Viral integration detection strategies and a technical update on Virus-Clip

Oncovirus infection is crucial in human malignancies. Certain oncoviruses can lead to structural variations in the human genome known as viral genomic integration, which can contribute to tumorigenesis. Existing viral integration detection tools differ in their underlying algorithms pinpointing different aspects or features of viral integration phenomenon. We discuss about major procedures in performing viral integration detection. More importantly, we provide a technical update on Virus-Clip to facilitate its usage on the latest human genome builds (hg19 and hg38) and the adoption of multi-thread mode for faster initial read alignment. By comparing the execution of Virus-Clip using single-thread and multi-thread modes of read alignment on targeted-panel sequencing data of HBV-associated hepatocellular carcinoma patients, we demonstrate the marked improvement of multi-thread mode in terms of significantly reduced execution time, while there is negligible difference in memory usage. Taken together, with the current update of Virus-Clip, it will continue supporting the in silico detection of oncoviral integration for better understanding of various human malignancies.     

Escherichia coli O157: H7 Growth in Laboratory Media as Affected by Phenolic Antioxidants

Five strains of Escherichia coli O157:H7 with ATCC 11775 E. coli were grown in brain heart infusion (BHI) broth (pH 5.8, adjusted with citric acid) and treated with butylated hydroxyanisole (BHA), butylated hy-droxytoluene (BHT), tertiary butylhydroquinone (TBHQ), and propyl gallate (PG) individually or combined. Additives ranged from 100–400 ppm with inocula levels between 5 and 104 CFU/mL in tissue culture plates or in flasks; samples were incubated at 4°C or 37°C for 24 hr. Additive antimicrobial efficacy varied with inoculum level and incubation temperature. BHA at <200 ppm was bactericidal on all strains. Poly-hydroxyl additives (TBHQ, PG) were less effective at 4°C. BHA-BHT combinations were synergistic at 4°C.     

PROGRESS CONFINED: Increases in Black Home Buying and the Persistence of Residential Segregation

ABSTRACT: In recent years, increasing homeownership among blacks, as well as other minority groups, has been a major federal policy objective in the United States. Black homeownership in the US has increased significantly in the 1990s, and the benefits of such increases to minority households are likely to be considerable. However, examining black home-buying patterns in the Chicago area in the early 1990s shows that an increasing proportion of black buyers are buying into segregated or soon-to-be segregated neighborhood's. The proportion of black home buyers in the Chicago area moving into tracts with 75% or more black buyers increased from 27% in 1990–1991 to 45% in 1995–1996. Although federal policies have shown promise in opening up financial access to minority home buyers, without more aggressive policies to open up home-selling markets, black homeownership is likely to remain highly segregated and likely to yield far fewer benefits than would more widely distributed settlement patterns.     

The Parallel Transfer of Task Knowledge Using Dynamic Learning Rates Based on a Measure of Relatedness

With a distinction made between two forms of task knowledge transfer, 'representational' and 'functional', eta MTL, a modified version of the multiple task learning (MTL) method of functional (parallel) transfer, is introduced. The eta MTL method employs a separate learning rate, etak, for each task output node k. etak varies as a function of a measure of relatedness, Rk, between the kth task and the primary task of interest. Results of experiments demonstrate the ability of eta MTL to dynamically select the most related source task(s) for the functional transfer of prior domain knowledge. The eta MTL method of learning is nearly equivalent to standard MTL when all parallel tasks are sufficiently related to the primary task, and is similar to single task learning when none of the parallel tasks are related to the primary task.     

Three‐dimensional bright‐field scanning transmission electron microscopy elucidate novel nanostructure in microbial biofilms

