scholarly journals Estimate of the sequenced proportion of the global prokaryotic genome

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Zheng Zhang ◽  
Jianing Wang ◽  
Jinlan Wang ◽  
Jingjing Wang ◽  
Yuezhong Li
Keyword(s):  
Large Scale ◽  
Prokaryotic Genome ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Basic Question ◽  
Prokaryotic Genomes ◽  
Efficient Exploration ◽  
The Many ◽  
Multiple Samples ◽  
Large Scale Alignment

Abstract Background Sequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. However, the cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases. Results Our results showed that the median proportions of the genome-sequenced cells and taxa (at 100% identities in the 16S-V4 region) in different biomes reached 38.1% (16.4–86.3%) and 18.8% (9.1–52.6%), respectively. The sequenced proportions of the prokaryotic genomes in biomes were significantly negatively correlated with the alpha diversity indices, and the proportions sequenced in host-associated biomes were significantly higher than those in free-living biomes. Due to a set of cosmopolitan OTUs that are found in multiple samples and preferentially sequenced, only 2.1% of the global prokaryotic taxa are represented by sequenced genomes. Most of the biomes were occupied by a few predominant taxa with a high relative abundance and much higher genome-sequenced proportions than numerous rare taxa. Conclusions These results reveal the current situation of prokaryotic genome sequencing for earth biomes, provide a more reasonable and efficient exploration of prokaryotic genomes, and promote our understanding of microbial ecological functions.

Integration of Ecological and Engineering Aspects in Planning Large Scale Tidal Power Development in the Bay of Fundy, Canada

1984 ◽  
Vol 16 (1-2) ◽  
pp. 281-295 ◽  
Author(s):  
Donald C Gordon
Keyword(s):  
Large Scale ◽  
Feasibility Studies ◽  
Bay Of Fundy ◽  
Final Decision ◽  
Power Development ◽  
Tidal Power ◽  
History Of ◽  
Scientists And Engineers ◽  
The Many ◽  
University Scientists

Large-scale tidal power development in the Bay of Fundy has been given serious consideration for over 60 years. There has been a long history of productive interaction between environmental scientists and engineers durinn the many feasibility studies undertaken. Up until recently, tidal power proposals were dropped on economic grounds. However, large-scale development in the upper reaches of the Bay of Fundy now appears to be economically viable and a pre-commitment design program is highly likely in the near future. A large number of basic scientific research studies have been and are being conducted by government and university scientists. Likely environmental impacts have been examined by scientists and engineers together in a preliminary fashion on several occasions. A full environmental assessment will be conducted before a final decision is made and the results will definately influence the outcome.

scholarly journals A Novel Unsupervised Classification Method for Sandy Land Using Fully Polarimetric SAR Data

2021 ◽  
Vol 13 (3) ◽  
pp. 355
Author(s):  
Weixian Tan ◽  
Borong Sun ◽  
Chenyu Xiao ◽  
Pingping Huang ◽  
Wei Xu ◽  
...  
Keyword(s):  
Spectral Clustering ◽  
Large Scale ◽  
Clustering Algorithm ◽  
Feature Vector ◽  
Unsupervised Classification ◽  
Classification Method ◽  
Sandy Land ◽  
Classification Methods ◽  
The Many ◽  
Representative Points

Classification based on polarimetric synthetic aperture radar (PolSAR) images is an emerging technology, and recent years have seen the introduction of various classification methods that have been proven to be effective to identify typical features of many terrain types. Among the many regions of the study, the Hunshandake Sandy Land in Inner Mongolia, China stands out for its vast area of sandy land, variety of ground objects, and intricate structure, with more irregular characteristics than conventional land cover. Accounting for the particular surface features of the Hunshandake Sandy Land, an unsupervised classification method based on new decomposition and large-scale spectral clustering with superpixels (ND-LSC) is proposed in this study. Firstly, the polarization scattering parameters are extracted through a new decomposition, rather than other decomposition approaches, which gives rise to more accurate feature vector estimate. Secondly, a large-scale spectral clustering is applied as appropriate to meet the massive land and complex terrain. More specifically, this involves a beginning sub-step of superpixels generation via the Adaptive Simple Linear Iterative Clustering (ASLIC) algorithm when the feature vector combined with the spatial coordinate information are employed as input, and subsequently a sub-step of representative points selection as well as bipartite graph formation, followed by the spectral clustering algorithm to complete the classification task. Finally, testing and analysis are conducted on the RADARSAT-2 fully PolSAR dataset acquired over the Hunshandake Sandy Land in 2016. Both qualitative and quantitative experiments compared with several classification methods are conducted to show that proposed method can significantly improve performance on classification.

