gebhart/patrepeval huggingface dataset:
A domain-specific language for modeling method definition: From requirements to grammar (2015)

The core process a modeling method engineer needs to accomplish starts with the acquisition of domain knowledge and requirements, and ends with the deployment of a usable modeling tool. In between, a key intermediate deliverable of this process is the modeling method specification which, ideally, should be platform independent. On one hand, it takes input from a structured understanding of the application domain and scenarios; on the other hand, it provides sufficiently structured input to support the implementation of tool support for modeling activities. It is quite common that such modeling methods are domain-specific, in the sense that they provide concepts from the domain as “first-class modeling citizens”. However, for the purposes of this paper, we raise the level of abstraction for “domain specificity” and consider “modeling method engineering” as the application domain. Consequently, we raise several research questions - whether a domain-specific language can support this domain, and what would be its requirements, properties, constructs and grammar. We propose an initial draft of such a language - one that abstracts away from meta-modeling platforms by establishing a meta <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> layer of abstraction where a modeling method can be defined in a declarative manner, then the final modeling tool is generated by automated compilation of the method definition for the meta-modeling environment of choice.
Ligation of Glycophorin A Generates Reactive Oxygen Species Leading to Decreased Red Blood Cell Function (2016)

Acute, inflammatory conditions associated with dysregulated complement activation are characterized by significant increases in blood concentration of reactive oxygen species (ROS) and ATP. The mechanisms by which these molecules arise are not fully understood. In this study, using luminometric- and fluorescence-based methods, we show that ligation of glycophorin A (GPA) on human red blood cells (RBCs) results in a 2.1-fold, NADPH-oxidase-dependent increase in intracellular ROS that, in turn, trigger multiple downstream cascades leading to caspase-3 activation, ATP release, and increased band 3 phosphorylation. Functionally, using 2D microchannels to assess membrane deformability, GPS-ligated RBCs travel 33% slower than control RBCs, and lipid mobility was hindered by 10% using fluorescence recovery after photobleaching (FRAP). These outcomes were preventable by pretreating RBCs with cell-permeable ROS scavenger glutathione monoethyl ester (GSH-ME). Our results obtained in vitro using anti-GPA antibodies were validated using complement-altered RBCs isolated from control and septic patients. Our results suggest that during inflammatory conditions, circulating RBCs significantly contribute to capillary flow dysfunctions, and constitute an important but overlooked source of intravascular ROS and ATP, both critical mediators responsible for endothelial cell activation, microcirculation impairment, platelet activation, as well as long-term dysregulated adaptive and innate immune responses.
A New Nonlinear Optical Borate Crystal K<sub>2</sub>Al<sub>2</sub>B<sub>2</sub>O<sub>7</sub> (KAB) (1998)

A new nonlinear optical (NLO) borate crystal K 2 Al 2 B 2 O 7 (Potassium Aluminum Borate, KAB) has been discovered. The structure has been established by 4-axis X-ray diffraction methods. The material crystallizes in the trigonal space group P321 with a = 8.5657(9) Å, C = 8.463(2) Å and Z = 3. KAB possesses a space arrangement similar to Sr 2 Be 2 B 2 O 7 (SBBO). A KAB crystal with a dimensions of 30×15×1 mm 3 was grown using the Top-Seeded Solution Growth (TSSG) method. The optical properties of KAB were measured.
Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism (2010)

Marinobacter adhaerens HP15 is the type strain of a newly identified marine species, which is phylogenetically related to M. flavimaris, M. algicola, and M. aquaeolei. It is of special interest for research on marine aggregate formation because it showed specific attachment to diatom cells. In vitro it led to exopolymer formation and aggregation of these algal cells to form marine snow particles. M. adhaerens HP15 is a free-living, motile, rod-shaped, Gram-negative gammaproteobacterium, which was originally isolated from marine particles sampled in the German Wadden Sea. M. adhaerens HP15 grows heterotrophically on various media, is easy to access genetically, and serves as a model organism to investigate the cellular and molecular interactions with the diatom Thalassiosira weissflogii. Here we describe the complete and annotated genome sequence of M. adhaerens HP15 as well as some details on flagella-associated genes. M. adhaerens HP15 possesses three replicons; the chromosome comprises 4,422,725 bp and codes for 4,180 protein-coding genes, 51 tRNAs and three rRNA operons, while the two circular plasmids are ~187 kb and ~42 kb in size and contain 178 and 52 protein-coding genes, respectively.
Check Reliability Based Bit-Flipping Decoding Algorithms for LDPC Codes (2010)

