Miracle-dz/UniFAR-FTUs huggingface dataset:
Type I Interferons Regulate the Magnitude and Functionality of Mouse Polyomavirus-Specific CD8 T Cells in a Virus Strain-Dependent Manner

ABSTRACT Mouse polyomavirus (MPyV) is a ubiquitous persistent natural mouse pathogen. A glutamic acid (E)-to-glycine (G) difference at position 91 of the VP1 capsid protein shifts the profile of tumors induced by MPyV from an epithelial to a mesenchymal cell origin. Here we asked if this tropism difference affects the MPyV-specific CD8 T cell response, which controls MPyV infection and tumorigenesis. Infection by the laboratory MPyV strain RA (VP1-91G) or a strain A2 mutant with an E-to-G substitution at VP1 residue 91 [A2(91G)] generated a markedly smaller virus-specific CD8 T cell response than that induced by A2(VP1-91E) infection. Mutant A2(91G)-infected mice showed a higher frequency of memory precursor (CD127hi KLRG1lo) CD8 T cells and a higher recall response than those of A2-infected mice. Using T cell receptor (TCR)-transgenic CD8 T cells and immunization with peptide-pulsed dendritic cells, we found that early bystander inflammation associated with A2 infection contributed to recruitment of the larger MPyV-specific CD8 T cell response. Beta interferon (IFN-β) transcripts were induced early during A2 or A2(91G) infections. IFN-β inhibited replication of A2 and A2(91G) in vitro. Using mice lacking IFN-αβ receptors (IFNAR−/−), we showed that type I IFNs played a role in controlling MPyV replication in vivo but differentially affected the magnitude and functionality of virus-specific CD8 T cells recruited by A2 and A2(91G) viral infections. These data indicate that type I IFNs are involved in protection against MPyV infection and that their effect on the antiviral CD8 T cell response depends on capsid-mediated tropism properties of the MPyV strain. IMPORTANCE Isolates of the human polyomavirus JC virus from patients with the frequently fatal demyelinating brain disease progressive multifocal leukoencephalopathy (PML) carry single amino acid substitutions in the domain of the VP1 capsid protein that binds the sialic acid moiety of glycoprotein/glycolipid receptors on host cells. These VP1 mutations may alter neural cell tropism or enable escape from neutralizing antibodies. Changes in host cell tropism can affect recruitment of virus-specific CD8 T cells. Using mouse polyomavirus, we demonstrate that a single amino acid difference in VP1 known to shift viral tropism profoundly affects the quantity and quality of the anti-polyomavirus CD8 T cell response and its differentiation into memory cells. These findings raise the possibility that CD8 T cell responses to infections by human polyomaviruses may be influenced by VP1 mutations involving domains that engage host cell receptors.
A robust algorithm for text extraction in color video

We report on the development and implementation of a new algorithm for extracting text in digitized color video. The algorithm operates by locating potential text line segments from horizontal scan lines. Detected text line segments are expanded or combined with text line segments from adjacent scan lines to form larger text blocks, which are then subject to filtering and refinement. Text pixels within text blocks are then found using bi-color clustering and connected-component analysis. Morphological contour smoothing and morphological resolution enhancement algorithms are then applied to the detected binary texts to enhance their visual quality. The implemented algorithm has fast execution time and is effective in detecting text in difficult cases, such as scenes with highly textured background, and scenes with small text. A variety of color images digitized from broadcast television are used to test the algorithm and excellent performance result was obtained.
The Kinetoplast Duplication Cycle in Trypanosoma brucei Is Orchestrated by Cytoskeleton-Mediated Cell Morphogenesis

ABSTRACT The mitochondrial DNA of Trypanosoma brucei is organized in a complex structure called the kinetoplast. In this study, we define the complete kinetoplast duplication cycle in T. brucei based on three-dimensional reconstructions from serial-section electron micrographs. This structural model was enhanced by analyses of the replication process of DNA maxi- and minicircles. Novel insights were obtained about the earliest and latest stages of kinetoplast duplication. We show that kinetoplast S phase occurs concurrently with the repositioning of the new basal body from the anterior to the posterior side of the old flagellum. This emphasizes the role of basal body segregation in kinetoplast division and suggests a possible mechanism for driving the rotational movement of the kinetoplast during minicircle replication. Fluorescence in situ hybridization with minicircle- and maxicircle-specific probes showed that maxicircle DNA is stretched out between segregated minicircle networks, indicating that maxicircle segregation is a late event in the kinetoplast duplication cycle. This new view of the complexities of kinetoplast duplication emphasizes the dependencies between the dynamic remodelling of the cytoskeleton and the inheritance of the mitochondrial genome.
The Leucine-rich Pentatricopeptide Repeat-containing Protein (LRPPRC) Does Not Activate Transcription in Mammalian Mitochondria*

