cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12936731.v1
title: Evaluation of the skin-sensitizing potential of gold nanoparticles and the impact of established dermal sensitivity on the pulmonary immune response to various forms of gold

description: Gold nanoparticles (AuNP) are largely biocompatible; however, many studies have demonstrated their potential to modulate various immune cell functions. The potential allergenicity of AuNP remains unclear despite the recognition of gold as a common contact allergen. In these studies, AuNP (29 nm) dermal sensitization potential was assessed via Local Lymph Node Assay (LLNA). Soluble gold (III) chloride (AuCl<sub>3</sub>) caused lymph node (LN) expansion (SI 10.9), whereas bulk particles (Au, 942 nm) and AuNP did not. Next, the pulmonary immune effects of AuNP (10, 30, 90 µg) were assessed 1, 4, and 8 days post-aspiration. All markers of lung injury and inflammation remained unaltered, but a dose-responsive increase in LN size was observed. Finally, mice were dermally-sensitized to AuCl<sub>3</sub> then aspirated once, twice, or three times with Au or AuNP in doses normalized for mass or surface area (SA) to assess the impact of existing contact sensitivity to gold on lung immune responses. Sensitized animals exhibited enhanced responsivity to the metal, wherein subsequent immune alterations were largely conserved with respect to dose SA. The greatest increase in bronchoalveolar lavage (BAL) lymphocyte number was observed in the high dose group – simultaneous to preferential expansion of BAL/LN CD8+ T-cells. Comparatively, the lower SA-based doses of Au/AuNP caused more modest elevations in BAL lymphocyte influx (predominantly CD4+ phenotype), exposure-dependent increases in serum IgE, and selective expansion/activation of LN CD4+ T-cells and B-cells. Overall, these findings suggest that AuNP are unlikely to cause sensitization; however, established contact sensitivity to gold may increase immune responsivity following pulmonary AuNP exposure.
DOI: 10.26036/cnp0000135
title: panda gut metagenome raw sequence reads

description: Composition of the gut microorganisms of Pandas and changes over time
DOI: 10.26036/cnp0000048
title: Integration of gut microbiome, host biomarkers, and metabolome reveals networks of interactions in metabolic diseases

description: Case-control studies have revealed microbial features characterizing a number of human diseases, but only in a limited number of studies have gut microbial signatures been integrated into comprehensive correlation networks encompassing multi-omics data based on host biomarkers, metabolites and gut microbiota composition and functional potential.
DOI: 10.26036/cnp0000134
title: 慢传输型便秘宏基因组学研究 （Slow transit constipation metagenomics research）

description: Clostridium difficile and Crohn’s disease are two chronic, often relapsing, immunologically mediated gastrointestinal disorders. Since fecal microbiota transplantation (FMT) has been proved to be efficient in treating Clostridium difficile infection disease, recently it is also being applied to other diseases such as Inflammatory bowel disease whose main forms are Crohn’s Disease (CD) and Ulcerative Colitis (UC). While the efficacy and safety of FMT for UC patients have been assessed, only a few case series were reported on CD patients. To describe and quantify the change of gut flora of IBD patients especially CD patients after FMT, we monitored strain populations in 44 fecal samples. We observed the transfer of donor strains to recipient was more abundant in UC than in CD patients, persisting the follow-up time points. Besides, same-donor recipient differs in the degree of microbiota transfer. Furthermore, we also tended to uncover the principles of microbiota engraftment via random forest classification and regression model. Results showed that both the presence and abundance of some post-FMT patients’ species were predicable, indicating a possibility of precision engineering of the recipients’ gut microbiota under the FMT treatment.
DOI: 10.26036/cnp0000139
title: Meta cooperation project of guangdong provincial hospital of traditional Chinese medicine

description: Ankylosing spondylitis is a disease that is still hard to cure. It is often found in teenagers and has a great impact on their image and life.The differences between gut microbes and healthy people in Ankylosing Spondylitis patients have been analyzed based on data and some individualized analyses.
DOI: 10.26036/cnp0000144
title: 宏基因组相关DNA提取和建库方法学初步评估研究

