cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29876800
title: Authentication Methods for Phytochemicals (Botanicals) in Plant Extracts and Dietary Supplements

description: Demand for high-quality and standardized phytochemicals (botanicals) and plant extracts if rising in both the food and dietary supplement industries. Ensuring the authenticity of the plant raw materials used in botanical and dietary supplement manufacturing is an important step before processing raw materials. However, authenticating phytochemicals (botanicals) are challenging due to their unique characteristics, including geographical location, seasonal variations, environmental conditions, and plant diversity. These factors cause variability in properties, making consistent authentication methods difficult to establish. The current review is centered on the utilization of multisource and qualitative methods for authenticating the identity of botanical and food ingredients. This review highlights the integral role of various botanicals and plant extracts authentication methods such as micro/macroscopy, chromatography, and spectroscopy technology, including DNA-based approaches. Further summarizing the current state of knowledge and importance its potential contributions to the field of botanical ingredient authentication system. This study also highlights the plants used in dietary supplement categories of weight management, memory enhancement and blood sugar regulation and their adulteration/admixture. Furthermore, discusses considerations for selecting appropriate methods and optimization steps in the implementation and standardization of botanical and plant extract authentication. In addition, we discussed the challenges and opportunities associated with the implementation and standardization of botanical and plant extracts authentication system. The future of botanical authentication will be shaped by advances in molecular diagnostics such as targeted DNA barcoding, Next-Generation Sequencing (NGS), and chemometric integration with spectroscopic techniques which are set to greatly enhance accuracy, traceability, and global compliance in botanical product safety and quality.
DOI: 10.6084/m9.figshare.29876800.v1
title: Authentication Methods for Phytochemicals (Botanicals) in Plant Extracts and Dietary Supplements

description: Demand for high-quality and standardized phytochemicals (botanicals) and plant extracts if rising in both the food and dietary supplement industries. Ensuring the authenticity of the plant raw materials used in botanical and dietary supplement manufacturing is an important step before processing raw materials. However, authenticating phytochemicals (botanicals) are challenging due to their unique characteristics, including geographical location, seasonal variations, environmental conditions, and plant diversity. These factors cause variability in properties, making consistent authentication methods difficult to establish. The current review is centered on the utilization of multisource and qualitative methods for authenticating the identity of botanical and food ingredients. This review highlights the integral role of various botanicals and plant extracts authentication methods such as micro/macroscopy, chromatography, and spectroscopy technology, including DNA-based approaches. Further summarizing the current state of knowledge and importance its potential contributions to the field of botanical ingredient authentication system. This study also highlights the plants used in dietary supplement categories of weight management, memory enhancement and blood sugar regulation and their adulteration/admixture. Furthermore, discusses considerations for selecting appropriate methods and optimization steps in the implementation and standardization of botanical and plant extract authentication. In addition, we discussed the challenges and opportunities associated with the implementation and standardization of botanical and plant extracts authentication system. The future of botanical authentication will be shaped by advances in molecular diagnostics such as targeted DNA barcoding, Next-Generation Sequencing (NGS), and chemometric integration with spectroscopic techniques which are set to greatly enhance accuracy, traceability, and global compliance in botanical product safety and quality.
DOI: 10.6084/m9.figshare.29672618
title: Vitamin K Nutritional Status and Disease Risk - A Mendelian Randomization Analysis

description: Vitamin K is an essential nutrient obtained from dietary sources and commonly included in mainstream dietary supplements, playing a key role in regulating physiological functions and maintaining overall health. However, the causal nature of such associations between vitamin K nutritional status and diseases remains obscure. The existence of causality helps to prove the possibility of vitamin K becoming a biomarker for predicting susceptibility to certain diseases. To investigate this hypothesis, we conducted a literature review to identify diseases previously reported to be associated with vitamin K nutritional status, including cardiovascular, musculoskeletal, liver diseases and cancer, as candidate outcome factors. We also selected specific vitamin K subtypes with distinct physiological functions as exposure factors. Subsequently, we utilized a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association studies (GWAS) statistics to clarify causal relationships and distinguish vitamin K’s role as a risk factor or protective factor for these diseases. Our results showed that genetically predicted circulating vitamin K1 levels were positively associated with ischemic heart disease, myocardial infarction, heart failure, and alcoholic liver disease (ALD) risk, and negatively associated with lung carcinoma risk. Additionally, matrix Gla protein (MGP), as a biomarker of vitamin K2 nutritional status, was found to be positively associated with the risk of breast carcinoma and ALD. Osteocalcin (OC), another vitamin K2 biomarker, was potentially protective against nonalcoholic fatty liver disease (NAFLD). This novel causality discovery highlighted the necessity for further exploration of vitamin K nutritional status as a crucial factor in the pathogenesis and potential as a predictive, diagnostic, and prognostic biomarker for disease, including carcinoma, liver disease, myocardial infarction, heart failure, and related disorders.
DOI: 10.6084/m9.figshare.29672618.v1
title: Vitamin K Nutritional Status and Disease Risk - A Mendelian Randomization Analysis

