Analysis of Gene Sets Based on the Underlying Regulatory Network

Networks are often used to represent the interactions among genes and proteins. These interactions are known to play an important role in vital cell functions and should be included in the analysis of genes that are differentially expressed. Methods of gene set analysis take advantage of external biological information and analyze a priori defined sets of genes. These methods can potentially preserve the correlation among genes; however, they do not directly incorporate the information about the gene network. In this paper, we propose a latent variable model that directly incorporates the network information. We then use the theory of mixed linear models to present a general inference framework for the problem of testing the significance of subnetworks. Several possible test procedures are introduced and a network based method for testing the changes in expression levels of genes as well as the structure of the network is presented. The performance of the proposed method is compared with methods of gene set analysis using both simulation studies, as well as real data on genes related to the galactose utilization pathway in yeast.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78147/1/cmb.2008.0081.pd

Chacterization of CU tube filled with Al alloy foam by means of X-ray computer tomography

Copper tubes filled with aluminium foams were prepared by directly foaming metal powder compacts inside them. Compressive behaviour and foam-shell interface, that characterizes mechanical properties of reinforced tubes, were investigated by means of variable focus X-ray computer tomography. Compression tests were performed on empty and filled samples at increasing deformation steps: at each stage the samples were observed by tomography. A geometric evaluation of porosity on 2D sections was performed by calculating, for each pore, its area, equivalent diameter and circularity

British HIV Association guidelines for the management of tuberculosis in adults living with HIV 2019

The overall purpose of these guidelines is to help physicians manage adults with tuberculosis (TB)/human immunodeficiency virus (HIV) co‐infection. Recommendations for the treatment of TB in HIV‐positive adults are similar to those in HIV‐negative adults. Of note, the term “HIV” refers to HIV‐1 throughout these guidelines

Muscle fibre type, size and satellite cell pool in male volleyball players

Introduction. Longitudinal volleyball training stimuli can cause an increase in muscle strength that is brought about by neurological and morphological adaptations, such as changes in muscle fibre composition percentage and cross-sectional area (CSA). Aim of Study. The aim of this study was to examine the biological adaptations of volleyball-players in terms of muscle fiber type composition, cross-sectional area, myonuclei and satellite cell pool in comparison to physically active controls. Material and Methods. Ten professional volleyball-players (VG) and five physically active-persons (CG) participated in this study. Muscle biopsies were obtained from the vastus-lateralis of the dominant leg. Results. Immunohistochemical analysis revealed that although MHC I and MHC IIC muscle fibre distribution was not different between the groups, MHC IIX and MHC IIAX were totally absent in VG and appeared only in the CG. The cross-sectional area revealed a slightly different pattern as both MHC I and IIA were larger for the volleyball players. In accordance, MHC II myonuclei number was moderately larger in the volleyball players, while the satellite cells and their ratio to number of fibres had a large and very large difference, respectively. Conclusions. In conclusion, our study reveals that volleyball training-induced hypertrophy for both type I and II muscle fibres in the vastus lateralis of volleyball players and resulted in a specific shift in muscle fibres containing MHC II isoforms. This hypertrophy of the muscle fibres is associated with an increase in the myonuclear number and satellite cells

Modified Mesoporous Silica Nanoparticles with a Dual Synergetic Antibacterial Effect

