gebhart/patrepeval huggingface dataset:
Automated segmentation of retinal blood vessels in spectral domain optical coherence tomography scans (2012)

The correct segmentation of blood vessels in optical coherence tomography (OCT) images may be an important requirement for the analysis of intra-retinal layer thickness in human retinal diseases. We developed a shape model based procedure for the automatic segmentation of retinal blood vessels in spectral domain (SD)-OCT scans acquired with the Spectralis OCT system. The segmentation procedure is based on a statistical shape model that has been created through manual segmentation of vessels in a training phase. The actual segmentation procedure is performed after the approximate vessel position has been defined by a shadowgraph that assigns the lateral vessel positions. The active shape model method is subsequently used to segment blood vessel contours in axial direction. The automated segmentation results were validated against the manual segmentation of the same vessels by three expert readers. Manual and automated segmentations of 168 blood vessels from 34 B-scans were analyzed with respect to the deviations in the mean Euclidean distance and surface area. The mean Euclidean distance between the automatically and manually segmented contours (on average 4.0 pixels respectively 20 µm against all three experts) was within the range of the manually marked contours among the three readers (approximately 3.8 pixels respectively 18 µm for all experts). The area deviations between the automated and manual segmentation also lie within the range of the area deviations among the 3 clinical experts. Intra reader variability for the experts was between 0.9 and 0.94. We conclude that the automated segmentation approach is able to segment blood vessels with comparable accuracy as expert readers and will provide a useful tool in vessel analysis of whole C-scans, and in particular in multicenter trials.
Characterization of GSK2334470, a novel and highly specific inhibitor of PDK1 (2010)

PDK1 (3-phosphoinositide-dependent protein kinase 1) activates a group of protein kinases belonging to the AGC [PKA (protein kinase A)/PKG (protein kinase G)/PKC (protein kinase C)]-kinase family that play important roles in mediating diverse biological processes. Many cancer-driving mutations induce activation of PDK1 targets including Akt, S6K (p70 ribosomal S6 kinase) and SGK (serum- and glucocorticoid-induced protein kinase). In the present paper, we describe the small molecule GSK2334470, which inhibits PDK1 with an IC₅₀ of ~10 nM, but does not suppress the activity of 93 other protein kinases including 13 AGC-kinases most related to PDK1 at 500-fold higher concentrations. Addition of GSK2334470 to HEK (human embryonic kidney)-293, U87 or MEF (mouse embryonic fibroblast) cells ablated T-loop residue phosphorylation and activation of SGK isoforms and S6K1 induced by serum or IGF1 (insulin-like growth factor 1). GSK2334470 also inhibited T-loop phosphorylation and activation of Akt, but was more efficient at inhibiting Akt in response to stimuli such as serum that activated the PI3K (phosphoinositide 3-kinase) pathway weakly. GSK2334470 inhibited activation of an Akt1 mutant lacking the PH domain (pleckstrin homology domain) more potently than full-length Akt1, suggesting that GSK2334470 is more effective at inhibiting PDK1 substrates that are activated in the cytosol rather than at the plasma membrane. Consistent with this, GSK2334470 inhibited Akt activation in knock-in embryonic stem cells expressing a mutant of PDK1 that is unable to interact with phosphoinositides more potently than in wild-type cells. GSK2334470 also suppressed T-loop phosphorylation and activation of RSK2 (p90 ribosomal S6 kinase 2), another PDK1 target activated by the ERK (extracellular-signal-regulated kinase) pathway. However, prolonged treatment of cells with inhibitor was required to observe inhibition of RSK2, indicating that PDK1 substrates possess distinct T-loop dephosphorylation kinetics. Our data define how PDK1 inhibitors affect AGC signalling pathways and suggest that GSK2334470 will be a useful tool for delineating the roles of PDK1 in biological processes.
True Three-Dimensional Animation In Motion Pictures (1987)

