gebhart/patrepeval huggingface dataset:
Framing Risk Regulation : A Critical Reflection (2013)

Over a decade ago I was involved in a group project that focused on developing a regulatory model concerning the implementation of the precautionary principle in the EU. The project involved a number of workshops and in those workshops I used to joke about the fact that while there were many different frameworks being produced to represent risk regulation, these diagrams basically fell into two different categories. In the first category there were those diagrams that characterised risk regulation as a linear process involving usually a scientific process of risk assessment and then political processes of risk management and risk communication. In the second category there were those diagrams that had lots of looping arrows going all over the place that represented the fact that risk regulation was an iterative process that constantly involved many scientific, socio-political and other inputs. Behind my joking was a sense of hope. The linear diagrams did have their minimalist appeal, but the messy diagrams captured much of the reality of this area of regulatory practice.
Iron Catalysts for the Growth of Carbon Nanofibers: Fe, Fe<sub>3</sub>C or Both? (2011)

Iron is a widely used catalyst for the growth of carbon nanotubes (CNTs) or carbon nanofibers (CNFs) by catalytic chemical vapor deposition. However, both Fe and Fe–C compounds (generally, Fe3C) have been found to catalyze the growth of CNTs/CNFs, and a comparison study of their respective catalytic activities is still missing. Furthermore, the control of the crystal structure of iron-based catalysts, that is α-Fe or Fe3C, is still a challenge, which not only obscures our understanding of the growth mechanisms of CNTs/CNFs, but also complicates subsequent procedures, such as the removal of catalysts for better industrial applications. Here, we show a partial control of the phase of iron catalysts (α-Fe or Fe3C), obtained by varying the growth temperatures during the synthesis of carbon-based nanofibers/nanotubes in a plasma-enhanced chemical vapor deposition reactor. We also show that the structure of CNFs originating from Fe3C is bamboo-type, while that of CNFs originating from Fe is not. Moreover, we directly compare the growth rates of carbon-based nanofibers/nanotubes during the same experiments and find that CNFs/CNTs grown by α-Fe nanoparticles are longer than CNFs grown from Fe3C nanoparticles. The influence of the type of catalyst on the growth of CNFs is analyzed and the corresponding possible growth mechanisms, based on the different phases of the catalysts, are discussed.
Fault-tolerance for Stateful Application Servers in the Presence of Advanced Transactions Patterns (2006)

Replication is widely used in application server products to tolerate faults. An important challenge is to correctly coordinate replication and transaction execution for stateful application servers. Many current solutions assume that a single client request generates exactly one transaction at the server. However, it is quite common that several client requests are encapsulated within one server transaction or that a single client request can initiate several server transactions. In this paper, we propose a replication tool that is able to handle these variations in request/transaction association. We have integrated our approach into the J2EE application server JBoss. Our evaluation using the ECPerf benchmark shows a low overhead of the approach.
Defect-oriented cell-internal testing (2010)

Industry is facing very high quality requirements for today's and tomorrow's ICs. Especially in the automotive market these quality requirements need to be fulfilled. To achieve this we need to improve currently used test methods and fault models to improve the overall defect coverage. This paper presents two new methodologies to significantly improve this situation. One method will focus on cell-internal Bridges over a wide range of Bridge resistor values and the second method concentrates on library cell-internal high-resistive Open defects. The fault models used during the ATPG are enhanced to directly target the layout-based intra-cell Open and Bridge defects. Both methods have been evaluated on 1500 library cells of a 65nm technology. In addition the wide range of intracell Bridges has been evaluated on 10 real industrial designs with up to 60 million faults. Various results are presented from all 1500 library cells and from the 10 industrial designs as well.
Heterochromatin protein 1 is recruited to various types of DNA damage (2009)