description: 该项目对三例正常成年人的粪便样本进行宏基因组学分析，开展方法学的验证实验，以期将来能够采用此DNA提取和建库方法为后续疾病-宏基因组关联进行针对性的研究
DOI: 10.26036/cnp0000156
title: Verticillium dahliae Genome sequencing

description: Verticillium dahilae resequencing
DOI: 10.26036/cnp0000175
title: T2D of Multi-omics

description: we collected 254 stool samples from a previous reported Chinese cohort , followed by shotgun metagenomics and metaproteomics analyses. Here, we characterized substantial alterations of the intestinal host-microbiome ecosystem in Pre-DM and Treat-native T2D (TN-T2D) patients compared to that of normal glucose tolerance (NGT) individuals. Several microbial compositional changes were both pronounced at DNA and protein levels, such as the enrichment of E. coli in Pre-DM and the increased Bacteroides spp. in TN-T2D. Importantly, integrated omics analyses uncovered several Pre-DM-specific features, such as the decreased functional potentials involved in energy metabolism and bacterial growth, and a smaller number of identified proteins compared to other groups. Additionally, the Pre-DM enriched Prevotella was only detectable on metaproteomes. The findings indicate a unique status of intestinal ecosystem in this pre-disease status Additionally, metaproteomics identified 425 human proteins including mucins and antimicrobial peptides (AMPs), which potentially mediates the host immune and metabolism. Altogether, our study will provide a comprehensive foundation for integration analyses of faecal metagenomics and metaproteomics and lead a better understanding to the underlying mechanism of how gut microbiota regulates T2D.
DOI: 10.26036/cnp0000204
title: Metagenomics wide association studies on multi-autoimmune diseases.( F16HTSNCWLJ1153-F16FTSNCWLJ0140)

description: Public description： Ankylosing spondylitis (AS) is a common autoimmune disease. Due to the early pathogenesis and long duration, patients suffer from morning stiffness, low back pain, chest pain, alternating hip pain and other symptoms. And the disability rate is high, which seriously affects the quality of life. According to statistics, the prevalence of ankylosing spondylitis in China is about 0.3%, mostly young men. On average, patients need to stop working after fifteen or six years of illness. After 20 years of illness, more than 85% of patients lose the ability to live independently and become so-called "puppet people." In response to key scientific issues, these datas is devoted to the use a metagenomic wide association studies to explore new key biomarkers and therapeutic targets of AS from intestinal micro-organisms, so as to improve early diagnosis, accurate prediction and classification, and improve prognosis.And combine with other datas which already published of autoimmune disease,we identified conflicts and contradicts points of RA ,AS ,behcet disease and T1D.
DOI: 10.26036/cnp0000273
title: Dusko Rumen metagenomics

description: 本项目首先采集10例牛瘤胃样本（法国INRA）进行高深度shotgun 宏基因组测序，组装构建牛瘤胃基因集；并完成对基因进行结构和功能注释；比较了牛瘤胃与、人、猪、小鼠肠道基因集在结构和功能上的异同。对另外77例包含4种饮食类别的牛瘤胃样本，进行常规深度测序，基于上述基因集，组装得到324个metagenomic assemblies；基于基因集和组装物种，对不同饮食下牛瘤胃微生态在结构、功能的异同进行了比较和阐述。
DOI: 10.26036/cnp0000282
title: F13ZOOYJSY1389

description: we collected 290 stool samples from a previous reported Chinese cohort , followed by shotgun metagenomics and metaproteomics analyses. Here, we characterized substantial alterations of the intestinal host-microbiome ecosystem in Pre-DM and newly-diagnosed T2D (ND-T2D) patients compared to that of normal glucose tolerance (NGT) individuals. Several microbial compositional changes were both pronounced at DNA and protein levels, such as the enrichment of E. coli in Pre-DM and the increased Bacteroides spp. in ND-T2D. Importantly, integrated omics analyses uncovered several Pre-DM-specific features, such as the decreased functional potentials involved in energy metabolism and bacterial growth, and a smaller number of identified proteins compared to other groups. Additionally, the Pre-DM enriched Prevotella was only detectable on metaproteomes. The findings indicate a unique status of intestinal ecosystem in this pre-disease status Additionally, metaproteomics identified 592 human proteins including mucins and antimicrobial peptides (AMPs), which potentially mediates the host immune and metabolism. Altogether, our study will provide a comprehensive foundation for integration analyses of faecal metagenomics and metaproteomics and lead a better understanding to the underlying mechanism of how gut microbiota regulates T2D.
DOI: 10.26036/cnp0000283
title: Establishment of a Minke whale (Balaenoptera acutorostrata) gut microbiome gene catalog