description: Vitamin K is an essential nutrient obtained from dietary sources and commonly included in mainstream dietary supplements, playing a key role in regulating physiological functions and maintaining overall health. However, the causal nature of such associations between vitamin K nutritional status and diseases remains obscure. The existence of causality helps to prove the possibility of vitamin K becoming a biomarker for predicting susceptibility to certain diseases. To investigate this hypothesis, we conducted a literature review to identify diseases previously reported to be associated with vitamin K nutritional status, including cardiovascular, musculoskeletal, liver diseases and cancer, as candidate outcome factors. We also selected specific vitamin K subtypes with distinct physiological functions as exposure factors. Subsequently, we utilized a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association studies (GWAS) statistics to clarify causal relationships and distinguish vitamin K’s role as a risk factor or protective factor for these diseases. Our results showed that genetically predicted circulating vitamin K1 levels were positively associated with ischemic heart disease, myocardial infarction, heart failure, and alcoholic liver disease (ALD) risk, and negatively associated with lung carcinoma risk. Additionally, matrix Gla protein (MGP), as a biomarker of vitamin K2 nutritional status, was found to be positively associated with the risk of breast carcinoma and ALD. Osteocalcin (OC), another vitamin K2 biomarker, was potentially protective against nonalcoholic fatty liver disease (NAFLD). This novel causality discovery highlighted the necessity for further exploration of vitamin K nutritional status as a crucial factor in the pathogenesis and potential as a predictive, diagnostic, and prognostic biomarker for disease, including carcinoma, liver disease, myocardial infarction, heart failure, and related disorders.
DOI: 10.6084/m9.figshare.29835382
title: Apple Polyphenols and Defecation in Overweight Adults with Constipation – A Randomized Controlled Trial

description: Constipation is a prevalent symptom in adults and has been linked to an increased risk of serious complications, including cardiovascular and renal diseases. This study evaluated the effect of apple polyphenols on defecation among Japanese adults with a body mass index of ≥25 kg/m<sup>2</sup> and &lt;30 kg/m<sup>2</sup> experiencing constipation who were otherwise healthy. After screening for eligibility, 24 participants were randomly assigned to either the Apple polyphenol or Placebo group in equal numbers. Participants consumed four tablets/day of either unripe apple-derived polyphenols (600 mg/day) or a placebo after breakfast with water for 12 wk. The primary outcome was weekly defecation frequency. Secondary outcomes included the number of days with defecation, the volume and feeling of defecation, the shape and smell of stools, fecal <i>Akkermansia muciniphila</i> counts, physical measurements, body composition, and blood lipid profile. The analysis included 12 participants in the Apple polyphenol and 11 in the Placebo group. After the 12-week intervention, the Apple polyphenol group had a significantly higher weekly defecation frequency versus the Placebo group (7.0 ± 2.1 <i>vs</i>. 4.9 ± 1.4 times; group difference: 2.2 times [95% CI 0.8–3.6], <i>p</i> = 0.004). No significant inter-group differences were observed in fecal <i>A. muciniphila</i> counts, physical measurements, body composition. While blood triglyceride levels tended to be lower in the Apple polyphenol group. These findings suggest that the consumption of polyphenols derived from immature apples may increase defecation frequency and ameliorate constipation; however, it appears not to affect <i>A. muciniphila</i>. <b>Clinical trial registry:</b> UMIN000050393.
DOI: 10.6084/m9.figshare.29835382.v1
title: Apple Polyphenols and Defecation in Overweight Adults with Constipation – A Randomized Controlled Trial

