gebhart/patrepeval huggingface dataset:
SDA-based neural network approach to digit classification (2016)

Image classification and object recognition are important issues in machine learning. With the increased usage of the internet and smart-based applications, image classification has become more important in various social, financial, and domestic spheres. Deep learning algorithms have proven useful and powerful, having successfully classified many types of images, objects, etc. This paper uses a type of deep neural network, stacked denoising autoencoders (SDA), to classify the handwritten digits in the MNIST database. The method proposed transforms the images into the wavelet domain, for faster, more efficient processing, as compared to the spatial domain. Furthermore, the low frequency and high frequency components separately provide pertinent feature details learned by the SDA to correctly classify each digit. The fusion of the learned low and high frequency features, and processing the combined feature mapping results in an increased detection accuracy. Compared to traditional (spatial) SDA and other classification algorithms, experimental results of this method show an increase in speed, efficiency, and accuracy in image classification and object recognition.
Low-noise CEO stabilization of a femtosecond DPSSL using an optically-pumped SESAM as fast opto-optical modulator (2013)

We present the first CEO-stabilization by optical feedback to the SESAM. This method overcomes bandwidth limitations of the standard pump current control and enables a CEO-locked Er:Yb:glass DPSSL with ten times lower residual phase noise.
Activity of purine analogs against Leishmania donovani in vivo (1987)

The dose of orally administered 9-deazainosine calculated to suppress 50% of Leishmania donovani amastigotes in hamster livers was 19 mg/kg (body weight) per day; 96 to 99% of Leishmania organisms were eliminated from the liver and spleen of squirrel monkeys by 50 mg/kg per day. Because these activities were greater than that of the experimental clinical agent allopurinol and comparable to that of the classical agent parenteral pentavalent antimony, 9-deazainosine should be considered for clinical development for visceral leishmaniasis.
The Core Histone N Termini Function Independently of Linker Histones during Chromatin Condensation (2000)

The relationships between the core histone N termini and linker histones during chromatin assembly and salt-dependent chromatin condensation were investigated using defined chromatin model systems reconstituted from tandemly repeated 5 S rDNA, histone H5, and either native "intact" core histone octamers or "tailless" histone octamers lacking their N-terminal domains. Nuclease digestion and sedimentation studies indicate that H5 binding and the resulting constraint of entering and exiting nucleosomal DNA occur to the same extent in both tailless and intact chromatin arrays. However, despite possessing a normal chromatosomal structure, tailless chromatin arrays can neither condense into extensively folded structures nor cooperatively oligomerize in MgCl(2). Tailless nucleosomal arrays lacking linker histones also are unable to either fold extensively or oligomerize, demonstrating that the core histone N termini perform the same functions during salt-dependent condensation regardless of whether linker histones are components of the array. Our results further indicate that disruption of core histone N termini function in vitro allows a linker histone-containing chromatin fiber to exist in a decondensed state under conditions that normally would promote extensive fiber condensation. These findings have key implications for both the mechanism of chromatin condensation, and the regulation of genomic function by chromatin.
Disulfide-linked high molecular weight protein associated with human cataract. (1978)

A major high molecular weight disulfide-linked protein has been isolated from cataractous lenses. It is only present in the water-insoluble protein fractions. This species has not been found in normal lenses of comparable age. Upon reduction of this fraction, polypeptides having molecular weights of approximately 60,000, 43,000, and 20,000 as well as a noncharacterized heterogeneous species are released. Similar sized polypeptides have been found in various noncovalently linked aggregates in both normal and cataractous lenses. Examination of the disulfide-linked protein fraction indicates that approximately 70% of the sulfhydryl groups are in the oxidized state. Although little change in the sizes of the other major polypeptides in the water-insoluble fraction is observed upon reduction, these components were also found to contain an appreciable disulfide content. Such results indicate that the only major lens fraction containing disulfide-linked polypeptide is the high molecular weight species and that the disulfides present in the remaining fractions are either intrachain disulfides or link polypeptides to small peptides.
Sensitive quantification of messenger RNA with a real-time ligase chain reaction by using a ribonucleotide-modified DNA probe (2014)

A highly sensitive and specific assay is developed for quantification of messenger RNA with a real-time fluorescence ligase chain reaction by using a ribonucleotide-modified DNA probe.
<title>Automated interactive microscopy: measuring and manipulating the chemical and molecular dynamics of cells and tissues</title> (1996)

The Automated Interactive Microscope is a robotic light microscope workstation that combines high performance light microscopy and computing to explore the chemical and molecular dynamics of cells and tissues.
Introduction (2014)

