scholarly journals Segmental Series and Size: Clade-Wide Investigation of Molar Proportions Reveals a Major Evolutionary Allometry in the Dentition of Placental Mammals

2021 ◽  
Author(s):  
Guillaume Billet ◽  
Jérémie Bardin
Keyword(s):  
Large Scale ◽  
Dietary Habits ◽  
Wide Spectrum ◽  
Biological Traits ◽  
Dental Morphology ◽  
Absolute Size ◽  
Developmental Models ◽  
Evolutionary Allometry ◽  
Proportional Increase ◽  
Living Organisms

Abstract Iterative segments such as teeth or limbs are a widespread characteristic of living organisms. While their proportions may be governed by similar developmental rules in vertebrates, there is no emerging pattern as regards their relation to size. Placental mammals span eight orders of magnitude in body size and show a wide spectrum of dietary habits associated with size and reflected in their dentitions, especially molars. Although variation in size constitutes an important determinant for variation in biological traits, few major allometric trends have been documented on placental molars so far. Molar proportions have been intensively explored in placentals in relation to developmental models, but often at a small phylogenetic scale. Here, we analyzed the diversity of upper molar proportions in relation to absolute size in a large sample of placental species ($n = 299$) encompassing most of the group’s dental diversity. Our phylogenetically informed analyses revealed a 2-fold pattern of evolutionary integration among upper molars: while molars covary in size with each other, their proportions covary with the absolute size of the entire molar field. With increasing absolute size, posterior molars increase in size relative to anterior ones, meaning that large-sized species have relatively large rear molars while the opposite is true for small-sized species. The directionality of proportional increase in the molar row exhibits a previously unsuspected allometric patterning among placentals, showing how large-scale variations in size may have influenced variation in dental morphology. This finding provides new evidence that processes regulating the size of individual molars are integrated with overall patterns of growth and calls for further testing of allometric variation in the dentition and in other segmental series of the vertebrate body. [Dentition; evolution; model; phylogeny; segmentation; size.]

Model and Method for Contributor’s Quality Assessment in Community Image Tagging Systems

2018 ◽  
pp. 45-51
Author(s):  
A. V. Ponomarev
Keyword(s):  
Large Scale ◽  
Wide Spectrum ◽  
Preference Relation ◽  
Pairwise Comparison ◽  
Ground Truth ◽  
Comparison Method ◽  
Characteristic Matrix ◽  
Image Tagging ◽  
Proposed Model

Introduction: Large-scale human-computer systems involving people of various skills and motivation into the information processing process are currently used in a wide spectrum of applications. An acute problem in such systems is assessing the expected quality of each contributor; for example, in order to penalize incompetent or inaccurate ones and to promote diligent ones.Purpose: To develop a method of assessing the expected contributor’s quality in community tagging systems. This method should only use generally unreliable and incomplete information provided by contributors (with ground truth tags unknown).Results:A mathematical model is proposed for community image tagging (including the model of a contributor), along with a method of assessing the expected contributor’s quality. The method is based on comparing tag sets provided by different contributors for the same images, being a modification of pairwise comparison method with preference relation replaced by a special domination characteristic. Expected contributors’ quality is evaluated as a positive eigenvector of a pairwise domination characteristic matrix. Community tagging simulation has confirmed that the proposed method allows you to adequately estimate the expected quality of community tagging system contributors (provided that the contributors' behavior fits the proposed model).Practical relevance: The obtained results can be used in the development of systems based on coordinated efforts of community (primarily, community tagging systems). 

A Large-scale Analysis of Hundreds of In-memory Key-value Cache Clusters at Twitter

2021 ◽  
Vol 17 (3) ◽  
pp. 1-35
Author(s):  
Juncheng Yang ◽  
Yao Yue ◽  
K. V. Rashmi
Keyword(s):  
Large Scale ◽  
Production Systems ◽  
Wide Spectrum ◽  
Use Cases ◽  
Scale Analysis ◽  
Business Logic ◽  
Traffic Pattern ◽  
Fine Grained ◽  
Memory Cache ◽  
Large Scale Analysis