The VISIDEP (TM) method of three-dimensional display has been applied to object and cel animation by the author. The VISIDEP method differs from other three-dimensional imaging techniqu1s in that it gives parallax information without requiring viewers to wear special glasses. The illusion of movement created by the various forms of animation has been used in motion pictures since the late 1800s. Based on persistence of vision, animation requires artwork replacement at a rate of 12 to 24 changes per second. Through the use of perspective and shading animators have been able to add a three-dimensional "look" to their films. This two-dimensional depth is "read" py the viewer through a learned process based on their cultural and sociological background. Until recently a true three-dimensional "look" could be achieved only through stereo-scopic filming. Most of the systems available require special projection and viewing optics. The subject matter is usually live-action. Only one3 animated feature film, "Star-chaser" (TM), has been produced using a stereoscopic process.
Aligning biological sequences and structures (2004)

The end of last century witnessed the booming of bioinformatics. Bioinformatics is now becoming one of the most active research fields. One of the major problems facing bioinformatians is how to align two or more biological sequences. The question of multiple sequence alignment has been studied for a long time, may algorithms have been proposed. One solution is to reduce the multiple sequence alignment to the problem of aligning two alignments. Whether the latter question is NP-complete or not is an open problem. In this thesis, we will prove that it is NP-complete, thus this open problem is solved. In addition, we will propose a fast approximation algorithm to solve the problem of aligning two alignments question. 
Aligning two RNA sequences could reveal the relatedness of them. However, during long time of revolution, the RNA sequences may have changed greatly, yet their structures may preserve the same shape. Thus aligning two RNA structures may exhibit more accurate relationship. Traditionally, an RNA secondary structure is modeled as a tree which is not suitable to align multiple RNA structures. In this thesis, we will propose a new model to align RNA structures which can also be applied to align RNA tertiary structures. We will also propose a series of algorithms to align pairwise RNA structures and multiple RNA structures which are based upon the new model.
The genetics of the Rhesus blood group system. (2007)

The Rhesus factor is clinically the most important protein-based blood group system. With 49 antigens so far described, it is the largest of all 29 blood group systems. The unusually large number of Rhesus antigens is attributable to its complex genetic basis. The antigens are located on two Rhesus proteins - RhD and RhCE - and are produced by differences in their protein sequences. In CD nomenclature, they are termed CD240D and CD240CE. Unlike proteins of other blood groups, Rhesus proteins are expressed only in the membranes of red blood cells and their immediate precursors1.

Rhesus is second in its clinical importance only to the ABO blood group. Since the introduction of postpartum anti-D prophylaxis in the late 1960s, and combined pre-and postpartum anti-D prophylaxis in the early 1990s, the incidence of haemolytic disease in newborns due to alloimmunization has been reduced by more than 90%. Up to 1% of all pregnant women have clinically significant anti-erythrocyte antibodies2,3.

Anti-D remains the main indication for phototherapy or exchange transfusions in newborns2,4, and pregnant women who are D negative show an above average incidence.

The five most important Rhesus antigens are the cause of most alloimmunizations following blood transfusion. According to the German haemotherapy guidelines [Richtlinien zur Gewinnung von Blut und Blutbestandteilen und zur Anwendung von Blutprodukten]5, D negative transfusion recipients must always be given D negative erythrocyte products.

Since 2000, women of reproductive age and girls have also received transfusions compatible for further Rhesus antigens such as C, c, E and e in addition to the K antigen of the Kell blood group5.

This procedure also applies to patients who receive regular transfusions or have immunohaematological problems, like anti-erythrocyte allo- and autoantibodies. In the case of autoantibodies, their exact specificity is not usually determined. Although one thirds of such autoantibodies are directed at Rhesus proteins, this has virtually no practical consequences for treatment1.

The D antigen, discovered in 1939, was the first Rhesus antigen to be described. D positive patients were termed Rhesus-positive. In 1946, a quantitative variant with a weakly expressed D antigen was discovered and termed “Du”. This variant, now called “weak D”, is of clinical and diagnostic importance.

