Comment on "Atomic Scale Structure and Chemical Composition across Order-Disorder Interfaces"

Interfaces have long been known to be the key to many mechanical and electric properties. To nickel base superalloys which have perfect creep and fatigue properties and have been widely used as materials of turbine blades, interfaces determine the strengthening capacities in high temperature. By means of high resolution scanning transmission electron microscopy (HRSTEM) and 3D atom probe (3DAP) tomography, Srinivasan et al. proposed a new point that in nickel base superalloys there exist two different interfacial widths across the {\gamma}/{\gamma}' interface, one corresponding to an order-disorder transition, and the other to the composition transition. We argue about this conclusion in this comment

StubCoder: Automated Generation and Repair of Stub Code for Mock Objects

Mocking is an essential unit testing technique for isolating the class under test (CUT) from its dependencies. Developers often leverage mocking frameworks to develop stub code that specifies the behaviors of mock objects. However, developing and maintaining stub code is labor-intensive and error-prone. In this paper, we present StubCoder to automatically generate and repair stub code for regression testing. StubCoder implements a novel evolutionary algorithm that synthesizes test-passing stub code guided by the runtime behavior of test cases. We evaluated our proposed approach on 59 test cases from 13 open-source projects. Our evaluation results show that StubCoder can effectively generate stub code for incomplete test cases without stub code and repair obsolete test cases with broken stub code.Comment: This paper was accepted by the ACM Transactions on Software Engineering and Methodology (TOSEM) in July 202

Escherichia coli infection indicates favorable outcomes in patients with infected pancreatic necrosis

IntroductionInfected pancreatic necrosis (IPN) is a severe complication of acute necrotizing pancreatitis with increasing morbidity. Escherichia coli is the most frequently cultured microorganism in IPN. However, the implications of Escherichia coli infection on the outcomes of patients with IPN remain unclear. Therefore, this study aimed to evaluate the clinical impacts of Escherichia coli infection on IPN.MethodsA prospective database with consecutive patients with IPN between January 2010 and April 2022 at a tertiary hospital was post-hoc analyzed. The clinical and microbiological characteristics, surgical management, and follow-up data of patients with and without Escherichia coli infection were compared.ResultsA total of 294 IPN patients were enrolled in this cohort. Compared with non-Escherichia coli infection cases (n=80, 27.2%), patients with Escherichia coli infection (n=214, 72.8%) were characterized by more frequent polymicrobial infections (77.5% vs. 65.0%, P=0.04) but a lower occurrence of severe acute pancreatitis (SAP) (42.5% vs. 61.7%, P=0.003). In addition, significantly lower mortality (12.5% vs. 30.4%, p=0.002), fewer step-up surgical interventions (73.8% vs. 85.1%, P=0.025), and a lower rate of multiple organ failure (MOF) (25.0% vs. 40.2%, P=0.016) were also observed in patients with Escherichia coli infection. Multivariate analysis of mortality predictors indicated that MOF (odds ratio [OR], 6.197; 95% confidence interval [CI], 2.373–16.187; P<0.001) and hemorrhage (OR, 3.485; 95% CI, 1.623–7.487; P=0.001) were independent predictors associated with higher mortality in patients with IPN. Escherichia coli infection was significantly associated with a lower mortality (OR, 0.302; 95% CI, 0.121–0.751; P= 0.01).ConclusionEscherichia coli infection indicates a favorable prognosis in patients with IPN, although the mechanism needs further investigation

The evolution of cloud and aerosol microphysics at the summit of Mt. Tai, China

The influence of aerosols, both natural and anthropogenic, remains a major area of uncertainty when predicting the properties and the behaviours of clouds and their influence on climate. In an attempt to better understand the microphysical properties of cloud droplets, the simultaneous variations in aerosol microphysics and their potential interactions during cloud life cycles in the North China Plain, an intensive observation took place from 17 June to 30 July 2018 at the summit of Mt. Tai. Cloud microphysical parameters were monitored simultaneously with number concentrations of cloud condensation nuclei (NCCN) at different supersaturations, PM2:5 mass concentrations, particle size distributions and meteorological parameters. Number concentrations of cloud droplets (NC), liquid water content (LWC) and effective radius of cloud droplets (reff) show large variations among 40 cloud events observed during the campaign. The low values of reff and LWC observed at Mt. Tai are comparable with urban fog. Clouds on clean days are more susceptible to the change in concentrations of particle number (NP), while clouds formed on polluted days might be more sensitive to meteorological parameters, such as updraft velocity and cloud base height. Through studying the size distributions of aerosol particles and cloud droplets, we find that particles larger than 150 nm play important roles in forming cloud droplets with the size of 5-10 μm. In general, LWC consistently varies with reff. As NC increases, reff changes from a trimodal distribution to a unimodal distribution and shifts to smaller size mode. By assuming a constant cloud thickness and ignoring any lifetime effects, increase in NC and decrease in reff would increase cloud albedo, which may induce a cooling effect on the local climate system. Our results contribute valuable information to enhance the understanding of cloud and aerosol properties, along with their potential interactions on the North China plain. © Author(s) 2020