Abstract The moments of Christ's life noticed in the Creeds—Christ was conceived, born, suffered, died, and buried—are regular stages along life's way. Thus, since Christ's life has been a subject of extended meditation within Christian life and thought, a particular conception of what it is to be human has been brought to imaginative realization within this tradition, explicitly or implicitly in contention with other accounts. If moral theology is to articulate the ethics of everyday life involved in its account of human being, a reconception of the tasks of moral theology will be required, and so too of its relations with moral philosophy and social anthropology. This chapter identifies some of the main themes and topics which will be important for this project.
Modeling and simulation of storage area networks (2002)

Storage area networks (SANs) are an emerging data communications platform which interconnects servers and storage devices (such as disks, disk arrays, and tape drives) to create a pool of storage that users can access directly. This networking approach reports benefits such as computer clustering, topological flexibility, fault tolerance, high availability, and remote management. In order to evaluate the performance of these systems it is necessary to have the adequate tools. Usually, performance evaluation may be based on analytical modeling or simulation. Each of them differs in their scope and applicability. However the simulation modeling technique offers more freedom, flexibility, and accuracy than the analytical methods. Thus, when evaluating the performance of SANs, simulation modeling should be used. In this paper the issues involved in the modeling and design of a very flexible and easy to use SAN simulator are presented. This tool is able to consider among others, both real-world I/O traces and synthetic I/O traffic, message packetization, faults in links and switches, virtual channels, different routing algorithms, etc. We describe its main internal organization, the basic modeling mechanisms the simulator is based on, the main input parameters and output performance variables. Also, the analysis of preliminary results using I/O traces is presented, showing that the storage network increases self-similarity of the traffic received by servers, latency variations are more important for control messages than for data messages, and links have a low utilization.
Alkyne–Carbene Chelate Complexes of Chromium: Arrested Intermediates in the Benzannulation Reaction and Precursors of Densely Functionalized Centrosymmetric Chrysenes (1997)

Abstract Tetracarbonyl‐π 2 ‐alkyne–carbene chromium(0) complexes 3a–c stabilized by a rigid C 2 ‐arene unit bridging the alkyne and the carbene ligands were synthesized from their pentacarbonyl precursors 2a–c by low‐temperature photodecarbonylation. The chelates 3a–c are the first stable alkyne–carbene complexes containing a Group VIB metal carbonyl unit, and can be regarded as arrested intermediates in the chromium‐mediated benzannulation reaction. Comparative X‐ray and 13 C NMR studies indicate only weak coordination of the alkyne, both in the solid state and in solution. Decomposition of chelates 3a–c as well as the thermal decarbonylation of their pentacarbonyl precursors 2a–c results in dimerization of the alkynylcarbene ligands to give densely substituted oxygenated chrysene derivatives. A modification of the substitution pattern in the central chrysene rings results in a gradual distortion of the arene system across the central CC arene bond.
Integrin α2-Deficient Mice Develop Normally, Are Fertile, but Display Partially Defective Platelet Interaction with Collagen (2002)

The integrin alpha(2)-subunit was ablated in mice by targeted deletion of the ITGA2 gene. alpha(2)-Deficient animals develop normally, are fertile, and reproduce. Surprisingly, no obvious anatomical or histological differences were observed in mutant mice. Besides its significance in tissue morphogenesis, integrin alpha(2)beta(1) has been reported to play a major role in hemostasis by mediating platelet adhesion and activation on subendothelial collagen. To define its role in hemostasis, alpha(2)-deficient platelets were analyzed for their capacity to adhere to and aggregate in response to fibrillar or soluble collagen type I. We show that aggregation of alpha(2)-deficient platelets to fibrillar collagen is delayed but not reduced, whereas aggregation to enzymatically digested soluble collagen is abolished. Furthermore, alpha(2)-deficient platelets normally adhere to fibrillar collagen. However, in the presence of an antibody against GPVI (activating platelet collagen receptor), adhesion of alpha(2)-deficient but not wild type platelets is abrogated. These results demonstrate that integrin alpha(2)beta(1) significantly contributes to platelet adhesion to (fibrillar) collagen, which is further confirmed by the abolished adhesion of alpha(2)-deficient platelets to soluble collagen. Thus, alpha(2)beta(1) plays a supportive rather than an essential role in platelet-collagen interactions. These results are in agreement with the observation that alpha(2)beta(1)-deficient animals suffer no bleeding anomalies.
Epigallocatechin-3-gallate (EGCG) Alters Histone Acetylation and Methylation and Impacts Chromatin Architecture Profile in Human Endothelial Cells (2020)

