Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotyping by Induced Förster Resonance Energy Transfer (iFRET) Mechanism and Simultaneous Mutation Scanning

Multiple genotyping techniques were developed on the basis of real‐time PCR. In this article, we present a genotyping technique extending the induced Förster resonance energy transfer (iFRET) mechanism in conjunction with simultaneous mutation scanning. Rapid, asymmetric PCR was performed with SYTO9, polymerase lacking 5′ → 3′ exonuclease activity, two primers, and a probe labeled with 6‐Carboxy‐X‐rhodamine. Six primers and probe sets were designed to detect germline mutations in BRCA1, a singular polymorphism in CCND1 and somatic mutations in KRAS and BRAF genes. The validation set consisted of 140 archival DNA samples from patients with previously confirmed BRCA1 mutation and 42 archival formalin‐fixed and paraffin‐embedded tissues from patients with colorectal cancer or malignant melanoma. BRCA1 and CCND1 genotyping by iFRET probe showed 100% agreement with Sanger sequencing and other validated methods. A combination of iFRET and high‐resolution melting analysis (HRMA) detected a spectrum of six different mutations in the KRAS gene and three different mutations in the BRAF gene. Due to an allele enrichment effect, the sensitivity of mutation detection of iFRET–HRMA genotyping and sequencing of iFRET–HRMA PCR products was significant, increasing from 1.5% to 6.2%, respectively. The technique presented in this article is a useful and cost‐effective method for the detection of both germline and somatic mutations.
Bayesian image reconstruction

A Bayesian method is described for solving problems in image reconstruction from projections. The approach utilizes a Gibbs distribution to incorporate a priori spatial information. The model has been used for reconstruction of simulated data, data from phantom studies, and real scanning data. The results indicate that the technique has the potential to provide both improvement in spatial resolution and reduction of noise. <<ETX>>
A System for 256-Channel in Vitro Recording of the Electrophysiological Activity of Brain Tissue

A measurement system for 256-channel in vitro recordings of brain tissue electrophysiological activity is presented in the paper. The system consists of the brain tissue life support system, Microelectrode Array (MEA), conditioning Application Specific Integrated Circuits (ASIC’s) for signals conditioning, Digitizer and PC application for measurement data presentation and storage. The life support system keeps brain tissue samples in appropriately saturated artificial cerebrospinal fluid at a very stable temperature. The MEA consists of two hundred and fifty-six 40 μm diameter tip-shaped electrodes. The ASIC’s performs amplification and filtering of the 256-field and action potential signals. The Digitizer performs simultaneous data acquisition from 256 channels 14 kS/s sample rate and 12-bit resolution. The resulting byte stream is transmitted to the PC via USB (Universal Serial Bus). Preliminary tests confirm that the system is capable of keeping the extracted brain tissue active (hippocampal formation slices) and simultaneously to record action potentials, as well as local theta field potentials with very small amplitudes from multiple neurons.
Screening of thiopurine S‐methyltransferase mutations by horizontal conformation‐sensitive gel electrophoresis

The genetic polymorphism of thiopurine S‐methyltransferase (TPMT) has had a highly significant clinical impact due to its association with individual variation in the toxicity and therapeutic efficiency of thiopurine drugs, which are pharmaceutical agents widely used in the treatment of several kinds of diseases. Until now, ten mutant alleles responsible for TPMT deficiency and several silent and intronic mutations have been described.
A Study of Vulnerabilities in E-Voting System

This paper discussed the vulnerabilities in e-voting system. E-voting is an electronic election or voting system that has strong implications in the life of the country that implement them that is classified in Safety Critical Systems. But there is some issues in the e-voting system. There are some vulnerabilities in this system that had been discuss by the previous authors. There is some propose solution provided by the previous author. In this paper some type of evoting has been chosen as the scope of the study. This study will discuss the type of vulnerabilities in e-voting and suggest some solution method to overcome the situation vulnerabilities.
DEVELOPMENT OF AN INTELLIGENT THREE DIMENSIONAL OPTICAL INSPECTION SYSTEM

Optical inspection is becoming more popular for quality assurance in manufacturing. Faster and more powerful computers help improve the speed of image processing and analysis. This dissertation presents the development of an intelligent three-dimensional optical inspection system. The main objective is to automate the inspection process. This dissertation work consists of three major tasks: new calibration procedure, fuzzy logic based fringe center locator (FCL), and object recognition. The accuracy and reliability of fringe center detection are critical to three dimensional geometry determination, whereas object recognition is to recognize an object's shape and size. With the new calibration procedure, the value of calibration factor can be automatically adjusted when the camera angle changed. The results indicate that two-dimensional objects can be successfully recognized, and the fringe centers can be automatically detected. The time needed to inspect the three dimensional geometry is about 30 seconds when using Matlab software. However, the same inspection can be completed in about 0.6 seconds if we convert the Matlab program into a C++ source code.
Extracellular matrix and nuclear localization of βig‐h3 in human bladder smooth muscle and fibroblast cells

