gebhart/patrepeval huggingface dataset:
Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool (2016)

In eukaryotic cells the genome is highly spatially organized. Functional relevance of higher order genome organization is implied by the fact that specific genes, and even whole chromosomes, alter spatial position in concert with functional changes within the nucleus, for example with modifications to chromatin or transcription. The exact molecular pathways that regulate spatial genome organization and the full implication to the cell of such an organization remain to be determined. However, there is a growing realization that the spatial organization of the genome can be used as a marker of disease. While global genome organization patterns remain largely conserved in disease, some genes and chromosomes occupy distinct nuclear positions in diseased cells compared to their normal counterparts, with the patterns of reorganization differing between diseases. Importantly, mapping the spatial positioning patterns of specific genomic loci can distinguish cancerous tissue from benign with high accuracy. Genome positioning is an attractive novel biomarker since additional quantitative biomarkers are urgently required in many cancer types. Current diagnostic techniques are often subjective and generally lack the ability to identify aggressive cancer from indolent, which can lead to over- or under-treatment of patients. Proof-of-principle for the use of genome positioning as a diagnostic tool has been provided based on small scale retrospective studies. Future large-scale studies are required to assess the feasibility of bringing spatial genome organization-based diagnostics to the clinical setting and to determine if the positioning patterns of specific loci can be useful biomarkers for cancer prognosis. Since spatial reorganization of the genome has been identified in multiple human diseases, it is likely that spatial genome positioning patterns as a diagnostic biomarker may be applied to many diseases.
An RGB color management concept based on an improved gamut mapping algorithm (2009)

In principal, color reproduction on specific devices can be divided into transformation of color coordinates and the adaptation of colors to a device, called gamut mapping. The well established ICC color management neglects the latter aspect. This paper presents a practical implementation addressing both an eficient color transformation and a sophisticated gamut mapping.
The Role of Focal Adhesion Kinase-Phosphatidylinositol 3-Kinase-Akt Signaling in Hepatic Stellate Cell Proliferation and Type I Collagen Expression (2003)

Following a fibrogenic stimulus, the hepatic stellate cell (HSC) undergoes a complex activation process associated with increased cell proliferation and excess deposition of type I collagen. The focal adhesion kinase (FAK)-phosphatidylinositol 3-kinase (PI3K)-Akt signaling pathway is activated by platelet-derived growth factor (PDGF) in several cell types. We investigated the role of the FAK-PI3K-Akt pathway in HSC activation. Inhibition of FAK activity blocked HSC migration, cell attachment, and PDGF-induced PI3K and Akt activation. Both serum- and PDGF-induced Akt phosphorylation was inhibited by LY294002, an inhibitor of PI3K. A constitutively active form of Akt stimulated HSC proliferation in serum-starved HSCs, whereas LY294002 and dominant-negative forms of Akt and FAK inhibited PDGF-induced proliferation. Transforming growth factor-beta, an inhibitor of HSC proliferation, did not block PDGF-induced Akt phosphorylation, suggesting that transforming growth factor-beta mediates its antiproliferative effect downstream of Akt. Expression of type I collagen protein and alpha1(I) collagen mRNA was increased by Akt activation and inhibited when PI3K activity was blocked. Therefore, FAK is important for HSC migration, cell attachment, and PDGF-induced cell proliferation. PI3K is positioned downstream of FAK. Signals for HSC proliferation are transduced through FAK, PI3K, and Akt. Finally, expression of type I collagen is regulated by the PI3K-Akt signaling pathway.
Visual bracketing for Web search result visualization (2004)

We introduce a novel visual bracketing method that provides detail-in-context views where the inner part contains the Focus bracketed by the context information at a lower semantic level. We demonstrate two designs for Web search result visualization that obviate the need to frequently select the next button for viewing multiple search results.
Broadband interference excision in spread spectrum communication systems via fractional Fourier transform (2002)

