gebhart/patrepeval huggingface dataset:
Proteins of human semen. I. Two-dimensional mapping of human seminal fluid. (1981)

The proteins in human seminal plasma were mapped by high-resolution two-dimensional electrophoresis (ISO-DALT and BASO-DALT systems). When analyzed under dissociating conditions, samples from normal fertile males revealed a pattern of over 200 proteins, ranging in mass from 10 000 to 100 000 daltons. Comparison of the mapped proteins from these males and those who had undergone vasectomy allowed us to identify one series of glycoproteins as missing from the semen from vasectomized individuals. Glycoproteins isolated by affinity chromatography with use of concanavalin A were also mapped. Some of the protein spots were identified either by co-electrophoresis with purified proteins or by the electrophoretic transfer of proteins to nitrocellulose sheets and subsequent detection by immunological procedures. The proteins identified include a number of serum proteins as well as prostatic acid phosphatase and creatine kinase. Proteolytic events shown to occur during the liquefaction of semen that occurs early after collection indicate the importance of carefully controlled collection and preparation methods for clinical evaluation of seminal plasma. Ethylenediaminetetraacetic acid and phenylmethylsulfonyl fluoride inhibit this proteolysis.
Codon catalog usage is a genome strategy modulated for gene expressivity (1981)

The nucleic acid sequence bank now contains 161 mRNAs, 43 new genes are added. One sequence, that of B. mori fibroin, is dropped due to uncertainty on the starting point for translation. Frequencies of all codons are given for each gene added and for each genome type in the total bank. A new series of correspondence analyses on codon use is presented, substantiating the genome hypothesis. Internal regulation of mRNA expression by different third base choices between quartet and duet codons is proposed for bacterial genes.
Olympia, Cairo and World Moral Leadership (2011)

At the Olympic Games in 380 BC, Isocrates gave to the Greek world the speech afterwards circulated as the Panegyricus. In 2009, on 4 June at Cairo University, Barack Obama gave a speech directed principally to the Muslim world. Both men spoke with passion and commitment regarding their vision for their respective societies. Ostensibly the disparity in historical era and context would seem to preclude any similarities between the two speeches, but on closer examination a number of common elements emerge, particularly in relation to both speakers' cultural programs, and their putative claims to moral leadership.
Catechol estrogen metabolites and conjugates in mammary tumors and hyperplastic tissue from estrogen receptor-alpha knock-out (ERKO)/Wnt-1 mice: implications for initiation of mammary tumors (2001)

A novel model of breast cancer was established by crossing mice carrying the Wnt-1 transgene (100% of adult females develop spontaneous mammary tumors) with the ERKO mouse line, in which mammary tumors develop despite a lack of functional estrogen receptor-alpha. To begin investigating whether metabolite-mediated genotoxicity of estrogens may play an important role in the initiation of mammary tumors, the pattern of estrogen metabolites and conjugates was examined in ERKO/Wnt-1 mice. Extracts of hyperplastic mammary tissue and mammary tumors were analyzed by HPLC with identification and quantification of compounds by multichannel electrochemical detection. Picomole amounts of the 4-catechol estrogens (CE) were detected, but their methoxy conjugates, as well as the 2-CE and their methoxy conjugates, were not. 4-CE conjugates with glutathione or its hydrolytic products (cysteine and N-acetylcysteine) were detected in picomole amounts in both tumors and hyperplastic mammary tissue, demonstrating the formation of CE-3,4-quinones. These preliminary findings show that the estrogen metabolite profile in the mammary tissue is unbalanced, in that the normally minor 4-CE metabolites were detected in the mammary tissue and not the normally predominant 2-CE. These results are consistent with the hypothesis that the mammary tumor development is primarily initiated by metabolism of estrogens to 4-CE and, then, to CE-3,4-quinones, which may react with DNA to induce oncogenic mutations.
Immortalization of Human Urethral Epithelial Cells: a Model for the Study of the Pathogenesis of and the Inflammatory Cytokine Response to Neisseria gonorrhoeae Infection (2002)