description: A previous study exploring the gut microbiota of different baleen whales using fecal 16S rRNA gene amplicon sequencing, demonstrating similarities to both terrestrial carnivores and herbivores (Sanders 2015), but information on gene identity and function of the whale gut microbiome is still lacking. Establishment of a Minke whale (Balaenoptera acutorostrata) gut microbiome gene catalog will be done
DOI: 10.26036/cnp0000290
title: The anti-cholesterolaemic effect of probiotics: A intragastric administration study in Golden Hamster.

description: Probiotic strains improve high-fat diet induced hypercholesterolemia through modulating gut microbiota in ways different form atorvastatin.
DOI: 10.26036/cnp0000279
title: Parasitic plants genome

description: In parasitic plants, the transfer from autotrophy to heterotrophy coincides with changes in genes or genomes to adapt the new lifestyle. To analyze the molecular evolution of parasites, the nuclear genome, plastome or mitogenome were analyzed to uncover the parasitic mechanism.
DOI: 10.26036/cnp0000345
title: A comparative study of the gut microbiota in mudskippers and other fish species

description: This study presents a comprehensive analysis of gastrointestinal microbiota composition in several fishes by using 16S amplicon and metagenome sequencing. The composition of the gut microbiota is altered in fish living in different habitats. Moreover, we also show that several microorganisms among groups demonstrated significant compositional differences. Further research into these microorganisms and their associated functions within the host are needed in order to establish any causality in fish disease pathogenesis and develop
DOI: 10.26036/cnp0000359
title: Transcriptome sequencing of gonads of Gobiopterus lacustris

description: Transcriptome sequencing of gonads of Gobiopterus lacustris
DOI: 10.26036/cnp0000421
title: Malus_baccata_v1.0

description: Genome of wild apple, Malus baccata
DOI: 10.26036/cnp0000434
title: 微生物检测整体解决方案

description: 某养殖基地的多只青山羊发生不明病原的感染，主要症状为口唇出现脓包并结痂。为迅速控制疫情，该养殖基地将几只病情较严重青山羊的拭子样本采用华大智造病原微生物整体解决方案进行检测，2天内得到微生物鉴定结果
DOI: 10.26036/cnp0000408
title: Gut Microbiota Dynamics in a Confined Bio-regenerative Life Support System

description: During long-term manned space exploration, challenges exist both on the need for full autonomy, provision and reprocessing of resources and protection of crews from illness and infection. Bio-regenerative life support systems (BLSS) are artificially confined ecosystems to provide food, oxygen and other basic necessities for human living. Aggravated research has identified that gut microbiome can affect various human health both from psychological and physiological. Investigations are forced to study gut microbial alterations in a confined BLSS to maintain human physical and mental health and provide guidance in universal explorations. Here we performed metagenomics sequencing of 55 samples from two males and females who underwent a 60-day experiment in a confined BLSS, Chinese Lunar Palace 1, to study the effect of co-diet and cohabitation on host gut microbiome and the association between these kinds of changes and individual or sexual phenotypes.
DOI: 10.26036/cnp0000119
title: A causal role of the gut microbiome in schizophrenia

description: The gut-brain axis has been enthusiastically discussed in recent years. Gut bacteria are known to promote serotonin biosynthesis from colonic enterochromaffin cells1. Germ-free mice are also known to have impaired blood-brain barrier, which could be rescued by short-chain fatty acids2. However, there has been little evidence from human studies, not to mention a study that combined human cohorts with animal models. Here we provide metagenomic shotgun sequencing data for a typical psychiatric disease, schizophrenia, for which tens of thousands of samples have been characterized in genome-association studies (GWAS). Metagenome-wide association studies (MWAS) identified bacteria that differ between patients and controls, which was partially recapitulated in mice transplanted with the human faeces. We show that the schizophrenic gut microbiome was causally responsible for core symptoms such as psychomotor hyperactivity and impaired learning and memory, whereas non-specific symptoms such as anxiety were lost in the mice model. Our findings pave the road for better diagnosis as well as mechanistic understandings of this devastating disease.
DOI: 10.6084/m9.figshare.12865601
title: <i>CAPN1</i> and hereditary spastic paraplegia: a novel variant in an Iranian family and overview of the genotype-phenotype correlation