We demonstrate the use of the fractional Fourier transform (FRFT) in excising broadband, linear FM (chirp) type interferences in spread spectrum communication systems. This method is predicated on the fact that the FRFT perfectly localizes a linear FM signal as an impulse when the angle parameter of the transform matches the sweep rate (chirp rate) of the linear chirp signal. Therefore, a transform domain thresholding can often eliminate linear-FM type interferences without severely affecting the desired part of the received signal. Thus we propose a preprocessing of the received signal by an FRFT-based excision scheme prior to demodulation. The simulations demonstrate that this technique often improves the bit error performance of the receiver when compared to the case where there is no preprocessing.
Implementing integrated services of networked home appliances using service oriented architecture (2004)

This paper presents a method to implement integrated services of networked home electric appliances, which provide more convenient and comfortable living for home users. The conventional methods generally employ a home server to achieve the integrated services. The server controls all the networked appliances in a centralized manner. However, as the number of sophisticated appliances increases, the centralized server suffers from the concentration of load, as well as a decline in the reliability and interoperability. To cope with this problem, we adopt the service-oriented architecture (SOA) for the implementation of the integrated services. In the proposed framework, the appliances export own features as services, and autonomously execute the exported services one another. Thus, the appliances are loosely coupled via the exported services without any centralized home server, which enables more flexible, balanced and reliable integrated services. We first present a framework to design and implement the integrated services based on SOA, and then illustrate a prototype system developed with Web services. We also define three kinds of metrics (i.e., reliability, workload, and coupling), and conduct a comparative evaluation between the proposed and the previous systems.
High‐Temperature Mechanical Behavior of Fiber‐Reinforced Glass‐Ceramic‐Matrix Composites (1985)

Lithium aluminosilicate glass‐ceramic‐matrix composites reinforced with Sic fibers were tested at 900° and 1000°C in flexural and tensile configurations. The composites showed severe thermomechanical degradation when tested in oxidizing atmospheres. This degradation was found to depend on oxygen partial pressure. For P o 2 ≳10 3 Pa the composites failed in a brittle fashion; a single crack initiated and propagated through the matrix and fibers. At lower P o2 , multiple matrix cracking was observed, and the fibers bridged the matrix cracks.
Masking with narrow-band FM noise (1974)

Masked thresholds were measured for signal frequencies below, within, and above two 190-Hz noise bands centered arithmetically at 1125 Hz. One noise band was computer synthesized and had amplitude fluctuations characteristic of analog noise bands typically used in masking experiments. The other noise band, matched in spectrum and level to the synthesized noise band, was generated by a frequency modulation (FM) process. The resulting waveform was free of envelope fluctuations. Masked thresholds in the FM noise were 5–10 dB lower than in the synthetic noise in the flat portions of the spectra. Synthesized noise resulted in trapezoidal appearing audiograms. The FM noise audiogram tended to be unimodal. Results are discussed with reference to envelope detection hypotheses.
Discovery and Role of a Novel Eicosanoid Family in Breast Cancer (2007)

Abstract : There is strong evidence for the induction of the pro-inflammatory enzymes 5-lipoxygenase (5-LOX) and cyclooxygenase-2 (COX-2) in many types of cancer, including breast cancer. Upregula-tion of both enzymes is associated with promoting tumorigenesis and a negative prognosis of the disease. The 5-LOX (leukotriene) and COX-2 (prostaglandin) pathways have traditionally been viewed as independent biosynthetic routes to eicosanoid lipid hormones, yet recent enzy-mological analyses establish that the 5-LOX product, 5-HETE, is an excellent COX-2 substrate, forming a novel double endoperoxide product that has the potential to evolve into a novel family of biomediators. In this funding period we have used LC-MS to detect two cellular metabolites that were derived from the novel di-endoperoxide product. The metabolites are similar in molecular weight to the parent di-endoperoxide, and their formation is blocked by presence of the COX-2 inhibitor indomethacin. Detection of these products is a major step forward in establishing a potential novel eicosanoid-forming pathway resulting from the cross-over of the leukotriene and prostaglandin pathways in breast cancer.
<title>Realization of a vertical integration scheme for polymer waveguides by a novel stacking technology</title> (2001)