Background: LRPPRC regulates mitochondrial mRNA stability and was recently reported to also stimulate mammalian mtDNA transcription. Results: Altered expression of LRPPRC in mice in vivo or addition of LRPPRC to a recombinant transcription system in vitro does not affect mtDNA transcription. Conclusion: LRPPRC is not a mitochondrial transcriptional activator. Significance: LRPPRC is an essential post-transcriptional regulator of metazoan mtDNA expression. Regulation of mtDNA expression is critical for controlling oxidative phosphorylation capacity and has been reported to occur at several different levels in mammalian mitochondria. LRPPRC (leucine-rich pentatricopeptide repeat-containing protein) has a key role in this regulation and acts at the post-transcriptional level to stabilize mitochondrial mRNAs, to promote mitochondrial mRNA polyadenylation, and to coordinate mitochondrial translation. However, recent studies have suggested that LRPPRC may have an additional intramitochondrial role by directly interacting with the mitochondrial RNA polymerase POLRMT to stimulate mtDNA transcription. In this study, we have further examined the intramitochondrial roles for LRPPRC by creating bacterial artificial chromosome transgenic mice with moderately increased LRPPRC expression and heterozygous Lrpprc knock-out mice with moderately decreased LRPPRC expression. Variation of LRPPRC levels in mice in vivo, occurring within a predicted normal physiological range, strongly affected the levels of an unprocessed mitochondrial precursor transcript (ND5-cytochrome b) but had no effect on steady-state levels of mitochondrial transcripts or de novo transcription of mtDNA. We further assessed the role of LRPPRC in mitochondrial transcription by performing size exclusion chromatography and immunoprecipitation experiments in human cell lines and mice, but we found no interaction between LRPPRC and POLRMT. Furthermore, addition of purified LRPPRC to a recombinant human in vitro transcription system did not activate mtDNA transcription. On the basis of these data, we conclude that LRPPRC does not directly regulate mtDNA transcription but rather acts as a post-transcriptional regulator of mammalian mtDNA expression.
Transforming growth factor beta, fibrogenesis and hyperglycemia in patients with chronic pancreatitis.

UNLABELLED It has been suggested that transforming growth factor beta (TGFb) mediates liver fibrosis, which can be monitored by the serum determination of the N-terminal peptide of type III procollagen (PIIIP) and laminin. Fibrosis is also an important phenomenon in patients with chronic pancreatitis (CP). In 23 patients with CP, 38 with liver cirrhosis (LC) and 20 healthy controls we compared the serum patterns of PIIIP, laminin and TGFb and assessed whether in CP these markers are correlated with exocrine and endocrine function. In patients with LC, PIIIP and laminin levels were significantly higher, whereas TGFb levels were significantly lower than those of controls. In CP patients, no significant variations were found for PIIIP and laminin, although levels were high in 7/23 and in 5/23 patients, respectively. TGFb levels in CP patients were higher than those in LC patients, levels being raised in 6/23 patients. In LC patients an inverse correlation was found between PIIIP and TGFb, whereas in CP patients, a direct correlation was found between TGFb and PIIIP. Moreover, in CP patients, there was also a positive correlation between TGFb and fasting serum glucose levels, while laminin was correlated with PABA test results. IN CONCLUSION serum biochemical markers of liver fibrosis can be considered of limited value in assessing pancreatic fibrosis; in liver cirrhosis there may be a negative feed-back regulation between TGFb production and the fibrogenetic process; and in chronic pancreatitis TGFb appears to favor fibrosis on the one hand and the development of hyperglycemia on the other.
Escaping the Natural Resource Curse and the Dutch Disease ? Norway ' s Catching up with and Forging ahead of Its Neighbors

