gebhart/patrepeval huggingface dataset:
Mit Sicherheit zum Dokument - Die Identifizierung von Online-Publikationen (2004)

Die postmoderne Gesellschaft ist gekennzeichnet durch ein Zuviel an Informationen. Es gibt weltweit mehr als 100.000 Zeitschriftentitel, jährlich erscheinen 80.000 neue Bücher. Neben diesen traditionellen gedruckten Publikationsformen existiert eine Vielzahl elektronischer Dokumente. Im WWW gibt es weltweit rund 170 Millionen Hosts mit geschätzten 500 Millionen Seiten. Die Zahl seriöser wissenschaftlicher Dokumente, die nur noch elektronisch erscheinen, steigt ständig. Das gezielte Auffinden von relevanten Informationen und Dokumenten wird immer schwieriger, da es eine eindeutige und verwechslungsfreie Kennzeichnung der Dokumente erfordert. Ist es bislang gelungen, die gedruckten Erzeugnisse nach einem weltweit einheitlichen Standard eindeutig zu kennzeichnen (ISBN, ISSN), so ist dies bei elektronischer Dokumenten noch lange nicht gesichert. Zur Zeit werden oft die Internetadressen zum Zitieren und Wiederauffinden der Dokumente benutzt. Doch die Internetadressen, Uniform Resource Locators (URLs) genannt, können sich verändern und häufig sind die Publikationen dann verschwunden. Damit die Online-Publikationen zitiert, wiedergefunden und genutzt werden können, sind eindeutige Identifizierungssysteme nötig. Besonders Bibliotheken, deren Aufgabe im gezielten Auffinden und Vermitteln von Informationen weltweit besteht, haben Interesse an einer eindeutigen und unverwechselbaren Kennzeichnung elektronischer Dokumente. Als Beispiel für die Identifizierung von elektronischer Publikationen werden zwei unterschiedliche Systeme, der Uniform Resource Name (URN) und der Digital Object Identifier vorgestellt. Der Beitrag enthält einen Praxisbericht zum Thema: Bibiliotheken als Verleger?-Einsatz von URNS am Beispiel der Zentralbibliothek des Forschungszentrums Jülich.
Novel Length Scales in Nanotube Devices (1999)

We calculate the properties of $p\ensuremath{-}n$ junctions, $n\ensuremath{-}i$ junctions, and Schottky barriers made on a single-wall carbon nanotube. In contrast to planar bulk junctions, the depletion width for nanotubes varies exponentially with inverse doping. In addition, there is a very long-range (logarithmic) tail in the charge distribution, extending over the entire tube. These effects can render traditional devices unworkable, while opening new possibilities for device design. Our general conclusions should apply to a broad class of nanotube heterojunctions, and to other quasi-one-dimensional ``molecular wire'' devices.
Reference plane parasitics modeling and their contribution to the power and ground path "effective" inductance as seen by the output drivers (1994)

Modeling of the current distribution in package reference (power and ground) planes and the extraction of the associated parasitics are presented. Electrical network and equivalent circuit are developed to model the chip-package interface including the effects of V/sub DD//V/sub SS/ planes. For single- and multichip packages, methods of calculating the "effective" inductance (L/sub eff/) as seen by the output drivers from their on-chip V/sub DD/ and V/sub SS/ buses to the tip of the package pin are explained. Variations from the conventional method (where all connections are assumed identical) of calculating L/sub eff/ are analyzed. Closed-form equations are given to estimate the simultaneous switching noise (SSN) on the on-chip V/sub DD//V/sub SS/ buses for packaged CMOS circuits. The contribution of reference plane (with and without perforation) parasitics on the SSN are investigated. Optimal package pin placement to minimize the plane inductance is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A programming course in bioinformatics for computer and information science students. (1996)