We introduce new reliability definitions for bit and check nodes. Maximizing global reliability, which is the sum reliability of all bit nodes, is shown to be equivalent to minimizing a decoding metric which is closely related to the maximum likelihood decoding metric. We then propose novel bit-flipping (BF) decoding algorithms that take into account the check node reliability. Both hard-decision (HD) and soft-decision (SD) versions are considered. The former performs better than the conventional BF algorithm and, in most cases, suffers less than 1 dB performance loss when compared with some well known SD BF decoders. For one particular code it even outperforms those SD BF decoders. The performance of the SD version is superior to that of SD BF decoders and is comparable to or even better than that of the sum-product algorithm (SPA). The latter is achieved with a complexity much less than that required by the SPA.
Microcalorimetry of Protein–Protein Interactions (2003)

Microcalorimetry can be used to determine directly the energetics and stoichiometry of macromolecular interactions by detecting the heat energy changes that, in most circumstances, accompany association or dissociation processes. These heat effects are small, but commercial instrumentation suitable for biological work is readily available and relatively easy to use. The fundamentals of modern microcalorimetry techniques have been covered earlier in this series and elsewhere (1–7), and some recent examples of its use for protein-protein and other interaction studies may be found in refs. 8–13. The two kinds of calorimetry most commonly used for investigating biomolecular systems are differential scanning calorimetry (DSC), in which changes brought about by increasing (or decreasing) temperature may be detected; and isothermal titration calorimetry (ITC), in which heat-energy changes during mixing of two solutions are measured. Both techniques can be used to examine protein-protein and other macromolecular interactions, though ITC is usually the more versatile and more readily interpretable technique.
Polyacrolein Microspheres as a New Solid Phase for Radioimmunoassay (1986)

Polyacrolein (PA) microspheres contain reactive aldehyde groups through which ligands containing primary amino groups such as proteins and drugs can be covalently bound in a single step at physiological pH. Antibodies against cyclic-AMP, digoxin and rabbit serum were thus coupled to PA microspheres. The immuno-microspheres were kept in suspension or freeze-dried, with insignificant decrease in their binding capacity. The conjugates were used in the respective radioimmunoassay (RIA) systems to facilitate the separation of the free and the antibody-bound 125I ligands, in comparison with precipitation of Protein A of Staphylococcus aureus. Cyclic-AMP was assayed using PA microspheres coupled either with the primary antibody or with anti-rabbit serum as a secondary antibody, in a buffer system, in chick plasma, in urine and in media in which avian dispersed kidney cells had been stimulated by various agents. The results obtained using the immuno-microspheres and the bacterial separation methods were indistinguishable. Other 125I-ligands, such as digoxin in buffer system or thyroxine and triiodothyronine in chick plasma, were assayed in the picogram range. Owing to the solubility of non crosslinked microspheres conjugates in toluene-based scintillation fluids, both the free and the bound fractions could be counted when using 3H-ligands. Corticosterone was assayed using this technique.
最轻保时捷——2010保时捷 Boxster Spyder (2009)

保时捷青睐于跑车的生产，但它似乎也更关注历史，或许很多人已经忘记或不清楚1953年那台扬名纽博格林赛道Eifel Race比赛的550 Spyder，但保时捷不会忘记。保时捷刚刚推出的这台全新的Boxster Spyder自然是最好的证据。
논문 : 질병 체험과 서사 (2010)