description: SPG76 is one of the rare forms of hereditary spastic paraplegia (HSP) which causes by mutations in the <i>CAPN1</i> gene. The mode of inheritance of SPG76 is autosomal recessive (AR) and so far, only 24 families and 25 mutations in this gene have been reported worldwide. These mutations have been associated with a spectrum of disorders from pure HSP to spastic ataxia. HSP genetically is one of the most heterogeneous neurological disorders and to date, 79 types of HSP (SPG1-SPG79) have been identified, however, it has been suggested that many HSP-genes, particularly in AR-HSPs, remained unknown. AR-HSPs clinically overlap with other neurodegenerative disorders, making an accurate diagnosis of the disease difficult. Therefore, in addition to clinical examination, a high throughout genetic method like whole exome sequencing (WES) may be necessary for the diagnosis of this type of neurodegenerative disorders. Herein, we present the clinical features and results of WES in the first Iranian family with a novel <i>CAPN1</i> variant, c.C853T:p.R285* and pure HSP. Some of the previous studies have mentioned that the “spasticity-ataxia phenotype might be conducted to the diagnosis of SPG76” but recently the number of pure HSP patients with <i>CAPN1</i> mutation is increasing. The present study also expands the mutation spectrum of pure <i>CAPN1</i>-related SPG76; emphasizing that <i>CAPN1</i> screening is required in both pure HSP and spasticity-ataxia phenotypes. As noted in some other literature, we suggest the clinical spectrum of this disorder to be considered as “<i>CAPN1</i>-associated neurodegeneration”.
DOI: 10.6084/m9.figshare.12865601.v1
title: <i>CAPN1</i> and hereditary spastic paraplegia: a novel variant in an Iranian family and overview of the genotype-phenotype correlation

description: SPG76 is one of the rare forms of hereditary spastic paraplegia (HSP) which causes by mutations in the <i>CAPN1</i> gene. The mode of inheritance of SPG76 is autosomal recessive (AR) and so far, only 24 families and 25 mutations in this gene have been reported worldwide. These mutations have been associated with a spectrum of disorders from pure HSP to spastic ataxia. HSP genetically is one of the most heterogeneous neurological disorders and to date, 79 types of HSP (SPG1-SPG79) have been identified, however, it has been suggested that many HSP-genes, particularly in AR-HSPs, remained unknown. AR-HSPs clinically overlap with other neurodegenerative disorders, making an accurate diagnosis of the disease difficult. Therefore, in addition to clinical examination, a high throughout genetic method like whole exome sequencing (WES) may be necessary for the diagnosis of this type of neurodegenerative disorders. Herein, we present the clinical features and results of WES in the first Iranian family with a novel <i>CAPN1</i> variant, c.C853T:p.R285* and pure HSP. Some of the previous studies have mentioned that the “spasticity-ataxia phenotype might be conducted to the diagnosis of SPG76” but recently the number of pure HSP patients with <i>CAPN1</i> mutation is increasing. The present study also expands the mutation spectrum of pure <i>CAPN1</i>-related SPG76; emphasizing that <i>CAPN1</i> screening is required in both pure HSP and spasticity-ataxia phenotypes. As noted in some other literature, we suggest the clinical spectrum of this disorder to be considered as “<i>CAPN1</i>-associated neurodegeneration”.
DOI: 10.6084/m9.figshare.13332615
title: Neutrophil activation by nanomaterials <i>in vitro</i>: comparing strengths and limitations of primary human cells with those of an immortalized (HL-60) cell line