The primary human urethral epithelial cells developed by our laboratory have been immortalized by transduction with a retroviral vector expressing the human papillomavirus E6E7 oncogenes. Analysis of telomerase expression and comparison to that in primary cells revealed detectable levels in the transduced human urethral epithelial cells. Immortalized urethral cells could be passaged over 20 times. Immunofluorescence microscopy studies showed that the immortalized cells were phenotypically similar and responded to gonococcal infection similarly to primary cells. Specifically, positive cytokeratin staining showed that the immortalized cells are keratinocytes; cell surface levels of human asialoglycoprotein receptor increase following gonococcal infection, and, like the primary cells, the immortalized urethral epithelial cells are CD14 negative. Using enzyme-linked immunosorbent assay, we found that interleukin-6 (IL-6) and IL-8 levels in primary urethral epithelial cell supernatants increase after challenge with N. gonorrhoeae. Likewise, the immortalized urethral epithelial cells produced higher levels of IL-6 and IL-8 cytokines in response to gonococcal infection. Cells challenged with a gonococcal lipid A msbB mutant produced reduced IL-6 and IL-8 levels when compared to the parent strain. Additionally, these data suggest that the 1291 msbB lipooligosaccharide may suppress cytokine induction.
High Aspect Ratio Silicon Wire Array Photoelectrochemical Cells (2007)

In an effort to develop low-cost solar energy conversion techniques, high uniformity vertically oriented silicon wire arrays have been fabricated. These arrays, which allow for radial diffusion of minority charge carriers, have been measured in a photoelectrochemical cell. Large photovoltages (∼400 mV) have been measured, and these values are significantly greater than those obtained from the substrate alone. Additionally, the wire array samples displayed much higher current densities than the underlying substrate, demonstrating that significant energy conversion was occurring due to the absorption and charge-carrier transport in the vertically aligned Si wires. This method therefore represents a step toward the use of collection-limited semiconductor materials in a wire array format in macroscopic solar cell devices.
Preparation and Characterization of Overcoated II–VI Quantum Dots (2005)

A convenient route for the synthesis of high-quality overcoated II-VI quantum dots (QDs) is reported in this paper. Simple salts, such as Cd(Ac)2 and Zn(Ac)2 were used to replace organometallics, whose disadvantage is obvious. Size-tunable core/shell structured QDs (CdSe/ZnS, CdSe/CdS, etc.) were synthesized. They were of narrow size distribution and had good monodispersivity and photoluminescence (PL) properties. The spectrum was symmetrical and sharp-pointed (with the full width at half-maximum (fwhm) of about 20-30 nm). The quantum yield (QY) was improved to 60-80% from 20-30% for bare QDs and remained stable at least for 6 months. The primary overcoated QDs were modified with biomacromolecules by a direct mechanical rubbing strategy, which is very simple and fast. The results obtained by UV-vis, PL, atomic force microscopy (AFM), and fluorescence microscopy imaging showed that the modified QDs were of good fluorescent and monodisperse characteristics. They are likely to be used further for biological labels.
Three dimensional imaging with randomly distributed sensors (2008)

As a promising three dimensional passive imaging modality, Integral Imaging (II) has been investigated widely within the research community. In virtually all of such investigations, there is an implicit assumption that the collection of elemental images lie on a simple geometric surface (e.g. flat, concave, etc), also known as pickup surface. In this paper, we present a generalized framework for 3D II with arbitrary pickup surface geometry and randomly distributed sensor configuration. In particular, we will study the case of Synthetic Aperture Integral Imaging (SAII) with random location of cameras in space, while all cameras have parallel optical axes but different distances from the 3D scene. We assume that the sensors are randomly distributed in 3D volume of pick up space. For 3D reconstruction, a finite number of sensors with known coordinates are randomly selected from within this volume. The mathematical framework for 3D scene reconstruction is developed based on an affine transform representation of imaging under geometrical optics regime. We demonstrate the feasibility of the methods proposed here by experimental results. To the best of our knowledge, this is the first report on 3D imaging using randomly distributed sensors.
Immunization with Alpha-Toxin Toxoid Protects the Cornea against Tissue Damage during Experimental Staphylococcus aureus Keratitis (2000)