description: Constipation is a prevalent symptom in adults and has been linked to an increased risk of serious complications, including cardiovascular and renal diseases. This study evaluated the effect of apple polyphenols on defecation among Japanese adults with a body mass index of ≥25 kg/m<sup>2</sup> and &lt;30 kg/m<sup>2</sup> experiencing constipation who were otherwise healthy. After screening for eligibility, 24 participants were randomly assigned to either the Apple polyphenol or Placebo group in equal numbers. Participants consumed four tablets/day of either unripe apple-derived polyphenols (600 mg/day) or a placebo after breakfast with water for 12 wk. The primary outcome was weekly defecation frequency. Secondary outcomes included the number of days with defecation, the volume and feeling of defecation, the shape and smell of stools, fecal <i>Akkermansia muciniphila</i> counts, physical measurements, body composition, and blood lipid profile. The analysis included 12 participants in the Apple polyphenol and 11 in the Placebo group. After the 12-week intervention, the Apple polyphenol group had a significantly higher weekly defecation frequency versus the Placebo group (7.0 ± 2.1 <i>vs</i>. 4.9 ± 1.4 times; group difference: 2.2 times [95% CI 0.8–3.6], <i>p</i> = 0.004). No significant inter-group differences were observed in fecal <i>A. muciniphila</i> counts, physical measurements, body composition. While blood triglyceride levels tended to be lower in the Apple polyphenol group. These findings suggest that the consumption of polyphenols derived from immature apples may increase defecation frequency and ameliorate constipation; however, it appears not to affect <i>A. muciniphila</i>. <b>Clinical trial registry:</b> UMIN000050393.
DOI: 10.6084/m9.figshare.29387830
title: Efficacy of a Probiotic Combination on Glycemic Index and Insulin Resistance in Adults: A Systematic Review and Meta-Analysis

description: Insulin resistance leads to increased glucose and insulin levels. Probiotics can reduce insulin resistance, but the presence of different probiotic strains and doses prevents the generalization to real-world scenario. The current systematic review and meta-analysis study investigated the efficacy of a triple probiotic combination (<i>Lactobacillus acidophilus</i>, <i>Lactobacillus casei</i>, and <i>Bifidobacterium bifidum</i>) on glycemic index and insulin resistance parameters in adults. Randomized controlled trials evaluating the efficacy of the probiotics combination on glycemic index and insulin resistance parameters were identified. Physiotherapy Evidence Database scale and the Cochrane Risk of Bias tool were used for risk of bias assessment and RevMan for meta-analysis. Fourteen good-quality clinical trials were included in the current study. Low-to-moderate risk of bias was observed. Data from 823 participants were included. Probiotics supplementation significantly reduced insulin resistance (MD: −1.05 HOMA-IR score, <i>p</i> &lt; 0.00001), serum glucose (MD: −3.99 mg/dl, <i>p</i> = 0.0003) and insulin levels (MD: −3.79 µIU/ml, <i>p</i> &lt; 0.00001), while significantly improved insulin sensitivity (MD: +0.02 QUICKI score, <i>p</i> &lt; 0.00001) and pancreatic β-cell functioning (MD: −14.71 HOMA-B score, <i>p</i> &lt; 0.00001) compared to the control group. Significant heterogeneity was observed for all evaluation parameters (except the HOMA-B score) while no significant publication bias was observed. The current study suggests that the probiotic combination of <i>Lactobacillus acidophilus</i>, <i>Lactobacillus casei</i>, and <i>Bifidobacterium bifidum</i> is effective in reducing insulin resistance, improving glycemic index parameters, and improving pancreatic β-cell functioning in adults by improving the gastrointestinal microbiome.
DOI: 10.6084/m9.figshare.29776096
title: Guar Gum β-Manno-Oligosaccharides Alleviate Ulcerative Colitis in Mice Models <i>via</i> Gut Microflora Modulation