Modern web services use in-memory caching extensively to increase throughput and reduce latency. There have been several workload analyses of production systems that have fueled research in improving the effectiveness of in-memory caching systems. However, the coverage is still sparse considering the wide spectrum of industrial cache use cases. In this work, we significantly further the understanding of real-world cache workloads by collecting production traces from 153 in-memory cache clusters at Twitter, sifting through over 80 TB of data, and sometimes interpreting the workloads in the context of the business logic behind them. We perform a comprehensive analysis to characterize cache workloads based on traffic pattern, time-to-live (TTL), popularity distribution, and size distribution. A fine-grained view of different workloads uncover the diversity of use cases: many are far more write-heavy or more skewed than previously shown and some display unique temporal patterns. We also observe that TTL is an important and sometimes defining parameter of cache working sets. Our simulations show that ideal replacement strategy in production caches can be surprising, for example, FIFO works the best for a large number of workloads.

Oxygen, hydrogen, and strontium isotope constraints on the origin of granites

1988 ◽  
Vol 79 (2-3) ◽  
pp. 317-338 ◽  
Author(s):  
Hugh P. Taylor
Keyword(s):  
Large Scale ◽  
Wide Spectrum ◽  
Volcanic Field ◽  
Parent Material ◽  
Rock Interaction ◽  
Metasedimentary Rocks ◽  
Clear Cut ◽  
End Members ◽  
Type 3

ABSTRACTOxygen isotope data are very useful in determining the source rocks of granitic magmas, particularly when used in combination with Sr, Pb, and Nd isotope studies. For example, unusually high δ18O values in magmas (δ18O> +8) require the involvement of some precursor parent material that at some time in the past resided on or near the Earth's surface, either as sedimentary rocks or as weathered or hydrothermally altered rocks. The isotopic systematics which are preserved in the Mesozoic and Cenozoic batholiths of western North America can be explained by grand-scale mixing of three broadly defined end-members: (1) oceanic island-arc magmas derived from a “depleted” (MORB-type?) source in the upper mantle (δ18O c. +6 and 87Sr/86Sr c. 0·703); (2) a high-18O (c. +13 to +17) source with a very uniform 87Sr/86Sr (c. 0·708 to 0·712), derived mainly from eugeosynclinal volcanogenic sediments and (or) hydrothermally altered basalts; and (3) a much more heterogeneous source (87Sr/86Sr c. 0·706 to 0·750, or higher) with a high δ18O (c. +9 to +15) where derived from supracrustal metasedimentary rocks and a much lower δ18O (c. +7 to +9) where derived from the lower continental crust of the craton. These end-members were successively dominant from W to E, respectively, within three elongate N–S geographic zones that can be mapped from Mexico all the way N to Idaho.18O/16O studies (together with D/H analyses) can, however, play a more important and certainly a unique role in determining the origins of the aqueous fluids involved in the formation of granitic and rhyolitic magmas. Fluid-rock interaction effects are most clear-cut when low-18O, low-D meteoric waters are involved in the isotopic exchange and melting processes, but the effects of other waters such as seawater (with a relatively high δD c. 0) can also be recognised. Because of these hydrothermal processes, rocks that ultimately undergo partial melting may exhibit isotopic signatures considerably different from those that they started with. We discuss three broad classes of potential source materials of such “hydrothermal-anatectic” granitic magmas, based mainly on water/rock (w/r), temperature (T), and the length of time (t) that fluid-rock interaction proceeds: (Type 1) epizonal systems with a wide variation in whole-rock δ18O and extreme 18O/16O disequilibrium among coexisting minerals (e.g. quartz and feldspar); (Type 2) deeper-seated and (or) longer-lived systems, also with a wide spectrum of whole-rock δ18O, but with equilibrated 18O/16O ratios among coexisting minerals; (Type 3) thoroughly homogenised and equilibrated systems with relatively uniform δ18O in all lithologies. Low-18O magmas formed by melting of rocks altered in a Type 2 or a Type 3 meteoric-hydrothermal system are the only kinds of “hydrothermal-anatectic” granitic magmas that are readily recognisable in the geological record. Analogous effects produced by other kinds of aqueous fluids may, however, be quite common, particularly in areas of extensional tectonics and large-scale rifting. The greatly enhanced permeabilities in such fractured terranes make possible the deep convective circulation of ground waters and sedimentary pore fluids. The nature and origin of low-18O magmas in the Yellowstone volcanic field and the Seychelles Islands are briefly reviewed in light of these concepts, as is the development of high-D, peraluminous magmas in the Hercynian of the Pyrenees.

