Generalization of matching extensions in graphs (II)

Proposed as a general framework, Liu and Yu(Discrete Math. 231 (2001) 311-320) introduced $(n,k,d)$-graphs to unify the concepts of deficiency of matchings, $n$-factor-criticality and $k$-extendability. Let $G$ be a graph and let $n,k$ and $d$ be non-negative integers such that $n+2k+d\leq |V(G)|-2$ and $|V(G)|-n-d$ is even. If when deleting any $n$ vertices from $G$, the remaining subgraph $H$ of $G$ contains a $k$-matching and each such $k$- matching can be extended to a defect-$d$ matching in $H$, then $G$ is called an $(n,k,d)$-graph. In \cite{Liu}, the recursive relations for distinct parameters $n, k$ and $d$ were presented and the impact of adding or deleting an edge also was discussed for the case $d = 0$. In this paper, we continue the study begun in \cite{Liu} and obtain new recursive results for $(n,k,d)$-graphs in the general case $d \geq0$.Comment: 12 page

CanPredict: a computational tool for predicting cancer-associated missense mutations

Various cancer genome projects are underway to identify novel mutations that drive tumorigenesis. While these screens will generate large data sets, the majority of identified missense changes are likely to be innocuous passenger mutations or polymorphisms. As a result, it has become increasingly important to develop computational methods for distinguishing functionally relevant mutations from other variations. We previously developed an algorithm, and now present the web application, CanPredict (http://www.canpredict.org/ or http://www.cgl.ucsf.edu/Research/genentech/canpredict/), to allow users to determine if particular changes are likely to be cancer-associated. The impact of each change is measured using two known methods: Sorting Intolerant From Tolerant (SIFT) and the Pfam-based LogR.E-value metric. A third method, the Gene Ontology Similarity Score (GOSS), provides an indication of how closely the gene in which the variant resides resembles other known cancer-causing genes. Scores from these three algorithms are analyzed by a random forest classifier which then predicts whether a change is likely to be cancer-associated. CanPredict fills an important need in cancer biology and will enable a large audience of biologists to determine which mutations are the most relevant for further study

Preparation and Characterization of a Lecithin Nanoemulsion as a Topical Delivery System

Purpose of this study was to establish a lecithin nanoemulsion (LNE) without any synthetic surfactant as a topical delivery vehicle and to evaluate its topical delivery potential by the following factors: particle size, morphology, viscosity, stability, skin hydration and skin penetration. Experimental results demonstrated that an increasing concentration of soybean lecithin and glycerol resulted in a smaller size LNE droplet and increasing viscosity, respectively. The droplet size of optimized LNE, with the glycerol concentration above 75% (w/w), changed from 92 (F10) to 58 nm (F14). Additionally, LNE, incorporated into o/w cream, improved the skin hydration capacity of the cream significantly with about 2.5-fold increase when the concentration of LNE reached 10%. LNE was also demonstrated to improve the penetrability of Nile red (NR) dye into the dermis layer, when an o/w cream, incorporated with NR-loaded LNE, applied on the abdominal skin of rat in vivo. Specifically, the arbitrary unit (ABU) of fluorescence in the dermis layer that had received the cream with a NR-loaded LNE was about 9.9-fold higher than the cream with a NR-loaded general emulsion (GE). These observations suggest that LNE could be used as a promising topical delivery vehicle for lipophilic compounds

Bi-Directional SIFT Predicts a Subset of Activating Mutations

Advancements in sequencing technologies have empowered recent efforts to identify polymorphisms and mutations on a global scale. The large number of variations and mutations found in these projects requires high-throughput tools to identify those that are most likely to have an impact on function. Numerous computational tools exist for predicting which mutations are likely to be functional, but none that specifically attempt to identify mutations that result in hyperactivation or gain-of-function. Here we present a modified version of the SIFT (Sorting Intolerant from Tolerant) algorithm that utilizes protein sequence alignments with homologous sequences to identify functional mutations based on evolutionary fitness. We show that this bi-directional SIFT (B-SIFT) is capable of identifying experimentally verified activating mutants from multiple datasets. B-SIFT analysis of large-scale cancer genotyping data identified potential activating mutations, some of which we have provided detailed structural evidence to support. B-SIFT could prove to be a valuable tool for efforts in protein engineering as well as in identification of functional mutations in cancer

GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database

GeneHub-GEPIS is a web application that performs digital expression analysis in human and mouse tissues based on an integrated gene database. Using aggregated expressed sequence tag (EST) library information and EST counts, the application calculates the normalized gene expression levels across a large panel of normal and tumor tissues, thus providing rapid expression profiling for a given gene. The backend GeneHub component of the application contains pre-defined gene structures derived from mRNA transcript sequences from major databases and includes extensive cross references for commonly used gene identifiers. ESTs are then linked to genes based on their precise genomic locations as determined by GMAP. This genome-based approach reduces incorrect matches between ESTs and genes, thus minimizing the noise seen with previous tools. In addition, the gene-centric design makes it possible to add several important features, including text searching capabilities, the ability to accept diverse input values, expression analysis for microRNAs, basic gene annotation, batch analysis and linking between mouse and human genes. GeneHub-GEPIS is available at http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/ or http://www.gepis.org/