Application of mesoporous silica nanoparticles (MSNs) as antifouling/antibacterial carriers is limited and specifically with a dual synergetic effect. In the present work, MSNs modified with quaternary ammonium salts (QASs) and loaded with the biocide Parmetol S15 were synthesized as functional fillers for antifouling/antibacterial coatings. From the family of the MSNs, MCM-48 was selected as a carrier because of its cubic pore structure, high surface area, and high specific pore volume. The QASs used for the surface modification of MCM-48 were dimethyloctadecyl[3-(trimethoxysilyl)propyl]ammonium chloride and dimethyltetradecyl[3-(triethoxysilyl)propyl]ammonium chloride. The QAS-modified MCM-48 reveals strong covalent bonds between the QAS and the surface of the nanoparticles. The surface functionalization was confirmed by Fourier transform infrared spectroscopy, thermogravimetric analysis, elemental analysis, and ζ-potential measurements. Additional loading of the QAS-modified MCM-48 with a commercially available biocide (Parmetol S15) resulted in a synergetic dual antibacterial/antifouling effect. Either loaded or unloaded QAS-modified MSNs exhibited high antibacterial performance confirming their dual activity. The QAS-modified MCM-48 loaded with the biocide Parmetol S15 killed all exposed bacteria after 3 h of incubation and presented 100% reduction at the antibacterial tests against Gram-negative and Gram-positive bacteria. Furthermore, the QAS-modified MCM-48 without Parmetol S15 presented 77–89% reduction against the exposed Gram-negative bacteria and 78–94% reduction against the exposed Gram-positive bacteria. In addition, the modified MCM-48 was mixed with coating formulations, and its antifouling performance was assessed in a field test trial in northern Red Sea. All synthesized paints presented significant antifouling properties after 5 months of exposure in real seawater conditions, and the dual antifouling effect of the nanoparticles was confirmed

Developmental features of cotton fibre middle lamellae in relation to cell adhesion and cell detachment in cultivars with distinct fibre qualities.

Background: Cotton fibre quality traits such as fibre length, strength, and degree of maturation are determined by genotype and environment during the sequential phases of cotton fibre development (cell elongation, transition to secondary cell wall construction and cellulose deposition). The cotton fibre middle lamella (CFML) is crucial for both cell adhesion and detachment processes occurring during fibre development. To explore the relationship between fibre quality and the pace at which cotton fibres develop, a structural and compositional analysis of the CFML was carried out in several cultivars with different fibre properties belonging to four commercial species: Gossypium hirsutum, G. barbadense, G. herbaceum and G. arboreum. Results: Cotton fibre cell adhesion, through the cotton fibre middle lamella (CFML), is a developmentally regulated process determined by genotype. The CFML is composed of de-esterified homogalacturonan, xyloglucan and arabinan in all four fibre-producing cotton species: G. hirsutum, G. barbadense, G. herbaceum and G. arboreum. Conspicuous paired cell wall bulges are a feature of the CFML of two G. hirsutum cultivars from the onset of fibre cell wall detachment to the start of secondary cell wall deposition. Xyloglucan is abundant in the cell wall bulges and in later stages pectic arabinan is absent from these regions. Conclusions: The CFML of cotton fibres is re-structured during the transition phase. Paired cell wall bulges, rich in xyloglucan, are significantly more evident in the G. hirsutum cultivars than in other cotton species

Identifiability of flow distributions from link measurements with applications to computer networks

We study the problem of identifiability of distributions of flows on a graph from aggregate measurements collected on its edges. This is a canonical example of a statistical inverse problem motivated by recent developments in computer networks. In this paper (i) we introduce a number of models for multi-modal data that capture their spatio-temporal correlation, (ii) provide sufficient conditions for the identifiability of nth order cumulants and also for a special class of heavy tailed distributions. Further, we investigate conditions on network routing for the flows that prove sufficient for identifiability of their distributions (up to mean). Finally, we extend our results to directed acyclic graphs and discuss some open problems.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/58107/2/ip7_5_004.pd

The Hepatitis B Virus Ribonuclease H Is Sensitive to Inhibitors of the Human Immunodeficiency Virus Ribonuclease H and Integrase Enzymes