Growth studies show, counter to intuition, that the discovery of a natural resource may be a curse rather than a blessing since resource-rich countries grow slower than others. Moreover, resource abundance may involve a displacement of a growth-essential manufacturing sector, leading to Dutch Disease. Norway is an important exception to the curse and the disease. Since oil production started in 1971 its overall growth has been remarkable side-by-side with phenomenal oil exports. At the same time, manufacturing has been performing well. This article uses neighbor countries Denmark and Sweden to highlight Norway's relative development. The article employs structural break techniques to demonstrate that Norway started a sudden acceleration in 1974, three years after having started oil extraction, and never slowed down. After catchingup with its neighbors, Norway surprisingly maintained a higher pace, and appears to have escaped the curse and the disease. This article establishes the fact through rigorous hypothesis testing before examining explanations of why Norway did escape.
Guidelines for Listeria testing of environmental, raw product and finished product samples in smoked seafood processing facilities

VIRGINIA N. SCOTT,1* MARTIN WIEDMANN,2 DORIS HICKS,3 ROBERT COLLETTE,4 MICHAEL L. JAHNCKE,5 and KEN GALL 6 1National Food Processors Association, Washington, D.C. 20005, USA; 2Department of Food Science, Cornell University, Ithaca, NY 14853, USA; 3University of Delaware Sea Grant College Program, Lewes, DE 19958, USA, 4National Fisheries Institute, McLean, VA 22102, USA; 5Virginia Seafood Agricultural Research and Extension Center, Hampton, VA 23669, USA; 6New York Sea Grant and Cornell Cooperative Extension, Stony Brook, New York 11794, USA Food Protection Trends, Vol. 25, No. 1, Pages 23–34 Copyright© 2005, International Association for Food Protection 6200 Aurora Ave., Suite 200W, Des Moines, IA 50322-2864
Identification and Characterization of a Pi Isoform of Glutathione S-Transferase (GSTP1) as a Zeaxanthin-binding Protein in the Macula of the Human Eye*

Uptake, metabolism, and stabilization of xanthophyll carotenoids in the retina are thought to be mediated by specific xanthophyll-binding proteins (XBPs). A membrane-associated XBP was purified from human macula using ion-exchange chromatography followed by gel-exclusion chromatography. Two-dimensional gel electrophoresis showed a prominent spot of 23 kDa and an isoelectric point of 5.7. Using mass spectral sequencing methods and the public NCBI database, it was identified as a Pi isoform of human glutathione S-transferase (GSTP1). Dietary (3R,3′R)-zeaxanthin displayed the highest affinity with an apparent Kd of 0.33 μm, followed by (3R,3′S-meso)-zeaxanthin with an apparent Kd of 0.52 μm. (3R,3′R,6′R)-Lutein did not display any high-affinity binding to GSTP1. Other human recombinant glutathione S-transferase (GST) proteins, GSTA1 and GSTM1, exhibited only low affinity binding of xanthophylls. (3R,3′S-meso)-Zeaxanthin, an optically inactive nondietary xanthophyll carotenoid present in the human macula, exhibited a strong induced CD spectrum in association with human macular XBP that was nearly identical to the CD spectrum induced by GSTP1. Like-wise, dietary (3R,3′R)-zeaxanthin displayed alterations in its CD spectrum in association with GSTP1 and XBP. Other mammalian xanthophyll carrier proteins such as tubulin, high-density lipoprotein, low-density lipoprotein, albumin, and β-lactoglobulin did not bind zeaxanthins with high affinity, and they failed to induce or alter xanthophyll CD spectra to any significant extent. Immunocytochemistry with an antibody to GSTP1 on human macula sections showed highest labeling in the outer and inner plexiform layers. These results indicate that GSTP1 is a specific XBP in human macula that interacts with (3R,3′S-meso)-zeaxanthin and dietary (3R,3′R)-zeaxanthin in contrast to apparently weaker interactions with (3R,3′R,6′R)-lutein.
Muscle fibre breakdown in venom‐induced muscle degeneration

We studied the early stages of the degeneration of skeletal muscles using the venom of Notechis scutatus as the myotoxic agent. The venom was used at a dose equivalent to the LD50 in the mouse. There was no mortality amongst the rats. Electron microscopy was used to show the progressive hypercontraction of sarcomeres and the loss of alignment of myofibrils in individual muscle fibres. Between areas of hypercontraction sarcomeres were torn, shedding loosened myofilaments into the cytosol. Western blotting and Coomassie staining were used to compare the respective rates of loss of desmin, titin, actin, myosin and dystrophin. We showed that desmin and titin were the first proteins to be degraded with a time to 50% loss of approximately 1 h and 3 h, respectively. The loss of major contractile proteins, myosin and actin, was rather slower. The loss of dystrophin was also slower than the loss of desmin and titin. Early damage to the plasma membrane of the muscle fibre caused the cells to depolarize, probably promoting the hypercontraction of the sarcomeres, but actual loss of membrane was incomplete even at 24 h. We suggest that the early degradation of desmin and titin was responsible for the disaggregation of the sarcomeres; the liberated contractile proteins myosin and actin were shed into the cytosol, where they were degraded. Phagocytic cells that had invaded the degenerating muscle fibres were primarily involved in the clearance of damaged mitochondria.
Antibodies as delivery vehicles for radioimmunotherapy of infectious diseases

