gebhart/patrepeval huggingface dataset:
Chromatic focal plane displacement in the parabolic chirped waveguide grating router (1997)

It is shown that the application of parabolic chirp to the arm lengths of the waveguide grating router is equivalent to placing a lens with chromatic aberration in the free-space region. By adjusting the focal plane for each port, performance equivalent to a nonchirped grating can be achieved in a desired grating order with significant passband suppression in unwanted grating orders.
Hardware-Efficient Coherent Digital Receiver Concept With Feedforward Carrier Recovery for $M$-QAM Constellations (2009)

This paper presents a novel digital feedforward carrier recovery algorithm for arbitrary <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> -ary quadrature amplitude modulation (M-QAM) constellations in an intradyne coherent optical receiver. The approach does not contain any feedback loop and is therefore highly tolerant against laser phase noise. This is crucial, especially for higher order QAM constellations, which inherently have a smaller phase noise tolerance due to the lower spacing between adjacent constellation points. In addition to the mathematical description of the proposed carrier recovery algorithm also a possible hardware-efficient implementation in a parallelized system is presented and the performance of the algorithm is evaluated by Monte Carlo simulations for square 4-QAM (QPSK), 16-QAM, 64-QAM, and 256-QAM. For the simulations ASE noise and laser phase noise are considered as well as analog-to-digital converter (ADC) and internal resolution effects. For a 1 dB penalty at BER = 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> , linewidth times symbol duration products of 4.1 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> (4-QAM), 1.4 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> (16-QAM), 4.0 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> (64-QAM) and 8.0 x 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-6</sup> (256-QAM) are tolerable.
Reverse Transcriptas (1975)

Recognition of RNA tumor viruses as causative agents of malignant disease started with the observation (by Ellerman and Bang in 1908) that a filterable agent transmitted avian leukemia1 and the subsequent isolation of chicken sarcoma virus by Rous in 1911.2 These findings were followed by an intense and continuous search for new isolates, the establishment of inbred strains of mice, and the development of tissue culture techniques. In the early 1960s, the significance of RNA tumor viruses was generally accepted, especially in avian and murine systems, but with some skepticism, probably because its role in natural disease was not yet evident. Moreover, the mode of replication of the RNA tumor viruses was still not understood. In recent years, the study of these viruses markedly intensified, principally because of a discovery which filled a major gap in the understanding of their replication. This is the independent discovery of the viral RNA-dependent DNA polymerase (reverse transcriptase) by Temin and Mizutani3 and by Baltimore4 in 1970. This discovery also extended our understanding of the mode of genetic information transfer, and it paved the way for the finding of viral-related components, reverse transcriptase5-11 and type-C viral related nucleic acids in human leukemic cells by Gallo, Spiegelman, and their co-workers (see later section10,12-17).
Naive automated machine learning (2022)

Abstract An essential task of automated machine learning ( $$\text {AutoML}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mtext>AutoML</mml:mtext> </mml:math> ) is the problem of automatically finding the pipeline with the best generalization performance on a given dataset. This problem has been addressed with sophisticated $$\text {black-box}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mtext>black-box</mml:mtext> </mml:math> optimization techniques such as Bayesian optimization, grammar-based genetic algorithms, and tree search algorithms. Most of the current approaches are motivated by the assumption that optimizing the components of a pipeline in isolation may yield sub-optimal results. We present $$\text {Naive AutoML}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mtext>Naive AutoML</mml:mtext> </mml:mrow> </mml:math> , an approach that precisely realizes such an in-isolation optimization of the different components of a pre-defined pipeline scheme. The returned pipeline is obtained by just taking the best algorithm of each slot. The isolated optimization leads to substantially reduced search spaces, and, surprisingly, this approach yields comparable and sometimes even better performance than current state-of-the-art optimizers.
Effects of Ultrasonic Vibrations on Nerve Tissues. (1951)

