Miracle-dz/UniFAR-FTUs huggingface dataset:
Upc2p and Ecm22p, Dual Regulators of Sterol Biosynthesis in Saccharomyces cerevisiae

ABSTRACT Sterol levels affect the expression of many genes in yeast and humans. We found that the paralogous transcription factors Upc2p and Ecm22p of yeast were sterol regulatory element (SRE) binding proteins (SREBPs) responsible for regulating transcription of the sterol biosynthetic genes ERG2 and ERG3. We defined a 7-bp SRE common to these and other genes, including many genes involved in sterol biosynthesis. Upc2p and Ecm22p activatedERG2 expression by binding directly to this element in the ERG2 promoter. Upc2p and Ecm22p may thereby coordinately regulate genes involved in sterol homeostasis in yeast. Ecm22p and Upc2p are members of the fungus-specific Zn[2]-Cys[6] binuclear cluster family of transcription factors and share no homology to the analogous proteins, SREBPs, that are responsible for transcriptional regulation by sterols in humans. These results suggest that Saccharomyces cerevisiae and human cells regulate sterol synthesis by different mechanisms.
Obtaining New Biopolymer Materials by Electrospinning

The paper covers aspects of the technology of fibre electrospinning for the production of nonwoven fabrics for various application areas. The conditions of forming nanoand microfibres from solutions of collagen hydrolyzate and dibutyrylchitine were studied as well as polymer-polymer complexes based on polyacrylic acid, polyvinyl alcohol and polyethylene oxide. A comparative analysis of different methods of electrospinning – electrocapillary, electric and NanospiderTM, was conducted. Promising application areas of non-woven fabrics in medicine sanitation as well as for clothing and footwear production are shown.
Early Alpha/Beta Interferon Production by Myeloid Dendritic Cells in Response to UV-Inactivated Virus Requires Viral Entry and Interferon Regulatory Factor 3 but Not MyD88

ABSTRACT Alpha/beta interferons (IFN-α/β) are key mediators of innate immunity and important modulators of adaptive immunity. The mechanisms by which IFN-α/β are induced are becoming increasingly well understood. Recent studies showed that Toll-like receptors 7 and 8 expressed by plasmacytoid dendritic cells (pDCs) mediate the endosomal recognition of incoming viral RNA genomes, a process which requires myeloid differentiation factor 88 (MyD88). Here we investigate the requirements for virus-induced IFN-α/β production in cultures of bone marrow-derived murine myeloid DCs (mDCs). Using recombinant Semliki Forest virus blocked at different steps in the viral life cycle, we show that replication-defective virus induced IFN-α/β in mDCs while fusion-defective virus did not induce IFN-α/β. The response to replication-defective virus was largely intact in MyD88−/− mDC cultures but was severely reduced in mDC cultures from mice lacking IFN regulatory factor 3. Our observations suggest that mDCs respond to incoming virus via a pathway that differs from the fusion-independent, MyD88-mediated endosomal pathway described for the induction of IFN-α/β in pDCs. We propose that events during or downstream of viral fusion, but prior to replication, can activate IFN-α/β in mDCs. Thus, mDCs may contribute to the antiviral response activated by the immune system at early time points after infection.
More and More Coronaviruses: Human Coronavirus HKU1

