Creating an instance of the project skeleton on GitHub.

On the project page of bertha [20], click on “Use this template”. In the following, enter the desired owner, repository name, and project description. The button “Create repository from template” will then create the instance.</p

Overview of best practices in software engineering for scientific software projects.

For each best practice, implementation candidates are listed where the selected choice is denoted in bold.</p

Overview of the project skeleton.

The source code and dependencies of a scientific software project are denoted in orange. These are the parts the developer has to provide. The presented skeleton guides the project from creation to deployment. Here, the arrows denote jobs that are created by the CMake build system. These jobs are triggered during the different continuous integration stages (build, tests, quality, deploy) or (in the case of the dashed arrows) by the conda-forge build service that follows the recipe [18]. The job names indicate the tools in use, where CXX represents one of the C++ compilers that are supported by CMake.</p

Creating an instance of the project skeleton in GitLab.

Click on the plus button to create a new project. After selecting the “Create from template” tab, choose bertha by clicking “Use this template” (currently in development, see [21]). Then, enter the project name and description and click “Create project”.</p

sj-docx-1-npx-10.1177_1934578X211045479 - Supplemental material for Geographical Discrimination of <i>Curcuma longa</i> L. in Vietnam Based on LC-HRMS Metabolomics

Supplemental material, sj-docx-1-npx-10.1177_1934578X211045479 for Geographical Discrimination of Curcuma longa L. in Vietnam Based on LC-HRMS Metabolomics by Kieu-Oanh Nguyen Thi, Hoang-Giang Do, Ngoc-Tu Duong, Tien Dat Nguyen and Quang-Trung Nguyen in Natural Product Communications</p

New anthracene-based Cu(I) dithiocarbamates as AIEgens

The syntheses and structural characterizations of a series of anthracene-tethered Cu(I) phosphine dithiocarbamate complexes, [CuL(PPh3)2], are described in this article. All complexes were readily prepared from corresponding ligands with various acyclic and cyclic N-alkyl substituents and [Cu(PPh3)2(NO3)]. Steric hindrance imposed on the anthracenyl rings by dithiocarbamate, N-alkyl substituents and triphenylphosphine moieties in complexes 1-6 are not detected, as evidenced by the sharp aromatic resonances in 1H NMR spectra. X-ray crystallography reveals distorted tetrahedral chelation environments around the Cu(I) centers in 2 and 3 as well as extensive C–S···π and C–H···π intermolecular interactions in their solid state packings. The complexes display characteristic anthracene-based absorption and emission properties. The emission quantum yields of the complexes are poor (1.0–2.7 × 10−2) but the aggregation-induced emission effects are perceived in aqueous DMSO solutions. Especially, 6 with N-substituted cyclohexyl group displays the largest increase in emission intensity (ca. 7 times).</p

Analysis of PCDD/Fs in environmental samples by using gas chromatography in combination with high resolution mass spectrometry: optimization of sample preparation

This study developed a simple, economical and time-saving clean-up procedure based on an in-house packed column system for the determination of the most toxic-relevant 17 PCDD (polychlorinated dibenzo-p-dioxin) and PCDF (polychlorinated dibenzofuran) congeners in environmental samples following accelerated solvent extraction. The extract solution was cleaned up using a manually packed column system consisting of a multi-layer silica gel column and an activated carbon column. After clean-up, dioxins and furans were analysed by using gas chromatography in combination with high-resolution mass spectrometry. Isotopic labelled spiking experiments investigated the recovery of all dioxin and furan congeners. Then, the clean-up procedure for environmental samples was validated by applying the analysis of both clean soil reference material (CRM EDF-5183) and heavily contaminated sediment reference material (CRM EDF-5184) samples, as well as participating in the proficiency test (PT) for sediment samples. The recovery efficiency of isotope-labelled standard compounds in certified reference material (CRM) samples and PT samples ranged from 35% to 101% and between 46.1% and 105%, respectively. The mass concentrations of 17 PCDD/Fs in CRM samples were in the acceptable range. The absolute z-score value for each PCDD/F congener in the PT samples was below 1, confirming the analytical procedure’s high accuracy. The applied clean-up procedure in this study has demonstrated accuracy, repeatability and a significant increase in sample extraction/preparation productivity by reducing the time for sample preparation.</p

<i>In vitro</i> and <i>in vivo</i> development of interspecies Asian elephant embryos reconstructed with pig enucleated oocytes

Interspecies somatic cell nuclear transfer (iSCNT) has an immense potential to rescue endangered animals and extinct species like mammoths. In this study, we successfully established an Asian elephant’s fibroblast cell lines from ear tissues, performed iSCNT with porcine oocytes and evaluated the in vitro and in vivo development of reconstructed embryos. A total of 7780 elephant–pig iSCNT embryos were successfully reconstructed and showed in vitro development with cleavage rate, 4-cell, 8-cell and blastocyst rate of 73.01, 30.48, 5.64, and 4.73%, respectively. The total number of elephant–pig blastocyte cells and diameter of hatched blastocyte was 38.67 and 252.75 μm, respectively. Next, we designed species-specific markers targeting EDNRB, AGRP and TYR genes to verify the genome of reconstructed embryos with donor nucleus/species. The results indicated that 53.2, 60.8, and 60.8% of reconstructed embryos (n = 235) contained elephant genome at 1-cell, 2-cell and 4-cell stages, respectively. However, the percentages decreased to 32.3 and 32.7% at 8-cell and blastocyst stages, respectively. Furthermore, we also evaluated the in vivo development of elephant–pig iSCNT cloned embryos and transferred 2260 reconstructed embryos into two surrogate gilts that successfully became pregnant and a total of 11 (1 and 10) fetuses were surgically recovered after 17 and 19 days of gestation, respectively. The crown-rump length and width of elephant–pig cloned fetuses were smaller than the control group. Unfortunately, none of these fetuses contained elephant genomes, which suggested that elephant embryos failed to develop in vivo. In conclusion, we successfully obtained elephant–pig reconstructed embryos for the first time and these embryos are able to develop to blastocyst, but the in vivo developmental failure needs further investigated.</p