Bacterial biofilms play key roles in environmental and biomedical processes, and understanding their activities requires comprehension of their nanoarchitectural characteristics. Electron microscopy (EM) is an essential tool for nanostructural analysis, but conventional EM methods are limited in that they either provide topographical information alone, or are suitable for imaging only relatively thin (<300 nm) sample volumes. For biofilm investigations, these are significant restrictions. Understanding structural relations between cells requires imaging of a sample volume sufficiently large to encompass multiple cells and the capture of both external and internal details of cell structure. An emerging EM technique with such capabilities is bright‐field scanning transmission electron microscopy (BF‐STEM) and in the present report BF‐STEM was coupled with tomography to elucidate nanostructure in biofilms formed by the polycyclic aromatic hydrocarbon‐degrading soil bacterium, Delftia acidovorans Cs1‐4. Dual‐axis BF‐STEM enabled high‐resolution 3‐D tomographic recontructions (6–10 nm) visualization of thick (1250 and 1500 nm) sections. The 3‐D data revealed that novel extracellular structures, termed nanopods, were polymorphic and formed complex networks within cell clusters. BF‐STEM tomography enabled visualization of conduits formed by nanopods that could enable intercellular movement of outer membrane vesicles, and thereby enable direct communication between cells. This report is the first to document application of dual‐axis BF‐STEM tomography to obtain high‐resolution 3‐D images of novel nanostructures in bacterial biofilms. Future work with dual‐axis BF‐STEM tomography combined with correlative light electron microscopy may provide deeper insights into physiological functions associated with nanopods as well as other nanostructures.     

Sintering of Monosized, Spherical Yttria Powders

Monosized, spherical Y₂O₃ was processed from raw commercial Y₂O₃ by homogeneous precipitation in aqueous solution via urea decomposition. Dry-pressed pellets of the synthesized and raw powders were sintered to 1500°, 1600°, and 1700°C for 7 to 720 min. Microstructural development was followed with scanning electron microscopy. The differences between sintering behavior of the two powders are discussed.     

Identification of faces obscured by noise: comparison of an artificial neural network with human observers

Face identification is easily accomplished by humans but is an exceptionally difficult task for machine vision algorithms. This report is the first to directly compare the face identification performance of humans with that of an artificialneural network,Dystal, using digitized images of the faces of eight individuals in an eight-alternative forced-response paradigm. The test images differed from the training images in facial expression, head tilt and rotation, amount and correlation of added noise, and the presence of a stocking mask in some of the images. The images were deliberately not preprocessed by a feature extraction algorithm to avoid confoundingthe performance of Dystal with the performance of the feature extraction algorithm.While human observers outperform Dystal at low noise levels, at high levels of correlated noise Dystal outperforms human observers, who score just above the chance level. The greater sensitivity to noise exhibited by human observers is attributed to the local feature extraction performed by human observers, but not by Dystal.     

Physicochemical and antioxidant properties of bovine caseinate hydrolysates obtained through microbial protease treatment

It is currently possible to obtain bioactive nutritional components through enzyme hydrolysis under well‐controlled and moderate conditions of pH and temperature. In this work, we aimed for the production and characterisation of bovine sodium caseinate (NaCAS) hydrolysates by means of an extracellular protease from Bacillus sp. P45. Antioxidant properties were evaluated through 2,2‐diphenyl‐1‐picrylhydrazyl and thiobarbituric acid reactive substances assays. A glucono‐δ‐lactone acid‐induced aggregation and gelation processes of the hydrolysates and their corresponding mixtures with NaCAS were also analysed. Hereby, we demonstrate that the presence of hydrolysates affects the kinetics of NaCAS aggregation processes but does not significantly alters the final state of the acid aggregates obtained.     

PREPARATORY STUDIES FOR THE IMPLEMENTATION OF NORM UNE 66020-1:2001 (OR NORM ISO 2859-1:1999) IN A CANNED MARINE FOOD FACTORY

The Spanish norm UNE 66020-1:2001 is equivalent to the international norm ISO 2859-1:1999 and deals with inspection by attributes of lots of material. In order to implement such a norm in a canned marine food factory (which manufactures mainly bluefin tuna in vegetal oil), some preliminary work was carried out. First, a careful study of the production process led to three possible sources of variation in the final weight of the cans produced, namely the canning machine, the cans used and the balance utilized for weighing. Afterward, each of these sources of variation was studied, which resulted in a value of the process average. This average shall enable the responsible authority of the company to set an acceptance quality limit, which should allow the application of the cited norm.

PRACTICAL APPLICATION

This work is expected to be considered an example of the studies that need to be carried out previously to the implementation of norm UNE 66020-1:2001 (i.e., norm ISO 2859-1:1999). Moreover, an additional point to highlight is the fact that this work is not a simulation but rather, it was developed in a real factory, devoted to the manufacturing of canned marine food.