After human coronaviruses OC43, 229E and NL63, human coronavirus HKU1 (HCoV-HKU1) is the fourth human coronavirus discovered. HCoV-HKU1 is a group 2a coronavirus that is still not cultivable. The G + C contents of HCoV-HKU1 genomes are 32%, the lowest among all known coronaviruses with complete genome sequences available. Among all coronaviruses, HCoV-HKU1 shows the most extreme codon usage bias, attributed most importantly to severe cytosine deamination. All HCoV-HKU1 genomes contain unique tandem copies of a 30-base acidic tandem repeat of unknown function at the N-terminus of nsp3 inside the acidic domain upstream of papain-like protease 1. Three genotypes, A, B and C, of HCoV-HKU1 and homologous recombination among their genomes, are observed. The incidence of HCoV-HKU1 infections is the highest in winter. Similar to other human coronaviruses, HCoV-HKU1 infections have been reported globally, with a median (range) incidence of 0.9 (0 – 4.4) %. HCoV-HKU1 is associated with both upper and lower respiratory tract infections that are mostly self-limiting. The most common method for diagnosing HCoV-HKU1 infection is RT-PCR or real-time RT-PCR using RNA extracted from respiratory tract samples such as nasopharyngeal aspirates (NPA). Both the pol and nucleocapsid genes have been used as the targets for amplification. Monoclonal antibodies have been generated for direct antigen detection in NPA. For antibody detection, Escherichia coli BL21 and baculovirus-expressed recombinant nucleocapsid of HCoV-HKU1 have been used for IgG and IgM detection in sera of patients and normal individuals, using Western blot and enzyme-linked immunoassay.
Histogram of gradient magnitudes: A rotation invariant texture-descriptor

We propose a new low-dimensional rotation invariant local texture-descriptor with a low computational complexity in this paper. Commonly used local texture features are sensitive to rotation of texture patterns in an image. On the other hand, rotation-invariant features are generally computationally expensive. The proposed feature descriptor is based on gradient of magnitude of pixel-intensities that is naturally rotation-neutral. Experiments with several datasets show better performance for the proposed texture-descriptor as compared to the existing texture-descriptors in image classification and segmentation tasks.
Geometric PCA of Images

We describe a method for analyzing the shape variability of images, called geometric PCA. Our approach is based on the use of deformation operators to model the geometric variability of images around a reference mean pattern. This leads to a new algorithm for estimating shape variability. Some numerical experiments on real images are proposed to highlight the benefits of this approach. The consistency of this procedure is also analyzed in statistical deformable models.
Comments on "Bayesian hierarchical error model for analysis of gene expression data"

Cho and Lee (2004) proposed a Bayesian hierarchical error model (HEM) to account for heterogeneous error variability in oligo-nucleotide microarray experiments. They estimated the parameters of their model using Markov Chain Monte Carlo (MCMC) and proposed an F-like summary statistic to identify differentially expressed genes under multiple conditions. Their HEM is one of the emerging Bayesian hierarchical modeling tools that have been developed for the analysis of multiple-level data structures and variation in microarray gene expression data (Broet et al., 2002; Tadesse and Ibrahim, 2004; Cho and Lee, 2004). In this letter, we first discuss the significance of the HEM developed by Cho and Lee. Then, we re-derive the fully conditional distributions for gene and conditional effects, since we think that these two fully conditional distributions were not presented properly in their paper. Finally, we expand the HEM to deal with biological or/and experimental correlations in gene expression data. A FORTRAN 90 program was developed to implement our extended method and it is available from the authors upon request.
Linking Sheet Music and Audio - Challenges and New Approaches

Score and audio files are the two most important ways to represent, convey, record, store, and experience music. While score describes a piece of music on an abstract level using symbols such as notes, keys, and measures, audio files allow for reproducing a specific acoustic realization of the piece. Each of these representations reflects different facets of music yielding insights into aspects ranging from structural elements (e.g., motives, themes, musical form) to specific performance aspects (e.g., artistic shaping, sound). Therefore, the simultaneous access to score and audio representations is of great importance. In this paper, we address the problem of automatically generating musically relevant linking structures between the various data sources that are available for a given piece of music. In particular, we discuss the task of sheet music-audio synchronization with the aim to link regions in images of scanned scores to musically corresponding sections in an audio recording of the same piece. Such linking structures form the basis for novel interfaces that allow users to access and explore multimodal sources of music within a single framework. As our main contributions, we give an overview of the state-of-the-art for this kind of synchronization task, we present some novel approaches, and indicate future research directions. In particular, we address problems that arise in the presence of structural differences and discuss challenges when applying optical music recognition to complex orchestral scores. Finally, potential applications of the synchronization results are presented.
Cooperative text and line-art extraction from a topographic map