A New Type of Quartz Smog Chamber : Design and Characterization

Publisher Copyright: ©Since the 1960s, many indoor and outdoor smog chambers have been developed worldwide. However, most of them are made of Teflon films, which have relatively high background contaminations due to the wall effect. We developed the world's first medium-size quartz chamber (10 m(3)), which is jointed with 32 pieces of 5 mm thick polished quartz glasses and a stainless-steel frame. Characterizations show that this chamber exhibits excellent performance in terms of relative humidity (RH) (2-80%) and temperature (15-30 +/- 1 degrees C) control, mixing efficiency of the reactants (6-8 min), light transmittance (>90% above 290 nm), and wall loss of pollutants. The wall loss rates of the gas-phase pollutants are on the order of 10(-4) min(-1) at 298 K under dry conditions. It is 0.08 h(-1) for 100-500 nm particles, significantly lower than those of Teflon chambers. The photolysis rate of NO2 (J(NO2)) is automatically adjustable to simulate the diurnal variation of solar irradiation from 0 to 0.40 min(-1). The inner surface of the chamber can be repeatedly washed with deionized water, resulting in low background contaminations. Both experiments (toluene-NOx and alpha-pinene-ozone systems) and box model demonstrate that this new quartz chamber can provide high-quality data for investigating SOA and O-3 formation in the atmosphere.Peer reviewe

Influence of organic aerosol molecular composition on particle absorptive properties in autumn Beijing

Publisher Copyright: © 2022 Jing Cai et al.Organic aerosol (OA) is a major component of fine particulate matter (PM), affecting air quality, human health, and the climate. The absorptive and reflective behavior of OA components contributes to determining particle optical properties and thus their effects on the radiative budget of the troposphere. There is limited knowledge on the influence of the molecular composition of OA on particle optical properties in the polluted urban environment. In this study, we characterized the molecular composition of oxygenated OA collected on filter samples in the autumn of 2018 in Beijing, China, with a filter inlet for gases and aerosols coupled to a high-resolution time-of-flight chemical ionization mass spectrometer (FIGAERO-CIMS). Three haze episodes occurred during our sampling period with daily maximum concentrations of OA of 50, 30, and 55 μg m-3. We found that the signal intensities of dicarboxylic acids and sulfur-containing compounds increased during the two more intense haze episodes, while the relative contributions of wood-burning markers and other aromatic compounds were enhanced during the cleaner periods. We further assessed the optical properties of oxygenated OA components by combining detailed chemical composition measurements with collocated particle light absorption measurements. We show that light absorption enhancement (Eabs) of black carbon (BC) was mostly related to more oxygenated OA (e.g., dicarboxylic acids), likely formed in aqueous-phase reactions during the intense haze periods with higher relative humidity, and speculate that they might contribute to lensing effects. Aromatics and nitro-aromatics (e.g., nitrocatechol and its derivatives) were mostly related to a high light absorption coefficient (babs) consistent with light-absorbing (brown) carbon (BrC). Our results provide information on oxygenated OA components at the molecular level associated with BrC and BC particle light absorption and can serve as a basis for further studies on the effects of anthropogenic OA on radiative forcing in the urban environment.Peer reviewe

Measurement of HbA1c and HbA2 by Capillarys 2 Flex Piercing HbA1c programme for simultaneous management of diabetes and screening for thalassemia

Introduction: Thalassemia could interfere with some assays for haemoglobin A1c (HbA1c) measurement, therefore, it is useful to be able to screen for thalassemia while measuring HbA1c. We used Capillarys 2 Flex Piercing (Capillarys 2FP) HbA1c programme to simultaneously measure HbA1c and screen for thalassemia. Materials and methods: Samples from 498 normal controls and 175 thalassemia patients were analysed by Capillarys 2FP HbA1c programme (Sebia, France). For method comparison, HbA1c was quantified by Premier Hb9210 (Trinity Biotech, Ireland) in 98 thalassaemia patients samples. For verification, HbA1c from eight thalassaemia patients was confirmed by IFCC reference method. Results: Among 98 thalassaemia samples, Capillarys 2FP did not provide an HbA1c result in three samples with HbH due to the overlapping of HbBart’s with HbA1c fraction; for the remaining 95 thalassaemia samples, Bland-Altman plot showed 0.00 ± 0.35% absolute bias between two systems, and a significant positive bias above 7% was observed only in two HbH samples. The HbA1c values obtained by Capillarys 2FP were consistent with the IFCC targets (relative bias below ± 6%) in all of the eight samples tested by both methods. For screening samples with alpha (α-) thalassaemia silent/trait or beta (β-) thalassemia trait, the optimal HbA2 cut-off values were ≤ 2.2% and > 2.8%, respectively. Conclusions: Our results demonstrated the Capillarys 2FP HbA1c system could report an accurate HbA1c value in thalassemia silent/trait, and HbA2 value (≤ 2.2% for α-thalassaemia silent/trait and > 2.8% for β-thalassemia trait) and abnormal bands (HbH and/or HbBart’s for HbH disease, HbF for β-thalassemia) may provide valuable information for screening