The field of infectious diseases is in crisis and there is a need for strategies that can facilitate the rapid development of new antimicrobial agents. Radioimmunotherapy (RIT), a therapeutic modality originally developed for cancer treatment, has recently been suggested as a novel therapy for the treatment of a variety of infectious diseases. Because specific antibodies are used in RIT as delivery vehicles of cytocidal radiation, their molecular weight influences the nonspecific accumulation in infectious foci and blood clearance, and their affinity-specific accumulation of antibodies in infectious foci. Like the problems encountered in oncology, relevant variables in the development of RIT of infectious diseases include target antigen-shedding; delivering radionuclides to infectious foci in organs, abscesses, granulomas, heart and brain, and potential safety concerns. Dadachova and Casadevall anticipate that RIT can be developed for many types of infectious diseases, including microbes resistant to conventional antimicrobial therapy and agents of biological warfare.
A STOCHASTIC INVENTORY MODEL WITH PERISHABLE AND AGING ITEMS LAKHDAR AGGOUN and LAKDERE BENKHEROUF

In this paper, we propose a single-product, discrete time inventory model for perishable items. Inventory levels are reviewed periodically and units in stock have a maximum lifetime of M periods. It is assumed that the dynamics of the inventory level is driven by a parameter process (reflecting perishability) and demands. By observing the history of the inventory level we obtain the conditional distribution of the perishability parameter by using the change of measure techniques. A special case is also presented.
Chemoprevention of Breast Cancer with Fenretinide (4-HPR): Study of Long-Term Visual and Ophthalmologic Tolerability

Background Fenretinide (4-HPR) is a synthetic retinoid being clinically tested in the chemoprevention of different tumors and precancerous lesions. Though safer than many other retinoids in experimental models, in humans 4-HPR may induce adverse effects that mainly affect the eye and visual function. Such effects are thought to be caused by the reduction of plasma retinol levels, which occurs after administration of the retinoid. Methods A series of 826 women treated with 4-HPR was studied to quantify the incidence and temporal pattern of occurrence of visual (dark adaptation) and ophthalmologic complaints (ocular dryness, lacrimation, conjunctivitis or photophobia) and to investigate the possible association between their occurrence and plasma retinol levels. Results The cumulative incidence of visual complaints reached nearly 20% at 5 years. The occurrence of these symptoms was more frequent at the start of treatment. The probability of developing visual complaints was significantly higher in patients with lower plasma retinol concentrations following 4-HPR treatment. The cumulative incidence of ophthalmologic complaints was 8% at 5 years. The occurrence of these complaints was evenly distributed during treatment. Ophthalmologic complaints were not associated with a greater degree of reduction of plasma retinol concentrations, but rather with the patient's age, since symptomatic patients were generally older than asymptomatic patients. Conclusions Visual and ophthalmologic complaints are common during 4-HPR treatment: their estimated 5-year cumulative incidence is close to 20% and 8%, respectively. However, the pattern of occurrence over time and the underlying mechanisms of these two types of complaints seem different.
An analysis of the posterior group of thalamic nuclei on the basis of its afferent connections

The distribution of the axonal and terminal degeneration in the posterior group and principal nuclei of the thalamus of the cat has been studied with the Nauta technique following lesions of the major ascending sensory pathways and of most areas of the cerebral cortex. The cellular changes occurring in the same parts of the thalamus after damage of the cortex of the somatic, auditory and visual sensory areas have also been investigated.
Design of a Broadband Quadrature Directional Coupler