Since 1953, is has been clear that there are also qualitative variants of the D antigen. Although patients with this partial D variant are positive for the D antigen, they can also form anti-D.
Securin induces genetic instability in colorectal cancer by inhibiting double-stranded DNA repair activity (2006)

Genetic instability (GI) is a hallmark feature of tumor development. Securin, also known as pituitary tumor transforming gene (PTTG), is a mitotic checkpoint protein which is highly expressed in numerous cancers, is associated with tumor invasiveness, and induces GI in thyroid cells. We used fluorescence inter-simple sequence repeat PCR to assess GI caused primarily by DNA breakage events in 19 colorectal tumors. GI values ranged significantly, with Dukes' stage C&D colorectal tumors exhibiting greater GI and higher securin expression than Dukes' stage A&B tumors. Consistent with these findings, we observed a dose-dependent increase in GI in HCT116 cells in response to securin overexpression, as well as in non-transformed human fibroblasts. As securin has been implicated in a novel DNA repair pathway in fission yeast, we investigated its potential role in chemotoxic DNA damage response pathways in mammalian cells, using host cell reactivation assays. Securin overexpression in HCT116 cells inhibited etoposide-induced double-stranded DNA damage repair activity, and repressed Ku heterodimer function. Additionally, we observed that securin and Ku70 showed a reciprocal cytosol-nuclear translocation in response to etoposide-induced dsDNA damage. Our data suggest that, by repressing Ku70 activity and inhibiting the non-homologous end-joining dsDNA repair pathway, securin may be a critical gene in the development of GI in colorectal cancer.
Pairwise Association of Seismic Arrivals with Convolutional Neural Networks (2019)

Correctly determining the association of seismic phases across a network is crucial for developing accurate earthquake catalogs. Nearly all established methods use travel time information as the main criterion for determining associations, and in problems in which earthquake rates are high and many false arrivals are present, many standard techniques may fail to resolve the problem accurately. As an alternative approach, in this work we apply convolutional neural networks (CNNs) to the problem of associations; we train CNNs to read earthquake waveform arrival pairs between two stations and predict the binary classification of whether the two waveforms are from a common source or different sources. Applying the method to a large training dataset of previously cataloged earthquakes in Chile, we obtain >80% true positive prediction rates for high-frequency data (>2 Hz) and stations separated in excess of 100 km. As a secondary benefit, the output of the neural network can also be used to infer predicted phase types of arrivals. Here, the method is ideally applied in conjunction with standard travel-time-based association routines and can be adapted for arbitrary network geometries and applications, so long as sufficient training data are available.
Concise Review: A Chemical Approach to Control Cell Fate and Function (2011)

Stem cells are essential for maintaining tissue homeostasis and mediating physiological and pathological regeneration. Recent breakthroughs in stem cell biology have generated tremendous enthusiasm and hope for the therapeutic potential of stem cells in regenerative medicine. However, this research is still in an early development stage. An improved understanding of stem cell biology is required to precisely manipulate stem cell fate and to harness these cells for regenerative medicine. Small molecules, targeting specific signaling pathways and mechanisms, are powerful tools for manipulating stem cells for desired outcomes. Those small molecules are increasingly important in probing the fundamental mechanisms of stem cell biology and facilitating the development of therapeutic approaches for regenerative medicine. These could involve cell replacement therapies with homogenous functional cells produced under chemically defined conditions in vitro and the development of small-molecule drugs that modulate patient's endogenous cells for therapeutic benefit.
A 90ns 1Mb DRAM with multi-bit test mode (1985)

A 1Mb DRAM using a half Vcc biased memory cell with a reduced electric field of 2MV/cm will be reported. A shared sense amplifier design and a continous nibble mode are also included. Additionally, a test pin allows testing as a 256K×4 memory. Die is 65mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
STDs in injecting drug users. (1992)

incidence of unwanted pregnancy should not social, medical and economic benefits.
Photogrammetry and Conventional Impressions for Recording Implant Positions: A Comparative Laboratory Study (2005)