We have created a course entitled "Representations and Algorithms for Computational Molecular Biology" with three specific goals in mind. First, we want to provide a technical introduction for computer science and medical information science students to the challenges of computing with molecular biology data, particularly the advantages of having easy access to real-world data sets. Second, we want to equip the students with the skills required of productive research assistants in molecular biology computing research projects. Finally, we want to provide a showcase for local investigators to describe their work in the context of a course that provide adequate background information. In order to achieve these goals, we have created a programming course, in which three major projects and six smaller assignments are assigned during the quarter. We stress fundamental representations and algorithms during the first part of the course in lectures given by the core faculty, and then have more focused lectures in which faculty research interests are highlighted. The course stressed issues of structural molecular biology, in order to better motivate the critical issues in sequence analysis. The culmination of the course was a challenge to the students to use a version of protein threading to predict which members of a set of unknown sequences were globins. The course was well received, and has been made a core requirement in the Medical Information Sciences program.
Sample purification on a microfluidic device (2001)

Sample preparation has long been recognized as a significant barrier to the implementation of macroscopic protocols on microfabricated devices. Macroscopically, such tasks as removing salts, primers and other contaminants are performed by methods involving precipitation, specialized membranes and centrifuges, none of which are readily performed in microfluidic structures. Although some microfluidic systems have been developed for performing sample purification, their complexity may hinder the degree to which they can be implemented. We present a method of microchip-based sample purification that can be performed with even the simplest microfluidic designs. The technique is demonstrated by removing primers from a sample of amplified DNA, leaving only the product DNA. This provides a new sample preparation capability for microfluidic systems.
GENETICALLY MODIFIED, LIVE ATTENUATED DENGUE VIRUS TYPE 3 VACCINE CANDIDATES (2004)

Three novel recombinant dengue type 3 (DEN3) virus vaccine candidates have been generated from a DEN3 virus isolated from a mild outbreak of dengue fever in the Sleman area of central Java in Indonesia in 1978. Antigenic chimeric viruses were prepared by replacing the membrane precursor and envelope (ME) proteins of recombinant DEN4 (rDEN4) virus with those from DEN3 Sleman/78 in the presence (rDEN3/4Delta30(ME)) and the absence (rDEN3/4(ME)) of the Delta30 mutation, a previously described 30-nucleotide deletion in the 3' untranslated region. In addition, a full-length infectious cDNA clone was generated from the DEN3 isolate and used to produce rDEN3 virus and the vaccine candidate rDEN3Delta30. The chimeric viruses rDEN3/4(ME) and rDEN3/4Delta30(ME) appear to be acceptable vaccine candidates since they were restricted in replication in severe combined immune deficiency mice transplanted with human hepatoma cells, in rhesus monkeys, and in Aedes and Toxorynchites mosquitoes, and each was protective in rhesus monkeys against DEN3 virus challenge. The rDEN3/4(ME) and rDEN3/4Delta30(ME) viruses were comparable in all parameters evaluated, indicating that antigenic chimerization resulted in the observed high level of attenuation. Surprisingly, rDEN3Delta30 was not attenuated in any model tested when compared with wild-type rDEN3 and therefore, is not a vaccine candidate at present. Thus, the rDEN3/4(ME) and rDEN3/4Delta30(ME) antigenic chimeric viruses can be considered for evaluation in humans and for inclusion in a tetravalent dengue vaccine.
Verification and comparison of probabilistic precipitation forecasts using the TIGGE data in the upriver of Huaihe Basin (2011)

Abstract. The precipitation forecasts of three ensemble prediction systems (EPS) and two multi-model ensemble prediction systems (MM EPS) were assessed by comparing with observations from 19 rain gauge stations located in the Dapoling-Wangjiaba sub-catchment of Huaihe Basin for the period from 1 July to 6 August 2008. The sample Probabilistic Distribution Functions (PDF) of gamma distribution, the Relative Operating Characteristic (ROC) diagrams, the percentile precipitation and a heavy rainfall event are analyzed to evaluate the performances of the single and multi-model ensemble prediction system (EPS). The three EPS were from the China Meteorological Administration (CMA); the United States National Centre for Environment Predictions (NCEP); and the European Centre for Medium-Range Weather Forecasts (ECMWF), all were obtained from the TIGGE-CMA archiving centre (THORPEX Interactive Grand Global Ensemble, TIGGE). The MM EPS were created using the equal weighting method for every ensemble member over the test area, the first ( MM-1) consisted of all three EPS, the second (MM-2) consisted of the ECMWF and NCEP EPS. The results demonstrate the level of correspondence between deterioration in predictive skill and extended lead time. Compared with observations and with a lead time of one day, ECMWF performs a little better than other centre's. With over five days in advance, all the three EPS and the two MM EPS don't give reliable probabilistic precipitation forecasts. Both MM EPS can outperform CMA and NCEP for most of the forecasted days, but still perform a little worse than ECMWF. Though variation of daily percentile precipitation and ROC areas show MM-2 outperforms MM-1, gamma distribution indicates much similar performances for all 10-day forecast, and neither is superior to ECMWF.
A Small Biped Entertainment Robot (2002)