Epigallocatechin gallate (EGCG), the main green tea polyphenol, exerts a wide variety of biological actions. Epigenetically, the catechin has been classified as a DNMTs inhibitor, however, its impact on histone modifications and chromatin structure is still poorly understood. The purpose of this study was to find the impact of EGCG on the histone posttranslational modifications machinery and chromatin remodeling in human endothelial cells of both microvascular (HMEC-1) and vein (HUVECs) origin. We analyzed the methylation and acetylation status of histones (Western blotting), as well as assessed the activity (fluorometric assay kit) and gene expression (qPCR) of the enzymes playing a prominent role in shaping the human epigenome. The performed analyses showed that EGCG increases histone acetylation (H3K9/14ac, H3ac), and methylation of both active (H3K4me3) and repressive (H3K9me3) chromatin marks. We also found that the catechin acts as an HDAC inhibitor in cellular and cell-free models. Additionally, we observed that EGCG affects chromatin architecture by reducing the expression of heterochromatin binding proteins: HP1α, HP1γ. Our results indicate that EGCG promotes chromatin relaxation in human endothelial cells and presents a broad epigenetic potential affecting expression and activity of epigenome modulators including HDAC5 and 7, p300, CREBP, LSD1 or KMT2A.
Self-recalibration of the camera pose via homography (2010)

In this paper, we propose a robust method to calculating camera pose via homography. We assuming the intrinsic parameters of the camera are known from initial calibration, and then we show that its camera pose parameters, in terms of translation vector and rotation matrix, can be determined from Homographic matrix. Our method is able to dynamic calibrating of the camera pose and arbitrary motion is allowed for the system. Results show robustness of the proposed method to be improved over those of the standard method.
A procedure for generation of three-dimensional half-toned computer graphics presentations (1970)

A description is given of an algorithm for producing computer generated half-tone presentations of three-dimensional polygonal surface structures. This algorithm achieves a significant increase in speed of computation over the Warnock algorithm developed at the University of Utah and implemented also on ~he Coordinated Science Laboratory CDC 1604 computer system at the University of Illinois. The history leading to the dg0rithm development and then the algorithm itself are described. Results are presented and are compared with computer runs achieved by the Warnock approach. An extension d the procedure to variable position illumination sources is also given.
Expression and polarized targeting of a rab3 isoform in epithelial cells. (1994)

Pathways of polarized membrane traffic in epithelial tissues serve a variety of functions, including the generation of epithelial polarity and the regulation of vectorial transport. We have identified a candidate regulator of polarized membrane traffic in epithelial cells (i.e., rab3B), which is a member of the rab family of membrane traffic regulators. Rab3B is highly homologous to a brain-specific rab3 isoform (rab3A) that targets in a polarized fashion to the presynaptic nerve terminal, where it probably regulates exocytosis. The coding region for human rab3B was cloned from epithelial mRNA using a reverse-transcription polymerase chain reaction strategy. This cDNA clone hybridized to a single mRNA species in Northern blots of poly(A)+ RNA isolated from epithelial cell lines. A rab3B-specific antibody that was raised against recombinant fusion protein recognized a 25-kD band in immunoblots of cell lysates prepared from cultured epithelial cells (e.g., T84 and HT29-CL19A), but not from a variety of nonepithelial cells (e.g., PC12 neuroendocrine cells). Immunofluorescence analysis confirmed that rab3B protein is preferentially expressed in cultured epithelial cells as well as in a number of native epithelial tissues, including liver, small intestine, colon, and distal nephron. Rab3B localized to the apical pole very near the tight junctions between adjacent epithelial cells within all of these cell lines and native epithelial tissues, as determined by immunofluorescence and immunoelectron microscopic analysis. Moreover, this pattern of intracellular targeting was regulated by cell contact; namely, rab3B was reversibly retrieved from the cell periphery as epithelial cell contact was inhibited by reducing the extracellular Ca2+ concentration. Our results indicate that neurons and epithelial cells express homologous rab3 isoforms that target in a polarized fashion within their respective tissues. The pattern and regulation of rab3B targeting in epithelial cells implicates this monomeric GTPase as a candidate regulator of apical and/or junctional protein traffic in epithelial tissues.
NIUST - Deepwater horizon oil spill response cruise (2010)

