scholarly journals Mitochondrial Phylogenomics of Fagales Provides Insights Into Plant Mitogenome Mosaic Evolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanlei Feng ◽  
Xiaoguo Xiang ◽  
Delara Akhter ◽  
Ronghui Pan ◽  
Zhixi Fu ◽  
...  
Keyword(s):  
Woody Plants ◽  
Large Scale ◽  
Size Variation ◽  
Nuclear Genome ◽  
Third Party ◽  
Plastid Genomes ◽  
Gene Sets ◽  
Almost All ◽  
Similar Gene ◽  
Specific Sequences

Fagales are an order of woody plants and comprise more than 1,100 species, most of which produce economically important timbers, nuts, and fruits. Their nuclear and plastid genomes are well-sequenced and provided valuable resources to study their phylogeny, breeding, resistance, etc. However, little is known about the mitochondrial genomes (mitogenomes), which hinder a full understanding of their genome evolution. In this study, we assembled complete mitogenomes of 23 species, covering five of the seven families of Fagales. These mitogenomes had similar gene sets but varied 2.4 times in size. The mitochondrial genes were highly conserved, and their capacity in phylogeny was challenging. The mitogenomic structure was extremely dynamic, and synteny among species was poor. Further analyses of the Fagales mitogenomes revealed extremely mosaic characteristics, with horizontal transfer (HGT)-like sequences from almost all seed plant taxa and even mitoviruses. The largest mitogenome, Carpinus cordata, did not have large amounts of specific sequences but instead contained a high proportion of sequences homologous to other Fagales. Independent and unequal transfers of third-party DNA, including nuclear genome and other resources, may partially account for the HGT-like fragments and unbalanced size expansions observed in Fagales mitogenomes. Supporting this, a mitochondrial plasmid-like of nuclear origin was found in Carpinus. Overall, we deciphered the last genetic materials of Fagales, and our large-scale analyses provide new insights into plant mitogenome evolution and size variation.

scholarly journals WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

2019 ◽  
Vol 47 (W1) ◽  
pp. W199-W205 ◽  
Author(s):  
Yuxing Liao ◽  
Jing Wang ◽  
Eric J Jaehnig ◽  
Zhiao Shi ◽  
Bing Zhang
Keyword(s):  
User Interfaces ◽  
Large Scale ◽  
Data Interpretation ◽  
R Package ◽  
Third Party ◽  
Gene Set Analysis ◽  
Functional Categories ◽  
User Friendliness ◽  
The Core ◽  
Gene Sets

Abstract WebGestalt is a popular tool for the interpretation of gene lists derived from large scale -omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers and 155 175 functional categories, as well as user-uploaded functional databases. To address the growing and unique need for phosphoproteomics data interpretation, we have implemented phosphosite set analysis to identify important kinases from phosphoproteomics data. We have completely redesigned result visualizations and user interfaces to improve user-friendliness and to provide multiple types of interactive and publication-ready figures. To facilitate comprehension of the enrichment results, we have implemented two methods to reduce redundancy between enriched gene sets. We introduced a web API for other applications to get data programmatically from the WebGestalt server or pass data to WebGestalt for analysis. We also wrapped the core computation into an R package called WebGestaltR for users to perform analysis locally or in third party workflows. WebGestalt can be freely accessed at http://www.webgestalt.org.

scholarly journals TP53 mutations promote immunogenic activity in breast cancer

2018 ◽  
Author(s):  
Zhixian Liu ◽  
Zehang Jiang ◽  
Yingsheng Gao ◽  
Lirui Wang ◽  
Cai Chen ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Large Scale ◽  
Therapeutic Option ◽  
Immune Gene ◽  
Survival Prognosis ◽  
Mutation Status ◽  
Gene Sets ◽  
Immunotherapeutic Strategy ◽  
Tumor Immunogenicity ◽  
Almost All

