gebhart/patrepeval huggingface dataset:
The Alignment Template Approach to Statistical Machine Translation (2004)

A phrase-based statistical machine translation approach — the alignment template approach — is described. This translation approach allows for general many-to-many relations between words. Thereby, the context of words is taken into account in the translation model, and local changes in word order from source to target language can be learned explicitly. The model is described using a log-linear modeling approach, which is a generalization of the often used source-channel approach. Thereby, the model is easier to extend than classical statistical machine translation systems. We describe in detail the process for learning phrasal translations, the feature functions used, and the search algorithm. The evaluation of this approach is performed on three different tasks. For the German-English speech Verbmobil task, we analyze the effect of various system components. On the French-English Canadian Hansards task, the alignment template system obtains significantly better results than a single-word-based translation model. In the Chinese-English 2002 National Institute of Standards and Technology (NIST) machine translation evaluation it yields statistically significantly better NIST scores than all competing research and commercial translation systems.
Signal shaping for peak-power and dynamics reduction in transmission schemes employing precoding (2002)

Precoding, i.e., nonlinear pre-equalization, at the transmitter side has been proved to be a very efficient strategy for channel equalization in single-carrier digital transmission schemes. It enables the application of coded modulation in a seamless fashion. A drawback of precoding is that the signal at the input of the decision device exhibits a huge dynamic range. Based on dynamics shaping, a combined precoding/shaping technique introduced in the paper by Fischer et al. (1995), a new shaping strategy is developed in this paper. This technique enables a flexible tradeoff among: (1) reduction of the average transmit power; (2) avoidance of peaks in the transmit signal in order to facilitate line driver implementation; and (3) restriction of the maximum amplitude at the receiver side to a prescribed value. Over a wide range, all three demands can be met simultaneously. As the scheme is fully compatible with Tomlinson-Harashima (1971, 1972) precoding, it can replace the precoder even in existing and standardized schemes. Simulation results for a typical digital subscriber line scenario show the achievable gains.
Pattern Based Analysis of BPEL4WS (2002)

Abstract. Web services composition is an emerging paradigm for en-abling application integration within and across organisational bound-aries. A landscape of languages and techniques for web services composi-tion has emerged and is continuously being enriched with new proposals from different vendors and coalitions. However, little or no effort has been dedicated to systematically evaluating the capabilities and limitations of these languages and techniques. The work reported in this paper is a first step in this direction. It presents an in-depth analysis of the Busi-ness Process Execution Language for Web Services (BPEL4WS). The framework used for this analysis is based on a collection of workflow and communication patterns. 1
The Phytase Subfamily of Histidine Acid Phosphatases: Isolation of Genes for Two Novel Phytases from the Fungi Aspergillus Terreus and Myceliophthora Thermophila (1997)

Phytases catalyse the hydrolysis of phytate (myo-inositol hexakisphosphate) to myo-inositol and inorganic phosphate. In this study genes encoding novel phytases from two different filamentous fungi, Aspergillus terreus strain 9A-1 and Myceliophthora thermophila were isolated. The encoded PhyA phytase proteins show 60% (A. terreus) and 48% (M. thermophila) identity, respectively, to the PhyA of Aspergillus niger and have 21-29% identity compared to other histidine acid phosphatases. All three PhyA proteins, in contrast to the A. niger pH 2.5-optimum acid phosphatase, prefer phytic acid as substrate and show enzyme activity at a broad range of acidic pH values. Based on their enzyme characteristics and protein sequence homology, the phytases form a novel subclass of the histidine acid phosphatase family.
Expression, purification and immunological characterization of the transforming protein E7, from cervical cancer-associated human papillomavirus type 16 (1999)