description: Assessment of nanomaterial (NM) induced inflammatory responses has largely relied on rodent testing via measurement of leukocyte accumulation in target organs. Despite observations that NMs activate neutrophil driven inflammatory responses <i>in vivo</i>, a limited number of studies have investigated neutrophil responses to NMs <i>in vitro</i>. We compared responses between the human neutrophil-like HL-60 cell line and human primary neutrophils following exposure to silver (Ag), zinc oxide (ZnO), copper oxide (CuO) and titanium dioxide (TiO<sub>2</sub>) NMs. NM cytotoxicity and neutrophil activation were assessed by measuring cellular metabolic activity, cytokine production, respiratory burst, and release of neutrophil extracellular traps. We observed a similar pattern of response between HL-60 cells and primary neutrophils, however we report that some neutrophil functions are compromised in the cell line. Ag NMs were consistently observed to stimulate neutrophil activation, with CuO NMs inducing similar though weaker responses. TiO<sub>2</sub> NMs did not induce a neutrophil response in either cell type. Interestingly, ZnO NMs readily induced activation of HL-60 cells but did not appear to activate primary cells. Our findings are relevant to the development of a tiered testing strategy for NM hazard assessment which promotes the use of non-rodent models. Whilst we acknowledge that HL-60 cells may not be a perfect substitute for primary cells and require further investigation regarding their ability to predict neutrophil activation, we recommend their use for initial screening of NM-induced inflammation. Primary human neutrophils can then be used for more focused assessments of neutrophil activation before progressing to <i>in vivo</i> models where necessary.
DOI: 10.6084/m9.figshare.13332615.v1
title: Neutrophil activation by nanomaterials <i>in vitro</i>: comparing strengths and limitations of primary human cells with those of an immortalized (HL-60) cell line

description: Assessment of nanomaterial (NM) induced inflammatory responses has largely relied on rodent testing via measurement of leukocyte accumulation in target organs. Despite observations that NMs activate neutrophil driven inflammatory responses <i>in vivo</i>, a limited number of studies have investigated neutrophil responses to NMs <i>in vitro</i>. We compared responses between the human neutrophil-like HL-60 cell line and human primary neutrophils following exposure to silver (Ag), zinc oxide (ZnO), copper oxide (CuO) and titanium dioxide (TiO<sub>2</sub>) NMs. NM cytotoxicity and neutrophil activation were assessed by measuring cellular metabolic activity, cytokine production, respiratory burst, and release of neutrophil extracellular traps. We observed a similar pattern of response between HL-60 cells and primary neutrophils, however we report that some neutrophil functions are compromised in the cell line. Ag NMs were consistently observed to stimulate neutrophil activation, with CuO NMs inducing similar though weaker responses. TiO<sub>2</sub> NMs did not induce a neutrophil response in either cell type. Interestingly, ZnO NMs readily induced activation of HL-60 cells but did not appear to activate primary cells. Our findings are relevant to the development of a tiered testing strategy for NM hazard assessment which promotes the use of non-rodent models. Whilst we acknowledge that HL-60 cells may not be a perfect substitute for primary cells and require further investigation regarding their ability to predict neutrophil activation, we recommend their use for initial screening of NM-induced inflammation. Primary human neutrophils can then be used for more focused assessments of neutrophil activation before progressing to <i>in vivo</i> models where necessary.
DOI: 10.6084/m9.figshare.12936810.v1
title: Probabilistic model for assessing occupational risk during the handling of nanomaterials

description: Exposure to nanomaterials (NMs) can be considered as human, occupational or environmental. Occupational exposure may be experienced by the workers and/or researchers who develop and produce these products and the hazards inherent to exposure are not yet fully known. Quantitative and qualitative methods are available to estimate the occupational risks associated with the handling of NMs, however, both have limitations. In this context, the objective of this study was to create a Bayesian network (BN) that will allow an assessment of the occupational risk associated with the handling of NMs in research laboratories. The BN was developed considered variables related to exposure, the hazards associated with NMs and also the existing control measures in the work environment, such as collective protection equipment (CPE), administrative measures and personal protection equipment (PPE). In addition to assessing the occupational risk, simulations were carried out by the laboratory manager to obtain information on which actions should be taken to reduce the risk. The development of a BN to assess the occupational risk associated with the handling of NMs is a novel aspect of this study. As a distinctive feature, the BN has measurement control variables in addition to considering CPE, administrative measures and PPE. An advantage of this network in relation to other risk assessment models is that it allows the easy execution of simulations and provides a guide for a decision making by identifying which actions should be taken to minimize the risk.