We propose a small biped entertainment robot prototype, Sony Dream Robot (SDR-3X) that realizes Motion Entertainment by entertaining people with its controlled dynamic motion performance. New key technologies developed for SDR-3X include the Intelligent Servo Actuator (ISA), the trine-actuator composed of a motor a built-in controller and a gear Another technology is Whole Body Coordinated Dynamic Motion Control. Both technologies realize dynamic, stable motion performance in dynamic biped walking, gymnastic motions and dancing. Human-rohot interactive performances are also described in this paper.
Biopharmaceutical Considerations In Topical Ocular Drug Delivery (2000)

1. Despite the accessibility of the front of the eye, efficient delivery of drug to treat various ocular disorders is a challenge to the formulation scientist. The majority of ophthalmic medications are formulated as eye drops. Due to anatomical constraints, the volume that can be administered is limited to approximately 30 microL. This, together with the efficient clearance system that exists in the front of the eye, makes it difficult to maintain an effective pre-ocular drug concentration for a desired length of time. Various formulation strategies have been used to increase pre-ocular retention of eye drops. The most successful of these has been the inclusion of viscosity enhancing polymers, particularly those able to interact with the mucous layer on the eye surface or those that can undergo a transition from a solution to a gel under the conditions of the pre-ocular area. 2. When the target site is intra-ocular, drug must be absorbed from the pre-ocular region into the eye. The main route for absorption is across the cornea. However, absorption of drug across the cornea is inefficient due to its impermeable nature and small surface area. Thus, the intra-ocular bioavailability of topically administered medications is typically less than 10%. 3. Corneal permeability favours moderately lipophilic compounds. These compounds often have a low aqueous solubility. Problems in ocular drug delivery and formulation are compounded for poorly soluble drugs that must be formulated as suspensions. 4. Reformulation of ophthalmic suspensions as solutions has many advantages. This may be achieved by complexation using cyclodextrins. Solubilization using cyclodextrins can overcome many of the formulation problems. However, it is unclear as to their potential for improving ocular bioavailability, which is seemingly drug dependent and may be influenced by both the physicochemical properties of the drug and the complex formed.
A brain–computer interface using electrocorticographic signals in humans (2004)

Brain-computer interfaces (BCIs) enable users to control devices with electroencephalographic (EEG) activity from the scalp or with single-neuron activity from within the brain. Both methods have disadvantages: EEG has limited resolution and requires extensive training, while single-neuron recording entails significant clinical risks and has limited stability. We demonstrate here for the first time that electrocorticographic (ECoG) activity recorded from the surface of the brain can enable users to control a one-dimensional computer cursor rapidly and accurately. We first identified ECoG signals that were associated with different types of motor and speech imagery. Over brief training periods of 3-24 min, four patients then used these signals to master closed-loop control and to achieve success rates of 74-100% in a one-dimensional binary task. In additional open-loop experiments, we found that ECoG signals at frequencies up to 180 Hz encoded substantial information about the direction of two-dimensional joystick movements. Our results suggest that an ECoG-based BCI could provide for people with severe motor disabilities a non-muscular communication and control option that is more powerful than EEG-based BCIs and is potentially more stable and less traumatic than BCIs that use electrodes penetrating the brain.
An implantable bolus infusion pump for use in freely moving, nontethered rats (2002)