Marine organic matter in the remote environment of the Cape Verde islands-an introduction and overview to the MarParCloud campaign

The project MarParCloud (Marine biological production, organic aerosol Particles and marine Clouds: a process chain) aims to improve our understanding of the genesis, modification and impact of marine organic matter (OM) from its biological production, to its export to marine aerosol particles and, finally, to its ability to act as ice-nucleating particles (INPs) and cloud condensation nuclei (CCN). A field campaign at the Cape Verde Atmospheric Observatory (CVAO) in the tropics in September-October 2017 formed the core of this project that was jointly performed with the project MARSU (MARine atmospheric Science Unravelled). A suite of chemical, physical, biological and meteorological techniques was applied, and comprehensive measurements of bulk water, the sea surface microlayer (SML), cloud water and ambient aerosol particles collected at a ground-based and a mountain station took place. Key variables comprised the chemical characterization of the atmospherically relevant OM components in the ocean and the atmosphere as well as measurements of INPs and CCN. Moreover, bacterial cell counts, mercury species and trace gases were analyzed. To interpret the results, the measurements were accompanied by various auxiliary parameters such as air mass back-trajectory analysis, vertical atmospheric profile analysis, cloud observations and pigment measurements in seawater. Additional modeling studies supported the experimental analysis. During the campaign, the CVAO exhibited marine air masses with low and partly moderate dust influences. The marine boundary layer was well mixed as indicated by an almost uniform particle number size distribution within the boundary layer. Lipid biomarkers were present in the aerosol particles in typical concentrations of marine background conditions. Accumulation-and coarse-mode particles served as CCN and were efficiently transferred to the cloud water. The ascent of ocean-derived compounds, such as sea salt and sugar-like compounds, to the cloud level, as derived from chemical analysis and atmospheric transfer modeling results, denotes an influence of marine emissions on cloud formation. Organic nitrogen compounds (free amino acids) were enriched by several orders of magnitude in submicron aerosol particles and in cloud water compared to seawater. However, INP measurements also indicated a significant contribution of other non-marine sources to the local INP concentration, as (biologically active) INPs were mainly present in supermicron aerosol particles that are not suggested to undergo strong enrichment during ocean-atmosphere transfer. In addition, the number of CCN at the supersaturation of 0.30 % was about 2.5 times higher during dust periods compared to marine periods. Lipids, sugar-like compounds, UV-absorbing (UV: ultraviolet) humic-like substances and low-molecularweight neutral components were important organic compounds in the seawater, and highly surface-active lipids were enriched within the SML. The selective enrichment of specific organic compounds in the SML needs to be studied in further detail and implemented in an OM source function for emission modeling to better understand transfer patterns, the mechanisms of marine OM transformation in the atmosphere and the role of additional sources. In summary, when looking at particulate mass, we see oceanic compounds transferred to the atmospheric aerosol and to the cloud level, while from a perspective of particle number concentrations, sea spray aerosol (i.e., primary marine aerosol) contributions to both CCN and INPs are rather limited. © Author(s) 2020

Marine organic matter in the remote environment of the Cape Verde islands – an introduction and overview to the MarParCloud campaign