Alpha-toxin is a major virulence factor in Staphylococcus aureus keratitis. Active or passive immunization with alpha-toxin toxoid could protect against corneal damage. Results show that either form of immunization did not kill bacteria but did significantly protect against corneal pathology, especially epithelial erosion.
Preface to the Second Edition (2006)

I am pleased to have this opportunity to express my appreciation to the following students and colleagues who assisted me at various stages: My former students Hanley Chiang, Ryan Mutter, and Sita Slavov discovered some glitches in the first edition and brought them to my attention. My current students David Hansen, Jonathan Kuzma, and Emma Murray helped me fill in many of the boxes that connect the theory to contemporary events, and Matthew Draper did some preliminary spadework for Chapter 9. I am grateful for the superb diagrams produced by Carrie Clingan, a student in the Masters in Public Policy program at William and Mary. Jerry Kelly of the Syracuse University Economics Department made copious comments on early drafts of Chapter 7. I have benefited from the insightful comments of Ed Nelson of the Tulane Economics Department, John Weymark of the Vanderbilt Economics Department, and David Ellerman of the World Bank. My colleague and coauthor for two undergraduate texts, Alfredo Pereira, taught me how to write textbooks. I express my deep gratitude to these people. I assume responsibility for any errors in the book.
BlueBoX (2003)

Detecting attacks against systems has, in practice, largely been delegated to sensors, such as network intrustion detection systems. However, due to the inherent limitations of these systems and the increasing use of encryption in communication, intrusion detection and prevention have once again moved back to the host systems themselves. In this paper, we describe our experiences with building BlueBox, a host-based intrusion detection system. Our approach, based on the technique of system call introspection, can be viewed as creating an infrastructure for defining and enforcing very fine-grained process capabilities in the kernel. These capabilities are specified as a set of rules (policies) for regulating access to system resources on a per executable basis. The language for expressing the rules is intuitive and sufficiently expressive to effectively capture security boundaries.We have prototyped our approach on Linux operating system kernel and have built rule templates for popular daemons such as Apache and wu-ftpd. Our design has been validated by testing against a comprehensive database of known attacks. Our system has been designed to minimize the kernel changes and performance impact and thus can be ported easily to new kernels. We describe the motivation and rationale behind BlueBox, its design, implementation on Linux, and how it relates to prior work on detecting and preventing intrusions on host systems.
Automatic Outlining of Regions on CT Scans (1981)

A computer software system for automatic outlining of borders between regions of differing CT numbers on computed tomography scans has been developed. The technique was originally intended for application in defining inhomogeneities for radiation therapy treatment planning; however, several other applications are possible. The system scans an image using a simple threshold model to locate initial outline points and then completes the outline with a border-following algorithm. Results of the automatic outlining system are given along with histograms of the enclosed regions, demonstrating several further applications of these techniques.
Dropout Improves Recurrent Neural Networks for Handwriting Recognition (2014)

Recurrent neural networks (RNNs) with Long Short-Term memory cells currently hold the best known results in unconstrained handwriting recognition. We show that their performance can be greatly improved using dropout - a recently proposed regularization method for deep architectures. While previous works showed that dropout gave superior performance in the context of convolutional networks, it had never been applied to RNNs. In our approach, dropout is carefully used in the network so that it does not affect the recurrent connections, hence the power of RNNs in modeling sequences is preserved. Extensive experiments on a broad range of handwritten databases confirm the effectiveness of dropout on deep architectures even when the network mainly consists of recurrent and shared connections.
Cis-Selective Ring-Opening Metathesis Polymerization with Ruthenium Catalysts (2012)