SummaryThe excised crayfish ventral nerve cord exposed to ultrasound (35 watts/ cm2, frequency 1 mc) exhibited a reduction of spontaneous activity after several seconds exposure and recovered its original activity about one minute after the ultrasound was turned off. Frogs positioned so that ultrasound was incident on the dorsal surface over the lumbar enlargement of the spinal cord exhibited paralysis of the hind legs after 4.3 sec. exposure (at room temperature) and exhibited paralysis after 7.3 sec. exposure (at 1°-2°C). Histological examination of the sciatic nerves showed extensive degeneration of nerves and examination of the spinal cord indicated destruction of the lower motor neurones. It was concluded that the effect of ultrasound on the systems studied is produced by physical factors other than temperature.
High power with high efficiency in a narrow single-lobed beam from a diode laser array in an external cavity (1987)

High output power (700 mW) in a nearly diffraction-limited (0.7°) single-lobed nonsteering output beam is obtained from a gain-guided diode laser array in a novel, easily fabricated external cavity configuration. The laser output beam is collimated in both lateral and vertical directions. Differential quantum efficiency as high as 70% has been measured along with excellent linearity of the optical power versus current characteristic. The power and efficiency are the highest reported for a coupled-stripe laser array emitting a narrow single-lobed beam.
Rationally designed strings of promiscuous CD4+ T cell epitopes provide help toHaemophilus influenzae type b oligosaccharide: a model for new conjugate vaccines (2001)

The age-related and T cell-independent immunological properties of most capsular polysaccharides limit their use as vaccines, especially in children under 2 years of age. To overcome these limitations, polysaccharide antigens have been successfully conjugated to a variety of carrier proteins, such as diphtheria toxoid or tetanus toxoid (TT) and the diphtheria mutant (CRM197) to produce very successful glycoconjugate vaccines. The increasing demand for new conjugate vaccines requires the availability of additional carriers providing high and long-lasting T helper cell immunity. Here we describe the design and construction of three recombinant carrier proteins (N6, N10, N19) constituted by strings of 6, 10 or 19 human CD4(+) T cell epitopes from various pathogen-derived antigens, including TT and proteins from Plasmodium falciparum, influenza virus and hepatitis B virus. Each of these epitopes is defined as universal in that it binds to many human MHC class II molecules. When conjugated to Haemophilus influenzae type b (Hib) oligosaccharide, these carriers elicit a potent anti-Hib antibody response in mice. In the case of the N19-Hib conjugate, this response is at least as good as that observed with CRM197-Hib, a conjugate vaccine currently used for mass immunization. We also show that some of the universal epitopes constituting the recombinant carriers are specifically recognized by two human in vitro systems, suggesting that T cell memory is provided by the selected epitopes. The data indicate that rationally designed recombinant polyepitope proteins represent excellent candidates for the development and clinical testing of new conjugate vaccines.
The Human Genome Project: Lessons from Large-Scale Biology (2003)

The Human Genome Project has been the first major foray of the biological and medical research communities into “big science.” In this Viewpoint, we present some of our experiences in organizing and managing such a complicated, publicly funded, international effort. We believe that many of the lessons we learned will be applicable to future large-scale projects in biology.
ATP-binding cassette (ABC) transporters in human metabolism and diseases. (2004)

The ATP-binding cassette (ABC) superfamily of active transporters involves a large number of functionally diverse transmembrane proteins. They transport a variety of substrates including amino acids, lipids, inorganic ions, peptides, saccharides, metals, drugs, and proteins. The ABC transporters not only move a variety of substrates into and out of the cell, but also are also involved in intracellular compartmental transport. Energy derived from the hydrolysis of ATP is used to transport the substrate across the membrane against a concentration gradient. The typical ABC transporter consists of two transmembrane domains and two nucleotide-binding domains. Defects in 14 of these transporters cause 13 genetic diseases (cystic fibrosis, Stargardt disease, adrenoleukodystrophy, Tangier disease, etc.). Mutations in three genes affect lipid levels expressively. Mutations in ABCA1 cause severe HDL deficiency syndromes called Tangier disease and familial high-density lipoprotein deficiency, which are characterized by a severe deficiency or absence of high-density lipoprotein in the plasma. Two other ABCG transporters, ABCG5 and ABCG8, mutations of which cause sitosterolemia, have been identified. The affected individuals absorb and retain plant sterols, as well as shellfish sterols.
Essentials of Glycobiology (1999)