The design of an edge-coupled quadrature directional coupler, which has a broadband performance and a relaxed coupled-line spacing, is presented. A slotted ground plane is used underneath the coupled region in order to relax the requirement for a narrow slot between the coupled lines. The simulated results show that the designed coupler exhibits a coupling of 3plusmn1 dB across the band 3.8 GHz to 9.8 GHz, when the spacing between the coupled lines is larger than 0.1 mm. Without the slot in the ground plane, the spacing should be less than 0.01 mm in order to achieve the same value of coupling across that band. This broadband coupling is accompanied by an isolation and return loss in the order of 14 dB or better. The designed device has a compact size with a dimension of 30 mmx20 mm.
Comparison of Methods for Probe Design

Biology is unveiling the fundamental laws of creature at molecule level. Examining gene expression patterns is one of the approaches to the fundamental laws. Therefore, it is important to analyze the gene expression patterns, quickly, massively, and accurately. Currently, cDNA arrays and DNA chips are the solutions to the requirement. Many works have been carried out for the techniques of composing oligo DNA on the DNA chips and the cDNA arrays. However, methods designing oligo DNA sequences for such systems have not been well studied, although they have great influence on the accuracy of the systems. Hence, it’s urgent work to establish effective and practical design methods. The prior work [3] on the probe design for the known genome, has shown the direction of the study. To observe gene expressions accurately, the probes have to hybridize exclusively to their target genes. Consequently, each probe must be distinctive. It introduced a metric for distinctiveness, which is Unique Sequence length (USL) defined for each position in the genome. If once we have the USLT, which is a table of the USLs for the whole genome, we can obtain a proper set of probes for the genome by choosing low-USL regions of the genes. The method of [3] is quite fast, but still not fast enough to satisfy the need to design a set of probes for a large genome. Then, we propose a new algorithmic method QT for constructing USLT. We also propose ST, a new approach for the probe design. ST directly produces a list of candidates for probes from a set of genes with out using USLT.
H2O2 increases sheep tracheal blood flow, permeability, and vascular response to luminal capsaicin.

Exogenous hydrogen peroxide (H2O2) causes airway epithelial damage in vitro. We have studied the effects of luminal H2O2 in the sheep trachea in vivo on tracheal permeability to low-molecular-weight hydrophilic (technetium-99m-labeled diethylenetriamine pentaacetic acid; 99mTc-DTPA) and lipophilic ([14C]antipyrine; [14C]AP) tracers and on the tracheal vascular response to luminal capsaicin, which stimulates afferent nerve endings. A tracheal artery was perfused, and tracheal venous blood was collected. H2O2 exposure (10 mM) reduced tracheal potential difference (-42.0 +/- 6.4 mV) to zero. It increased arterial and venous flows (56.7 +/- 6.1 and 57.3 +/- 10.0%, respectively; n = 5, P < 0.01, paired t-test) but not tracheal lymph flow (unstimulated flow 5.0 +/- 1.2 microliters.min-1.cm-1, n = 4). During H2O2 exposure, permeability to 99mTc-DTPA increased from -2.6 to -89.7 x 10(-7) cm/s (n = 5, P < 0.05), whereas permeability to [14C]AP (-3,312.6 x 10(-7) cm/s, n = 4) was not altered significantly (-2,565 x 10(-7) cm/s). Luminal capsaicin (10 microM) increased tracheal blood flow (10.1 +/- 4.1%, n = 5) and decreased venous 99mTc-DTPA concentration (-19.7 +/- 4.0, P < 0.01), and these effects were significantly greater after epithelial damage (28.1 +/- 6.0 and -45.7 +/- 4.3%, respectively, P < 0.05, unpaired t-test). Thus H2O2 increases the penetration of a hydrophilic tracer into tracheal blood and lymph but has less effect on a lipophilic tracer. It also enhances the effects of luminal capsaicin on blood flow and tracer uptake.
Using multi time-scale electro-thermal simulation approach to evaluate SiC-MOSFET power converter in virtual prototyping design tool

Using virtual prototyping (VP) design tool to evaluate power converter electro-thermal performance can help designers to validate prototype in a quick way. However, different system time-scale requires efficient electro-thermal simulation techniques. Thus, an approach by using average power losses of one switching cycle is presented in the paper to decouple electrical and thermal simulation so as to evaluate the influence of the parasitic inductance on device junction temperature quickly. This approach is validated by comparing with a method to obtain device junction temperature by using instantaneous power losses. By implementing it in the VP design tool, where a SiC-MOSFET behavioural model is developed and validated, it is shown the parasitic inductance influence on power converter electro-thermal waveforms. Thus, designers can evaluate power converter electro-thermal performance more quickly than other commercial software.