E7 is the major oncogenic protein produced in cervical cancer-associated human papillomavirus type 16 (HPV16). This protein was expressed in Escherichia coli as a glutathione-S-transferase (GST) fusion protein. E7-enriched inclusion bodies were collected from bacterial lysates, were solubilized in 10 M urea, and the protein was purified using anion exchange column chromatography. After removal of endotoxin with serial Triton X-114 extractions, material of high purity (about 90%) was obtained, which is suitable for use in a human clinical trial. This material was immunogenic, and when used as a vaccine, protected mice against challenge with an HPV16 E7 DNA transfected tumour cell line. Based on this observation, the E7GST fusion protein is currently being used in a human clinical trial of a vaccine against HPV16-induced cervical cancer. This fusion protein could be cleaved with thrombin to remove the GST fusion part and further purified by preparative SDS gel electrophoresis to obtain free E7 with > 98% purity.
New Cephalotaxus Alkaloids from Cephalotaxus harringtonia var. drupacea (1996)

The cytotoxic alkaloids nordeoxyharringtonine (2), homodeoxyharringtonine (3), and bishomodeoxyharringtonine (4) were isolated from the leaves and stems of Cephalotaxus harringtonia var. drupacea. Their structures were established on the basis of spectral data and chemical evidence.
Control of Blood Sugar in Insulin-Dependent Diabetes: Comparison of an Artificial Endocrine Pancreas, Continuous Subcutaneous Insulin Infusion, and Intensified Conventional Insulin Therapy (1980)

We compared the ability of closed-loop intravenous insulin infusion (i.e., an artificial "pancreas"), open-loop continuous subcutaneous insulin infusion, and intensified conventional insulin therapy (preprandial injections of regular insulin, with injection of long-acting zinc-suspension insulin before breakfast) to bring the hyperglycemia of insulin-dependent diabetic subjects to a level comparable to that of normal, nondiabetic subjects. The mean circadian levels of plasma glucose, mean amplitude of glycemic excursions, and M values (defined in Methods) did not significantly differ among the three regimens. Although these levels in the diabetic subjects approximated those in the normal subjects, the levels of plasma insulin, mean amplitude of glycemic excursions, and M values were significantly higher than those in normal subjects (P < 0.01). Therefore, at least on a short-term basis, all three regimens can produce comparable, nearly normal levels of blood sugar in such patients; moreover, closed-loop devices can be used to determine insulin requirements for conventional therapy.
Preclinical Evaluation of the α-Particle Generator Nuclide 225Ac for Somatostatin Receptor Radiotherapy of Neuroendocrine Tumors (2008)

225Ac might be suitable to improve PRRT in neuroendocrine tumors.
Silver-Coated Dye-Embedded Silica Beads: A Core Material of Dual Tagging Sensors Based on Fluorescence and Raman Scattering (2010)

We have developed a new type of dual-tag sensor for immunoassays, operating via both fluorescence and surface-enhanced Raman scattering (SERS). A one-shot fluorescence image over the whole specimen allows us to save considerable time because any unnecessary time-consuming SERS measurements can be avoided from the signature of the fluorescence. Dye-embedded silica beads are prepared initially, and then SERS-active silver is coated onto them via a very simple electroless-plating method. The Raman markers are subsequently assembled onto the Ag-coated silica beads, after which they are stabilized by silanization via a biomimetic process in which a poly(allylamine hydrochloride) layer formed on the Raman markers by a layer-by-layer deposition method acting as a scaffold for guiding silicification. In the final stage, specific antibodies are attached to the silica surface in order to detect target antigens. The fluorescence signal of the embedded dye can be used as a fast readout system of molecular recognition, whereas the SERS signals are subsequently used as the signature of specific molecular interactions. In this way, the antibody-grafted particles were found to recognize antigens down to 1 × 10(-10) g mL(-1) solely by the SERS peaks of the Raman markers.
Beam search for feature selection in automatic SVM defect classification (2003)

Often in pattern classification problems, one tries to extract a large number of features and base the classifier decision on as much information as possible. This yields an array of features that are 'potentially' useful. Most of the time however, large feature sets are sub-optimal in describing the samples since they tend to over-represent the data and model noise along with the useful information in the data. Selecting relevant features from the available set of features is, therefore, a challenging task. In this paper, we present an innovative feature selection algorithm called Smart Beam Search (SBS), which is used with a support vector machine (SVM) based classifier for automatic defect classification. This feature selection approach not only reduces the dimensionality of the feature space substantially, but also improves the classifier performance.
Phytochrome E Influences Internode Elongation and Flowering Time in Arabidopsis (1998)