General principles - historical background and overview saccharide structure and nomenclature evolution of glycan diversity protein-glycan Interactions exploring the biological roles of glycans biosynthesis, metabolism, and function - monosaccharide metabolism N-glycans O-glycans glycosphingolipids glycophospholipid anchors proteoglycans and glycosaminoglycans other classes of golgi-derived glycans nuclear and cytoplasmic glycosylation the O-GlcNAc modification sialic acids structures common to different types of glycans glycosyltransferases degradation and turnover of glycans glycosylation in model organisms glycobiology of plant cells bacterial polysaccharides proteins that recognize glycans - discovery and classification of animal lectins P-type lectins I-type lectins C-type lectins selectins S-type lectins (galectins) microbial glycan-binding proteins glycosaminoglycan-binding proteins plant lectins glycans in genetic disorders and disease - genetic disorders of glycosylation in cultured cells naturally occurring genetic disorders of glycosylation in animals determining glycan function using genetically modified mice glycosylation changes in ontogeny and cell activation glycosylation changes in cancer glycobiology of protozoal and helminthic parasites acquired glycosylation changes in human disease methods and applications - structural analysis and sequencing of glycans chemical and enzymatic synthesis of glycans natural and synthetic inhibitors of glycosylation glycobiology in biotechnology and medicine.
Delayed dark-adaptation and lipofuscin accumulation in abcr+/- mice: implications for involvement of ABCR in age-related macular degeneration. (2001)

Partial loss of the ABCR or rim protein is sufficient to cause a phenotype in mice similar to recessive Stargardt's disease (STGD) and age-related macular degeneration (AMD) in humans. These data are consistent with the suggestion that the STGD carrier-state may predispose to the development of AMD.
A Novel Antiretroviral Class (Fusion Inhibitors) in the Management of HIV Infection. Present Features and Future Perspectives of Enfuvirtide (T-20) (2006)

Enfuvirtide (Fuzeon, Roche), is the first member of a novel class of antiretroviral agents, the so-called fusion inhibitors, which act against HIV with a completely novel (extra cellular) mechanism of action, and can therefore be easily added to all anti-HIV association therapies including all other antiretroviral agents belonging to nucleoside/nucleotide reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, and protease inhibitors, since no interactions of any type are expected with enfuvirtide. Despite the need of a twice-daily parenteral (subcutaneous) delivery due to the polypeptide structure of the drug, and its proportionally short elimination lifetime, two extensive multicentre randomized clinical trials and a huge amount of other clinical and laboratory experiences confirmed the elevated potency and the safety profile of enfuvirtide in appropriate samples of HIV-infected patients (both adults and children), who failed and/or became intolerant to all previously available anti-HIV regimens, and had a very restricted choice of antiviral compounds showing residual activity. As a consequence, enfuvirtide is recommended as an adjunct to an "optimized background" containing at least one or two antiretroviral drugs, which are still active against the isolated viral strain, as assessed by resistance testing. The extremely promising profile of this novel anti-HIV drug and the reduced potential for the development of viral resistance (with no possibility of cross-resistance with the other anti-HIV classes) however warrant further pharmacokinetic, pharmacodynamic, pharmacogenomic, and pharmacoeconomic investigation. Also more extensive and prolonged clinical and quality of life studies are strongly needed to establish the best positioning of enfuvirtide in the current therapeutic guidelines of HIV disease and its future role, besides its current approval for salvage therapy of adult and pediatric HIV-infected patients with limited therapeutic options.
DNA copy number amplifications in human neoplasms: review of comparative genomic hybridization studies. (1998)