Photogrammetry is a valid option for recording implant positions and has a precision comparable to that of conventional impression techniques. At present, however, it is limited to framework fabrication techniques that are based on digital platforms.
The kinetics and mechanism of the oxidation of amines and alcohols at oxide-covered nickel, silver, copper, and cobalt electrodes (1972)

A series of alcohols and amines have been oxidised at oxide-covered nickel, silver, copper, and cobalt anodes in aqueous alkaline solutions. The kinetics of these electrode processes have been studied and it is shown that the mechanism of these oxidations involves hydrogen abstraction from the substrate by an oxide species rather than direct electron transfer to the anode. The mechanism put forward is compared with those commonly suggested for the chemical reactions of transition-metal oxides and for heterogeneous catalysis.
Image evaluation of the high resolution VUV spectrometer at SURF II by ray tracing (1998)

A high resolution VUV spectroscopic facility has been in use for several years at SURF II, the Synchrotron Ultraviolet Radiation Facility at the National Institute of Standards and Technology in Gaithersburg, Maryland. At this facility, a combination of three cylindrical mirrors is utilized to focus the light originating in the storage ring onto the horizontal entrance slit of the spectrometer. The spectrometer uses a 6.65 m concave grating having a groove density of 4800 lines/mm in the off-plane Eagle mounting. In preparation for the installation of an array detector in the exit image plane, a ray tracing program has been formulated and spot diagrams have been constructed by plotting the coordinates of the points of intersection of the diffracted rays with the image plane, which is tangent to the Rowland circle. In creating the spot diagrams, we have considered both parallel and tilted configurations of the entrance slit with respect to the grating grooves. It is shown that the line widths of the spectral images can be reduced when the entrance slit is properly tilted. Finally, we have estimated the spectral widths of the images when they are recorded on an array detector placed tangent to the Rowland circle. We conclude that an image spectral width of 0.41 pm to 0.88 pm in first order can be achieved over the wavelength region of 40 nm to 120 nm.
Asymmetric Transfer Hydrogenation of α, β-Acetylenic Ketones (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAsymmetric Transfer Hydrogenation of α, β-Acetylenic KetonesKazuhiko Matsumura, Shohei Hashiguchi, Takao Ikariya, and Ryoji NoyoriView Author Information ERATO Molecular Catalysis Project Japan Science and Technology Corporation 1247 Yachigusa, Yakusa-cho, Toyota 470-03, Japan Cite this: J. Am. Chem. Soc. 1997, 119, 37, 8738–8739Publication Date (Web):September 17, 1997Publication History Received15 May 1997Published online17 September 1997Published inissue 1 September 1997https://pubs.acs.org/doi/10.1021/ja971570ahttps://doi.org/10.1021/ja971570arapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views11133Altmetric-Citations633LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Catalysts,Ketones,Redox reactions,Transfer reactions Get e-Alerts
Analysis of the kinase-related protein gene found at human chromosome 3q21 in a multi-gene cluster: Organization, expression, alternative splicing, and polymorphic marker (1999)