scholarly journals Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hua Zha ◽  
Fengping Liu ◽  
Zongxin Ling ◽  
Kevin Chang ◽  
Jiezuan Yang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Vital Role ◽  
Rrna Gene ◽  
Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

scholarly journals Grounding semantic transparency in context

Morphology ◽  
2021 ◽  
Author(s):  
Rossella Varvara ◽  
Gabriella Lapesa ◽  
Sebastian Padó
Keyword(s):  
Large Scale ◽  
Point Of View ◽  
Distributional Semantics ◽  
Semantic Transparency ◽  
Inclusion Measure ◽  
The Difference ◽  
Semantic Point ◽  
The Many ◽  
The Relationship

AbstractWe present the results of a large-scale corpus-based comparison of two German event nominalization patterns: deverbal nouns in -ung (e.g., die Evaluierung, ‘the evaluation’) and nominal infinitives (e.g., das Evaluieren, ‘the evaluating’). Among the many available event nominalization patterns for German, we selected these two because they are both highly productive and challenging from the semantic point of view. Both patterns are known to keep a tight relation with the event denoted by the base verb, but with different nuances. Our study targets a better understanding of the differences in their semantic import.The key notion of our comparison is that of semantic transparency, and we propose a usage-based characterization of the relationship between derived nominals and their bases. Using methods from distributional semantics, we bring to bear two concrete measures of transparency which highlight different nuances: the first one, cosine, detects nominalizations which are semantically similar to their bases; the second one, distributional inclusion, detects nominalizations which are used in a subset of the contexts of the base verb. We find that only the inclusion measure helps in characterizing the difference between the two types of nominalizations, in relation with the traditionally considered variable of relative frequency (Hay, 2001). Finally, the distributional analysis allows us to frame our comparison in the broader coordinates of the inflection vs. derivation cline.

scholarly journals Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components

2021 ◽  
Vol 11 (1) ◽  
pp. 35
Author(s):  
Zahra A. Barandouzi ◽  
Joochul Lee ◽  
Kendra Maas ◽  
Angela R. Starkweather ◽  
Xiaomei S. Cong
Keyword(s):  
Irritable Bowel Syndrome ◽  
Gut Microbiota ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Cross Sectional Study ◽  
Caffeine Intake ◽  
Caffeine Consumption ◽  
Cross Sectional ◽  
Food Components ◽  
Irritable Bowel

The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as well as to explore the associations of food components and microbiota profiles. A cross-sectional study was conducted with 80 young adults with IBS and 21 HC recruited. The food frequency questionnaire was used to measure food components. Fecal samples were collected and profiled by 16S rRNA Illumina sequencing. Food components were similar in both IBS and HC groups, except in caffeine consumption. Higher alpha diversity indices and altered gut microbiota were observed in IBS compared to the HC. A negative correlation existed between total observed species and caffeine intake in the HC, and a positive correlation between alpha diversity indices and dietary fiber in the IBS group. Higher alpha diversity and gut microbiota alteration were found in IBS people who consumed caffeine more than 400 mg/d. Moreover, high microbial diversity and alteration of gut microbiota composition in IBS people with high caffeine consumption may be a clue toward the effects of caffeine on the gut microbiome pattern, which warrants further study.

scholarly journals Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota

2021 ◽  
Vol 22 (4) ◽  
pp. 2131
Author(s):  
Stefania Pane ◽  
Anna Sacco ◽  
Andrea Iorio ◽  
Lorenza Romani ◽  
Lorenza Putignani
Keyword(s):  
Gut Microbiota ◽  
Bacterial Species ◽  
Alpha Diversity ◽  
Strongyloides Stercoralis ◽  
Pulmonary Involvement ◽  
Diversity Indices ◽  
Parasite Infection ◽  
Intestinal Nematode ◽  
Immune Mediated ◽  
Stool Samples

