643,531 Works

Challenges in modeling complexity of neglected tropical diseases: a review of dynamics of visceral leishmaniasis in resource limited settings

Swati DebRoy, Olivia Prosper, Austin Mishoe & Anuj Mubayi
Abstract Objectives Neglected tropical diseases (NTD), account for a large proportion of the global disease burden, and their control faces several challenges including diminishing human and financial resources for those distressed from such diseases. Visceral leishmaniasis (VL), the second-largest parasitic killer (after malaria) and an NTD affects poor populations and causes considerable cost to the affected individuals. Mathematical models can serve as a critical and cost-effective tool for understanding VL dynamics, however, complex array of...

Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity

Shuting Zhang, Xiaojiao Liu, Qipeng Jiang, Guihua Shen & Wei Ding
Abstract Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high throughput Illumina sequencing and Biolog ECO microplates to determine the bacterial community and microbial metabolic activity in ginger harvest fields of non-fumigation (NF), chloropicrin-fumigation for 1 year (F_1) and continuous...

Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

Balรกzs Brankovics, Peter Van Dam, Martijn Rep, G. Sybren De Hoog, Theo A. J. Van Der Lee, Cees Waalwijk & Anne D. Van Diepeningen
Abstract Background The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. Results A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that...

Homocysteine exaggerates microglia activation and neuroinflammation through microglia localized STAT3 overactivation following ischemic stroke

Shuang Chen, Zhiping Dong, Man Cheng, Yaqian Zhao, Mengying Wang, Na Sai, Xuan Wang, Huan Liu, Guowei Huang & Xumei Zhang
Abstract Background Elevated plasma homocysteine (Hcy) levels have been indicated as a strong and modifiable risk factor of ischemic stroke; the previous studies have shown that exposure to Hcy activates cultured microglia. However, whether neurotoxicity of Hcy involves microglia activation following brain ischemia and the underlying mechanisms remains incompletely understood. Methods The cerebral damage was evaluated by staining with 2,3,5-triphenyltetrazolium chloride, hematoxylin-eosin, and Fluoro Jade B. The activation state of microglia was assessed via immunoreaction...

Data integration from pathology slides for quantitative imaging of multiple cell types within the tumor immune cell infiltrate

Zhaoxuan Ma, Stephen Shiao, Emi Yoshida, Steven Swartwood, Fangjin Huang, Michael Doche, Alice Chung, Beatrice Knudsen & Arkadiusz Gertych
Abstract Background Immune cell infiltrates (ICI) of tumors are scored by pathologists around tumor glands. To obtain a better understanding of the immune infiltrate, individual immune cell types, their activation states and location relative to tumor cells need to be determined. This process requires precise identification of the tumor area and enumeration of immune cell subtypes separately in the stroma and inside tumor nests. Such measurements can be accomplished by a multiplex format using immunohistochemistry...

The role of the two-component systems Cpx and Arc in protein alterations upon gentamicin treatment in Escherichia coli

Emina Ćudić, Kristin Surmann, Gianna Panasia, Elke Hammer & Sabine Hunke
Abstract Background The aminoglycoside antibiotic gentamicin was supposed to induce a crosstalk between the Cpx- and the Arc-two-component systems (TCS). Here, we investigated the physical interaction of the respective TCS components and compared the results with their respective gene expression and protein abundance. The findings were interpreted in relation to the global proteome profile upon gentamicin treatment. Results We observed specific interaction between CpxA and ArcA upon treatment with the aminoglycoside gentamicin using Membrane-Strep-tagged protein...

Additional file 4: Table S3. of The role of the two-component systems Cpx and Arc in protein alterations upon gentamicin treatment in Escherichia coli

Emina ĆUdić, Kristin Surmann, Gianna Panasia, Elke Hammer & Sabine Hunke
Correlation studies between intensities of CpxA or ArcA and other detected proteins including WT condition, Cpx induction, and gentamicin treatment. (XLSX 496 kb)

Increasing educational attainment and mortality reduction: a systematic review and taxonomy

Elena Byhoff, Mary Hamati, Robyn Power, Sarah Burgard & Vineet Chopra
Abstract Background Understanding the relationship between increasing educational attainment and mortality reduction has important policy and public health implications. This systematic review of the literature establishes a taxonomy to facilitate evaluation of the association between educational attainment and early mortality. Methods Following PRISMA guidelines, we searched Ovid Medline, Embase, PubMed and hand searches of references for English-language primary data analyses using education as an independent variable and mortality as a dependent variable. Initial searches were...

