gebhart/patrepeval huggingface dataset:
Exergy as a means for process integration in integrated steel plants and process industries (2009)

Exergy analysis can be a useful tool for process comparison and improvement in industrial energy systems. Examples from three branches are given: pulp and paper, bio refineries (ethanol) and steel production. The application and development of exergy analysis in an integrated steel plant is shown together with description and explanations on destroyed and lost exergy. Implementation for energy conservation and use as a pedagogic tool is discussed.
Disturbed Matrix Metalloproteinase Activity of Bruch's Membrane in Age-Related Macular Degeneration (2011)

The reduction in the levels of activated MMP2 and -9 may be responsible for impaired matrix degradation of Bruch's membrane, leading to the pathology associated with AMD. The degradation pathway is therefore a viable therapeutic target for future intervention.
Etude morphologique du futur des verbes irreguliers en moyen francais (1997)

본 연구는 중세 불어에서의 불규칙 동사 단순 미래 시제의 형태론적 연구이다. 본 연구에서 우리는 14-15세기의 불문학 작품을 자료체로 선정하였고, 이들 자료체에 나타난 불규칙 동사의 미래형을 추출하여 유사한 통사적 특성에 따라 -ir, -re, -oir의 세 그룹으로 분류하였다. 자료체 분석의 결과, 첫째로 -ir 동사의 경우, 직설법 현재의 어간+ai의 형태론적 형성은 venir, tenir 그룹의 동사에서만 가능하며, 부정법+ai 의 형태론적 형성은 그 외의 -ir 동사에서 가능하였다. 둘째로, -ir 동사의 경우, 모음 e의 존재 여부가 미래 형태에서 중요한 변수로 작용하고 있어, 고대 불어의 흔적을 여전히 간직하고 있음을 알 수 있다. 아울러 부정법+ai 의 형태는 -re, -oir의 두 동사 그룹에서 가능하지만, -oir 그룹의 동사에서 더 안정된 모습을 보인다. 마지막으로 조동사 avoir와 e＾tre의 경우, e＾tre 동사의 현대적 용법은 중세불어기 내내 널리 사용되었지만, avoir 동사의 현대적 용법은 15세기부터 등장하여 e＾tre 동사보다 발전과정이 뒤지고 있음을 알 수 있었다. 이상의 중세불어에서의 불규칙 동사에 대한 형태론적 분석은 미래형태가 어떠한 변화 발전과정을 거쳐 중세불어의 용법에 이르고 있으며, 이들 동사가 어느 시기에 현대적 용법으로 사용되었는지를 구체적으로 고찰해 볼 수 있었다.
Lipid‐induced conformational changes in glucagon, secretin, and vasoactive intestinal peptide (1982)

Abstract The CD of glucagon, secretin, and vasoactive intestinal peptide has been studied as a function of temperature in water and in aqueous solutions of dodecyl sulfate, phosphatidyl glycerol, and L ‐α‐phosphatidic acid (dipalmitoyl). The anionic detergent and lipids induce helix formation in all three peptides, with the amount of induced helical content increasing in the order glucagon < secretin < vasoactive intestinal peptide. These observations are subject to quantitative rationalization using a matrix formulation for the configuration partition function. In this formulation the major conformational consequences of the interaction with anionic lipids or detergents is an increase in the probability for helix formation by arginyl, histidyl, and lysyl residues. The region in which helix formation is maximal is found to be at amino acid residues 13–20 in all three peptides. Other studies have implicated this portion of the polypeptide chain in receptor binding. Thus, the helical segment induced by interaction with anionic lipids may play an important physiological role.
Xaa-Arg-Gly Triplets in the Collagen Triple Helix Are Dominant Binding Sites for the Molecular Chaperone HSP47 (2002)

HSP47 is an essential procollagen-specific molecular chaperone that resides in the endoplasmic reticulum of procollagen-producing cells. Recent advances have revealed that HSP47 recognizes the (Pro-Pro-Gly)(n) sequence but not (Pro-Hyp-Gly)(n) and that HSP47 recognizes the triple-helical conformation. In this study, to better understand the substrate recognition by HSP47, we synthesized various collagen model peptides and examined their interaction with HSP47 in vitro. We found that the Pro-Arg-Gly triplet forms an HSP47-binding site. The HSP47 binding was observed only when Arg residues were incorporated in the Yaa positions of the Xaa-Yaa-Gly triplets. Amino acids in the Xaa position did not largely affect the interaction. The recognition of the Arg residue by HSP47 was specific to its side-chain structure because replacement of the Arg residue by other basic amino acids decreased the affinity to HSP47. The significance of Arg residues in HSP47 binding was further confirmed by using residue-specific chemical modification of types I and III collagen. Our results demonstrate that Xaa-Arg-Gly sequences in the triple-helical procollagen molecule are dominant binding sites for HSP47 and enable us to predict HSP47-binding sites in homotrimeric procollagen molecules.
A novel RGB-Z camera for high-quality motion picture applications (2013)