Background: Strongyloidiasis is a neglected tropical disease caused by the intestinal nematode Strongyloides stercoralis and characterized by gastrointestinal and pulmonary involvement. We report a pediatric case of strongyloidiasis to underline the response of the host microbiota to the perturbation induced by the nematode. Methods: We performed a 16S rRNA-metagenomic analysis of the gut microbiota of a 7-year-old female during and after S. stercolaris infection, investigating three time-point of stool samples’ ecology: T0- during parasite infection, T1- a month after parasite infection, and T2- two months after parasite infection. Targeted-metagenomics were used to investigate ecology and to predict the functional pathways of the gut microbiota. Results: an increase in the alpha-diversity indices in T0-T1 samples was observed compared to T2 and healthy controls (CTRLs). Beta-diversity analysis showed a shift in the relative abundance of specific gut bacterial species from T0 to T2 samples. Moreover, the functional prediction of the targeted-metagenomics profiles suggested an enrichment of microbial glycan and carbohydrate metabolisms in the T0 sample compared with CTRLs. Conclusions: The herein report reinforces the literature suggestion of a putative direct or immune-mediated ability of S. stercolaris to promote the increase in bacterial diversity.

scholarly journals Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 463
Author(s):  
Mariusz Sikora ◽  
Albert Stec ◽  
Magdalena Chrabaszcz ◽  
Aleksandra Knot ◽  
Anna Waskiel-Burnat ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Large Scale ◽  
Skin Diseases ◽  
Intestinal Barrier ◽  
Alpha Diversity ◽  
Current Data ◽  
Intestinal Microbiome ◽  
Microbial Composition ◽  
Alpha And Beta Diversity

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.

Toolkit for Epidemiologic Response to an Acute Chemical Release

2016 ◽  
Vol 10 (4) ◽  
pp. 631-632 ◽  
Author(s):  
Mary Anne Duncan ◽  
Maureen F. Orr
Keyword(s):  
Public Health ◽  
Large Scale ◽  
Technical Assistance ◽  
Local Health ◽  
Toxic Substances ◽  
Public Health Action ◽  
Public Health Agencies ◽  
Chemical Release ◽  
State And Local ◽  
The Many

AbstractWhen a large chemical incident occurs and people are injured, public health agencies need to be able to provide guidance and respond to questions from the public, the media, and public officials. Because of this urgent need for information to support appropriate public health action, the Agency for Toxic Substances and Disease Registry (ATSDR) of the US Department of Health and Human Services has developed the Assessment of Chemical Exposures (ACE) Toolkit. The ACE Toolkit, available on the ATSDR website, offers materials including surveys, consent forms, databases, and training materials that state and local health personnel can use to rapidly conduct an epidemiologic investigation after a large-scale acute chemical release. All materials are readily adaptable to the many different chemical incident scenarios that may occur and the data needs of the responding agency. An expert ACE team is available to provide technical assistance on site or remotely. (Disaster Med Public Health Preparedness. 2016;10:631–632)

Large scale alignment of a lamellar block copolymer thin film via electric fields: a time-resolved SFM study

Soft Matter ◽  
2006 ◽  
Vol 2 (12) ◽  
pp. 1089-1094 ◽  
Author(s):  
Violetta Olszowka ◽  
Markus Hund ◽  
Volker Kuntermann ◽  
Sabine Scherdel ◽  
Larisa Tsarkova ◽  
...  
Keyword(s):  
Thin Film ◽  
Block Copolymer ◽  
Electric Fields ◽  
Large Scale ◽  
Time Resolved ◽  
Large Scale Alignment

The Politics of The Grain Trade in Iraq c. 1840-1917

1991 ◽  
Vol 6 ◽  
pp. 151-165 ◽  
Author(s):  
Hala Fattah
Keyword(s):  
Local Governments ◽  
Large Scale ◽  
Grain Trade ◽  
The Many ◽  
Difficult Terrain ◽  
The Military

Anyone who watched the televison coverage of, or read about the African famine some years ago could not help but be appalled by the many obstacles erected to impede the progress of getting food to the starving millions in Ethiopia, Somalia and the Sudan. While it is true that the difficult terrain, an inhospitable climate and the lack of rain were partly responsible for the large-scale spread of famine and dearth in the African sub-continent, it is also true that local governments were responsible for creating impediments to the alleviation of mass hunger and starvation. Governments waging war against secessionist regimes and rebel armies used political means—primarily blockades of grain and other foodstuffs—to starve the enemy forces, creating misery among the military as well as civilian populations in the rebel areas.

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