The extracellular matrix (ECM) plays an essential role in bladder structure and function. In this study, expression of βig‐h3, a recently identified extracellular matrix protein, was investigated in human bladder tissue, and human bladder smooth‐muscle (SMC) and fibroblast cells in vitro. SMCs secreted greater than three times the level of this protein compared with fibroblasts. The relative levels of βig‐h3 mRNA in the two cell types reflected the protein expression. Immunohistochemical analysis demonstrated protein deposition in the ECM as well as cytoplasmic localization and, unexpectedly, nuclei. Anti‐βig‐h3 antibodies also stained the matrix surrounding the detrusor SMCs and nuclei of bladder fibroblasts, SMCs, and urothelium in intact bladder tissue. Western blot analyses of medium and matrix fractions obtained from cells in vitro revealed protein of ∼70–74 kDa, whereas nuclear extracts contained a 65‐kDa reactive protein band. We propose that although this protein is a structural component of bladder ECM, its nuclear localization suggests that it has other regulatory and/or structural functions. J. Cell. Biochem. 79:261–273, 2000. © 2000 Wiley‐Liss, Inc.
Microglial and macrophage reactions mark progressive changes and define the penumbra in the rat neocortex and striatum after transient middle cerebral artery occlusion

Transient middle cerebral artery occlusion in rats leads to infarction of the lateral part of the striatum and adjacent neocortex, with selective neuronal necrosis in the bordering penumbral zones. Administration of glutamate, cytokine, and leukocyte antagonists have rescued mainly neocortical neurons, indicating differences in the degenerative processes. The aim of this study was, therefore, to describe the microglial/macrophage activation and polymorphonuclear leukocyte recruitment patterns and to correlate these with the ischemia‐induced degenerative processes. The analysis showed significant differences in the characteristics and timing of the microglial/macrophage responses between the caudate putamen and neocortical infarct zones, the infarct zones and their associated penumbral zones, as well as between the striatal and the neocortical penumbral zone. Infiltrations with polymorphonuclear leukocytes into the infarct zones were limited and shortlasting and confined to the acutely degenerating striatum and piriform cortex. A delayed, massive infiltration with lipid phagocytes into the caudate putamen infarct markedly contrasted an early recruitment and activation of microglia/macrophages in the adjacent penumbra. Within the neocortex, a later onset of degeneration along the insular‐parietal axis was marked by neuronal expression of heat shock protein and a progressive microglial activation with induction of the full repertoire of microglial activation markers, including a widespread microglial major histocompatibility complex (MHC) class II antigen expression. We interpret the present results as delineating two differentially progressing penumbral zones, which are likely to reflect differences in the underlying degenerative processes. Differences in the microglial/macrophage activation pattern attract special attention, as these cells may constitute specific targets for therapeutic intervention. J. Comp. Neurol. 386:461‐476, 1997. © 1997 Wiley‐Liss, Inc.
Neurotransmitter-Mediated Collective Rhythms in Grouped Drosophila Circadian Clocks

Over the past decades, fly Drosophila melanogaster has being used as a premier model organism to study molecular and genetic bases of circadian rhythms. Here the authors propose a multicellular heterogeneous model for which the network of Drosophila circadian oscillators consists of two groups, the self-sustained lateral neurons (LNs) communicating to each other and the damped dorsal neurons (DNs) receiving neurotransmitters only from the LNs without interaction within this group. By simulating different experimental conditions, the authors find that the proposed model, except for being capable of reproducing some known experimental results well, also can predict some interesting phenomena: 1) The DNs need neuronal projections from the LNs to be rhythmic and to synchronize; 2) the effect of communication on mean amplitude and mean period of two oscillatory groups is different; 3) communication delay can facilitate the network synchronization of the LNs; and 4) only the LNs lose rhythmicity under constant light conditions. These results reveal the mechanism of an integrated pacemaker that would govern behavioral and physiological rhythmicity of the model organism.
Aberrant expression of muc1 mucin in ductal hyperplasia and ductal carcinoma In situ of the breast