Heterochromatin protein 1 (HP1) family members are chromatin-associated proteins involved in transcription, replication, and chromatin organization. We show that HP1 isoforms HP1-alpha, HP1-beta, and HP1-gamma are recruited to ultraviolet (UV)-induced DNA damage and double-strand breaks (DSBs) in human cells. This response to DNA damage requires the chromo shadow domain of HP1 and is independent of H3K9 trimethylation and proteins that detect UV damage and DSBs. Loss of HP1 results in high sensitivity to UV light and ionizing radiation in the nematode Caenorhabditis elegans, indicating that HP1 proteins are essential components of DNA damage response (DDR) systems. Analysis of single and double HP1 mutants in nematodes suggests that HP1 homologues have both unique and overlapping functions in the DDR. Our results show that HP1 proteins are important for DNA repair and may function to reorganize chromatin in response to damage.
Upregulation of interferon-alpha receptor expression in hydroxyurea-treated leukemia cell lines. (1997)

Thus, HU may have an ability to enhance the response to IFN-alpha probably because of its ability to upregulate the IFN-alpha receptors, suggesting that this may be involved in the mechanism of effective combination therapy of IFN-alpha with HU.
Feature-based off-line programming of coordinate measuring machines (2002)

The paper describes an off-line programming system for coordinate measuring machines based on a novel approach. Input data to the system is the geometric model produced by a CAD system. Using the picture of the part, the user can select the surface elements to be inspected. He or she has to provide the tolerance data as additional information. First the workpiece setup is decided: the position, orientation, and accessibility of the part is determined. Next the system automatically generates an optimal distribution of the measuring points for the surfaces to be inspected and the local probe path. Probe clusters are built together on an interactive way using a set of building blocks. A time optimal sequence of the inspection operations is computed using heuristic algorithms. At this stage all information needed for the CMM program is available and will be combined in a device independent DMIS format, which in turn can be converted into equipment specific programs.
Reminiscing View: Event-Based Browsing of Consumer's Photo and Video-Clip Collections (2008)

The "Reminiscing View" is a visualization system for browsing hierarchically organized photo and video-clip collections. The current Reminiscing View prototype supports browsing of hierarchical temporal event clusters. Users simply upload their pictures and video clips to a server and their collection is automatically clustered into hierarchical temporal events. They can then browse events in a chronologically ordered spiral or grid view and explore details of each event. They can also filter the displayed media by date, text-based search, and sharing group. The addition of a remote control interface to the system allows users to browse their collection in a ldquolean backrdquo setting such as a living room environment. This paper describes the system and interface of the Reminiscing View. It also presents results and implications of a user study conducted on an earlier version of the system.
Cell Separation Science and Technology (1991)

There are several reasons for isolating subpopulations of living cells, including biochemical study, product analysis in non-clonogenic cells, selection of fused cells, isolation of rare cell types for cloning, preparation of pure cells for transplantation, and bioreactor maintenance. Methods for separating cells include flow sorting, sedimentation, biphasic extraction, field-flow fractionation, affinity methods, magnetically enhanced affinity methods, and electrophoresis. Each method can be considered in terms of its resolution, purity, gentleness, convenience and cost. Recent advances in each of these methods improves its utility in routine cell-separation practice and its potential for scale-up.
Pump Speed Waveform Analysis to Detect Aortic Valve Opening in Patients on Ventricular Assist Device Support (2015)

As the aortic valve (AV) opens, the pump pressure head remains constant, which is reflected as a "notch/plateau" in pump pressure and flow signals. However, instantaneous flow estimation may be influenced by friction and is particularly difficult in axial pumps. Therefore, a new method to determine the duration of AV opening based on the area under the curve (AUC) of the power spectral density analysis of pump speed signal was developed. Data from patients implanted with HeartWare HVAD left ventricular assist device were studied at different pump speeds, with simultaneous transthoracic echocardiography in two cohorts. In the first group, pump data of 15 patients were used to investigate the ability to discriminate between an open and closed AV. In the second cohort of a further 13 patients, the duration of AV opening was measured from digitized M-mode images, and the relationship between the AV opening time and the new method assessed. In 14 of the initial 15 patients, AV status could be discriminated using only one threshold for all patients. In the second cohort, gradual speed reduction resulted in aortic valve opening in 12 of the 13 patients. The correlation between AV opening duration and AUC was 0.96 ± 0.03. Regression analysis indicated a linear relationship in each of the patients with a small error between the fit and the measured opening time (root mean square error = 11.0 ± 7.6 ms). However, the slopes (69.0 ± 52.8) and intercepts (-31.4 ± 78.0) varied widely between patients. The sensitivity and specificity for the new method using AUC threshold of 0.95 for aortic valve closure was 95% and 91%, respectively. The newly developed method to detect AV opening not only provides information on the AV status during LVAD support (open/closed) but also gives insight into the duration of AV opening. Because the slope of the relationship varies from patient to patient, initial training and adaptation of the method to each patient seems to be required.
The stereographic projection with primitive radius of 50 centimeters (1940)