scholarly journals A Multi-Scale Modelling of Aggregation of TiO2 Nanoparticle Suspensions in Water

2021 ◽  
Author(s):  
Giulia Mancardi ◽  
Matteo Alberghini ◽  
Neus Aguilera-Porta ◽  
Monica Calatayud ◽  
Pietro Asinari ◽  
...  
Keyword(s):  
Titanium Dioxide ◽  
Density Functional ◽  
Large Scale ◽  
Molecular Descriptors ◽  
Titanium Dioxide Nanoparticles ◽  
Accurate Determination ◽  
Multi Scale ◽  
Spherical Bead ◽  
Living Organisms ◽  
Dynamics Simulations

Titanium dioxide nanoparticles have risen concerns about their possible toxicity and the European Food Safety Authority recently banned the use of TiO2 nano-additive in food products. Following the intent of relating nanomaterials atomic structure with their toxicity without having to conduct large scale experiments on living organisms, we investigate the aggregation of titanium dioxide nanoparticles using a multi-scale technique: starting from ab initio Density Functional Theory to get an accurate determination of the energetics and electronic structure, we switch to classical Molecular Dynamics simulations to calculate the Potential of Mean Force for the connection of two identical nanoparticles in water; the fitting of the latter by a set of mathematical equations is the key for the upscale. Lastly, we perform Brownian Dynamics simulations where each nanoparticle is a spherical bead. This coarsening strategy allows studying the aggregation of a few thousand nanoparticles. Applying this novel procedure, we find three new molecular descriptors, namely, the aggregation free energy and two numerical parameters used to correct the observed deviation from the aggregation kinetic described by the Smoluchowski theory. Molecular descriptors can be fed into QSAR models to predict the toxicity of a material knowing its physicochemical properties, without having to conduct large scale experiments on living organisms.

scholarly journals Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

2020 ◽  
Author(s):  
Youwen Qin ◽  
Aki S Havulinna ◽  
Yang Liu ◽  
Pekka Jousilahti ◽  
Scott C Ritchie ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Dietary Habits ◽  
Population Based ◽  
Genome Wide ◽  
Scale Population ◽  
Important Health ◽  
Disease Analysis

Co-evolution between humans and the microbial communities colonizing them has resulted in an intimate assembly of thousands of microbial species mutualistically living on and in their body and impacting multiple aspects of host physiology and health. Several studies examining whether human genetic variation can affect gut microbiota suggest a complex combination of environmental and host factors. Here, we leverage a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial shotgun metagenomes, dietary information and health records up to 16 years post-sampling, to characterize human genetic variations associated with microbial abundances, and predict possible causal links with various diseases using Mendelian randomization (MR). Genome-wide association study (GWAS) identified 583 independent SNP-taxon associations at genome-wide significance (p<5.0×10-8), which included notable strong associations with LCT (p=5.02×10-35), ABO (p=1.1×10-12), and MED13L (p=1.84×10-12). A combination of genetics and dietary habits was shown to strongly shape the abundances of certain key bacterial members of the gut microbiota, and explain their genetic association. Genetic effects from the LCT locus on Bifidobacterium and three other associated taxa significantly differed according to dairy intake. Variation in mucin-degrading Faecalicatena lactaris abundances were associated with ABO, highlighting a preferential utilization of secreted A/B/AB-antigens as energy source in the gut, irrespectively of fibre intake. Enterococcus faecalis levels showed a robust association with a variant in MED13L, with putative links to colorectal cancer. Finally, we identified putative causal relationships between gut microbes and complex diseases using MR, with a predicted effect of Morganella on major depressive disorder that was consistent with observational incident disease analysis. Overall, we present striking examples of the intricate relationship between humans and their gut microbial communities, and highlight important health implications.