Cis-selective ring-opening metathesis polymerization of several monocyclic alkenes as well as norbornene and oxanorbornene-type monomers using a C-H activated, ruthenium-based metathesis catalyst is reported. The cis content of the isolated polymers depended heavily on the monomer structure and temperature. A cis content as high as 96% could be obtained by lowering the temperature of the polymerization.
The small world inside large metabolic networks (2001)

The metabolic network of the catabolic, energy and biosynthetic metabolism of Escherichia coli is a paradigmatic case for the large genetic and metabolic networks that functional genomics efforts are beginning to elucidate. To analyse the structure of previously unknown networks involving hundreds or thousands of components by simple visual inspection is impossible, and quantitative approaches are needed to analyse them. We have undertaken a graph theoretical analysis of the E. coli metabolic network and find that this network is a small-world graph, a type of graph distinct from both regular and random networks and observed in a variety of seemingly unrelated areas, such as friendship networks in sociology, the structure of electrical power grids, and the nervous system of Caenorhabditis elegans. Moreover, the connectivity of the metabolites follows a power law, another unusual but by no means rare statistical distribution. This provides an objective criterion for the centrality of the tricarboxylic acid cycle to metabolism. The small-world architecture may serve to minimize transition times between metabolic states, and contains evidence about the evolutionary history of metabolism.
Causes and Outcome of Upper and Lower Gastrointestinal Bleeding (1999)

The causes of gastrointestinal bleeding remain little changed over the past several decades, though in our large series the need for surgical therapy and the mortality from both upper and lower GI bleeding were low.
Plant sterols lower LDL cholesterol without improving endothelial function in prepubertal children with familial hypercholesterolaemia (2003)

In adults with familial hypercholesterolaemia (FH), cholesterol lowering with statins has been shown to improve the endothelial function, a hallmark of early atherogenesis. Currently, therapeutic options for treating high cholesterol levels in FH children are limited. Plant sterols safely and effectively reduce serum cholesterol concentrations by inhibiting cholesterol absorption. Therefore, we evaluated the effect of plant sterols on cholesterol and vascular function in prepubertal children with FH. We included 41 children (5-12 years old) with FH in a double-blind crossover trial using spreads containing 2.3 g of plant sterols (mainly sitosterol and campesterol) per 15 g spread and a placebo spread for a 4-week period, separated by a 6-week washout period. Lipid levels and endothelial function were assessed after both 4-week treatment periods. Endothelial function was assessed as flow-mediated dilation (FMD) of the brachial artery using a wall tracking system. Data were compared to those of 20 healthy controls. Intake of 2.3 g plant sterols per day decreased total cholesterol (-11%) and low-density cholesterol (-14%) as compared to placebo spread in FH children. FH children treated with placebo spread were characterized by an impaired FMD compared to healthy control children (7.2% +/- 3.4% versus 10.1% +/- 4.2%, p < 0.005). However, the reduction of LDL in FH children did not improve FMD (placebo: 7.2% +/- 3.4% versus plant sterols: 7.7% +/- 4.1%). In conclusion, the present study shows a clear reduction of LDL cholesterol by plant sterol treatment. However, short-term plant sterol treatment does not improve the endothelial function in FH children.
Protein and pharmaceutical engineering : proceedings of an Upjohn-UCLA Symposium, held at Park City, Utah January 17-22, 1989 (1990)

PHYSICAL ANALYSIS OF PROTEIN STRUCTURE: Assignment of Histidine Resonances in the NMR Spectrum of Staphylococcal Nuclease Using Site-Directed Mutagenesis Detection of Conformational Changes in Active Site Mutants of Staphylococcal Nuclease The Acetylcholine Receptor CHEMICAL ASPECTS OF PROTEIN FUNCTION: HIV1 Protease: Bacterial Expression, Purification and Characterization Stereospecific Catalysis by an Antibody Enzyme Mimics Manipulative Mutagenesis of Enzymes.
Structural and Microtubule Binding Properties of Tau Mutants of Frontotemporal Dementias (2007)

