system showed that methods CP and M&P yielded high integrity RNA from both P. capsici and N. crassa. In contrast, method QP and lyophilized sample-based methods resulted in inconsistent RNA integrity between the two organisms, indicating they are not safe alternatives for method M&P. Microarray mRNA profiling for P. capsici revealed alterations in global mRNA profiles in those samples that the chip-based electrophoresis detected slight decreases in RNA integrity. Despite this, RNA integrity of these samples could still be high enough to pass conventional stringent quality control measures. This demonstrated the necessity of global mRNA profiling for the evaluation of RNA extraction protocols

Accounting conservatism and banking expertise on board of directors

Previous studies show mixed evidence of the role of banking expertise on the board of directors on accounting conservatism. In this paper, we add to this growing literature by providing an innovative way to measure banking expertise based on life-time working history in banks of all individual directors on the board. We find that accounting conservatism is negatively affected by banking expertise on the board. Also, the results indicate that banking expertise on the board has a more pronounced impact on accounting conservatism when firms have high bankruptcy risk and when firms have high financial leverage. The evidence has some implications for boards of directors

Biological activities of in vitro liverwort Marchantia polymorpha L. extracts

To overcome the problems in liverwort collecting such as small size and easily mixed with other species in the wild, we have successfully cultivated Marchantia polymorpha L. under in vitro conditions in the previous study. The aim of this study is to evaluate the biological activities of this in vitro biomass as a confirmation of the sufficient protocol in cultivation this species. Cultured biomass was dried at a temperature of 45-50 oC to constant weight and ground into a fine powder. The coarse powder was extracted with organic solvents of increasing polarization including n-hexane, chloroform, ethyl acetate, and ethanol using the maceration technique. Four extracts were investigated antioxidant (iron reduction power, DPPH), antibacterial (agar diffusion), tyrosinase inhibitory activity, anti-proliferation on MCF-7 cells. Additionally, the presence of natural metabolite groups of the extracts was detected by using specific reagents. For antioxidant activity, ethyl acetate fraction extract had the highest iron reducing power and DPPH free radical scavenging ability with IC50 = 439.31 µg ml-1. All three n-hexane, chloroform, and ethyl acetate extracts possessed resistance to the bacterial strain tested. At a concentration of 2 mg ml-1, n-hexane and chloroform extracts had the highest percentage of tyrosinase inhibition (69.54 and 69.10%, respectively). The n-hexane extract is a potent extract that inhibits the proliferation of MCF-7 cells with the lowest IC50 of 38.15 µg ml-1. A preliminary chemical composition survey showed that the cultured biomass liverwort contains many bioactive compounds, particularly the compounds of range of non- and less-polarized fractions

A cohesive zone model for fracture initiation and propagation of fused silica direct bonding interface

International audienceFused silica direct bonding is of particular interest for optical system manufacturing for spatial applications. However, in order to validate the European Space Agency standards, a better understanding of the assemblies mechanical behavior is required. Therefore, it is important to develop some predictive tools to determine numerically mechanical strength of complex assemblies. In this paper, a cohesive zone model is proposed to model the direct bonding interface behavior. In order to determine the mechanical strength of the interface, a propagation test, and an initiation test on a free edge the cleavage test have been performed on direct bonded fused silica samples. The FIT test (Flexible Initiation Test) is also used to identify the properties of the direct bonding joint. At the end, a comparative analyses is proposed between experimental results and finite elements models of the propagation and initiation tests

Preparation and Foliar Application of Oligochitosan - Nanosilica on the Enhancement of Soybean Seed Yield

Oligochitosan with weight average molecu-lar weight (Mw) of 5000 g/mol was prepared by gamma Co-60 radiation degradation of 4% chitosan solution containing 0.5% H2O2 at 21 kGy. Nanosilica with size of 10 – 30 nm was synthesized by calcination of acid treated rice husk at 700o C for 2 h. The mixture of 2% oligo-chitosan-2% nanosilica was prepared by dispersion of nanosilica in oligochitosan solution. Oligochitosan, nanosilica and their mixture were characterized by gel permeation chromatography (GPC), transmission electr-on microscopy (TEM), X-ray diffraction (XRD), energy dispersive x-ray spectroscopy (EDX), Ultraviolet-visible spectroscopy (UV-Vis), and Furrier transform infrared spectroscopy (FT-IR). Effect of foliar application of oli-gochitosan and oligochitosan-nanosilica on soybean seed yield was conducted in experimental field. Results indi-cated that soybean seed yield increased 10.5 and 17.0% for oligochitosan and oligochitosan-nanosilica, respect-tively for the control. Radiation degraded oligo-chitosan and its mixture with nanosilica can be potentially used for cultivation of soybean with enhanced seed yield

Pathogenicity of an H5N1 avian influenza virus isolated in Vietnam in 2012 and reliability of conjunctival samples for diagnosis of infection