The black layer is digitized from a USGS topographic map digitized at 1000 dpi. The connected components of this layer are analyzed and separated into line art, text, and icons in two passes. The paired street casings are converted to polylines by vectorization and associated with street labels from the character recognition phase. The accuracy of character recognition is shown to improve by taking account of the frequently occurring overlap of line art with street labels. The experiments show that complete vectorization of the black line-layer bitmap is the major remaining problem.
Inducing Immune Protection Against Trichomonas vaginalis: A Novel Vaccine Approach to Prevent HIV Transmission

Human immunodeficiency virus (HIV) infection is a pandemic that affects all parts of the globe. Current treatments fail to cure disease and for this reason there is significant interest in producing a vaccine to prevent HIV transmission, but clinical trials have proved disappointing. For this reason it is important to consider alternative measures to control incidence and prevalence of the disease. Trichomonas vaginalis is a highly prevalent and under-diagnosed sexually transmitted infection that facilitates transmission of and susceptibility to HIV infection (McClelland et al., 2007; Mavedzenge et al., 2010). Although current treatment is effective the disease is still poorly controlled and there are concerns about increasing levels of drug resistance (Upcroft & Upcroft, 2001). Efforts to research disease mechanisms and immune response with consideration to a rational vaccine design approach should be investigated as a potential method to reduce global incidence of T. vaginalis infection. A reliable murine model of T. vaginalis infection has been established with symptoms in female mice mimicking those seen in women (from vaginitis/vulvitis and discharge to asymptomatic but culture-positive for infection). Using this model it has been shown that vaccinating mice (by injection of trichomonad cells with adjuvant) protects the animals from subsequent vaginal infection (Abraham et al., 1996). By studying immune responses in mice, factors that are critical for immunological protection can be elucidated to create a “blueprint” for an effective human vaccine. Herein we provide an overview of the current understanding of T. vaginalis infection and epidemiology, methods of diagnosis and treatment, and implications of animal models for understanding disease mechanisms . We discuss how and why current T. vaginalis treatment protocols fail to control infection incidence with consideration as to how a T. vaginalis vaccine could overcome these obstacles and reduce disease burden. The association between T. vaginalis and HIV is examined and the potential for reducing HIV infection rates by lowering T. vaginalis incidence is elucidated. A vaccine against T. vaginalis would provide long term protection that could be more successful than treatment in controlling the spread of this very common disease. As T. vaginalis infection is a clear risk factor for HIV acquisition, it is our belief that this approach would also be effective in ameliorating HIV incidence and prevalence, especially in areas such as South and Southeast Asia and sub-Saharan Africa where HIV and T. vaginalis are endemic (United Nations, 2009; World Health Organization, 2001).
Progression of Carotid Stenosis Detected by Duplex Ultrasonography Predicts Adverse Outcomes in Cardiovascular High-Risk Patients

Background and Purpose— The progression of carotid stenosis reflects the activity of atherosclerotic disease and may indicate a risk for systemic atherothrombotic complications. We investigated whether progressive carotid stenosis determined by duplex ultrasonography predicts adverse outcomes in cardiovascular high-risk patients. Methods— We prospectively studied 1065 of 1268 consecutive patients initially asymptomatic with respect to carotid disease. Carotid ultrasound investigations at baseline and after a median of 7.5 months (range, 6 to 9 months) were performed to identify patients with progressive stenosis as defined by Doppler velocity criteria. Patients were then followed up clinically for a median of 3.2 years for the occurrence of major adverse cardiovascular events (composite MACEs: myocardial infarction, percutaneous coronary or peripheral interventions, coronary or vascular surgery, amputation, stroke, and all-cause mortality). Results— We found progressive carotid stenosis in 93 patients (9%) by ultrasound and thereafter recorded 495 MACEs in 421 patients (40%) during clinical follow-up. Patients with progressive carotid stenosis had a significantly increased risk for cardiovascular events compared with patients with nonprogressive disease: adjusted hazard ratios and confidence intervals were 2.01 for composite MACEs (95% CI, 1.48 to 2.67, P<0.001), 2.38 for myocardial infarction (95% CI, 1.07 to 5.35, P=0.044), 1.59 for any coronary event (95% CI, 1.10 to 2.28, P=0.011), 2.00 for stroke (95% CI, 1.02 to 4.11, P=0.035), 2.42 for any peripheral vascular event (95% CI, 1.61 to 3.62, P<0.001), and 1.75 for cardiovascular death (95% CI, 1.03 to 2.97, P=0.039). Conclusion— Progression of carotid stenosis within a 6- to 9-month interval detected by duplex ultrasound predicts midterm clinical adverse events of atherosclerosis in high-risk patients affecting the coronary, cerebrovascular, and peripheral circulations.
Selecting manual regression test cases automatically using trace link recovery and change coverage