In May 2010, the National Institute for Undersea Science and Technology (NIUST) had a 17-day research cruise aboard the UNOLS vessel R/V Pelican scheduled. NIUST is a partnership of the University of Mississippi, the University of Southern Mississippi and NOAA. Before sailing, the Deepwater Horizon oil platform burned and sank, resulting in an uncontrolled oil spill at a depth of 5000 ft at Mississippi Canyon Block 252. Subsequently, the decision was made to abort the planned hydrate and ship wreck research in favor of an oil spill response. The primary goals of the redefined cruise were to acquire baseline and early impact data for seafloor sediments and subsurface distribution of oil and gas hydrates as close as possible in time and space to the origin of the oil spill. Investigating an oil spill nearly a mile deep in the ocean presents special benthic sampling and subsurface oil detection challenges. NIUST's AUV's were unloaded from the ship and a larger main winch installed to allow operation of a large box corer for collecting sediment samples in water depths up to 2000 m. During the first five-day leg of the cruise, a total of 28 box cores were collected. The Pelican returned to port (Cocodrie, LA) to drop off sediment and water samples for immediate analyses, and to take on more sampling gear and supplies for the second leg of the cruise, including an Acrobat, a CDOM fluorometer, a Video Ray ROV, and a C02 sensor in addition to the already installed CTD Rosette with 02 sensor and light transmissometer. During Leg 2, box core samples were collected until weather prohibited safe operations. CTD stations were plotted to cover the area surrounding the wreck site and at various depths to cover the water column in order to map the subsurface water column structure and chemistry as baseline values for future investigations and especially to look for submerged oil and/or gas hydrates. Early in the water column sampling, a subsurface feature was discovered at 1200 to 1400 m depth. This layer was detected by three independent sensors, CDOM (colored dissolved organic matter) fluorometer, light transmissometer, and oxygen sensor. All three instruments responded in unison with greater fluorescence and beam attenuation and decreased 02 concentration. These signals were first observed at a station 5 miles from the accident site. Second and third station measurements, exactly half the distance to the spill site from the previous one, at 2.5 miles, and at 1.25 miles, showed the same signal but with significantly greater magnitude. Following this discovery, the sampling plan for the remaining days of the cruise was changed to map the newly discovered feature. This paper will discuss methods, pursuit of leads, gear and instrumentation utilized, resulting in the initial discovery of deep hydrocarbon plume features resulting from the uniquely deep oil spill.
Masked Inverse Folding with Sequence Transfer for Protein Representation Learning (2022)

A bstract Self-supervised pretraining on protein sequences has led to state-of-the art performance on protein function and fitness prediction. However, sequence-only methods ignore the rich information contained in experimental and predicted protein structures. Meanwhile, inverse folding methods reconstruct a protein’s amino-acid sequence given its structure, but do not take advantage of sequences that do not have known structures. In this study, we train a masked inverse folding protein masked language model parameterized as a structured graph neural network. During pretraining, this model learns to reconstruct corrupted sequences conditioned on the backbone structure. We then show that using the outputs from a pretrained sequence-only protein masked language model as input to the inverse folding model further improves pretraining perplexity. We evaluate both of these models on downstream protein engineering tasks and analyze the effect of using information from experimental or predicted structures on performance.
Occurrence of blood cells and serum proteins in bovine fetuses and calves. (1971)

Hematological values of peripheral blood were determined for bovine fetuses and calves of various ages. Erythrocyte values increased through gestation. Fetuses 100 days or older had total values within the ranges of those reported for normal adult cattle. Mature erythrocytes were not observed in embryos and only a few were observed in fetuses 40 days of age. Fetuses 250 days or older had only a few rubricytes (<10/100 WBC). Leukocytes were first identified in the peripheral blood of a 45-day old fetus. Absolute leukocyte values increased through gestation and reached maximum values shortly before parturition. Granulocytes were first observed at 130 days of gestation and reached maximum values near parturition. Total serum protein and gamma-globulin concentrations of colostrum-deprived calves were similar to serum protein and gammaglobulin concentrations of fetuses older than 265 days and were lower than values for the colostrum-fed calves. The immunoelectrophoretic pattern of 59-day old fetuses, the earliest age at which serum samples were obtained, demonstrated albumin, an alpha1 globulin and a beta globulin, possibly transferrin. Additional alpha and beta globulins appeared in the older fetuses and by 175 days of gestation serum electophoretic patterns of the fetuses were similar to patterns normally found with adult bovine serum except for the absence of the gammaglobulins in fetal serum. Immunoglobulin M was detected in 39 of 95 fetal serum samples by radial diffusion and in 13 of 95 samples by immunoelectrophoresis. Immunoglobulin G was detected in ten of 95 fetal serum samples by radial diffusion and in six of 95 samples by immunoelectrophoresis.
Innovative combustion analysis of a micro-gas turbine burner supplied with hydrogen-natural gas mixtures (2017)

The author discusses in this paper the potential of a micro gas turbine (MGT) combustor when operated under unconventional fuel supplied. The combustor of C30 gas turbine is a reverse flow annular combustor. The CFD analysis of the reacting flow is performed with the 3D ANSYS-FLUENT solver. Specific computational experiments refer to the use of hydrogen – natural gas mixtures in order to define the optimal conditions for pilot and main injections in terms of combustion stability and NOx production. The author's methodology relies on an advanced CFD approach that compares different schemes like eddy dissipation concept, together with the flamelet-PDF based approach coupled with an accurate study of the turbulent chemistry interaction. Extended kinetic mechanisms are also included in the combustion model. Some test cases are examined to make a comparison of combustion stability and efficiency and pollutant production with high hydrogen / natural gas ratios.