This review summarizes reports of recurrent DNA sequence copy number amplifications in human neoplasms detected by comparative genomic hybridization. Some of the chromosomal areas with recurrent DNA copy number amplifications (amplicons) of 1p22-p31, 1p32-p36, 1q, 2p13-p16, 2p23-p25, 2q31-q33, 3q, 5p, 6p12-pter, 7p12-p13, 7q11.2, 7q21-q22, 8p11-p12, 8q, 11q13-q14, 12p, 12q13-q21, 13q14, 13q22-qter, 14q13-q21, 15q24-qter, 17p11.2-p12, 17q12-q21, 17q22-qter, 18q, 19p13.2-pter, 19cen-q13.3, 20p11.2-p12, 20q, Xp11.2-p21, and Xp11-q13 and genes therein are presented in more detail. The paper with more than 150 references and two tables can be accessed from our web site http://www.helsinki.fi/lglvwww/CMG.html. The data will be updated biannually until the year 2001.
An Analysis of Traditional Operational Testing to Project How Testing Will be Conducted in the Future (1993)

The purpose of this thesis is to analyze current operational testing and to alert the reader to how testing will be conducted in the future. This analysis is conducted from a tester's point of view and is targeted at program offices so that Program Managers will be able to ensure that beneficial operational testing is conducted on their programs. The thesis also provides a detailed description of current and future systems used to instrument development systems, analyze the test data, and produce a final test report. It also provides a detailed analysis of a testing tool called Model-Test-Model (M- T-M). The goal of M-T-M is to save the Army time and money by using a validated model to provide operational test data. Finally, the thesis provides an analysis of the changes that will need to be made in the T&amp;E community as a result of a new defense environment. These areas include the need for minimizing duplication between development and operational testing, using modeling and simulation, and taking advantage of other areas where testing costs can be reduced. Operational testing, User testing, Model-test-model, Test instrumentation, Real-time casualty assessment, Future testing.
Human Colorectal Cancers Express a Constitutively Active Cholecystokinin-B/Gastrin Receptor That Stimulates Cell Growth (2000)

Although ectopic expression of the cholecystokinin B/gastrin receptor (CCK-BR) is widely reported in human colorectal cancers, its role in mediating the proliferative effects of gastrin1-17 (G-17) on these cancers is unknown. Here we report the isolation of a novel splice variant of CCK-BR that exhibits constitutive (ligand-independent) activation of pathways regulating intracellular free Ca(2+) ([Ca(2+)](i)) and cell growth. The splice variant (designated CCK-BRi4sv for intron 4-containing splice variant) is expressed in colorectal cancers but not in normal colonic mucosa adjacent to the cancer. Balb3T3 cells expressing CCK-BRi4sv exhibited spontaneous, ligand-independent, oscillatory increases in [Ca(2+)](i), whereas cells expressing wild-type CCK-BR did not. Primary cultures of cells isolated from resected colorectal cancers also exhibited a similar pattern of spontaneous [Ca(2+)](i) oscillations. For both Balb3T3 and primary tumor cells, application of G-17 (10 and 200 nm, respectively) caused an increase in [Ca(2+)](i). Selective CCK-BR antagonists blocked the G-17-stimulated Ca(2+) responses but not the spontaneous [Ca(2+)](i) oscillations. Cells expressing CCK-BRi4sv exhibited an increased growth rate ( approximately 2.5-fold), in the absence of G-17, compared with cells expressing wild-type CCK-BR. The selective pattern of expression, constitutive activity, and trophic action associated with CCK-BRi4sv suggest that this variant may regulate colorectal cancer cell proliferation though a gastrin-independent mechanism.
Increased hemoglobin O2affinity protects during acute hypoxia (2012)