scholarly journals Rationale and Design of the Hamburg City Health Study

2019 ◽  
Vol 35 (2) ◽  
pp. 169-181 ◽  
Author(s):  
Annika Jagodzinski ◽  
Christoffer Johansen ◽  
Uwe Koch-Gromus ◽  
Ghazal Aarabi ◽  
Gerhard Adam ◽  
...  
Keyword(s):  
Digital Media ◽  
Chronic Diseases ◽  
Large Scale ◽  
Dietary Habits ◽  
Routine Data ◽  
Health Care Use ◽  
Health Study ◽  
Imaging Biomarker ◽  
Risk And Resilience

Abstract The Hamburg City Health Study (HCHS) is a large, prospective, long-term, population-based cohort study and a unique research platform and network to obtain substantial knowledge about several important risk and prognostic factors in major chronic diseases. A random sample of 45,000 participants between 45 and 74 years of age from the general population of Hamburg, Germany, are taking part in an extensive baseline assessment at one dedicated study center. Participants undergo 13 validated and 5 novel examinations primarily targeting major organ system function and structures including extensive imaging examinations. The protocol includes validate self-reports via questionnaires regarding lifestyle and environmental conditions, dietary habits, physical condition and activity, sexual dysfunction, professional life, psychosocial context and burden, quality of life, digital media use, occupational, medical and family history as well as healthcare utilization. The assessment is completed by genomic and proteomic characterization. Beyond the identification of classical risk factors for major chronic diseases and survivorship, the core intention is to gather valid prevalence and incidence, and to develop complex models predicting health outcomes based on a multitude of examination data, imaging, biomarker, psychosocial and behavioral assessments. Participants at risk for coronary artery disease, atrial fibrillation, heart failure, stroke and dementia are invited for a visit to conduct an additional MRI examination of either heart or brain. Endpoint assessment of the overall sample will be completed through repeated follow-up examinations and surveys as well as related individual routine data from involved health and pension insurances. The study is targeting the complex relationship between biologic and psychosocial risk and resilience factors, chronic disease, health care use, survivorship and health as well as favorable and bad prognosis within a unique, large-scale long-term assessment with the perspective of further examinations after 6 years in a representative European metropolitan population.

scholarly journals Recent advances in functional genome analysis

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1968 ◽  
Author(s):  
Roderic Guigo ◽  
Michiel de Hoon
Keyword(s):  
Functional Genomics ◽  
Human Genome ◽  
Large Scale ◽  
Massively Parallel Sequencing ◽  
Genome Project ◽  
Biological Traits ◽  
Cellular Behavior ◽  
Sequencing Technologies ◽  
Recent Advances ◽  
The Human Genome Project

At the beginning of this century, the Human Genome Project produced the first drafts of the human genome sequence. Following this, large-scale functional genomics studies were initiated to understand the molecular basis underlying the translation of the instructions encoded in the genome into the biological traits of organisms. Instrumental in the ensuing revolution in functional genomics were the rapid advances in massively parallel sequencing technologies as well as the development of a wide diversity of protocols that make use of these technologies to understand cellular behavior at the molecular level. Here, we review recent advances in functional genomic methods, discuss some of their current capabilities and limitations, and briefly sketch future directions within the field.

Looking at Nature from the Perspective of Physical Sciences

2020 ◽  
pp. 1-103
Keyword(s):  
Liquid Crystals ◽  
Soft Matter ◽  
Wide Spectrum ◽  
General Information ◽  
Physical Sciences ◽  
Living Organisms ◽  
Near Future ◽  
The Universe

This chapter of the book looks at the structure of our environment, including our bodies, by examining the wide spectrum of dimensions of objects. Themes discussed provide some general information about concepts of data, information, and knowledge; dimensions of objects and the ways to look on and interpret them; ways to watch events and how they depend on various factors, especially within a nano-world. These issues are further examined with reference to our bodies and microbes that used to inhabit or attack us. Discussion involves materials such as soft matter, liquid crystals, and colloids, and then events occurring as waves in the quantum world, including the very beginnings of the universe, processes going now in nature, and plans concerning Mars colonization in the near future. Further text tells about carbon in its various forms, dimensions, existing reservoirs, and its role in living organisms.