Image_2_Production of Triple-Gene (GGTA1, B2M and CIITA)-Modified Donor Pigs for Xenotransplantation.tif

Activation of human immune T-cells by swine leukocyte antigens class I (SLA-I) and class II (SLA-II) leads to xenograft destruction. Here, we generated the GGTA1, B2M, and CIITA (GBC) triple-gene-modified Diannan miniature pigs, analyzed the transcriptome of GBC-modified peripheral blood mononuclear cells (PBMCs) in the pig's spleen, and investigated their effectiveness in anti-immunological rejection. A total of six cloned piglets were successfully generated using somatic cell nuclear transfer, one of them carrying the heterozygous mutations in triple genes and the other five piglets carrying the homozygous mutations in GGTA1 and CIITA genes, but have the heterozygous mutation in the B2M gene. The autopsy of GBC-modified pigs revealed that a lot of spot bleeding in the kidney, severe suppuration and necrosis in the lungs, enlarged peripulmonary lymph nodes, and adhesion between the lungs and chest wall were found. Phenotyping data showed that the mRNA expressions of triple genes and protein expressions of B2M and CIITA genes were still detectable and comparable with wild-type (WT) pigs in multiple tissues, but α1,3-galactosyltransferase was eliminated, SLA-I was significantly decreased, and four subtypes of SLA-II were absent in GBC-modified pigs. In addition, even in swine umbilical vein endothelial cells (SUVEC) induced by recombinant porcine interferon gamma (IFN-γ), the expression of SLA-I in GBC-modified pig was lower than that in WT pigs. Similarly, the expression of SLA-II DR and DQ also cannot be induced by recombinant porcine IFN-γ. Through RNA sequencing (RNA-seq), 150 differentially expressed genes were identified in the PBMCs of the pig's spleen, and most of them were involved in immune- and infection-relevant pathways that include antigen processing and presentation and viral myocarditis, resulting in the pigs with GBC modification being susceptible to pathogenic microorganism. Furthermore, the numbers of human IgM binding to the fibroblast cells of GBC-modified pigs were obviously reduced. The GBC-modified porcine PBMCs triggered the weaker proliferation of human PBMCs than WT PBMCs. These findings indicated that the absence of the expression of α1,3-galactosyltransferase and SLA-II and the downregulation of SLA-I enhanced the ability of immunological tolerance in pig-to-human xenotransplantation.</p

Image_1_Production of Triple-Gene (GGTA1, B2M and CIITA)-Modified Donor Pigs for Xenotransplantation.tif

Activation of human immune T-cells by swine leukocyte antigens class I (SLA-I) and class II (SLA-II) leads to xenograft destruction. Here, we generated the GGTA1, B2M, and CIITA (GBC) triple-gene-modified Diannan miniature pigs, analyzed the transcriptome of GBC-modified peripheral blood mononuclear cells (PBMCs) in the pig's spleen, and investigated their effectiveness in anti-immunological rejection. A total of six cloned piglets were successfully generated using somatic cell nuclear transfer, one of them carrying the heterozygous mutations in triple genes and the other five piglets carrying the homozygous mutations in GGTA1 and CIITA genes, but have the heterozygous mutation in the B2M gene. The autopsy of GBC-modified pigs revealed that a lot of spot bleeding in the kidney, severe suppuration and necrosis in the lungs, enlarged peripulmonary lymph nodes, and adhesion between the lungs and chest wall were found. Phenotyping data showed that the mRNA expressions of triple genes and protein expressions of B2M and CIITA genes were still detectable and comparable with wild-type (WT) pigs in multiple tissues, but α1,3-galactosyltransferase was eliminated, SLA-I was significantly decreased, and four subtypes of SLA-II were absent in GBC-modified pigs. In addition, even in swine umbilical vein endothelial cells (SUVEC) induced by recombinant porcine interferon gamma (IFN-γ), the expression of SLA-I in GBC-modified pig was lower than that in WT pigs. Similarly, the expression of SLA-II DR and DQ also cannot be induced by recombinant porcine IFN-γ. Through RNA sequencing (RNA-seq), 150 differentially expressed genes were identified in the PBMCs of the pig's spleen, and most of them were involved in immune- and infection-relevant pathways that include antigen processing and presentation and viral myocarditis, resulting in the pigs with GBC modification being susceptible to pathogenic microorganism. Furthermore, the numbers of human IgM binding to the fibroblast cells of GBC-modified pigs were obviously reduced. The GBC-modified porcine PBMCs triggered the weaker proliferation of human PBMCs than WT PBMCs. These findings indicated that the absence of the expression of α1,3-galactosyltransferase and SLA-II and the downregulation of SLA-I enhanced the ability of immunological tolerance in pig-to-human xenotransplantation.</p