AbstractBackgroundAlthough immunotherapy has recently achieved clinical successes in a variety of cancers, thus far there is no any immunotherapeutic strategy for breast cancer (BC). Thus, it is important to discover biomarkers for identifying the BC patients responsive to immunotherapy. TP53 mutations were often associated with worse clinical outcome in BC, of which the triple-negative BC (TNBC) has a high TP53 mutation rate (approximately 80%). TNBC is high-risk due to its high invasiveness, and lack of targeted therapy. To explore a potentially promising therapeutic option for the TP53-mutated BC subtype, we studied the associations between TP53 mutations and immunogenic activity in BC.MethodsWe compared enrichment levels of 26 immune gene-sets that indicated activities of diverse immune cells, functions, and pathways between TP53-mutated and TP53-wildtype BCs based on two large-scale BC multi-omics data. Moreover, we explored the molecular cues that were associated with the differences in immunogenic activity between TP53-mutated and TP53-wildtype BCs. Furthermore, we performed experimental validation of the findings from bioinformatics analysis.ResultsWe found that almost all analyzed immune gene-sets had significantly higher enrichment levels in TP53-mutated BCs compared to TP53-wildtype BCs. Moreover, our experiments confirmed that mutant p53 could increase BC immunogenicity. Furthermore, our computational and experimental results showed that TP53 mutations could promote BC immunogenicity via regulation of the p53-mediated pathways including cell cycle, apoptosis, Wnt, Jak-STAT, NOD-like receptor, and glycolysis. Interestingly, we found that elevated immune activities were likely to be associated with better survival prognosis in TP53-mutated BCs, but not necessarily in TP53-wildtype BCs.ConclusionsTP53 mutations promote immunogenic activity in breast cancer. This finding demonstrates a different effect of p53 dysfunction on tumor immunogenicity from that of previous studies, suggesting that the TP53 mutation status could be a useful biomarker for stratifying BC patients responsive to immunotherapy.

scholarly journals Projection of incinerators for medical waste processing during a pandemic: a case study of COVID-19 in Jakarta Province

2021 ◽  
Vol 909 (1) ◽  
pp. 012011
Author(s):  
M H Aryantie ◽  
T Widodo ◽  
R Wahyuni ◽  
B Purwanto ◽  
M Y Hidayat
Keyword(s):  
Waste Management ◽  
Large Scale ◽  
Disease Outbreaks ◽  
Data Retrieval ◽  
Medical Waste ◽  
Third Party ◽  
Budget Planning ◽  
Infectious Disease Outbreaks ◽  
Referral Hospitals ◽  
Almost All

Abstract Medical waste management due to the COVID-19 pandemic is important and urgent. An approach is needed to assess the weight of medical waste and to design appropriate waste management. The research was conducted in 2020 when the pandemic was still ongoing and had not yet reached the peak of the outbreak. Thus, the analysis was built based on assumptions and available data. The research was quantitative. Data were collected digitally (by big data retrieval and web survey) on the COVID-19 referral hospitals in Jakarta Province. The results showed that before the pandemic the weight of inpatients' medical waste was 1.57 kg/bed/day, while for COVID-19 inpatients was 1.84 kg/bed/day. The last number was processed with a limited projection of Jakarta population in 2020, then tested using two scenarios. First scenario was a pandemic condition without treatment. Second scenario was a pandemic condition plus vaccinations on D11. First scenario resulted that on D75, almost all residents of Jakarta would be infected with the SARS-COV2 virus and the maximum capacity of hospital incinerators in Jakarta was reached on D11. Second scenario resulted that the plague rate is resolved so that it does not infect all residents of Jakarta, but the capacity of hospital incinerators in Jakarta is still not adequate (limit on D11). Research has implications for environmental management budget planning in dealing with infectious disease outbreaks. The research recommendation is to calculate the weight of COVID-19 medical waste according to current conditions, which includes parameters such as the maximum hospital occupancy rate and the availability of large-scale incinerators belong to third-party.

scholarly journals Modelling Tree Growth in Monospecific Forests from Forest Inventory Data

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 753
Author(s):  
Guadalupe Sáez-Cano ◽  
Marcos Marvá ◽  
Paloma Ruiz-Benito ◽  
Miguel A. Zavala
Keyword(s):  
Tree Growth ◽  
Large Scale ◽  
Temporal Dynamics ◽  
Carbon Sink ◽  
Size Variation ◽  
Biotic Interactions ◽  
Richards Equation ◽  
Tree Level ◽  
Forest Inventories ◽  
Large Scale Data

The prediction of tree growth is key to further understand the carbon sink role of forests and the short-term forest capacity on climate change mitigation. In this work, we used large-scale data available from three consecutive forest inventories in a Euro-Mediterranean region and the Bertalanffy–Chapman–Richards equation to model up to a decade’s tree size variation in monospecific forests in the growing stages. We showed that a tree-level fitting with ordinary differential equations can be used to forecast tree diameter growth across time and space as function of environmental characteristics and initial size. This modelling approximation was applied at different aggregation levels to monospecific regions with forest inventories to predict trends in aboveground tree biomass stocks. Furthermore, we showed that this model accurately forecasts tree growth temporal dynamics as a function of size and environmental conditions. Further research to provide longer term prediction forest stock dynamics in a wide variety of forests should model regeneration and mortality processes and biotic interactions.