MUC1 mucin is a high molecular weight transmembrane glycoprotein expressed on the apical cell surface of normal glandular epithelia. In many human adenocarcinomas, this protein is up‐regulated and/or underglycosylated, and its expression changes from apical to the entire cell membrane. It is thought that entire cell membrane expression of MUC1 reduces cell–cell and cell–extracellular matrix interactions and therefore may facilitate invasive growth and development of metastases. In this study, we determined immunohistochemically the expression of normal and underglycosylated MUC1 in normal breast tissue (n = 8) and in a spectrum of breast lesions, including usual ductal hyperplasia (n = 23), atypical ductal hyperplasia (n = 7), and ductal carcinoma in situ (DCIS) (n = 22). We used 4 monoclonal antibodies; 115D8 is directed to a glycopeptide, the other 3 to the peptide core of the molecule, of which 139H2 is not affected by the degree of glycosylation of MUC1, whereas SM3 and VU‐4‐H5 stain only underglycosylated forms. All cases showed apical positivity for 115D8 and 139H2. Entire cell membrane expression of fully (normal) glycosylated MUC1 was mainly found in DCIS lesions. Apical staining of SM3 was found in 38% of normal cases and 60% of the ductal lesions with no difference between the different subgroups. Apical staining of VU‐4‐H5 was found more often in DCIS (27%) than in normal tissue or ductal hyperplasia (3%). Membrane expression of underglycosylated MUC1 was found only in poorly differentiated DCIS. In conclusion, aberrant expression of MUC1, i.e., on the entire cell membrane and/or underglycosylated forms, can be found in ductal hyperplasia with atypia and especially in DCIS of the breast. This finding implies that these lesions with aberrant expression are at higher risk for developing subsequent invasive breast carcinoma. Int. J. Cancer (Pred. Oncol.) 84:466–469, 1999. © 1999 Wiley‐Liss, Inc.
Metabolism of nitric oxide in soil and denitrifying bacteria

Production and consumption of NO was measured under anaerobic conditions in a slightly alkaline and an acidic soil as well as in pure cultures of denitrifying Pseudomonas aeruginosa, P. stutzeri, P. fluorescens, Paracoccus denitrificans, Azospirillum brasilense, and A. lipoferum. Growing bacterial cultures reduced nitrate and intermediately accumulated nitrite, NO, N2O, but not NO2. Addition of formaldehyde inhibited NO production and NO consumption. In the presence of acetylene NO was reduced to N2O. Net NO release rates in denitrifying bacterial suspensions and in soil samples decreased hyperbolically with increasing NO up to mixing ratios of about 5 ppmv NO. This behaviour could be modelled by assuming a constant rate of NO production simultaneously with a NO consumption activity that increased with NO until Vmax was reached. The data allowed calculation of the gross rates (P) of NO production, of the rate constants (k), Vmax and Km of NO consumption, and of the NO compensation mixing ratio (mc). In soil, P was larger than Vmax resulting in net NO release even at high NO mixing ratios unless P was selectively inhibited by chlorate + chlorite or by aerobic incubation conditions. In bacteria, Vmax was somewhat larger than P resulting in net NO uptake at high NO mixing ratios. Both P and Vmax were dependent on the supply of electron donor (e.g. glucose). Both in soil (aerobic or anaerobic) and in pure culture, the Km values of NO consumption were in a similar low range of about 0.5–6.0 nM. Anaerobic soil and denitrifying bacteria exhibited mc values of 1.6–2.1 ppmv NO and 0.2–4.0 ppmv NO, respectively.
Rhodopsin Transport and Rab Expression in the Carotenoid-Deprived Drosophila melanogaster

Abstract Drosophila rhodopsin consists of an apoprotein, opsin, and a chromophore, 11-cis-3-hydroxyretinal. When flies are raised in carotenoid-free medium, rhodopsin transport is blocked between the rough endoplasmic reticulum (rER) and the Golgi body, and immature opsin accumulates in the rER. To elucidate how carotenoid controls the protein transport between these organelles, we investigated the morphological and molecular-biological defects caused by carotenoid deprivation. The results demonstrated that this deprivation causes rER elongation and a shortening of the rhabdomeric microvilli, whereas the density and morphological features of the Golgi body are not significantly affected. Moreover, the content of rhabdomeric proteins other than rhodopsin is not decreased by the deprivation. These results indicate that carotenoid deprivation does not affect the overall traffic of vesicle transport, but selectively suppresses rhodopsin transport between the rER and the Golgi body. We further investigated the gene and protein expression of Rab proteins that control the vesicle transport between cell organelles. The results demonstrated that neither gene nor protein expression of RAB1 and RAB2 is influenced by carotenoid deprivation, which also supports the above conclusion.
The Spermatogonial Stem Cell Niche