The rapid growth of communication continuously demands an increasing number of data transport channels. We present an approach towards a substantial growth of channel numbers within the integrated optical waveguide chip. This is accomplished by introducing a vertical integration scheme, which is implemented with stacked polymer waveguides. To meet the requirements of stacked optical waveguide devices concerning index distributions, cross-sections and alignment precision, a novel fabrication technology has been developed. During the stacking process several fundamental problems, e.g., index inhomogenities caused by diffusion effects and distortion of the desired waveguide structures with increasing stack height, have to be avoided. In addition, the non-linear index change of the polymer materials during polymerization has to be carefully considered to come to well defined index distributions, which are the same in all layers. A solution meeting these requirements is presented using standard processes like UV patterning in combination with thermal curing steps.
Blue Light Acts as a Double-Edged Sword in Regulating Sexual Development of Hypocrea jecorina (Trichoderma reesei) (2012)

The industrially important cellulolytic filamentous fungus Trichoderma reesei is the anamorph of the pantropical ascomycete Hypocrea jecorina. H. jecorina CBS999.97 strain undergoes a heterothallic reproductive cycle, and the mating yields fertilized perithecia imbedded in stromata. Asci in the perithecia contain 16 linearly arranged ascospores. Here, we investigated H. jecorina sexual development under different light regimes, and found that visible light was dispensable for sexual development (stroma formation and ascospore discharge). By contrast, constant illumination inhibited stroma formation, and an interruption of the darkness facilitated timely stroma formation in a 12 h/12 h light-dark photoperiod. The results of genetic analyses further revealed that H. jecorina blue-light photoreceptors (BLR1, BLR2) and the photoadaptation protein ENV1 were not essential for sexual development in general. BLR1, BLR2 and ENV1 are orthologues of the conserved Neurospora crassa WC-1, WC-2 and VVD, respectively. Moreover, BLR1 and BLR2 mediate both positive and negative light-dependent regulation on sexual development, whereas ENV1 is required for dampening the light-dependent inhibitory effect in response to changes in illumination. Comparative genome-wide microarray analysis demonstrated an overview of light-dependent gene expression versus sexual potency in CBS999.97 (MAT1-2) haploid cells. Constant illumination promotes abundant asexual conidiation and high levels of hpp1 transcripts. hpp1 encodes a h (hybrid)-type propheromone that exhibits features of both yeast a and a pheromone precursors. Deletion of hpp1 could rescue stroma formation but not ascospore generation under constant illumination. We inferred that the HPP1-dependent pheromone signaling system might directly prevent stroma formation or simply disallow the haploid cells to acquire sexual potency due to abundant asexual conidiation upon constant illumination.
Bcl-2 and Bcl-xL Inhibit CD95-mediated Apoptosis by Preventing Mitochondrial Release of Smac/DIABLO and Subsequent Inactivation of X-linked Inhibitor-of-Apoptosis Protein (2002)

Bcl-2 and Bcl-x(L) are reported to inhibit CD95-mediated apoptosis in "type II" but not in "type I" cells. In the present studies, we found that stimulation of CD95 receptors, with either agonistic antibody or CD95 ligand, resulted in the activation of caspase-8, which in turn processed caspase-3 between its large and small subunits. However, in contrast to control cells, those overexpressing either Bcl-2 or Bcl-x(L) displayed a distinctive pattern of caspase-3 processing. Indeed, the resulting p20/p12 caspase-3 was not active and did not undergo normal autocatalytic processing to form p17/p12 caspase-3, because it was bound to and inhibited by endogenous X-linked inhibitor-of-apoptosis protein (XIAP). Importantly, Bcl-2 and Bcl-x(L) inhibited the release of both cytochrome c and Smac from mitochondria. However, since Smac alone was sufficient to promote caspase-3 activity in vitro by inactivating XIAP, we proposed the existence of a death receptor-induced, Smac-dependent and apoptosome-independent pathway. This type II pathway was subsequently reconstituted in vitro using purified recombinant proteins at endogenous concentrations. Thus, mitochondria and associated Bcl-2 and Bcl-x(L) proteins may play a functional role in death receptor-induced apoptosis by modulating the release of Smac. Our data strongly suggest that the relative ratios of XIAP (and other inhibitor-of-apoptosis proteins) to active caspase-3 and Smac may dictate, in part, whether a cell exhibits a type I or type II phenotype.
Cryogenic current comparator bridge for quantum Hall resistance ratio measurements (2002)