From a screen of M2 seedlings derived from gamma-mutagenesis of seeds doubly null for phytochromes phyA and phyB, we isolated a mutant lacking phyE. The PHYE gene of the selected mutant, phyE-1, was found to contain a 1-bp deletion at a position equivalent to codon 726, which is predicted to result in a premature stop at codon 739. Immunoblot analysis showed that the phyE protein was undetectable in the phyE-1 mutant. In the phyA- and phyB-deficient background, phyE deficiency led to early flowering, elongation of internodes between adjacent rosette leaves, and reduced petiole elongation. This is a phenocopy of the response of phyA phyB seedlings to end-of-day far-red light treatments. Furthermore, a phyE deficiency attenuated the responses of phyA phyB seedlings to end-of-day far-red light treatments. Monogenic phyE mutants were indistinguishable from wild-type seedlings. However, phyB phyE double mutants flowered earlier and had longer petioles than did phyB mutants. The elongation and flowering responses conferred by phyE deficiency are typical of shade avoidance responses to the low red/far-red ratio. We conclude that in conjunction with phyB and to a lesser extent with phyD, phyE functions in the regulation of the shade avoidance syndrome.
Photoactivatable Antisense DNA: Suppression of Ampicillin Resistance in Normally Resistant Escherichia coli (1991)

Antisense oligodeoxyribonucleotides complementary to a segment of the beta-lactamase gene and containing psoralen monoadducts at specific sites were examined for their ability to make normally resistant bacteria sensitive to ampicillin. Irradiation of oligonucleotides and psoralens with long-wavelength ultraviolet radiation (380-400 nm) produced monoadducted antisense molecules. High-performance liquid chromatography was used to purify microgram quantities of photoactivatable antisense DNA. Escherichia coli transformed with a plasmid containing the gene for beta-lactamase were used to test a series of oligonucleotides containing psoralen monoadducts after additional exposure to the photoactivating effects of long-wavelength ultraviolet radiation (320-400 nm). Normally resistant bacteria treated with this photoactivatable form of antisense DNA (0.4 microM) were specifically sensitized to ampicillin. The reduction in colony formation ranged from 31 to 79% in comparison to control oligonucleotides which did not contain photoactivatable monoadduct moieties. Bacteria treated in a similar manner but in the presence of tetracycline instead of ampicillin were not affected. The activity of beta-galactosidase, whose gene is located on the same plasmid as beta-lactamase, was not affected.
Alveolar hemostasis in patients with species-specific bacterial-mediated ventilator-associated pneumonia* (2007)

Song, Yuanlin MD; Wiener-Kronish, Jeanine P. MD; Flanagan, Judith PhD; Lynch, Susan V. PhD Author Information
Recently elucidated energy catabolism pathways provide opportunities for novel treatments in hepatocellular carcinoma (2004)

It has long been known that tumors depend on energy production pathways that are different from those of normal cells. These unique pathways require the expression and function of tumor-specific enzymes. Some of these glycolytic enzymes, as well as other modulators of tumor behavior, have recently been elucidated. In theory, inhibiting such enzymes or appropriately affecting such modulators should deprive tumors of energy, while leaving nontransformed cells unaffected. These factors include certain hexokinases that catalyze glycolysis in tumors and can be inhibited by 3-bromopyruvate. 2-deoxyglucose is another modulator that depletes hexokinase stores and cannot undergo further catabolism, thus depriving tumors of their energy source. Other enzymes or modulators are under scrutiny and have shown promise. Preliminary experiments on animals with hepatocellular carcinoma have indeed shown very encouraging results. It appears that modulating the energy production pathways of tumors is poised to become a substantial research area for cancer treatment. This review will focus on the energy production pathways of transformed cells, highlight the differences between transformed and normal cells in this regard and summarize recent experiments that take advantage of these disparities in cancer treatment.
Laser Beams and Resonators (1966)