Enkev Beheer BV (of the Netherlands) v. Republic of Poland

ICSID Reports ◽  
2021 ◽  
Vol 19 ◽  
pp. 630-648
Keyword(s):  
Due Process ◽  
The State ◽  
Third Party ◽  
Waiting Period ◽  
Content Type ◽  
Fair And Equitable Treatment ◽  
Just Compensation ◽  
Default Rules ◽  
Equitable Treatment ◽  
Almost All

630Procedure — Addition of a party — Conditional application — UNCITRAL Rules, Article 22 — UNCITRAL Rules, Article 17 — Whether the UNCITRAL Rules or lex loci arbitri allowed for applications to be made conditional on a tribunal’s future decision — Whether the application was consistent with the State’s procedural rights — Whether the amendment to a claim under Article 22 of the UNCITRAL Rules allowed for the addition of a third party as claimantJurisdiction — Investment — Shares — Whether an investor’s shares and rights derived from those shares were protected investments under the BITJurisdiction — Investment — Assets of subsidiary — Whether profits, goodwill or know-how of a local subsidiary constituted investments of the investor protected by the BITJurisdiction — Consent — Cooling-off period — Premature claims — Whether the investor had communicated its own claims rather than those of its local subsidiary — Whether the investor’s failure to comply with a waiting period of six months under the BIT required a tribunal to deny jurisdiction or admissibility — Whether the negotiation of a local subsidiary’s dispute in good faith was relevant to jurisdiction over a foreign investor’s claimsInterpretation — Cooling-off period — VCLT, Article 31 — Object and purpose — Whether the object and purpose of the BIT required a tribunal not to adopt a strict or formalistic interpretation of the waiting period of six monthsRemedies — Declaratory award — Interpretation — Just compensation — Whether the tribunal had jurisdiction under the BIT to make a declaratory award on the interpretation and application of the term “just compensation”Jurisdiction — Dispute — Whether the tribunal had jurisdiction under the BIT to advise the parties of an imminent disputeExpropriation — Direct deprivation — Shares — Rights derived from shares — Whether the State directly deprived the investor of its rights as a shareholder in its local subsidiaryExpropriation — Indirect deprivation — Shares — Rights derived from shares — Whether the shares had lost all or almost all significant commercial value — Whether the measures were adopted in the public interest — Whether due process had been followed — Whether there were any undertakings by the StateExpropriation — Interpretation — “Just compensation” — Whether there was any difference between the terms of the BIT and general international law — Whether the meaning of just compensation could be determined in the abstract631Fair and equitable treatment — Whether the impending expropriation constituted a breach of the standard of fair and equitable treatment — Whether the claim concerned the investor’s rights derived from sharesFull protection and security — Whether the State failed to protect an investment from expropriation by local authorities — Whether the claim concerned the investor’s rights derived from sharesUmbrella clause — Whether there was any assurance directed at the investor that created any legal obligations — Whether the claim concerned the investor’s rights derived from sharesCosts — Arbitration costs — Variation by agreement — UNCITRAL Rules — Whether the terms of the BIT varied the default rules for the allocation of arbitration costs

RESEARCH OF EXTERNAL MASS TRANSFER PROCESSES FOR ADSORPTION FROM SOLUTIONS IN A APPARATUS WITH STIRRING

2021 ◽  
pp. 11-20
Author(s):  
V. Solovej ◽  
K. Gorbunov ◽  
V. Vereshchak ◽  
O. Gorbunova
Keyword(s):  
Mass Transfer ◽  
Energy Spectrum ◽  
Energy Dissipation ◽  
Large Scale ◽  
Isotropic Turbulence ◽  
Wave Number ◽  
Wave Form ◽  
Local Isotropy ◽  
Stirred Vessel ◽  
Almost All

A study has been mode of transport-controlled mass transfer-controlled to particles suspended in a stirred vessel. The motion of particle in a fluid was examined and a method of predicting relative velocities in terms of Kolmogoroff’s theory of local isotropic turbulence for mass transfer was outlined. To provide a more concrete visualization of complex wave form of turbulence, the concepts of eddies, of eddy velocity, scale (or wave number) and energy spectrum, have proved convenient. Large scale motions of scale contain almost all of the energy and they are directly responsible for energy diffusion throughout the stirring vessel by kinetic and pressure energies. However, almost no energy is dissipated by the large-scale energy-containing eddies. A scale of motion less than is responsible for convective energy transfer to even smaller eddy sires. At still smaller eddy scales, close to a characteristic microscale, both viscous energy dissipation and convection are the rule. The last range of eddies has been termed the universal equilibrium range. It has been further divided into a low eddy size region, the viscous dissipation subrange, and a larger eddy size region, the inertial convection subrange. Measurements of energy spectrum in mixing vessel are shown that there is a range, where the so called -(5/3) power law is effective. Accordingly, the theory of local isotropy of Kolmogoroff can be applied because existence of the internal subrange. As the integrated value of local energy dissipation rate agrees with the power per unit mass of liquid from the impeller, almost all energy from the impeller is viscous dissipated in eddies of microscale. The correlation for mass transfer to particles suspended in a stirred vessel is recommended. The results of experimental study are approximately 12 % above the predicted values.

