A network approach for managing and processing big cancer data in clouds

Translational cancer research requires integrative analysis of multiple levels of big cancer data to identify and treat cancer. In order to address the issues that data is decentralised, growing and continually being updated, and the content living or archiving on different information sources partially overlaps creating redundancies as well as contradictions and inconsistencies, we develop a data network model and technology for constructing and managing big cancer data. To support our data network approach for data process and analysis, we employ a semantic content network approach and adopt the CELAR cloud platform. The prototype implementation shows that the CELAR cloud can satisfy the on-demanding needs of various data resources for management and process of big cancer data

Synthesis of 5-azaindoles via a cycloaddition reaction between nitriles and donor-acceptor cyclopropanes.

A new method for the synthesis of 5-azaindole derivatives is reported. A [3+2] dipolar cycloaddition between nitriles and a 3,4-cyclopropanopiperidine followed by SeO(2) oxidation affords the target compounds in moderate to excellent yields. The divergent nature and cost effectiveness of this method makes it very suitable for combinatorial applications in the pharmaceutical industry

Ytterbium triflate catalyzed synthesis of alkoxy-substituted donor-acceptor cyclobutanes and their formal [4 + 2] cycloaddition with imines: stereoselective synthesis of piperidines.

A new synthesis of 2-alkoxy-1,1-cyclobutane diesters and their first use in dipolar cycloadditions is reported. Both the formation of the donor-acceptor cyclobutanes and their subsequent annulation with in situ formed imines are catalyzed by Yb(OTf)(3). Cyclobutanes with carbon donor groups give piperidines with high trans stereoselectivity

The influence of tropospheric biennial oscillation on mid-tropospheric CO_2

Mid-tropospheric CO_2 retrieved from the Atmospheric Infrared Sounder (AIRS) was used to investigate CO_2 interannual variability over the Indo-Pacific region. A signal with periodicity around two years was found for the AIRS mid-tropospheric CO_2 for the first time, which is related to the Tropospheric Biennial Oscillation (TBO) associated with the strength of the monsoon. During a strong (weak) monsoon year, the Western Walker Circulation is strong (weak), resulting in enhanced (diminished) CO_2 transport from the surface to the mid-troposphere. As a result, there are positive (negative) CO2 anomalies at mid-troposphere over the Indo-Pacific region. We simulated the influence of the TBO on the mid-tropospheric CO_2 over the Indo-Pacific region using the MOZART-2 model, and results were consistent with observations, although we found the TBO signal in the model CO_2 is to be smaller than that in the AIRS observations

The Mechanical Energies of the Global Atmosphere in El Niño and La Niña Years

Two meteorological reanalysis datasets are analyzed to determine the mechanical energies of the global atmosphere in the El Niño and La Niña years. The general consistency of the mean energy components between the two datasets reveals ~1%–3% increase and ~2%–3% decrease in the mean energies in the El Niño years and La Niña years, respectively. These analyses further reveal that the tropospheric temperature responds to the sea surface temperature anomaly with a time lag of two months, which leads to the varying mean atmospheric energies in the El Niño and La Niña years

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection.

Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity

THE MOST ECONOMICAL CONFIGURATION OF PUSHED BARGE CONVOY SYSTEM THROUGH CAIRO-ASWAN WATERWAY

In the recent years, as a result of the economical situation in Egypt, fuel price is rapidly increased. Consequently, the cost of cargo transport is also increased. Therefore, the aim of the present paper is to check the feasibility of a pushed barge convoy system working through Cairo-Aswan waterway as an alternative mean of cargo transport in order to encourage the transport companies to transport their cargoes through river Nile which is considered the cheapest transport mode in Egypt. In this paper, the current situation of the river transport and the characteristics of the Egyptian inland waterways network are reviewed and investigated to identify the navigation problems and constraints which affect the navigation through Cairo-Aswan waterway. The basic concept of ship controllability is reviewed to clarify the maneuver characteristics of a pushed barge convoy system in shallow waterways. Also, different configurations for pushed barge convoy system are proposed and the required power of each configuration is calculated using a specially developed computer program. A technical and operational measure called transport efficiency is used as a criterion to get the most economical configuration of the desired pushed barge convoy system. Finally, a comparison between the pushed barge convoy system and the existing river transport means in Egypt is made to clarify the feasibility of using pushed barge convoy system through Cairo-Aswan waterway

Formal [4 + 2] cycloaddition of alkoxy-substituted donor-acceptor cyclobutanes and aldehydes catalyzed by Yb(OTf)3.

The cycloaddition between 2-alkoxy-1,1-cyclobutane diesters and aromatic, heteroaromatic, or aliphatic aldehydes under Yb(OTf)(3) catalysis generates tetrahydropyrans in high yields with exclusive cis-stereochemistry

Electricity generation by microorganisms in the sediment-water interface of an extreme acidic microcosm

The attachment of microorganisms to electrodes is of great interest for electricity generation in microbial fuel cells (MFC) or other applications in bioelectrochemical systems (BES). In this work, a microcosm of the acidic ecosystem of Río Tinto was built and graphite electrodes were introduced at different points. This allowed the study of electricity generation in the sediment/water interface and the involvement of acidophilic microorganisms as biocatalysts of the anodic and cathodic reactions in a fuel-cell configuration. Current densities and power outputs of up to 3.5 A/m2 and 0.3 W/m2, respectively, were measured at pH 3. Microbial analyses of the electrode surfaces showed that Acidiphilium spp., which uses organic compounds as electron donors, were the predominant biocatalysts of the anodic reactions, whereas the aerobic iron oxidizers Acidithiobacillus ferrooxidans and Leptospirillum spp. were detected mainly on the cathode surface.&nbsp

Discovery of a Histidine‐Based Scaffold as an Inhibitor of Gut Microbial Choline Trimethylamine‐Lyase

This is the peer reviewed version of the following article: Discovery of a Histidine‐Based Scaffold as an Inhibitor of Gut Microbial Choline Trimethylamine‐Lyase, which has been published in final form at https://doi.org/10.1002/cmdc.202000571. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.Anaerobic choline metabolism by human gut microbiota to produce trimethylamine (TMA) has recently evolved as a potential therapeutic target because of its association with chronic kidney disease and increased cardiovascular risks. Limited examples of choline analogues have been reported as inhibitors of bacterial enzyme choline TMA‐lyase (CutC), a key enzyme regulating choline anaerobic metabolism. We used a new workflow to discover CutC inhibitors based on focused screening of a diversified library of small molecules for intestinal metabolic stability followed by in vitro CutC inhibitory assay. This workflow identified a histidine‐based scaffold as a CutC inhibitor with an IC50 value of 1.9±0.2 μM. Remarkably, the identified CutC inhibitor was able to reduce the production of TMA in whole‐cell assays using various bacterial strains as well as in complex gut microbiota environment. The improved efficiency of the new scaffold identified in this study in comparison to previously reported CutC inhibitors would enable optimization of potential leads for in vivo screening and clinical translation. Finally, docking studies and molecular‐dynamic simulations were used to predict putative interactions created between inhibitor and CutC