Regression tests ensure that existing functionality is not impaired by changes to an existing software system. However, executing complete test suites often takes much time. Therefore, a subset of tests has to be found that is sufficient to validate whether the system under test is still valid after it has been changed. This test case selection is especially important if regression tests are executed manually, since manual execution is time intensive and costly. To select manual test cases, many regression testing techniques exist that aim on achieving coverage of changed or even new code. Many of these techniques base on coverage data from prior test runs or logical properties such as annotated pre and post conditions in the source code. However, coverage information becomes outdated if a system is changed extensively. Also annotated logical properties are often not available in industrial software systems. We present an approach for test selection that is based on static analyses of the test suite and the system's source code. We combine trace link recovery using latent semantic indexing with the metric change coverage, which assesses the coverage of source code changes. The proposed approach works automatically without the need to execute tests beforehand or annotate source code. Furthermore, we present a first evaluation of the approach.
A fast fuzzy keyword spotting algorithm based on syllable confusion network

This paper presents a fast fuzzy search algorithm to extract keyword candidates from syllable confusion networks (SCNs) in Mandarin spontaneous speech. Since the recognition accuracy of spontaneous speech is quite poor, syllable confusion matrix (SCM) is applied to compensate for the recognition errors and to improve recall. For fast retrieval, an efficient vocabulary-independent index structure is designed, which selects individual arcs of syllable confusion network as indexing units. An inverted search algorithm that uses syllable confusion matrix to calculate relevance score and search in this index structure is proposed. In experiments performed on a telephone conversational task, the equal error rate (EER) was reduced by about 33% relative over the baseline where keywords are directly extracted from phoneme lattices. Additionally, it only took computer one or two seconds to search 100 keywords in one hour speech data.
Current approaches to enhance CNS delivery of drugs across the brain barriers

Although many agents have therapeutic potentials for central nervous system (CNS) diseases, few of these agents have been clinically used because of the brain barriers. As the protective barrier of the CNS, the blood–brain barrier and the blood–cerebrospinal fluid barrier maintain the brain microenvironment, neuronal activity, and proper functioning of the CNS. Different strategies for efficient CNS delivery have been studied. This article reviews the current approaches to open or facilitate penetration across these barriers for enhanced drug delivery to the CNS. These approaches are summarized into three broad categories: noninvasive, invasive, and miscellaneous techniques. The progresses made using these approaches are reviewed, and the associated mechanisms and problems are discussed.
Further Validation of the Self-Defeating Personality Scale

In a sample of 51 women and 35 men those who scored higher on the Self-defeating Personality Scale reported having “dropped out” of useful activities more often and scored as less assertive on the Assertiveness Self-report Inventory. Women were more likely than men to report having experienced at least one self-defeating relationship. Attempts to replicate gender differences reported earlier were partially successful. The results provide additional validation for the Self-defeating Personality Scale.
Investigation of the Surface Passivation of P+-Type Si Emitters by PECVD Silicon Carbide Films