Joseph F. Cohalan, S.J., formerly at Georgetown University and now at Woodstock College, Maryland, in his master's dissertation entitled “The seismologist's problem and the method of Saint Hilaire,” studied the question of securing a more open scale for the graphical determination of epicenters from reported epicentral distances. He found that the use of navigator's plotting charts was not practical, but that a stereographlc projection with a primitive radius of 50 cm was very promising. This allows 4.4 mm for a degree at the center of the map, and an area 40° each way in latitude and longitude can be constructed on an ordinary typewriting sheet. Throughout this area 1/64 inch = 10 km.
Functionalization of Bispecific Therapeutic Antibodies Based on Protein Engineering (2015)

Although antibodies have been used as molecularly targeted agents for difficult-to-treat diseases such as cancers, the high production costs associated with mammalian expression systems continue to be a drawback. In addition, the clinical efficacy of conventional IgG antibodies is limited. Several types of recombinant antibody (e.g. fused with anticancer drugs, multivalent, or multispecific) have been designed in efforts to develop next-generation antibodies with higher functionality. We used protein engineering to construct several anticancer recombinant antibodies by developing bispecific antibodies that induced specific antitumor effects against cancer cells through the recruitment of lymphocytes. We found that a humanized small bispecific antibody (Ex3) that targets epidermal growth factor receptor on tumor cells and CD3 on T lymphocytes had marked anticancer activity. Furthermore, the function of Ex3 was enhanced by fusion with the human Fc region, domain rearrangement, multimerization, and affinity maturation; a combination of these modifications showed at least additive cytotoxic effects. Interestingly, merely rearranging the domain order of Ex3 induced substantial cytotoxic enhancements, even though the structural format remained the same. Here, we describe our efforts to develop highly functional bispecific antibodies as next-generation therapeutic antibodies using protein engineering.
Preparation, Electronic Structure, and Photoluminescence Properties of Eu<sup>2+</sup>- and Ce<sup>3+</sup>/Li<sup>+</sup>-Activated Alkaline Earth Silicon Nitride MSiN<sub>2</sub> (M = Sr, Ba) (2008)

The electronic structure of alkaline-earth silicon nitride MSiN2 (M = Sr, Ba) was calculated using the CASTEP code. BaSiN2 is calculated to be an intermediate band gap semiconductor with a direct energy gap of about 2.9 eV, while SrSiN2 is an intermediate band gap semiconductor with an indirect energy gap of about 3.0 eV. As expected, the calculated optical band gaps of MSiN2 (M = Ba, Sr) are lower compared to the experimentally determined values (about 4.1 eV for BaSiN2 and 4.2 eV for SrSiN2). In addition, the luminescence properties of Eu2+ and Ce3+ in MSiN2 (M = Sr, Ba) have been studied. Ba1−xEuxSiN2 (0 < x ≤ 0.1) shows a broad emission band in the wavelength range of 500–750 nm with maxima from about 600 to 630 nm with increaseing Eu2+ concentration, while Sr1−xEuxSiN2 (0 < x ≤ 0.1) shows a broad emission band in the wavelength range of 550–850 nm with maxima from 670 to 685 nm with increasing Eu2+ concentration. The high absorption and strong excitation bands of M1−xEuxSiN2 (0 < x ≤ 0.1; M = Sr, Ba) in the wavelength range of 300–530 m are very favorable properties for application as light-emitting-diode conversion phosphors. Ce3+- and Li+- codoped MSiN2 (M = Sr, Ba) exhibits a broad emission band in the wavelength range of 400–700 nm with a peak center at about 485 nm for BaSiN2 and about 535 nm for SrSiN2. A comparison is made between the luminescence properties of Eu2+ and Ce3+ in the Sr versus Ba compounds. The long-wavelength excitation and emission of Eu2+ and Ce3+ ions in the host of MSiN2 (M = Sr, Ba) are attributed to the effect of a high covalency and a large crystal field splitting on the 5d bands of Eu2+ and Ce3+ in the nitrogen coordination environment.
Activation of Human O6-Alkylguanine-DNA Alkyltransferase by DNA (1994)