Why Do People Stay Poor?

2021 ◽  
Author(s):  
Clare Balboni ◽  
Oriana Bandiera ◽  
Robin Burgess ◽  
Maitreesh Ghatak ◽  
Anton Heil
Keyword(s):  
Occupational Choice ◽  
Large Scale ◽  
Choice Model ◽  
Effective Means ◽  
Threshold Level ◽  
Poverty Traps ◽  
Asset Transfer ◽  
Small Livestock ◽  
Program Costs ◽  
Almost All

Abstract There are two broad views as to why people stay poor. One emphasizes differences in fundamentals, such as ability, talent, or motivation. The other, the poverty traps view, emphasizes differences in opportunities which stem from access to wealth. To test between these two views, we exploit a large-scale, randomized asset transfer and an 11-year panel of 6,000 households who begin in extreme poverty. The setting is rural Bangladesh and the assets are cows. The data supports the poverty traps view—we identify a threshold level of initial assets above which households accumulate assets, take on better occupations (from casual labor in agriculture or domestic services to running small livestock businesses), and grow out of poverty. The reverse happens for those below the threshold. Structural estimation of an occupational choice model reveals that almost all beneficiaries are misallocated in the work they do at baseline and that the gains arising from eliminating misallocation would far exceed the program costs. Our findings imply that large transfers which create better jobs for the poor are an effective means of getting people out of poverty traps and reducing global poverty.

Opuntia ficus-indica (prickly pear).

2021 ◽  
Author(s):  
Nick Pasiecznik
Keyword(s):  
Vitamin C ◽  
Large Scale ◽  
Time Lag ◽  
Prickly Pear ◽  
Invasive Weeds ◽  
Historical Records ◽  
Opuntia Ficus Indica ◽  
Actual Risk ◽  
Invasive Spread ◽  
Almost All

Abstract O. ficus-indica is highly valued as a fruit-producing cactus, also yielding 'leaves' that are used as a vegetable and browsed by livestock. It has been introduced widely from its native Mexico to almost all countries where the climate is suitable. The fruit is very rich in vitamin C and is exploited commercially in many areas. Many countries, especially in Asia, have recently established large-scale commercial plantations. However, O. ficus-indica, like several other species of Opuntia, have been known to spread and become invasive weeds. Historical records, however, appear to indicate a time-lag of about 100 years between introduction and the beginnings of invasive spread thus the actual risk may be low.

What Kind of Friction Model Is Needed to Predict Brake Squeal?

2012 ◽  
Author(s):  
Tore Butlin ◽  
Jim Woodhouse
Keyword(s):  
Large Scale ◽  
Dynamic Properties ◽  
Theoretical Work ◽  
Friction Model ◽  
Coupled Systems ◽  
Brake Squeal ◽  
Model Framework ◽  
Wide Range ◽  
Pin On Disc ◽  
Almost All

Predictive models of friction-induced vibration have proved elusive despite decades of research. There are many mechanisms that can cause brake squeal; friction coupled systems can be highly sensitive to small perturbations; and the dynamic properties of friction at the contact zone seem to be poorly understood. This paper describes experimental and theoretical work aimed at identifying the key ingredients of a predictive model. A large-scale experiment was carried out to identify squeal initiations using a pin-on-disc test rig: approximately 30,000 squeal initiations were recorded, covering a very wide range of frequencies. The theoretical model allows for completely general linear systems coupled at a single sliding point by friction: squeal is predicted using a linearised stability analysis. Results will be presented that show that almost all observed squeal events can be predicted within this model framework, but that some subsets require innovative friction modelling: predictions are highly dependent on the particular choice of friction model and its associated parameters.

Nuclear genome size variation in fleshy-fruited Neotropical Myrtaceae

2008 ◽  
Vol 276 (3-4) ◽  
pp. 209-217 ◽  
Author(s):  
Itayguara Ribeiro da Costa ◽  
Marcelo Carnier Dornelas ◽  
Eliana Regina Forni-Martins
Keyword(s):  
Genome Size ◽  
Size Variation ◽  
Nuclear Genome ◽  
Genome Size Variation
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