Spermatogonial stem cells (SSCs; As spermatogonia) and their direct descendants (Apr and Aal spermatogonia) are preferentially located in those areas of the seminiferous tubules that border on the interstitial tissue. Fewer of these cells are present in tubule areas directly bordering on another tubule. Therefore, the SSC niche is related to the presence of interstitial tissue. The somatic cells within the seminiferous tubules, the Sertoli cells, are able to produce growth factors that stimulate self-renewal (GDNF, FGF2) and differentiation (activin A, BMP4, and SCF) of the SSCs. As Sertoli cells are everywhere on the basal membrane of the tubules, other factors coming from outside the tubules must determine, either directly or indirectly via Sertoli cells, whether in a particular area self-renewal of SSCs will be preferred or differentiation in the form of Apr formation. Self-renewal will be preferred in the stem cell niche and differentiation outside of the niche. Factors that could link the niche to the interstitial tissue are CSF1, produced by Leydig cells that stimulate stem cell proliferation and FSH, the concentration of which will be highest near blood vessels and that stimulates GDNF production by Sertoli cells. Microsc. Res. Tech. 72:580– 585, 2009. VC 2009 Wiley-Liss, Inc.
Digitally controlled compressive receiver

An adaptive compressive receiver with electronically controlled parameter adjustment for applications like spectrum monitoring of frequency hopped spread spectrum signals is presented. For fast real time signal processing with high time-bandwidth product a SAW convolver is used. We achieve a resolution of 125 kHz over an 80 MHz bandwidth. The system presented employs some new digital concepts for the generation of the RF signals, and signal windowing and weighting due to the use of the high performance convolver. The system shows satisfactory performance and applicability in a wide range of realtime signal analysis.
Molecular characterization of bacterial virulence factors and the consequences for vaccine design (the 1988 Fleming lecture)

In this review I have attempted to illustrate, using selected examples, how molecular biology has changed the approaches taken to study bacterial virulence factors. By analysing in detail the virulence determinants of individual pathogens we have been able, in many cases, to piece together the complex way in which highly evolved pathogens interact with their host. This detailed information will in the future aid the development of new therapies against infectious diseases and other human and veterinary illnesses
Effects of Rhizobium innoculation, lime and molybdenum on nitrogen fixation of nodulated Phaseolus vulgaris L.

A field and glass house experiment was conducted with the aim of evaluatingRhizobium inoculation, molybdenum (Mo) and lime supply on growth and nitrogen fixation of nodulated Phaseolus vulgaris. The experiment was laid in a split-split plot design. The experimental treatments consisted of 2 levels ofRhizobium inoculation (with rhizobia and without rhizobia) 3 levels of Mo (0, 6 and 12 g kg-1 of seeds) and 3 levels of lime (0, 2 and 3 t ha-1). Rhizobiuminoculation showed significant increase in dry matter yield of different organs and decreased δ15N values in all organs assessed, thus resulting to improved % nitrogen derived from atmosphere (%Ndfa) in all organs and the amount of N derived from fixation. Molybdenum and lime were significantly effective in promoting plant growth in most organs and decreased δ15N values in all organs for glasshouse and field experiment. Lowest δ15N values were recorded in Mo and lime supplied at the highest rates of 6 and 12 g kg-1 of seeds and 2 and 3 t lime per ha, respectively. Molybdenum and lime application also significantly improved %Ndfa in all organs and N derived from N-fixation in most organs. Significant responses in N nutrition were also reported in treatments involving the combination of Rhizobium x Mo x lime with better result being recorded in treatments involving Rhizobium inoculation and higher levels of Mo and lime. Key words: Nodulated root, δ15N, %Ndfa, total N.
Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures

One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life.
Diagnóstico molecular de herpesvírus ovino tipo 2 em surto de febre catarral malígna em bovinos do Rio Grande do Norte

Molecular findings that confirmed the participation of ovine herpesvirus 2 (OVH-2) in the lesions that were consistent with those observed in malignant catarrhal fever of cattle are described. Three mixed-breed cattle from Rio Grande do Norte state demonstrated clinical manifestations that included mucopurulent nasal discharge, corneal opacity and motor incoordination. Routine necropsy examination demonstrated ulcerations and hemorrhage of the oral cavity, corneal opacity, and lymph node enlargement. Significant histopathological findings included widespread necrotizing vasculitis, non-suppurative meningoencephalitis, lymphocytic interstitial nephritis and hepatitis, and thrombosis. PCR assay performed on DNA extracted from kidney and mesenteric lymph node of one animal amplified a product of 423 base pairs corresponding to a target sequence within the ovine herpesvirus 2 (OVH-2) tegument protein gene. Direct sequencing of the PCR products, from extracted DNA of the kidney and mesenteric lymph node of one cow, amplified the partial nucleotide sequences (423 base pairs) of OVH-2 tegument protein gene. Blast analysis confirmed that these sequences have 98-100% identity with similar OVH-2 sequences deposited in GenBank. Phylogenetic analyses, based on the deduced amino acid sequences, demonstrated that the strain of OVH-2 circulating in ruminants from the Brazilian states of Rio Grande do Norte and Minas Gerais are similar to that identified in other geographical locations. These findings confirmed the active participation of OVH-2 in the classical manifestations of sheep associated malignant catarrhal fever.