The effect of DNA on the activity of human O6-alkylguanine-DNA alkyltransferase was investigated by using O6-benzylguanine as a substrate or inhibitor. The sensitivity of the alkyltransferase to inactivation by O6-benzylguanine was increased by addition of calf thymus DNA. In order to investigate this phenomenon in more detail, the ability of the alkyltransferase to convert O6-benzyl[8-3H]guanine to [8-3H]guanine was measured. The rate of guanine production was increased about 6-fold by addition of DNA. The effect of DNA was completely abolished by addition of 0.2 M NaCl, which had no effect on the reaction in the absence of DNA. When a mutant P140A alkyltransferase, which is known to be less sensitive to inactivation by O6-benzylguanine presumably as a result of steric hindrance, was used, the rate of reaction was increased by a considerably larger amount, about 16-fold. Oligodeoxynucleotides were able to stimulate the production of guanine from O6-benzylguanine. Single-stranded oligodeoxynucleotides were as effective as double-stranded, and a maximal stimulation was obtained with a 12-mer. These results demonstrate that the alkyltransferase binds to a region of DNA covering at most 12 bases and undergoes a conformational change which facilitates the reaction of adducts at the O6-position of guanine with the cysteine acceptor site on the protein. When O6-benzyl[8-3H]deoxyguanosine was used as a substrate, the addition of DNA decreased the rate of formation of 2'-deoxy[8-3H]guanosine. Inactivation of the alkyltransferase by O6-benzyldeoxyguanosine was also inhibited by DNA addition.(ABSTRACT TRUNCATED AT 250 WORDS)
A Rb 532 nm Stark anomalous dispersion optical filter for doubled Nd:YAG lasers (2002)

A Rb 532 nm Stark anomalous dispersion optical filter consists of an atomic vapor cell between crossed polarizers subjected to an electrical field transverse to the optical path, and a constant magnetic field along the optical path. The color glass filters are used to reject the infrared radiation. The 795 nm optical pumping is needed to populate the lower level of the filter transition. When linearly polarized light travels through a dispersive atomic vapor cell, a polarization rotation occurs. This polarization rotation is mainly due to the resonant Faraday effect.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Loop‐folding scheduling by using BOTTOM‐UP approach (1998)

This paper proposes an effective scheduling algorithm called BOTTOM-UP for loop-folding scheduling. The loop-folding is a scheduling algorithm for higher-layer VLSI synthesis to shorten the latency of operations which have such processing sequence dependency as DSP algorithm, and repeat the same process (process unit) many times in a restricted hardware resource. The proposed algorithm, BOTTOM-UP, makes a scheduling to minimize the latency and execution time by using loop-folding effectively. BOTTOM-UP uses the result of the ALAP scheduling as an initial scheduling, and makes it possible to operate in high speed by reassigning operations from the latest control step while fulfilling the resource constraints and maintaining data sequence dependency. Furthermore, latency and execution time are minimized by giving high priority to the longest path operation. © 1998 Scripta Technica. Electron Comm Jpn Pt 3, 81(6): 39–51, 1998
Dissection of the structure and activity of the tyrosyl-tRNA synthetase by site-directed mutagenesis (1987)