Acclimatization to hypoxia requires time to complete the adaptation mechanisms that influence oxygen (O(2)) transport and O(2) utilization. Although decreasing hemoglobin (Hb) O(2) affinity would favor the release of O(2) to the tissues, increasing Hb O(2) affinity would augment arterial O(2) saturation during hypoxia. This study was designed to test the hypothesis that pharmacologically increasing the Hb O(2) affinity will augment O(2) transport during severe hypoxia (10 and 5% inspired O(2)) compared with normal Hb O(2) affinity. RBC Hb O(2) affinity was increased by infusion of 20 mg/kg of 5-hydroxymethyl-2-furfural (5HMF). Control animals received only the vehicle. The effects of increasing Hb O(2) affinity were studied in the hamster window chamber model, in terms of systemic and microvascular hemodynamics and partial pressures of O(2) (Po(2)). Pimonidazole binding to hypoxic areas of mice heart and brain was also studied. 5HMF decreased the Po(2) at which the Hb is 50% saturated with O(2) by 12.6 mmHg. During 10 and 5% O(2) hypoxia, 5HMF increased arterial blood O(2) saturation by 35 and 48% from the vehicle group, respectively. During 5% O(2) hypoxia, blood pressure and heart rate were 58 and 30% higher for 5HMF compared with the vehicle. In addition, 5HMF preserved microvascular blood flow, whereas blood flow decreased to 40% of baseline in the vehicle group. Consequently, perivascular Po(2) was three times higher in the 5HMF group compared with the control group at 5% O(2) hypoxia. 5HMF also reduced heart and brain hypoxic areas in mice. Therefore, increased Hb O(2) affinity resulted in hemodynamics and oxygenation benefits during severe hypoxia. This acute acclimatization process may have implications in survival during severe environmental hypoxia when logistic constraints prevent chronic acclimatization.
A single amino acid difference is sufficient to elicit vegetative incompatibility in the fungus Podospora anserina. (1993)

Vegetative incompatibility is known to limit heterokaryosis in filamentous fungi. It results from genetic differences between incompatible strains at specific loci. The proteins encoded by the two incompatible alleles het-s and het-S of the fungus Podospora anserina differ from each other by 14 amino acids. Two approaches have been used to identify how many and which of these differences are necessary to elicit incompatibility. Twelve alleles of the het-s locus of wild-type isolates of P. anserina and of the related species Podospora comata have been sequenced to determine the extent of the variability of genes controlling s and S specificities. Expression of hybrid het-s/het-S genes and site-specific mutagenesis revealed that the specificities of het-s and het-S are under the control of a limited number of amino acid differences. The results show that vegetative incompatibility between s and S strains can be attributed to a single amino acid difference in the proteins encoded by the het-s locus.
Submillimeter-wave sideband generation using a planar diode array (2002)

A 36 element array of planar Schottky diodes is used to mix the output of a CO/sub 2/ pumped far infrared laser with a 1-20 GHz microwave source to generate tunable sidebands at 1.6 THz. The double sideband power was measured by heterodyne detection with a 1T23 corner cube Schottky diode for a calculated output power of 5.9 /spl mu/W with a 28 dB conversion loss.
Peptide Inhibitor of Complement C1, a Novel Suppressor of Classical Pathway Activation: Mechanistic Studies and Clinical Potential (2014)

The classical pathway of complement plays multiple physiological roles including modulating immunological effectors initiated by adaptive immune responses and an essential homeostatic role in the clearance of damaged self-antigens. However, dysregulated classical pathway activation is associated with antibody-initiated, inflammatory diseases processes like cold agglutinin disease, acute intravascular hemolytic transfusion reaction (AIHTR), and acute/hyperacute transplantation rejection. To date, only one putative classical pathway inhibitor, C1 esterase inhibitor (C1-INH), is currently commercially available and its only approved indication is for replacement treatment in hereditary angioedema, which is predominantly a kinin pathway disease. Given the variety of disease conditions in which the classical pathway is implicated, development of therapeutics that specifically inhibits complement initiation represents a major unmet medical need. Our laboratory has identified a peptide that specifically inhibits the classical and lectin pathways of complement. In vitro studies have demonstrated that these peptide inhibitors of complement C1 (PIC1) bind to the collagen-like region of the initiator molecule of the classical pathway, C1q. PIC1 binding to C1q blocks activation of the associated serine proteases (C1s-C1r-C1r-C1s) and subsequent downstream complement activation. Rational design optimization of PIC1 has resulted in the generation of a highly potent derivative of 15 amino acids. PIC1 inhibits classical pathway mediated complement activation in ABO incompatibility in vitro and inhibiting classical pathway activation in vivo in rats. This review will focus on the pre-clinical development of PIC1 and discuss its potential as a therapeutic in antibody-mediated classical pathway disease, specifically AIHTR.