description: Gut dysbiosis is a key feature in ulcerative colitis, a globally prevalent subtype of inflammatory bowel disease. Microbiota-directed dietary supplements can restore the dysbiotic gut and alleviate ulcerative colitis. We aimed to delineate whether prebiotic guar gum β-manno-oligosaccharides [GG-β-MOS(i) 500 mg/kg, (ii) 1000 mg/kg] favors gut microflora and microflora associated characteristics (MACs) and can prevent dextran sodium sulfate (DSS) induced ulcerative colitis in mice model. DSS challenged adult male C57BL/6 mice were used as model for colon inflammation evaluation. Food and water consumption, disease activity index (DAI), histopathological changes, cytokines in sera and colonic tissues, microflora associated characteristics (MACs; post-fermentation metabolites, short-chain fatty acids, etc.) and gut microflora profiles were studied. We found that GG-β-MOS successfully attenuated colonic inflammation, reduced inflammatory proteins, improved the ratio of Firmicutes to Bacteroidetes and promoted the colonization of probiotics like <i>Lactobacillus</i> and <i>Bifidobacteria</i>. Furthermore, GG-β-MOS enriched beneficial bacteria <i>viz.</i>, <i>Lactobacillus</i>, <i>Bifidobacteria</i>, <i>Bacillus</i> and <i>Enterococcus</i> showed positive correlation with anti-inflammatory metabolites like D-mannose, coprostanol, pentadecane, alpha-linolenic acid, dihomo-γ-linolenic acid, D-ribose, L-fucose, D-arabinose, N-acetyl-D-glucosamine, acetate and butyrate and negative correlation with oxalate, palmitic acid, arachidonic acid and erythritol. Overall, GG-β-MOS supplementation restored altered gut microflora and metabolome leading to improved mucosal repair and reduced intestinal inflammation in DSS induced ulcerative colitis mice model. GG-β-MOS effectively alleviated intestinal inflammation in UC mice.<i>Lactobacillus</i> and <i>Bifidobacteria</i> restored while <i>Bacteroides</i> reduced by GG-β-MOS.Disturbed gut microflora associated characteristics restored in UC mice by GG-β-MOS.ALA, DGLA, SCFAs, coprostanol enriched by GG-β-MOS.Carbohydrate, fatty acid, amino acid metabolism impacted by GG-β-MOS. GG-β-MOS effectively alleviated intestinal inflammation in UC mice. <i>Lactobacillus</i> and <i>Bifidobacteria</i> restored while <i>Bacteroides</i> reduced by GG-β-MOS. Disturbed gut microflora associated characteristics restored in UC mice by GG-β-MOS. ALA, DGLA, SCFAs, coprostanol enriched by GG-β-MOS. Carbohydrate, fatty acid, amino acid metabolism impacted by GG-β-MOS.
DOI: 10.6084/m9.figshare.29776096.v1
title: Guar Gum β-Manno-Oligosaccharides Alleviate Ulcerative Colitis in Mice Models <i>via</i> Gut Microflora Modulation