One of the current constraints on functional neuroimaging in animals is that to avoid movement artifacts during data acquisition, subjects need to be immobilized, sedated, or anesthetized. Such measures limit the behaviors that can be examined, and introduce the additional variables of stress or anesthetic agents that may confound meaningful interpretation. This study provides a description of the design and characteristics of a self-contained, implantable microbolus infusion pump (MIP) that allows triggering of a bolus injection at a distance in conscious, behaving rats that are not restrained or tethered. The MIP is externally triggered by a pulse of infrared light and allows in vivo bolus drug delivery. We describe application of this technology to the intravenous bolus delivery of iodo[(14)C]antipyrine in a freely moving animal, followed immediately by lethal injection, rapid removal of the brain, and analysis of regional cerebral blood flow tissue radioactivity with the use of autoradiography. The ability to investigate changes in brain activation in nonrestrained animals makes the MIP a powerful tool for evaluation of complex behaviors.
Shape sensing using distributed fiber optic strain measurements (2004)

The two-dimensional shape of a multicore optical fiber is estimated from distributed strain measurements. The fiber's shape is calculated based on the local curvature of the fiber and assuming practical strain sensitivities.
Surrogate predictive biomarkers for response to anti-EGFR agents: state of the art and challenges (2007)

The epidermal growth factor receptor (EGFR) plays a key role in cancer development and progression in several human malignancies including non-small cell lung cancer (NSCLC). Several strategies aimed at inhibiting the EGFR have been investigated in the last years, including the use of small tyrosine kinase inhibitors (TKIs) directed against the intracellular domain of the receptor and monoclonal antibodies targeting its extracellular portion. Subgroups of patients who are more likely to respond to TKIs have been identified based on both clincal and biological features. Never-smoking history has emerged as the most relevant clinical characteristic predictive of response to TKIs in NSCLC, while presence of drugsensitive EGFR mutations and EGFR gene gain represent critical biological variables associated with an improved outcome for patients exposed to these agents. Recent studies have highlighted the existence of biological factors involved in intrinsic and acquired resistance to TKIs, including k-ras, HER-2 and EGFR exon 20 mutations. Increasing knowledge of EGFR biology and drug-receptor interactions will allow to identify individuals who are likely to derive a clinical benefit from the proposed targeted therapy, sparing refractory patients expensive and potentially toxic treatment.
The remarkable catalytic activity of the saturated metal organic framework V-MIL-47 in the cyclohexene oxidation (2010)

The remarkable catalytic activity of the saturated metal organic framework MIL-47 in the epoxidation of cyclohexene is elucidated by means of both experimental results and theoretical calculations.
Phosphorylation of thePseudomonas aeruginosaResponse Regulator AlgR Is Essential for Type IV Fimbria-Mediated Twitching Motility (2002)

The response regulator AlgR is required for both alginate biosynthesis and type IV fimbria-mediated twitching motility in Pseudomonas aeruginosa. In this study, the roles of AlgR signal transduction and phosphorylation in twitching motility and biofilm formation were examined. The predicted phosphorylation site of AlgR (aspartate 54) and a second aspartate (aspartate 85) in the receiver domain of AlgR were mutated to asparagine, and mutant algR alleles were introduced into the chromosome of P. aeruginosa strains PAK and PAO1. Assays of these mutants demonstrated that aspartate 54 but not aspartate 85 of AlgR is required for twitching motility and biofilm initiation. However, strains expressing AlgR D85N were found to be hyperfimbriate, indicating that both aspartate 54 and aspartate 85 are involved in fimbrial biogenesis and function. algD mutants were observed to have wild-type twitching motility, indicating that AlgR control of twitching motility is not mediated via its role in the control of alginate biosynthesis. In vitro phosphorylation assays showed that AlgR D54N is not phosphorylated by the enteric histidine kinase CheA. These findings indicate that phosphorylation of AlgR most likely occurs at aspartate 54 and that aspartate 54 and aspartate 85 of AlgR are required for the control of the molecular events governing fimbrial biogenesis, twitching motility, and biofilm formation in P. aeruginosa.
Machine models and registration (1994)