인간은 이야기를 하는 동물이다. 서사는 삶을 살아가면서 인간이 겪게 되는 경험을 이해하고 재구성하여 전달하는 역할을 하고, 이를 바탕으로 삶의 의미를 찾도록 해준다. 의학에서도 환자의 이야기를 귀담아 듣고 그 이야기를 통해 환자의 고통에 다가가려는 ``서사적 전통``이 오랜 기간 존재해 왔다. 그러나 의료 기술의 발달과 더불어 현대 의학이 점점 더 기계화되고 비인간화되는 오늘날, 의학의 ``서사적 전통``은 점차 빛을 잃어가고 있다. 하지만 서사는 생의학의 질병 개념으로는 포착할 수 없는 질병 체험의 문제를 이해하는데 유용하다. 질병 체험 서사는 질병이 몸, 시간, 자아의 측면에서 한 인간에게 얼마나 큰 영향을 주는 사건인지를 이해할 수 있게 해 준다. 그런 의미에서 현대 의학은 질병 체험서사를 자신의 영역으로 끌어들어야 한다. 현대 의학의 큰 결함으로 일컬어지는 환자 소외, 비인간화 등의 현상은 생의학이 환자나 의료인들의 주관성과 감성을 수용하지 못한 것에 기인하기 때문이다. 질병 체험 서사를 통해 환자는 질병이 자신의 삶에 갖게 되는 의미를 적극적으로 해석하고 탐구하는 기회를 갖게 된다. 의료인 또한 서사를 통해 환자의 실존적 고통에 다가갈 수 있을 뿐 아니라, 의료인이 갖추어야 할 실천적 지혜와 공감 등의 태도와 감수성을 기를 수 있다.
Optimizing oxygen extraction by vent gas analysis: process control and safety (1986)

On a developpe une methode permettant d'evaluer la quantite d'oxygene residuel dans l'espace de tete de la tour d'extraction apres une extraction oxygene-alcali. On presente les resultats obtenus dans plusieurs installations et on etudie les parametres influant sur l'oxygene residuel. On a aussi mesure la teneur en CO, sous-produit de la reaction E 0 . Le controle des teneurs en O 2 et CO dans les gaz residuels de E 0 est un element de securite et d'efficacite
Controlled Nucleation and Growth Process of Li<sub>2</sub>S<sub>2</sub>/Li<sub>2</sub>S in Lithium-Sulfur Batteries (2013)

Lithium-sulfur battery is a very promising energy storage system because of its high specific energy density. However, the dissolution and precipitation of soluble polysulfides during cycling initiate a series of chain reactions that significantly shorten battery lifespan. In order to understand the interfacial reactions occuring on the electrode surfaces, we employ a convenient electrochemical strategy to regulate the nucleation and precipitation of polysulfides on the electrode surface. The accumulation of detrimental Li2S on cathode is largely alleviated thus enabling very stable cycling of Li-S batteries. For example, more than 760 stable cycling are demonstrated with a reversible capacity of 500 mAh g−1. More importantly, the exposure of new lithium metal surface to the S-containing electrolyte is also greatly reduced through this strategy, largely minimizing the anode corrosion caused by polysulfides. The fundamental findings of this work provide valuable information on the electrochemical redistribution process of sulfur, which is unavoidable, during cycling and the corresponding anode evolutions under different testing conditions.
Nondestructive Measurement of Moisture Content Using a Parallel-Plate Capacitance Sensor for Grain and Nuts (2010)

A simple, low-cost instrument that measures impedance and phase angle was used along with a parallel-plate capacitance system to estimate the moisture content (MC) of in-shell peanuts and yellow-dent field corn. Moisture content of the field crops is important and is measured at various stages of their processing and storage. A sample of about 150 g of in-shell peanuts or corn was placed separately between a set of parallel plate electrodes and the impedance and phase angle of the system were measured at frequencies 1 and 5 MHz. A semi-empirical equation was developed for peanuts and corn separately using the measured impedance and phase angle values, and the computed capacitance and the MC values obtained by standard air-oven method. The multilinear regression (MLR) method was used for the empirical equation development using an Unscrambler 9.7 data analyzer. In this paper, a low-cost impedance analyzer designed and assembled in our laboratory was used to measure the impedance and phase angles. MC values of corn samples in the moisture range of 7% to 18% and in-shell peanuts in the moisture range of 9% to 20%, not used in the calibration, were predicted by the equations and compared with their standard air-oven values. For over 96% of the samples tested from both crops, the predicted MC values were within 1% of the air-oven values. This method, being nondestructive and rapid, will have considerable application in the drying and storage processes for peanuts, corn, and similar field crops.
Translation initiation at a downstream AUG occurs with increased efficiency when the upstream AUG is located very close to the 5' cap (1990)