scholarly journals Evaluation of different phenotypic tests for detection of metallo-β-lactamases in imipenem-resistant Pseudomonas aeruginosa

2017 ◽  
Vol 9 (04) ◽  
pp. 249-253 ◽  
Author(s):  
Rohit Sachdeva ◽  
Babita Sharma ◽  
Rajni Sharma
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Large Scale ◽  
Wide Spectrum ◽  
Carbapenem Resistance ◽  
Resistance Mechanisms ◽  
Clinical Samples ◽  
Resistant Strains ◽  
Synergy Test ◽  
Phenotypic Tests ◽  
Simple Screening

Abstract PURPOSE: Pseudomonas aeruginosa causes a wide spectrum of infections including bacteremia, pneumonia, urinary tract infection, etc., Metallo-beta-lactamase (MBL) producing P. aeruginosa is an emerging threat and cause of concern as they have emerged as one of the most feared resistance mechanisms. This study was designed to know the prevalence of MBL production in P. aeruginosa and to evaluate the four phenotypic tests for detection of MBL production in imipenem-resistant clinical isolates of P. aeruginosa. METHODS: Totally, 800 isolates of P. aeruginosa isolated from various clinical samples were evaluated for carbapenem resistance and MBL production. All imipenem-resistant strains were tested for carabapenemase production by modified Hodge test. Screening for MBL production was done by double-disc synergy test and combined disc test (CDT). Confirmation of MBL production was done by the E-test (Ab BioDisk, Solna, Sweden). RESULTS: Out of the 800 isolates of P. aeruginosa, 250 isolates were found resistant to imipenem. Based on the results of E-test, 147 (18.37%) isolates of P. aeruginosa were positive for MBL production. The CDT has the highest sensitivity and specificity for the detection of MBL production as compared to other tests. CONCLUSION: The results of this study are indicative that MBL production is an important mechanism of carbapenem resistance among P. aeruginosa. Use of simple screening test like CDT will be crucial step toward large-scale monitoring of these emerging resistant determinants. Phenotypic test for MBL production has to be standardized, and all the isolates should be routinely screened for MBL production.

Oxidative Stress, Mitochondrial DNA Mutation, and Impairment of Antioxidant Enzymes in Aging

2002 ◽  
Vol 227 (9) ◽  
pp. 671-682 ◽  
Author(s):  
Yau-Huei Wei ◽  
Hsin-Chen Lee
Keyword(s):  
Oxidative Stress ◽  
Mitochondrial Dna ◽  
Antioxidant Enzymes ◽  
Oxidative Damage ◽  
Large Scale ◽  
Wide Spectrum ◽  
Radical Scavenging ◽  
Mtdna Mutations ◽  
Enhanced Production ◽  
Age Related

Mitochondria do not only produce less ATP, but they also increase the production of reactive oxygen species (ROS) as byproducts of aerobic metabolism in the aging tissues of the human and animals. It is now generally accepted that aging-associated respiratory function decline can result in enhanced production of ROS in mitochondria. Moreover, the activities of free radical-scavenging enzymes are altered in the aging process. The concurrent age-related changes of these two systems result in the elevation of oxidative stress in aging tissues. Within a certain concentration range, ROS may induce stress response of the cells by altering expression of respiratory genes to uphold the energy metabolism to rescue the cell. However, beyond the threshold, ROS may cause a wide spectrum of oxidative damage to various cellular components to result in cell death or elicit apoptosis by induction of mitochondrial membrane permeability transition and release of apoptogenic factors such as cytochrome c. Moreover, oxidative damage and large-scale deletion and duplication of mitochondrial DNA (mtDNA) have been found to increase with age in various tissues of the human. Mitochondria act like a biosensor of oxidative stress and they enable cell to undergo changes in aging and age-related diseases. On the other hand, it has recently been demonstrated that impairment in mitochondrial respiration and oxidative phosphorylation elicits an increase in oxidative stress and causes a host of mtDNA rearrangements and deletions. Here, we review work done in the past few years to support our view that oxidative stress and oxidative damage are a result of concurrent accumulation of mtDNA mutations and defective antioxidant enzymes in human aging.

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