To understand an enzyme reaction, one has to characterize the bound substrates, intermediates, products, and transition states on the reaction pathway and determine the interaction energies between them and the enzyme as the reaction proceeds. Site-directed mutagenesis is invaluable in this task, enabling the systematic dissection of the active site. Residues involved in catalysis may be detected and the energetics probed. The contributions of each hydrogen-bonding site chain in the active site of the tyrosyl-tRNA synthetase to binding and catalysis are being determined by making sensible mutations, which remove defined interactions with the substrates. The difference in free energy between complexes of wild-type and mutant enzymes gives the apparent binding energy of the relevant side chain in each complex. By this means, the following have been determined: the contributions of different types of hydrogen bonds to specificity; their roles in catalysis; the importance of enzyme--substrate versus enzyme--transition-state versus enzyme--intermediate complementarity; the fine tuning of enzyme catalysis during "evolution"; and the existence of linear free energy relationships between rate and binding constants. Prior to these studies, the mechanism of activation by the aminoacyl-tRNA synthetases was totally unknown. It is now seen that catalysis results solely from the use of binding energy. There are residues that do not bind the substrates in the ground state but stabilize just the transition state, consistent with the classical ideas of Haldane and Pauling of enzyme--transition-state complementarity. There are, however, regions of the protein that bind the ribose ring more tightly in the intermediate tyrosyl adenylate than in the transition state.(ABSTRACT TRUNCATED AT 250 WORDS)
When the lights go out: the evolutionary fate of free‐living colorless green algae (2015)

The endosymbiotic origin of plastids was a launching point for eukaryotic evolution. The autotrophic abilities bestowed by plastids are responsible for much of the eukaryotic diversity we observe today. But despite its many advantages, photosynthesis has been lost numerous times and in disparate lineages throughout eukaryote evolution. For example, among green algae, several groups have lost photosynthesis independently and in response to different selective pressures; these include the parasitic/pathogenic trebouxiophyte genera Helicosporidium and Prototheca, and the free-living chlamydomonadalean genera Polytomella and Polytoma. Here, we examine the published data on colorless green algae and argue that investigations into the different evolutionary routes leading to their current nonphotosynthetic lifestyles provide exceptional opportunities to understand the ecological and genomic factors involved in the loss of photosynthesis.
Participation of the molecular chaperone DnaK in intracellular growth of <i>Brucella suis</i> within U937‐derived phagocytes (1996)

In the intracellular bacterium Brucella suis, the molecular chaperone DnaK was induced under heat-shock conditions and at low pH. Insertional inactivation of dnaK and dnaJ within the dnaK/J locus led to the conclusion that DnaK, but not DnaJ, was required for growth at 37 degrees C in vitro. Viability of the dnaK null mutant was also greatly affected at low pH. Under conditions allowing intracellular multiplication, the infection of U937-derived phagocytes resulted in long-lasting DnaK induction in the wild-type bacteria. In infection experiments performed with both mutants at the reduced temperature of 30 degrees C, the dnaK mutant of B. suis survived but failed to multiply within U937 cells, whereas the wild-type strain and the dnaJ mutant multiplied normally. Complementation of the dnaK mutant with the cloned dnaK gene restored growth at 37 degrees C, increased resistance to acid pH, and increased intracellular multiplication. This is the first report of the effects of dnaK inactivation in a pathogenic species, and of the temperature-independent contribution of DnaK to intracellular multiplication of the pathogen B. suis.
Clindamycin-Induced Enterocolitis in Hamsters (1978)

A lethal enterocolitis was induced in hamsters by oral or parenteral administration of clindamycin in amounts comparable to those used in treatment of humans. The intestinal lesions were characterized histologically as an acute inflammatory reaction with pseudomembrane formation and resembled the lesions seen in humans with antibiotic-induced colitis. Results of quantitative stool cultures showed the numbers of Peptostreptococcus and Corynebacterium decreased in animals with colitis after challenge with 100 mg of clindamycin/kg, while numbers of Escherichia coli, Streptococcus faecalis, and clindamycin-resistant Clostridium sordellii and Clostridium difficile increased. Bacteria were not seen within the intestinal lesions. Viruses were not isolated from hamsters with colitis. Although the pathogenesis of this syndrome is not completely established, the evidence is consistent with the hypothesis that the disease is caused by clostridial toxins and that the production of these toxins by organisms within the intestines is enhanced by the effects of clindamycin upon the bowel flora.