This paper is a review of the theory-of laser beams and resonators. It is meant to be tutorial in nature and useful in scope. No attempt is made to be exhaustive in the treatment. Rather, emphasis is placed on formulations and derivations which lead to basic understanding and on results which bear practical significance.
Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene. (1992)

The human salivary amylase genes are associated with two inserted elements, a gamma-actin-processed pseudogene and an endogenous retroviral-like element. To test the contribution of these inserted elements to tissue specificity, 25 lines of transgenic mice carrying 10 amylase constructs were established. A 1-kb fragment of AMY1C (-1003 to +2) was found to be sufficient for parotid-specific expression of a human growth hormone reporter gene. The 1-kb fragment is entirely derived from inserted sequences. Deletion from -1003 to -826 resulted in reduced levels of transgene expression and loss of tissue specificity. The fragment -1003 to -327 was sufficient to transfer parotid specificity to the thymidine kinase promoter. The data demonstrate that the functional tissue-specific promoter of human AMY1C is derived from inserted sequences and that parotid expression can be conferred by sequences derived solely from the retrovirus. A role for retrotransposition in the evolution of gene regulation is indicated by these and other recent observations.
COLLISION AVOIDANCE THROUGH IMPROVED COMMUNICATION BETWEEN TRACTOR AND TRAILER (1998)

On September 2 1994, the National Highway Traffic Safety Administration (NHTSA) issued a notice in the Federal Register to promote a cooperative program which would foster the development, evaluation, and deployment of heavy vehicle intelligent communication and powering enhancement system(s). In response to this solicitation, Delco Electronics Corporation, on behalf of its potential project partners, submitted a proposal detailing a collaborative, jointly governed venture between industry and Government to develop and evaluate heavy-duty technology vehicles using two-way communication between the tractor and the trailer. The object of this cooperative agreement was to foster the development, evaluation, and deployment of intelligent communication and powering, also requiring the installation of several advanced electrical sub-systems on the trailers in order to properly exercise these communciation and powering techniques between the tractor and trailer in the real world. Among the devices installed on the vehicles, of particular interest to the government agencies, were the Side Collision Warning System, Brake Stroke Indicator, Head-up Display, and a Rear View Video Camera as collision avoidance devices. A unique feature of this program was the in-fleet operational testing of the systems, using real truck drivers, who faced real driver problems and performance pressures. The drivers introduced a recordable human factors element into the evaluation system with regard to the safety and productivity value of many of the tested systems. If something bothered them, it got shutoff or broken. (A) For the covering abstract see IRRD E102514.
Proteomic Analysis of Exosomes Isolated from Human Malignant Pleural Effusions (2004)

Exosomes are membrane vesicles from endosomal origin secreted by various cells such as hematopoietic, epithelial, and tumor cells. Exosomes secreted by tumor cells contain specific antigens potentially useful for immunotherapeutic purposes. Our aim was to determine if exosomes are present in human cancerous pleural effusions and to identify their proteomic content. Exosomes were purified by sucrose gradient ultracentrifugation, and electron microscopy was used to check both concentration and purity of exosomes. Proteins were separated by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and protein bands were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and Western blotting. Exosomes were present in pleural fluid obtained from patients suffering from mesothelioma (n = 4), lung cancer (n = 2), breast cancer (n = 2), and ovarian cancer (n = 1). As previously reported by others, antigen-presenting molecules, cytoskeletal proteins, and signal transduction-involved proteins were present. Proteins not previously reported were identified (SNX25, BTG1, PEDF, thrombospondin 2). Different types of immunoglobulins and complement factors were abundantly present in the sucrose fractions containing exosomes. Exosome-directed specificity of these immunoglobulins was not observed. In conclusion, sucrose gradient ultracentrifugation allows isolation of exosomes from malignant pleural effusions. However, pleural fluid proteins and especially immunoglobulins are coisolated and may hamper the use of exosomes isolated from malignant effusion for immunotherapy programs.
Aggregometry detects platelet hyperreactivity in healthy individuals (2005)