Several mutations in the gene encoding the microtubule-associated protein tau are responsible for the formation of neurofibrillary inclusions in frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTDP-17). Here we present the high-resolution characterization of the conformational properties of two FTDP-17 mutants of the four-repeat domain of tau, P301L and DeltaK280, and their properties for binding to polyanions and microtubules. Multidimensional NMR spectroscopy shows that the mutations do no lead to a significant increase in the level of beta-structure in their monomeric state, even though the mutations strongly promote beta-structure during aggregation. However, local structural changes are induced in the second repeat. These changes only weakly affect the binding to the polyanion heparin, which promotes paired helical filament formation. The extent of binding to microtubules, however, is strongly decreased. Our results demonstrate that the reversible binding of tau to microtubules involves specific interactions, which are not essential for binding to polyanions.
Discoidin domain receptors: structural relations and functional implications (1999)

Multicellular life relies on the presence of extracellular matrix to provide scaffolding for cells and tissue compartments. To provide communication between cells and tissues, a multitude of cell surface receptors are triggered by soluble ligands and components of the extracellular matrix. A large family of these receptors transmit signals through the use of an intrinsic tyrosine kinase function. The subgroup of discoidin domain receptors (DDRs) is distinguished from other members of the receptor tyrosine kinase family by a discoidin homology repeat in their extracellular domains that is also found in a variety of other transmembrane and secreted proteins. Sequence comparisons show that non-mammalian orthologs of DDRs exist: three closely related genes in Caenorhabditis and one in the sponge Geodia cydonium. Recently, various types of collagen have been identified as the ligands for the two mammalian discoidin domain receptor tyrosine kinases, DDR1 and DDR2. The binding of collagen to DDRs results in a delayed but sustained tyrosine kinase activation. Both receptors display several potential tyrosine phosphorylation sites that are able to relay the signal by interacting with cytoplasmic effector proteins. The potential cross-talk to other receptors for collagen and the clinical aspects of DDR function are discussed.
Formal Total Synthesis of (±)-α- and β-Cedrene by Preparation of Cedrone. Construction of the Tricyclic Carbon Skeleton by the Use of a Highly Efficient Intramolecular Khand Annulation (2001)

The cedrene carbon skeleton was rapidly assembled from a simple monocyclic precursor by the strategic use of a high yielding intramolecular Khand cyclization reaction. Further synthetic manipulations provided a concise formal total synthesis of alpha- and beta-cedrene. Reaction: see text.
Preparation of a new thermo‐responsive adsorbent with maltose as a ligand and its application to affinity precipitation (1998)

A thermo-responsive polymer on which maltose was covalently immobilized as an affinity ligand was newly synthesized for purification of thermolabile proteins from the crude solution by affinity precipitation. Among the thermo-responsive polymers synthesized as carriers for adsorbent, poly(N-acryloylpiperidine)–cysteamine (pAP) has a lower critical solution temperature (LCST) of around 4°C, at which its solubility exhibits a sharp change. Adsorbent for affinity precipitation was prepared by combining pAP with maltose using trimethylamine–borane as a reducing reagent. This adsorbent (pAPM) obtained showed a good solubility response: pAPM in the basal buffer (pH 7.0) became soluble below 4°C and was completely insoluble above 8°C. The affinity precipitation method using pAPM consisted of the following four steps: adsorption at 4°C, precipitation of the complex at 10°C, desorption by adding the desorption reagent at 4°C, and recovery of a target protein at 10°C. In the affinity precipitation of Con A from the crude extract of jack bean meal, 82% of Con A added was recovered with 80% purity by addition of 0.2 M methyl-α-D-mannopyranoside as a desorption reagent. In the repeated purification of Con A from the crude extract, pAPM could be satisfactorily reused without decrease in the affinity performance. Moreover, when pAPM was used for the purification of thermolabile α-glucosidase from the cell-free extract of Saccharomyces cerevisiae, 68% of total activity added was recovered and the specific activity per amount of protein of the purified solution was enhanced 206-fold higher than that of the cell-free extract without thermal deactivation of the enzyme. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 60: 568–579, 1998.