The surface passivation of an industrial applicable (e.g. screen printing) 60 Omegasq/ p+ boron emitter on Cz n-type c-Si wafers by amorphous SiCx films is investigated. A partial optimization of the deposition conditions of the SiCx films was performed resulting in an improved passivation quality of the SiCx films which also serves as anti-reflection coating. Passivation quality is determined by measuring the injection level dependency of the effective minority carrier lifetime using the quasi-steady state photoconductance method. Combining the information form the boron diffusion profile measured by SIMS and injection level dependent lifetime curves it can be concluded that a boron depletion layer formed during in-situ drive-in and oxidation has a detrimental effect on the passivation quality. Changing the diffusion conditions to prepare an improved boron profile with a similar sheet resistance should result in a further improvement of the passivation quality. This could include a reduction or a removal of the boron depletion layer at the emitter surface
Spin fluctuations and heavy fermion behavior

A heuristic approach to the relation of spin fluctuations (SF) and the heavy fermion (HF) state will be presented. The appearance of SF in the eigenstates of the periodic Anderson model is discussed in terms of relevant length scales, something already known for the Kondo problem but this time presented in a slightly more general framework. It will be shown that a specific form of SF can produce a HF-like state. The magnetic ordering, its small magnetic moment (using a Stoner-like criterion), charge transfer, and the magnetic field effect will be discussed.
Comprehensive Analysis of Human Cells Motion under an Irrotational AC Electric Field in an Electro-Microfluidic Chip

AC electrokinetics is a versatile tool for contact-less manipulation or characterization of cells and has been widely used for separation based on genotype translation to electrical phenotypes. Cells responses to an AC electric field result in a complex combination of electrokinetic phenomena, mainly dielectrophoresis and electrohydrodynamic forces. Human cells behaviors to AC electrokinetics remain unclear over a large frequency spectrum as illustrated by the self-rotation effect observed recently. We here report and analyze human cells behaviors in different conditions of medium conductivity, electric field frequency and magnitude. We also observe the self-rotation of human cells, in the absence of a rotational electric field. Based on an analytical competitive model of electrokinetic forces, we propose an explanation of the cell self-rotation. These experimental results, coupled with our model, lead to the exploitation of the cell behaviors to measure the intrinsic dielectric properties of JURKAT, HEK and PC3 human cell lines.
CENPA a Genomic Marker for Centromere Activity and Human Diseases

Inheritance of genetic material requires that chromosomes segregate faithfully during cell division. Failure in this process can drive to aneuploidy phenomenon. Kinetochores are unique centromere macromolecular protein structures that attach chromosomes to the spindle for a proper movement and segregation. A unique type of nucleosomes of centromeric chromatin provides the base for kinetochore formation. A specific histone H3 variant, CENPA, replaces conventional histone H3 and together with centromere-specific-DNA-binding factors directs the assembly of active kinetochores. Recent studies on CENPA nucleosomal structure, epigenetic inheritance of centromeric chromatin and transcription of pericentric heterochromatin provide new clues to our understanding of centromere structure and function. This review highlights the role and dynamics of CENPA assembly into centromeres and the potential contribution of this kinetochore protein to autoimmune and cancer diseases in humans.
Three-dimensional localization of cochlear implant electrodes using epipolar stereophotogrammetry

Three-dimensional (3-D) localization of individual cochlear implant electrodes within the inner ear is of importance for modeling the electrical field of the cochlea, designing the electrode array, and programming the associated speech processor. A 3-D reconstruction method of cochlear implant electrodes is proposed to localize individual electrodes from two X-ray views in combination with the spiral computed tomography technique. By adapting epipolar geometry to the configuration of an X-ray imaging system, we estimate individual electrode locations in the least square sense without using a patient attachment required by an existing stereophotogrammetry technique. Furthermore, our method does not require any knowledge of the intrinsic and extrinsic parameters of the imaging system. The performance of our method is studied in numerical simulation and with patient data and is found to be sufficiently accurate for clinical use. The maximum root mean-square errors measured are 0.0445 and 0.214 mm for numerical simulation and patient data, respectively.