The project MarParCloud (Marine biological production, organic aerosol Particles and marine Clouds: a process chain) aims to improve our understanding of the genesis, modification and impact of marine organic matter (OM) from its biological production, to its export to marine aerosol particles and, finally, to its ability to act as ice-nucleating particles (INPs) and cloud condensation nuclei (CCN). A field campaign at the Cape Verde Atmospheric Observatory (CVAO) in the tropics in September–October 2017 formed the core of this project that was jointly performed with the project MARSU (MARine atmospheric Science Unravelled). A suite of chemical, physical, biological and meteorological techniques was applied, and comprehensive measurements of bulk water, the sea surface microlayer (SML), cloud water and ambient aerosol particles collected at a ground-based and a mountain station took place. Key variables comprised the chemical characterization of the atmospherically relevant OM components in the ocean and the atmosphere as well as measurements of INPs and CCN. Moreover, bacterial cell counts, mercury species and trace gases were analyzed. To interpret the results, the measurements were accompanied by various auxiliary parameters such as air mass back-trajectory analysis, vertical atmospheric profile analysis, cloud observations and pigment measurements in seawater. Additional modeling studies supported the experimental analysis. During the campaign, the CVAO exhibited marine air masses with low and partly moderate dust influences. The marine boundary layer was well mixed as indicated by an almost uniform particle number size distribution within the boundary layer. Lipid biomarkers were present in the aerosol particles in typical concentrations of marine background conditions. Accumulation- and coarse-mode particles served as CCN and were efficiently transferred to the cloud water. The ascent of ocean-derived compounds, such as sea salt and sugar-like compounds, to the cloud level, as derived from chemical analysis and atmospheric transfer modeling results, denotes an influence of marine emissions on cloud formation. Organic nitrogen compounds (free amino acids) were enriched by several orders of magnitude in submicron aerosol particles and in cloud water compared to seawater. However, INP measurements also indicated a significant contribution of other non-marine sources to the local INP concentration, as (biologically active) INPs were mainly present in supermicron aerosol particles that are not suggested to undergo strong enrichment during ocean–atmosphere transfer. In addition, the number of CCN at the supersaturation of 0.30 % was about 2.5 times higher during dust periods compared to marine periods. Lipids, sugar-like compounds, UV-absorbing (UV: ultraviolet) humic-like substances and low-molecular-weight neutral components were important organic compounds in the seawater, and highly surface-active lipids were enriched within the SML. The selective enrichment of specific organic compounds in the SML needs to be studied in further detail and implemented in an OM source function for emission modeling to better understand transfer patterns, the mechanisms of marine OM transformation in the atmosphere and the role of additional sources. In summary, when looking at particulate mass, we see oceanic compounds transferred to the atmospheric aerosol and to the cloud level, while from a perspective of particle number concentrations, sea spray aerosol (i.e., primary marine aerosol) contributions to both CCN and INPs are rather limited

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Identification of Rab7 as an autophagy marker: potential therapeutic approaches and the effect of Qi Teng Xiao Zhuo granule in chronic glomerulonephritis

AbstractContext Qi Teng Xiao Zhuo granule (QTXZG) is a traditional Chinese medicine (TCM) used for therapeutic effects on chronic glomerulonephritis (CGN). However, the underlying mechanism remains unclear.Objective To investigate the molecular mechanism of QTXZG on CGN by proteomics.Materials and methods The CGN model was induced in Sprague–Dawley rats by injecting adriamycin (3.5 mg/kg, Day 1; 3.0 mg/kg, Day 14) twice through the tail vein. Urine samples were collected on the 21st day; and the rats divided randomly into control, adriamycin, QTXZG administration groups. Rats in the QTXZG group received QTXZG (10.8 g/kg); control and adriamycin groups were given physiological saline once per day for 30 days. Proteomics was applied to identify the candidate proteins combined with autophagy database and verified by immunofluorescence (IF) and western blots (WB).Results 278 differentially expressed proteins (DEPs) were identified based on proteomics and Rab7 was screened as an autophagy protein biomarker. In vitro cell experiments, we found that QTXZG (20%, IC50 = 23.47%) could decrease the expression of NLRP3, Caspase-1, IL-18, IL-1β, while increasing the expression of Pink1, Parkin, Rab7, Podocalyxin. The cell apoptosis rate increased from 6.68 ± 0.07 to 11.03 ± 0.36%. Overexpression of Rab7 resulted in an increase in autophagy relevant protein expression.Discussion and conclusion TCM CGN-regulating herbs (QTXZG) can exert therapeutic effects by affecting the Rab7/Pink1/Parkin pathway to promote mitochondrial autophagy. New breakthroughs in targeted Rab7 may eventually enable such applications