The continued spread of highly pathogenic avian influenza virus (HPAIV) subtype H5N1 among poultry in Vietnam poses a potential threat to animals and public health. To evaluate the pathogenicity of a 2012 H5N1 HPAIV isolate and to assess the utility of conjunctival swabs for viral detection and isolation in surveillance, an experimental infection with HPAIV subtype H5N1 was carried out in domestic ducks. Ducks were infected with 10[superscript 7.2] TCID[subscript 50] of A/duck/Vietnam/QB1207/2012 (H5N1), which was isolated from a moribund domestic duck. In the infected ducks, clinical signs of disease, including neurological disorder, were observed. Ducks started to die at 3 days-post-infection (dpi), and the study mortality reached 67%. Viruses were recovered from oropharyngeal and conjunctival swabs until 7 dpi and from cloacal swabs until 4 dpi. In the ducks that died or were sacrificed on 3, 5, or 6 dpi, viruses were recovered from lung, brain, heart, pancreas and intestine, among which the highest virus titers were in the lung, brain or heart. Results of virus titration were confirmed by real-time RT-PCR. Genetic and phylogenetic analysis of the HA gene revealed that the isolate belongs to clade 2.3.2.1 similarly to the H5N1 viruses isolated in Vietnam in 2012. The present study demonstrated that this recent HPAI H5N1 virus of clade 2.3.2.1 could replicate efficiently in the systemic organs, including the brain, and cause severe disease with neurological symptoms in domestic ducks. Therefore, this HPAI H5N1 virus seems to retain the neurotrophic feature and has further developed properties of shedding virus from the oropharynx and conjunctiva in addition to the cloaca, potentially posing a higher risk of virus spread through cross-contact and/or environmental transmission. Continued surveillance and diagnostic programs using conjunctival swabs in the field would further verify the apparent reliability of conjunctival samples for the detection of AIV.Japan Society for the Promotion of Science (Grant-in-Aid for Bilateral Joint Projects)Heiwa Nakajima FoundationNational Institute of Allergy and Infectious Diseases (U.S.) (Contract HHSN2662007000010C

Satellites May Underestimate Rice Residue and Associated Burning Emissions in Vietnam

In this study, we estimate rice residue, associated burning emissions, and compare results with existing emissions inventories employing a bottom-up approach. We first estimated field-level post-harvest rice residues, including separate fuel-loading factors for rice straw and rice stubble. Results suggested fuel-loading factors of 0.27 kg/sq m (+/-0.033), 0.61 kg/sq m (+/-0.076), and 0.88 kg/sq m (+/-0.083) for rice straw, stubble, and total post-harvest biomass, respectively. Using these factors, we quantified potential emissions from rice residue burning and compared our estimates with other studies. Our results suggest total rice residue burning emissions as 2.24 Gg PM2.5, 36.54 Gg CO and 567.79 Gg CO2 for Hanoi Province, which are significantly higher than earlier studies. We attribute our higher emission estimates to improved fuel-loading factors; moreover, we infer that some earlier studies relying on residue-to-product ratios could be underestimating rice residue emissions by more than a factor of 2.3 for Hanoi, Vietnam. Using the rice planted area data from the Vietnamese government, and combining our fuel-loading factors, we also estimated rice residue PM2.5 emissions for the entirety of Vietnam and compared these estimates with an existing all-sources emissions inventory, and the Global Fire Emissions Database (GFED). Results suggest 75.98 Gg of PM2.5 released from rice residue burning accounting for 12.8% of total emissions for Vietnam. The GFED database suggests 42.56 Gg PM2.5 from biomass burning with 5.62 Gg attributed to agricultural waste burning indicating satellite-based methods may be significantly underestimating emissions. Our results not only provide improved residue and emission estimates, but also highlight the need for emissions mitigation from rice residue burning

Long-term outcomes of primary cardiac malignant tumors: Difference between African American and Caucasian population

BACKGROUND: The survival outcome for primary cardiac malignant tumors (PMCTs) based on race has yet to be fully elucidated in previously published literature. This study aimed to address the general long-term outcome and survival rate differences in PMCTs among African Americans and Caucasian populations. METHODS: The 18 cancer registries database from the Surveillance, Epidemiology, and End Results (SEER) Program from 1975 to 2016 were utilized. Ninety-four African American (AA) and 647 Caucasian (CAU) patients from the SEER registry were available for survival analysis. The log-rank test was used to compare the difference in mortality between two populations and presented by the Kaplan-Meier curves. A multivariate Cox proportional hazards regression was used to determine the independent predictors of all-cause mortality. RESULTS: The overall 30-day, 1-year, and 5-year survival rates were 74%, 44.3%, and 16.6%, respectively, with a median survival of 10 months. There was no significant difference in survival rate between the two races (p-value = 0.55). The 1-year survival rate improved significantly during the study timeline in the AA population (13.3% during 1975-1998, 40.9% during 1999-2004, 50% during 2005-2010, and 59.7% during 2011-2016, p-value = 0.0064). Age of diagnosis, type of tumor, disease stage, and chemotherapy administration are the main factors that predict survival outcomes of PMCT patients. Interactive nomogram was developed based on significant predictors. CONCLUSIONS: PMCTs have remained one of the most lethal diseases with poor survival outcome. Survival rate improved during the timeline in AA patients, but in general, racial differences in survival outcome were not observed

HierarchyNet : learning to summarize source code with heterogeneous representations

Code representation is important to machine learning models in the code-related applications. Existing code summarization approaches primarily leverage Abstract Syntax Trees (ASTs) and sequential information from source code to generate code summaries while often overlooking the critical consideration of the interplay of dependencies among code elements and code hierarchy. However, effective summarization necessitates a holistic analysis of code snippets from three distinct aspects: lexical, syntactic, and semantic information. In this paper, we propose a novel code summarization approach utilizing Heterogeneous Code Representations (HCRs) and our specially designed HierarchyNet. HCRs adeptly capture essential code features at lexical, syntactic, and semantic levels within a hierarchical structure. HierarchyNet processes each layer of the HCR separately, employing a Heterogeneous Graph Transformer, a Tree-based CNN, and a Transformer Encoder. In addition, HierarchyNet demonstrates superior performance compared to fine-tuned pre-trained models, including CodeT5, and CodeBERT, as well as large language models that employ zero/few-shot settings, such as CodeLlama, StarCoder, and CodeGen. Implementation details can be found at https://github.com/FSoft-AI4Code/HierarchyNet