Nucleos(t)ide analog therapy blocks DNA synthesis by the hepatitis B virus (HBV) reverse transcriptase and can control the infection, but treatment is life-long and has high costs and unpredictable long-term side effects. The profound suppression of HBV by the nucleos(t)ide analogs and their ability to cure some patients indicates that they can push HBV to the brink of extinction. Consequently, more patients could be cured by suppressing HBV replication further using a new drug in combination with the nucleos(t)ide analogs. The HBV ribonuclease H (RNAseH) is a logical drug target because it is the second of only two viral enzymes that are essential for viral replication, but it has not been exploited, primarily because it is very difficult to produce active enzyme. To address this difficulty, we expressed HBV genotype D and H RNAseHs in E. coli and enriched the enzymes by nickel-affinity chromatography. HBV RNAseH activity in the enriched lysates was characterized in preparation for drug screening. Twenty-one candidate HBV RNAseH inhibitors were identified using chemical structure-activity analyses based on inhibitors of the HIV RNAseH and integrase. Twelve anti-RNAseH and anti-integrase compounds inhibited the HBV RNAseH at 10 μM, the best compounds had low micromolar IC50 values against the RNAseH, and one compound inhibited HBV replication in tissue culture at 10 μM. Recombinant HBV genotype D RNAseH was more sensitive to inhibition than genotype H. This study demonstrates that recombinant HBV RNAseH suitable for low-throughput antiviral drug screening has been produced. The high percentage of compounds developed against the HIV RNAseH and integrase that were active against the HBV RNAseH indicates that the extensive drug design efforts against these HIV enzymes can guide anti-HBV RNAseH drug discovery. Finally, differential inhibition of HBV genotype D and H RNAseHs indicates that viral genetic variability will be a factor during drug development. © 2013 Tavis et al

New records of rare species in the Mediterranean Sea (October 2021)

This Collective Article presents information about 27 taxa belonging to five Phyla (one Ochrophyta, one Cnidaria, three Arthropoda, two Mollusca and twenty Chordata) and extending from the Western Mediterranean Sea to the Levantine Sea and theBlack Sea (Sea of Marmara). The new records were reported from 11 countries as follows: Algeria: occurrence of the Africanstriped grunt Parapristipoma octolineatum; Spain: new records of eight uncommon fish species (Gadella maraldi, Hypleurochilusbananensis, Lobotes surinamensis, Parapristipoma octolineatum, Selene dorsalis, Sphoeroides marmoratus, Tetragonuruscuvieri, and Trachyrincus scabrus) from the Spanish Mediterranean; Italy: new record of the football octopus Ocythoe tuberculatafrom the Southern Tyrrhenian Sea; a rare sighting of a juvenile phase of a moray eel of the genus Gymnothorax, tentativelyidentified as Gymnothorax cf. unicolor in the Ligurian Sea; first record of adult Facciola’s sorcerer Facciolella oxyrhynchus inthe Adriatic Sea; occurrence of the tope shark Galeorhinus galeus in the Northern Adriatic Sea; Libya: first confirmed recordof the pen shell Pinna rudis; first documented record of the palaemonid shrimp Brachycarpus biunguiculatus; first record of thefish Sudis hyalina; Malta: new records of Grant’s rockling, Gaidropsarus granti; multiple concomitant reports of the rare hydromedusanspecies Aequorea forskalea; Croatia: a record of the skipjack tuna Katsuwonus pelamis in the Southern Adriatic Sea;Albania: new record of the bigeye thresher shark Alopias superciliosus; Greece: confirmation of the rare brown alga Sargassumflavifolium occurrence in the Eastern Mediterranean Sea; first record of the scaleless dragonfish Bathophilus nigerrimus; Turkey:first occurrence of the calanoid copepod Pteriacartia josephinae in the Aegean Sea; first documented record of the Cremona’s seaslug Placida cremoniana for the easternmost Mediterranean Sea; new record of the yellow-headed goby Gobius xanthocephalusin the Sea of Marmara; Cyprus: first record of the Liechtenstein’s goby Corcyrogobius liechtensteini; an individual of the Yellowfintuna Thunnus albacares captured with handline by an artisanal fisher; Lebanon: an individual of the Black marlin Istiompaxindica captured in a gill ne