Equipment for pattern generation in the semiconductor industry have long been a critical part of the manufacturing process. As the industry matured and finer features were required on larger exposure fields, the complexity of these machines grew. The requirements of calibration soon taxed the ability of statistics to understand the complexities of and control required by the tools. In response, the industry adopted an analytical method of data analysis. Mathematical models describing the operation, design and behavior of these tools were developed. These models are called machine models and herein is contained a critical review of the technology to date. The development of machine models is shownfrom a historical standpoint. First the concepts of metrology and a clear explanation of the analytical method are presented. Then the development of modeling and how it was influenced by the automation of metrology in the mid 1980’s. The later sections describe models and their application to machine characterization and matching. These are followed by recent concepts in model building and evaluation. In doing so, it is shown how the concept of machine models are critical to the continued advancement of lithography and equipment development. A final section presents some previously unpublished work on the determination of machine precision. The work is supported by an appendix of derivations for the basic model elements.
High-efficiency oligonucleotide-directed plasmid mutagenesis. (1990)

A number of single- and double-base substitutions have been introduced into either the polylinker region or the lacZ gene in the plasmid vector pUC19. The efficiencies of these changes upon transfection of TG-1 bacterial cells were generally 70-80%. A strategy has been devised by which the wild-type DNA can be selectively destroyed. It is primarily based on the resistance of phosphorothioate internucleotide linkages to some restriction enzymes. A mismatch oligonucleotide is introduced into a gapped region and the gap is filled using three deoxynucleoside 5'-triphosphates and one deoxynucleoside 5'-[alpha-thio]triphosphate. Reaction with a restriction enzyme that is unable to hydrolyze phosphorothioates ensures that the DNA containing the mismatch oligonucleotide is only nicked. Concomitantly, the DNA that does not contain the desired mutation is linearized. Subsequent reactions with an exonuclease and DNA polymerase I yield mutant homoduplex DNA for transfection.
Bumpless Build-Up Layer Packaging (2001)

Abstract Bumpless Build-Up Layer (BBUL) is a novel package developed to meet future packaging technology requirements. The BBUL package provides the advantages of small electrical loop inductance and reduced thermomechanical stresses on low dielectric constant (low-k) die materials. Furthermore, it allows for high lead count, ready integration of multiple electronic and optical components [such as logic, memory, radio frequency, microelectromechanical systems (MEMS), among others], and inherent scalability. In the present paper we investigate and discuss some of the process, routing, electrical, thermal, and mechanical attributes of BBUL.
Comparable detection of acute myocardial infarction by creatine kinase MB isoenzyme and cardiac troponin I (1994)

Although measurement of cardiac troponin I (cTnI) is, in some situations, more specific for detection of cardiac injury than is measurement of the MB isoenzyme of creatine kinase (MBCK), its sensitivity and specificity relative to MBCK for detection of myocardial infarction has not been established. Accordingly, we studied prospectively 199 consecutive patients admitted to the coronary care unit. Values of MBCK and cTnI mass were determined in all samples. Of the 188 patients admitted with a suspicion of acute myocardial ischemia, 89 were diagnosed as having an acute myocardial infarction on the basis of the patterns of MBCK values. Eighty-six of these patients also had increased cTnI (concordance, 96.6%); three did not. Of the patients diagnosed as without infarction, five with unstable angina and symptoms in the day(s) prior to admission had increased cTnI, for a cTnI specificity of 94.9%. Receiver operating characteristic curve analysis indicated that cTnI and MBCK had statistically indistinguishable diagnostic accuracies for the detection of acute myocardial infarction.
Protection by Trehalose of DNA from Radiation Damage (1997)

The most serious damage to cells exposed to radiation is attributed mostly to effects on the structure of cellular DNA. We found that trehalose protects DNA from irradiation. In the presence of 10 mM trehalose, DNA can be protected from about 4 times higher doses of beta- and gamma-ray irradiation. The protective effect increases with the amount of the sugar. Other disaccharides, sucrose, and maltose had similar effects.
Synthesis of Pseudopeptides with Sulfoximines as Chiral Backbone Modifying Elements (2001)

The synthesis of pseudopeptides with a chiral alpha-sulfonimidoylcarboxy moiety in the backbone is described. Starting from readily available (Ss)-S-methyl S-phenyl sulfoximine and various cyclic and acyclic alpha-amino acids the desired products are obtained in good yields with peptide coupling methodology. Specific secondary structures caused by intramolecular hydrogen bonds may be adopted. Results of NMR studies to reveal conformational preferences will be discussed.