description: Gut dysbiosis is a key feature in ulcerative colitis, a globally prevalent subtype of inflammatory bowel disease. Microbiota-directed dietary supplements can restore the dysbiotic gut and alleviate ulcerative colitis. We aimed to delineate whether prebiotic guar gum β-manno-oligosaccharides [GG-β-MOS(i) 500 mg/kg, (ii) 1000 mg/kg] favors gut microflora and microflora associated characteristics (MACs) and can prevent dextran sodium sulfate (DSS) induced ulcerative colitis in mice model. DSS challenged adult male C57BL/6 mice were used as model for colon inflammation evaluation. Food and water consumption, disease activity index (DAI), histopathological changes, cytokines in sera and colonic tissues, microflora associated characteristics (MACs; post-fermentation metabolites, short-chain fatty acids, etc.) and gut microflora profiles were studied. We found that GG-β-MOS successfully attenuated colonic inflammation, reduced inflammatory proteins, improved the ratio of Firmicutes to Bacteroidetes and promoted the colonization of probiotics like <i>Lactobacillus</i> and <i>Bifidobacteria</i>. Furthermore, GG-β-MOS enriched beneficial bacteria <i>viz.</i>, <i>Lactobacillus</i>, <i>Bifidobacteria</i>, <i>Bacillus</i> and <i>Enterococcus</i> showed positive correlation with anti-inflammatory metabolites like D-mannose, coprostanol, pentadecane, alpha-linolenic acid, dihomo-γ-linolenic acid, D-ribose, L-fucose, D-arabinose, N-acetyl-D-glucosamine, acetate and butyrate and negative correlation with oxalate, palmitic acid, arachidonic acid and erythritol. Overall, GG-β-MOS supplementation restored altered gut microflora and metabolome leading to improved mucosal repair and reduced intestinal inflammation in DSS induced ulcerative colitis mice model. GG-β-MOS effectively alleviated intestinal inflammation in UC mice.<i>Lactobacillus</i> and <i>Bifidobacteria</i> restored while <i>Bacteroides</i> reduced by GG-β-MOS.Disturbed gut microflora associated characteristics restored in UC mice by GG-β-MOS.ALA, DGLA, SCFAs, coprostanol enriched by GG-β-MOS.Carbohydrate, fatty acid, amino acid metabolism impacted by GG-β-MOS. GG-β-MOS effectively alleviated intestinal inflammation in UC mice. <i>Lactobacillus</i> and <i>Bifidobacteria</i> restored while <i>Bacteroides</i> reduced by GG-β-MOS. Disturbed gut microflora associated characteristics restored in UC mice by GG-β-MOS. ALA, DGLA, SCFAs, coprostanol enriched by GG-β-MOS. Carbohydrate, fatty acid, amino acid metabolism impacted by GG-β-MOS.
DOI: 10.6084/m9.figshare.29387830.v1
title: Efficacy of a Probiotic Combination on Glycemic Index and Insulin Resistance in Adults: A Systematic Review and Meta-Analysis

description: Insulin resistance leads to increased glucose and insulin levels. Probiotics can reduce insulin resistance, but the presence of different probiotic strains and doses prevents the generalization to real-world scenario. The current systematic review and meta-analysis study investigated the efficacy of a triple probiotic combination (<i>Lactobacillus acidophilus</i>, <i>Lactobacillus casei</i>, and <i>Bifidobacterium bifidum</i>) on glycemic index and insulin resistance parameters in adults. Randomized controlled trials evaluating the efficacy of the probiotics combination on glycemic index and insulin resistance parameters were identified. Physiotherapy Evidence Database scale and the Cochrane Risk of Bias tool were used for risk of bias assessment and RevMan for meta-analysis. Fourteen good-quality clinical trials were included in the current study. Low-to-moderate risk of bias was observed. Data from 823 participants were included. Probiotics supplementation significantly reduced insulin resistance (MD: −1.05 HOMA-IR score, <i>p</i> &lt; 0.00001), serum glucose (MD: −3.99 mg/dl, <i>p</i> = 0.0003) and insulin levels (MD: −3.79 µIU/ml, <i>p</i> &lt; 0.00001), while significantly improved insulin sensitivity (MD: +0.02 QUICKI score, <i>p</i> &lt; 0.00001) and pancreatic β-cell functioning (MD: −14.71 HOMA-B score, <i>p</i> &lt; 0.00001) compared to the control group. Significant heterogeneity was observed for all evaluation parameters (except the HOMA-B score) while no significant publication bias was observed. The current study suggests that the probiotic combination of <i>Lactobacillus acidophilus</i>, <i>Lactobacillus casei</i>, and <i>Bifidobacterium bifidum</i> is effective in reducing insulin resistance, improving glycemic index parameters, and improving pancreatic β-cell functioning in adults by improving the gastrointestinal microbiome.
DOI: 10.22002/227hz-8dd54
title: JV7967

description: Legionella thyA ΔdotI ΔdotJ
description: <strong>Tilt Series Date:</strong> 2016-08-11</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.50°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at Janelia Krios.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0.</p>
<strong>Sample Preparation:</strong> 8 grids were frozen for the JV7967 strain at OD~3.3. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 3 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2016-08-11-43/rawdata/</p>7967-gridb-atlas3a0030.mrc,  Tilt Series (Pixel Size 0.42 nm), 2.3 GB  
        
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        7967-gridb-atlas3a0030_full.rec,  Reconstruction (Pixel Size 1.68 nm), 445.4 MB  
        
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