A cryogenic current comparator (CCC) bridge for quantum Hall resistance ratio measurement has been constructed. Compared to previous CCC systems at the National Physical Laboratory, UK, the new system differs in two aspects. Firstly, it uses a type-II CCC, i.e. the ratio windings are on the outside and the detection winding is on the inside. This has the advantage that the CCC can be made very compact and fits into a standard storage Dewar. Secondly, the bridge electronics uses a digital servo and the SQUID feedback loop is disabled during current reversals. The overall relative measurement uncertainty of the system is of the order of 10−9.
Catalytic effect of metal oxides on the oxidation resistance in carbon nanotube–inorganic hybrids (2010)

Hybridising carbon nanotubes (CNTs) with metal oxide nanostructures creates a new class of multifunctional materials with greatly enhanced performances as photocatalysts, chemical sensors, and in fuel cells and batteries. The low resistance of CNT towards oxidation often limits their applicability. On the other hand, exactly this ability to degrade CNTs at low temperatures is beneficial when using them as sacrificial templates for the synthesis of inorganic nanotubes. In this work, we investigate the oxidation resistance of 20 new hybrids and reveal that the presence of metal oxides can both inhibit and catalyse the oxidation of CNTs. As a result, the oxidation temperatures range from nearly 800 °C with Al2O3 to values as low as 330 °C with PbO and Bi2O3. We further demonstrate that the catalytic activity of the metal oxides correlates directly with their reducibility, i.e. the ability to create oxygen vacancies, and propose a mechanistic model based on Mars and van Krevelen, which allows prediction of the chemical stability of a wide range of CNT–metal oxide hybrids.
Three-dimensional structure of dendritic spines and synapses in rat hippocampus (CA1) at postnatal day 15 and adult ages: implications for the maturation of synaptic physiology and long-term potentiation. (1992)

It has long been hypothesized that changes in dendritic spine structure may modify the physiological properties of synapses located on them. Due to their small size, large number, and highly variable shapes, standard light microscopy of Golgi impregnations and electron microscopy (EM) of single thin sections have not proved adequate to identify most spines in a sample or to quantify their structural dimensions and composition. Here we describe a new approach, the series sample, that was developed to classify by shape and subcellular composition all of the spines and synapses in a sample of neuropil by viewing them through serial EM sections. Spines in each class are then randomly selected for serial reconstruction and measurement in three dimensions. This approach was used to assess whether structural changes in hippocampal CA1 spines could contribute to the enhanced synaptic transmission and the greater endurance of long-term potentiation (LTP) that occur with maturation. Our results show a near doubling in the total density of synapses in the neuropil and along reconstructed dendrites between postnatal day 15 (PND 15) and adult ages. However, this doubling does not occur uniformly across all spine and synapse morphologies. Thin spines, mushroom spines containing perforated postsynaptic densities (PSDs) and spine apparatuses, and branched spines increase by about four-fold in density between PND 15 and adult ages. In contrast, stubby spines decrease by more than half and no change occurs in mushroom spines with macular PSDs or in dendritic shaft synapses. The stubby spines that remain are smaller in adults than at PND 15 and the mushroom spines are larger, while no change occurs in the three-dimensional structure of thin spines. Only a few spine necks at either age are constricted or long enough to attenuate charge transfer; therefore, the doubling in synapses should mediate the enhancement of synaptic transmission that occurs with maturation. In addition, LTP is not likely to be mediated by widening of spine necks at either age. However, the constricted spine necks could serve to concentrate specific molecules at activated synapses, thereby enhancing the specificity and endurance of LTP with maturation. These results demonstrate that the new series sample method combined with three-dimensional reconstruction reveals quantitative changes in the frequency and structure of spines and synapses that are not discernable by other methods and are likely to have dramatic effects on synaptic physiology and plasticity.
Prognostic significance of S100A4 expression in gallbladder cancer (2002)