Aggregometry is widely used to assess platelet function, but its use in identifying platelet hyperreactivity is poorly defined. We studied platelet aggregation in 359 healthy individuals using the agonists adenosine diphosphate (ADP), epinephrine, collagen, collagen-related peptide, and ristocetin. We also assessed the reproducibility of these assays in 27 subjects by studying them repeatedly on at least 4 separate occasions. Healthy subjects exhibited considerable interindividual variability in aggregation response to agonists, especially at concentrations lower than those typically used in clinical laboratories. For each agonist tested at these submaximal concentrations, a small proportion of individuals demonstrated an unusually robust aggregation response. Subjects who exhibited such in vitro hyperreactivity to one agonist tended to demonstrate a similar response to others, suggesting that hyperreactivity is a global characteristic of platelets. Epinephrine and collagen-related peptide were especially reliable and efficient in detecting hyperreactivity. For epinephrine, excellent reproducibility persisted for up to 3 years, and hyperreactivity was associated with female sex and higher fibrinogen levels (P < .02). We recommend these assays as appropriate candidates for future studies requiring accurate assessment of increased platelet reactivity. These include clinical studies to improve risk assessment for arterial thrombosis, as well as genetic studies to establish determinants of the hyperreactive platelet phenotype.
Biosynthesis of Poly(3-hydroxybutyrate-co-3-hydroxyalkanoates) by Metabolically Engineered Escherichia coli Strains (2004)

Biosynthesis of polyhydroxyalkanoates (PHAs) consisting of 3-hydroxy-alkanoates (3HAs) of 4 to 10 carbon atoms was examined in metabolically engineered Escherichia coli strains. When the fadA and/or fadB mutant E. coli strains harboring the plasmid containing the Pseudomonas sp. 61-3 phaC2 gene and the Ralstonia eutropha phaAB genes were cultured in Luria-Bertani (LB) medium supplemented with 2 g/L of sodium decanoate, all the recombinant E. coli strains synthesized PHAs consisting of C4, C6, C8, and C10 monomer units. The monomer composition of PHA was dependent on the E. coli strain used. When the fadA mutant E. coli was employed, PHA containing up to 63 mol% of 3-hydroyhexanoate was produced. In fadB and fadAB mutant E. coli strains, 3-hydroxybutyrate (3HB) was efficiently incorporated into PHA up to 86 mol%. Cultivation of recombinant fadA and/or fadB mutant E. coli strains in LB medium containing 10 g/L of sodium gluconate and 2 g/L of sodium decanoate resulted in the production of PHA copolymer containing a very high fraction of 3HB up to 95 mol%. Since the material properties of PHA copolymer consisting of a large fraction of 3HB and a small fraction of medium-chain-length 3HA are similar to those of low-density polyethylene, recombinant E. coli strains constructed in this study should be useful for the production of PHAs suitable for various commercial applications.
Molecular pathways as novel therapeutic targets in systemic sclerosis (2007)

The identification of novel signaling pathways and mediators that are altered in systemic sclerosis and contribute to tissue damage allows their selective targeting. This in turn opens the door for novel therapeutic strategies utilizing novel compounds, or innovative ways of using already-approved drugs. In light of the complex pathogenesis of systemic sclerosis, however, only carefully designed clinical trials with appropriate biomarkers and outcome measures will be able to clarify the clinical utility of these innovative approaches.
No Retroviremia or Pathology in Long-Term Follow-Up of Monkeys Exposed to a Murine Amphotropic Retrovirus (1991)

Four monkeys were exposed to a retroviral vector and replication-competent murine amphotropic retrovirus in a bone marrow transplantation/gene transfer protocol (Kantoff et al., 1987). We have studied these animals 2 and 3 years post-transplantation and did not detect replicating virus in serum, peripheral blood mononuclear cells, or bone marrow cells. Amphotropic envelope sequences could not be detected in blood or bone marrow cells by Southern blotting or the polymerase chain reaction. Antibodies directed against the p30 and gp70 viral antigens were detected by Western blot and immunoprecipitation. The animals remain alive and well. Our findings suggest that primates can clear murine amphotropic retroviruses even when exposure occurs during a time of severe immunosuppression.