The major late 16S mRNA species of simian virus 40 encodes both a 61-amino-acid protein, LP1, and the major virion protein, VP1. Although the initiation signal GCCAUGG is usually utilized at high efficiency, at least one-third of 40S ribosomal subunits bypass it when it is present on the major 16S mRNA of simian virus 40 (S. A. Sedman, P. J. Good, and J. E. Mertz, J. Virol. 63:3884-3893, 1989). The LP1 translation initiation codon is situated 10 bases from the 5' end of this mRNA. To determine whether the short length of the untranslated leader of this mRNA affects the efficiency of translation initiation at the LP1 initiation signal, monkey cells were transfected with plasmids which encode major late 16S-like mRNAs with 5' untranslated regions (UTRs) of 6 or 44 bases. Decreasing the length of the 5' UTR from 44 to 6 bases resulted in a 30% decrease in translation initiation at the LP1 AUG and a threefold increase in synthesis of VP1. When the VP1 open reading frame was replaced with the chloramphenicol acetyltransferase open reading frame, the reduction in 5' UTR length resulted in a 70% decrease in translation initiation at the LP1 AUG and a 30% increase in chloramphenicol acetyltransferase synthesis. Therefore, ribosomes bypass an AUG codon more efficiently when it is located very close to the 5' end of the mRNA.
Wireless smart power saving system for home automation (2012)

Mostly in home and office appliances like light and fan are manually controlled which leads to power wastage. They are left ON even if there is no usage and even when the appliances are in use their operation is not controlled by environmental conditions like daylight and temperature variation. By making a smart automated controlling system for appliances we can save the power by huge amount. In this paper we are providing a solution for preventing the wastage of power in a comfortable and cost effective way. Our system consists of an electronic door lock and power saving module. When the person enters the correct password in door lock the power saving module is switched on. The power saving module switches the appliances in the room based on the presence of the person. It also controls the power delivered to fan and light according to temperature of room and natural daylight intensity.
Assessment of the thrombin generation assay in haemophilia: Comparative study between fresh and frozen platelet‐rich plasma (2012)

The severity of haemophilia A has traditionally been classified by the dosage of factor VIII (FVIII) by one-step coagulation tests. However, an homogeneous group of patients with similar FVIII levels show clinical heterogeneity and 10-15% of the patients classified as severe haemophilia do not have a severe bleeding phenotype. Traditional tests used for measuring FVIII are not capable of detecting other prohaemorrhagic or prothrombotic factors. Global tests as the thrombin generation assay (TGA) may detect these haemostatic factors. So TGA may be an additional tool for classifying the actual severity of haemophilia. Our group is carrying out correlation tests between FVIII and TGA in platelet-poor and -rich plasmas (PPP and PRP, respectively). PRP has the inconvenience that must be done freshly soon after blood extraction. Our aim is to study the differences between TGA performed with fresh and frozen PRP and PPP and its implementation in multicenter studies. We included 70 patients with severe haemophilia A in prophylactic treatment. Venous blood drawing was obtained prior to administration of FVIII, at the trough levels. FVIII measurement and TGA were performed in fresh and frozen PRP and PPP. The platelet absence caused a significant decrease in TGA although PPP and PRP correlated well. Frozen samples gave different results in PPP, but there were no significant differences between fresh and frozen PRP. This fact enables using frozen PRP in multicenter studies with a TGA-specialized laboratory for reclassifying haemophilia severity and for pharmacokinetic studies with TGA.
Co-Expression of Yersinia pestis F1- and V-Ags by the Same Salmonella Vaccine Protects Against Nasal Y. pestis Challenge (41.14) (2007)

Abstract To test whether the protective antigens (Ags) to Yersinia pestis can be simultaneously delivered, the Y. pestis cafI operon encoding the F1 Ag, and virulence Ag (V-Ag) were cloned into attenuated Salmonella vaccine vector. F1-Ag expression was controlled under its endogenous promoter from the cafI operon and amply expressed; a chimeric promoter consisting of ptetS and pphoP in the pV55 plasmid showed enhanced V-Ag expression. Immunofluorescence data showed that the single construct, Salmonella-(F1-V)Ags, could co-express both Ags. When orally tested, the Salmonella-(F1-V)Ags vaccine elicited elevated Ab titers to both F1- and V-Ags. Supportive CD4+ T cell responses showed that IFN-γ was elevated in response to F1-Ag restimulation and to a lesser degree, IL-4 and IL-13. V-Ag restimulation showed much less IFN-γ and IL-4 production. IL-10 responses were equivalent to both Ags. IgG1 and IgG2a subclass responses to both Ags were equivalent. Upon nasal challenge, immunized mice required immunity to both F1- and V-Ags because the mice vaccinated with Salmonella-(F1-V)Ags protected against 100 LD50 Y. pestis, but mice immunized with Salmonella constructs bearing a single Ag showed impaired efficacies. These results show that a single Salmonella vaccine can deliver both F1- and V-Ags to effect immune protection against Y. pestis. This work is supported by AI-56286 and NIH 1U54 AI-06537.
Technological hybridization for efficient runtime reconfigurable FPGAs (2007)