Endoplasmic reticulum stress cooperates with Toll-like receptor ligation in driving activation of rheumatoid arthritis fibroblast-like synoviocytes

Pawel Kabala, Chiara Angiolilli, Nataliya Yeremenko, Aleksander Grabiec, Barbara Giovannone, Desiree Pots, Timothy Radstake, Dominique Baeten & Kris Reedquist
Abstract Background Endoplasmic reticulum (ER) stress has proinflammatory properties, and transgenic animal studies of rheumatoid arthritis (RA) indicate its relevance in the process of joint destruction. Because currently available studies are focused primarily on myeloid cells, we assessed how ER stress might affect the inflammatory responses of stromal cells in RA. Methods ER stress was induced in RA fibroblast-like synoviocytes (FLS), dermal fibroblasts, and macrophages with thapsigargin or tunicamycin alone or in combination with Toll-like...

Additional file 2: Figure S2. of Endoplasmic reticulum stress cooperates with Toll-like receptor ligation in driving activation of rheumatoid arthritis fibroblast-like synoviocytes

Pawel Kabala, Chiara Angiolilli, Nataliya Yeremenko, Aleksander Grabiec, Barbara Giovannone, Desiree Pots, Timothy Radstake, Dominique Baeten & Kris Reedquist
ER stress effects on TLR-proximal signaling pathways. (TIF 875 kb)

Additional file 1: Video S1. of Homocysteine exaggerates microglia activation and neuroinflammation through microglia localized STAT3 overactivation following ischemic stroke

Shuang Chen, Zhiping Dong, Man Cheng, Yaqian Zhao, Mengying Wang, Na Sai, Xuan Wang, Huan Liu, Guowei Huang & Xumei Zhang
Rat tail vein injection. Homocysteine was injected into the tail vein of a rat. (MP4 8751 kb)

Additional file 3 of Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

Balรกzs Brankovics, Peter Van Dam, Martijn Rep, G. Sybren De Hoog, Theo A. J. Van Der Lee, Cees Waalwijk & Anne D. Van Diepeningen
Boxplot of the length of the conserved part of the mitogenome of the three clades of the FOSC. (PDF 111 kb)

Additional file 1: Figure S1. of Comparison of volar-flexion, ulnar-deviation and functional position cast immobilization in the non-operative treatment of distal radius fracture in elderly patients: a pragmatic randomized controlled trial study protocol

Lauri Raittio, Antti Launonen, Teemu Hevonkorpi, Toni Luokkala, Juha Kukkonen, Aleksi Reito, Bakir Sumrein, Minna Laitinen & Ville Mattila
The first picture of flexion-ulnar deviation cast. (TIFF 35156 kb)

Additional file 1: Figure S1. of Increasing educational attainment and mortality reduction: a systematic review and taxonomy

Elena Byhoff, Mary Hamati, Robyn Power, Sarah Burgard & Vineet Chopra
Search Strategy. Screen shot of pubmed search strategy for conducting the review. (DOCX 140 kb) Additional file 2: Figure S2.

Additional file 3: Table S2. of The role of the two-component systems Cpx and Arc in protein alterations upon gentamicin treatment in Escherichia coli

Emina ĆUdić, Kristin Surmann, Gianna Panasia, Elke Hammer & Sabine Hunke
Proteins regulated upon gentamicin treatment. (XLSX 210 kb)

Additional file 3: Figure S3. of Endoplasmic reticulum stress cooperates with Toll-like receptor ligation in driving activation of rheumatoid arthritis fibroblast-like synoviocytes

Pawel Kabala, Chiara Angiolilli, Nataliya Yeremenko, Aleksander Grabiec, Barbara Giovannone, Desiree Pots, Timothy Radstake, Dominique Baeten & Kris Reedquist
Tunicamycin-induced ER stress synergizes with LPS in regulation of gene expression and restricts mRNA decay in the same way as when induced by thapsigargin. (TIF 391 kb)

Additional file 2: Table S2. of Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor

Y. Daguerre, E. Levati, J. Ruytinx, E. Tisserant, E. Morin, A. Kohler, B. Montanini, S. Ottonello, A. Brun, C. Veneault-Fourrey & F. Martin
Number of proteins within each TF family for 70 fungal genomes. Data used to generate Fig. 1. (XLSX 32 kb)

Additional file 2 of Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

Balรกzs Brankovics, Peter Van Dam, Martijn Rep, G. Sybren De Hoog, Theo A. J. Van Der Lee, Cees Waalwijk & Anne D. Van Diepeningen
Scalable Genealogical Concordance Phylogenetic Species Recognition: Detailed description of the new implementation of the GCPSR method, including algorithm overview and recommended workflow. (PDF 420 kb)

Additional file 1: of The role of the two-component systems Cpx and Arc in protein alterations upon gentamicin treatment in Escherichia coli

Emina ĆUdić, Kristin Surmann, Gianna Panasia, Elke Hammer & Sabine Hunke
Supporting information and supporting figures. (DOCX 2129 kb)

Development and evaluation of an efficient heterologous gene knock-in reporter system in Lactococcus lactis

Yifei Lu, Hongxiang Yan, Jiezhong Deng, Zhigang Huang, Xurui Jin, Yanlan Yu, Qiwen Hu, Fuquan Hu & Jing Wang
Abstract Background Lactococcus lactis is a food grade probiotics and widely used to express heterologous proteins. Generally, target genes are knocked into the L. lactis genome through double-crossover recombination to express heterologous proteins stably. However, creating marker-less heterologous genes knocked-in clones is laborious. In this study, an efficient heterologous gene knock-in reporter system was developed in L. lactis NZ9000. Results Our knock-in reporter system consists of a temperature-sensitive plasmid pJW and a recombinant L. lactis...

MOESM1 of Development and evaluation of an efficient heterologous gene knock-in reporter system in Lactococcus lactis

Yifei Lu, Hongxiang Yan, Jiezhong Deng, Zhigang Huang, Xurui Jin, Yanlan Yu, Qiwen Hu, Fuquan Hu & Jing Wang
Additional file 1. Additional tables and figures.

Additional file 2: Table S1. of The role of the two-component systems Cpx and Arc in protein alterations upon gentamicin treatment in Escherichia coli

Emina Ćudić, Kristin Surmann, Gianna Panasia, Elke Hammer & Sabine Hunke
Proteome profile of E. coli MG1655 and its isogenic cpxAR mutant with and without incubation with 5 μg ml−1 gentamicin. (XLSX 882 kb)

Additional file 1:Fig. S1 of Data integration from pathology slides for quantitative imaging of multiple cell types within the tumor immune cell infiltrate

Zhaoxuan Ma, Stephen Shiao, Emi Yoshida, Steven Swartwood, Fangjin Huang, Michael Doche, Alice Chung, Beatrice Knudsen & Arkadiusz Gertych
Visualization of staining components used to generate a 3-D cell density map of cancer areas. (a) A whole-slide multicolor RGB bright-field image of breast cancer tissue stained for CD45 (brown), Pan-CK (red) and a hematoxylin nuclear counter-stain (blue). (b-d) The whole-slide multicolor RGB image was color-deconvoluted to separate the staining components: (b) CD45+ image, (c) Pan-CK+ image, and (d) hematoxylin image. (e) A 3-D cell density map of Pan-CK-positive cells (which demarcates areas of epithelial...

Characterization of a secreted cystatin of the parasitic nematode Haemonchus contortus and its immune-modulatory effect on goat monocytes

Yujian Wang, Lingyan Wu, Xinchao Liu, Shuai Wang, Muhammad Ehsan, RuoFeng Yan, XiaoKai Song, LiXin Xu & XiangRui Li
Abstract Background Haemonchosis is a disease of the small ruminant caused by a nematode parasite Haemonchus contortus, and it is most important and alarming challenges to the small ruminant’s production. The infection of the H. contortus could cause high economic losses worldwide. H. contortus is a blood feeding parasite which penetrates into the abomasal mucosa to feed the blood of the host and causing the anemia and decreased total plasma protein. Modulation and suppression of...

Additional file 1 of Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

Balรกzs Brankovics, Peter Van Dam, Martijn Rep, G. Sybren De Hoog, Theo A. J. Van Der Lee, Cees Waalwijk & Anne D. Van Diepeningen
Strains analyzed and accession numbers of the NGS data used. (XLSX 9 kb)

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