The calcium-binding protein S100A4 has been characterized as a metastasis-inducing molecule, and regulates cell motility and invasiveness of cancer cells. In order to clarify the significance of the expression of S100A4 as a prognostic factor in gallbladder cancer, S100A4 expression in resected gallbladder cancers were examined using an immunohistochemical staining technique. The relationship between S100A4 expression and clinicopathological factors including prognosis were evaluated. Twenty-five of 60 cases (42%) demonstrated positive staining for S100A4. There was no statistically significant association between S100A4 and histological grade, T, N, M factor, presence of stone, or stage. Kaplan-Meier method showed the 5-year survival rate of the group staining positive for S100A4 (31.5%) to be statistically poorer than that of the group staining negative for S100A4 (78.2%). Also in T2 cases, the 5-year survival rate of the group staining positive for S100A4 (57.1%) was statistically poorer than that of the group staining negative for S100A4 (83.3%). On univariate analysis, positive staining for S100A4 was a significant prognostic factor, and the hazard ratio was 4.05. On multivariate analysis, positive staining for S100A4 is also a significant predictor of prognosis second to T factor. These results indicate that positive staining for S100A4 is useful in assessing the prognosis of patients with gallbladder cancer as well as TNM factors.
Alfresco—A Workbench for Comparative Genomic Sequence Analysis (2000)

Comparative analysis of genomic sequences provides a powerful tool for identifying regions of potential biologic function; by comparing corresponding regions of genomes from suitable species, protein coding or regulatory regions can be identified by their homology. This requires the use of several specific types of computational analysis tools. Many programs exist for these types of analysis; not many exist for overall view/control of the results, which is necessary for large-scale genomic sequence analysis. Using Java, we have developed a new visualization tool that allows effective comparative genome sequence analysis. The program handles a pair of sequences from putatively homologous regions in different species. Results from various different existing external analysis programs, such as database searching, gene prediction, repeat masking, and alignment programs, are visualized and used to find corresponding functional sequence domains in the two sequences. The user interacts with the program through a graphic display of the genome regions, in which an independently scrollable and zoomable symbolic representation of the sequences is shown. As an example, the analysis of two unannotated orthologous genomic sequences from human and mouse containing parts of the UTY locus is presented.
A web enabled secured system for attendance monitoring and real time location tracking using Biometric and Radio Frequency Identification (RFID) technology (2015)

Automated Information Systems has played a major role in the growth, advancement, and modernization of our daily work processes. The main purpose of this paper is to develop a safe and secure web based attendance monitoring system using Biometrics and Radio Frequency Identification (RFID) Technology based on multi-tier architecture, for both computers and smartphones. The system can maintain the attendance records of both students and teachers/staff members of an institution. The system can also detect the current location of the students, faculties, and other staff members anywhere within the domain of institution campus. With the help of android application one can receive live feeds of various campus activities, keep updated with the current topics in his/her enrolled courses as well as track his/her friends on a real time basis. An automated SMS service is facilitated in the system, which sends an SMS automatically to the parents in order to notify that their ward has successfully reached the college. Parents as well as student will be notified via e-mail, if the student is lagging behind in attendance. There is a functionality of automatic attendance performance graph in the system, which gives an idea of the student's consistency in attendance throughout the semester.