The goal of this paper is to propose an FPGA using emerging non volatile technologies for its configuration memory. Studies on magnetic memories have already been carried out (Bruchon et al., 2006) but solid electrolyte and phase change memories are also good candidates for such type of application. Features of these technologies can provide some interesting characteristics to the FPGA such as short writing time with non volatile technology. A small structure (RSRAM) for remanent SRAM is used to convert information from these technologies into electrical information. This structure naturally provides some more features like partial and shadowed reconfiguration
Air-induced fluorescence bursts from single semiconductor nanocrystals (2004)

We observe a dramatic enhancement of the fluorescence intensity from single core∕shell CdSe∕ZnS nanocrystals upon sudden exposure to air from an evacuated surrounding. Both the number of particles contributing to emission increases as well as the average emission intensity from a single particle, leading to an overall fluorescence rise by a factor of 60. A common power-law distribution of both on- and off times of single nanocrystals is observed independent of shell thickness and environment. We propose that electron transfer to oxygen, which is facilitated by the presence of water, leads to a neutralization of charged, nonemissive nanocrystals.
Germline Stem Cells Anchored by Adherens Junctions in the <i>Drosophila</i> Ovary Niches (2002)

How stem cells are recruited to and maintained in their niches is crucial to understanding their regulation and use in regenerative medicine. Here, we demonstrate that DE-cadherin-mediated cell adhesion is required for anchoring germline stem cells (GSCs) in their niches in the Drosophila ovary. Two major components of this adhesion process, DE-cadherin and Armadillo/beta-catenin, accumulate at high levels in the junctions between GSCs and cap cells, one of the niche components. Removal of these proteins from GSCs results in stem cell loss. Furthermore, DE-cadherin is required for recruiting GSCs to their niche. Our study demonstrates that anchorage of GSCs in their niche by DE-cadherin-mediated adhesion is important for stem cell maintenance and function.
Synthesis of new quinoline derivatives as antimicrobial agents. (1986)

2-Hydroxyquinoline-4-hydrazide was condensed with some aromatic aldehydes and acetophenones to give the hydrazones 1a-h. It was also reacted with HCOOH, PhCOCl and p-CH3O-PhCOCl to afford 2a-c. Cyclization of 2b was completed by using PPA, POCl3 and/or P2S5, which gave compounds 3, 4, and 6 respectively. Reaction of 4 with some amines gave the corresponding derivatives 5a-f. The thiosemicarbazide 7 was cyclized under acid and basic condition to give the thiadiazolyl-8 and triazolyl-10 derivatives.
A linear time erasure-resilient code with nearly optimal recovery (1996)

We develop an efficient scheme that produces an encoding of a given message such that the message can be decoded from any portion of the encoding that is approximately equal to the length of the message. More precisely, an (n,c,l,r)-erasure-resilient code consists of an encoding algorithm and a decoding algorithm with the following properties. The encoding algorithm produces a set of l-bit packets of total length cn from an n-bit message. The decoding algorithm is able to recover the message from any set of packets whose total length is r, i.e., from any set of r/l packets. We describe erasure-resilient codes where both the encoding and decoding algorithms run in linear time and where r is only slightly larger than n.
Theory of 3‐D angle gathers in wave‐equation imaging (2004)

I present two methods for constructing angle gathers in 3‐D seismic imaging by downward extrapolation. Angles in angle gathers refer to the scattering angle at the reflector and provide a natural access to analyzing migration velocity and amplitudes. In the first method, angle gathers are extracted at each downward‐continuation step by mapping transformations in constant‐depth frequency slices. In the second method, one extracts angle gathers after applying the imaging condition by transforming local offset gathers in the depth domain. The second approach generalizes previously published algorithms for angle‐gather construction in 2‐D and common‐azimuth imaging.