We report the amino acid sequence, genomic organization, tissue expression, and alternative splice patterns for the human kinase related protein (KRP) gene, as well as the discovery of a new CA repeat sequence polymorphic marker in an upstream intron of the myosin light chain kinase (MLCK) gene. The KRP/MLCK genetic locus is a prototype for a recently discovered paradigm in which an independently regulated gene for a non-enzymic protein is embedded within a larger gene for a signal transduction enzyme, and both classes of proteins are involved in the regulation of the same cellular structure. The MLCK/KRP gene cluster has been found only in higher vertebrates and is localized to human chromosome 3q21. The determination of the human KRP amino acid sequence through cDNA sequence analysis and its comparison to the exon/intron organization of the human KRP gene revealed an alternative splice pattern at the start of KRP exon 2, resulting in the insertion of a single glutamic acid in the middle of the protein. Examination of tissue distribution using Northern blot analysis revealed that the human expression pattern is more similar to the well-characterized chicken KRP gene expression pattern than to rodent or rabbit. Unexpected differences of the human gene from other species is the apparent expression of the human gene products in adult cardiac muscle, an observation that was pursued further by the production of a site-directed antiserum and immunohistochemistry analysis. The results reported here provide insight into the conserved and variable features of this late evolving genetic paradigm, raise new questions about the molecular aspects of cardiac muscle regulation, and provide tools needed for future clinical studies. The comparative analysis of the MLCK/KRP locus, combined with the recent discovery of a similar genomic relationship among other signal transduction proteins, suggest a diverse distribution of this theme among signal transduction systems in higher vertebrate genomes and indicate the utility of comparative genomics in revealing late evolving genetic paradigms.
X‐ray Absorption Spectroscopy of Bimetallic Pt–Re Catalysts for Hydrogenolysis of Glycerol to Propanediols (2010)

Abstract Bimetallic Pt–Re nanoparticles supported on Norit carbon were effective at converting aqueous glycerol to 1,3 (34 %) and 1,2 (33 %) propanediol at 443 K under 4 MPa of H 2 . Results from X‐ray absorption spectroscopy and analytical transmission electron microscopy confirmed that the nanoparticles were indeed bimetallic, with a particle size less than 2 nm in diameter. The Pt L III near edge spectra indicated that the Pt was reduced to the metallic state by treatment in H 2 at 473 K, but that a partial positive charge remained on the Re. These oxidized Re species could be associated with charged Re atoms dispersed on the carbon support because spillover of H atoms from Pt was required to reduce Re in the bimetallic particles.
BEAMS: Battery Exhaustion Anomaly Monitoring System model in SENSORNET (2012)

Wireless Sensor Network (SENSORNET) is vulnerable to various security threats due to its deployment in open and hostile environment. Fast battery exhaustion of sensor nodes in SENSORNET is a challenging issue because it shortens the normal lifetime of sensor network. Affected nodes give rise to denial of service that resists to get the objective of SENSORNET in real life. In this paper, Battery Exhaustion Anomaly Monitoring System (BEAMS) model based on Absorbing Markov Chain (AMC) is proposed to detect battery exhaustion attack in SENSORNET. A mathematical model is considered to analyze whether SENSORNET is affected by battery exhaustion attack.
Respiratory Syncytial Virus Infection of Alveolar Macrophages in Adult Transplant Patients (1992)

Pulmonary epithelial cells are thought to be the primary cellular targets for infection by respiratory syncytial virus (RSV) in vivo. To determine whether other pulmonary cells are infected by RSV, bronchoalveolar lavage cells from six adult transplant patients, four of whom had acute RSV infection, were examined by in situ immunohistochemistry to identify infected lung cells. Both alveolar macrophages and epithelial cells were infected with RSV in vivo. At the single-cell level, three-color immunofluorescent studies revealed that both RSV-infected epithelial cells and alveolar macrophages expressed Class II molecules of the major histocompatibility complex, but only the alveolar macrophage coexpressed interleukin-1 beta. Paraformaldehyde-fixed bronchoalveolar lavage cells from RSV-infected but not uninfected patients induced a marked proliferative response by cloned T cells indicating that in vivo infected cells expressed bioactive interleukin-1. Together, these studies indicate that the alveolar macrophage may have a critical role in the lung immune response to RSV.
Environmental aspects of the combustion of sewage sludge in a utility boiler (1986)

Abstract This paper discusses the environmental aspects of the combustion of dewatered municipal sewage sludge in a utility boiler. The information presented is based on the results of laboratory scale combustion tests performed on both sludge/coal and sludge/oil mixtures. Air pollution control and solid waste disposal considerations are discussed.