The combination of 2D high-resolution RGB image sensors with 3D Time-of-Flight imagers has become an increasing field of research in the past ten years. This paper describes the next step of sensor fusion by providing flawlessly matching RGB and Z images. Our novel RGB-Z camera is based on a high-quality 2.8k motion picture camera which is optically extended to provide the same perspective for a depth camera by means of a rotating mirror principle. In the scope of this paper technical details are explained and a common interface is proposed for integrating RGB-Z data in the professional post-production workflow. Thereby, this RGB-Z camera addresses typical problems in the movie production chain where depth information is essential. Finally, the Z image quality is evaluated using a cine-style full format lens.
Self-Assembly of a Hexagonal Boron Nitride Nanomesh on Ru(0001) (2007)

Hexagonal boron nitride (h-BN) nanostructures were grown on Ru(0001), and are very similar to those previously reported on Rh(111). They show a highly regular 12 x 12 superstructure, comprising 2 nm wide apertures with a depth of about 0.1 nm. Valence band photoemission reveals two distinctly bonded h-BN species, and X-ray photoelectron spectroscopy indicates an h-BN monolayer film. The functionality of the h-BN/Ru(0001) nanomesh is demonstrated by using this structure for the assembly of gold nanoclusters.
Every laboratory with a fluorescence microscope should consider counting molecules (2014)

Protein numbers in cells determine rates of biological processes, influence the architecture of cellular structures, reveal the stoichiometries of protein complexes, guide in vitro biochemical reconstitutions, and provide parameter values for mathematical modeling. The purpose of this essay is to increase awareness of methods for counting protein molecules using fluorescence microscopy and encourage more cell biologists to report these numbers. We address the state of the field in terms of utility and accuracy of the numbers reported and point readers to references for details of specific techniques and applications.
Assigning Tasks in a 24-Hour Software Development Model (2005)

With the advent of globalization and the Internet, the concept of global software development is gaining ground. The global development model opens up the possibility of 24-hour software development by effectively utilizing the time zone differences. To harness the potential of the 24-hour software development model for reducing the overall development time, a key issue is the allocation of project tasks to the resources in the distributed team. In this paper, we examine this issue of task allocation in order to minimize the completion time of a project. We discuss a model for distributed team across time-zones and propose a task allocation algorithm for the same. We apply the approach on tasks of a few synthetic projects and two real projects and show that there is a potential to reduce the project duration as well as improve the resource utilization through 24-hour development.
Amazing Stability of the Arginine−Phosphate Electrostatic Interaction (2005)

Electrostatic interactions between a basic epitope containing adjacent arginine residues and an acidic epitope containing a phosphorylated serine are involved in receptor heteromerization. In the present study, we demonstrate that this arginine-phosphate electrostatic interaction possesses a "covalent-like" stability. Hence, these bonds can withstand fragmentation by mass spectrometric collision-induced dissociation at energies similar to those that fragment covalent bonds and they demonstrate an extremely low dissociation constant by plasmon resonance. The present work also highlights the importance of phosphorylation-dephosphorylation events in the modulation of this electrostatic attraction. Phosphorylation of the acidic epitope, a casein kinase one consensus site, makes it available to interact with the basic epitope. On the other hand, phosphorylation of serine and/or threonine residues adjacent to the basic epitope, a protein kinase A consensus site, slows down the attraction between the epitopes. Although analyzed here in the frame of receptor heteromerization, the arginine-phosphate electrostatic interaction most likely represents a general mechanism in protein-protein interactions.
Introducing the Infant’s First Solid Food (1993)

The introduction of solid food to an infant is usually addressed in terms of a “correct” time for introduction. There is usually also a discussion of “appropriate” foods which may be introduced to the infant; these foods will change according to prevailing health priorities. Concentrates on the contribution made by the infant to the timing and type of the first foods introduced. Places emphasis on the development of the infant′s taste preferences which determine the infant′s response to foods which may be offered by the parent.
Nanofabrication of grating and dot patterns by electron holographic lithography (1995)

Line and dot patterns with about a 100 nm period are exposed on poly-methyl methacrylate (PMMA) resist by electron holographic lithography with a W〈100〉 thermal field emission (TFE) gun and an electron biprism. Subsequent atomic force microscope (AFM) observation has confirmed that both patterns are successfully fabricated. This technique allows one to produce nanoscale periodic patterns simultaneously, whose spacing could be, in principle, comparable to a lattice spacing.
The TNFR family members OX40 and CD27 link viral virulence to protective T cell vaccines in mice (2010)

Induction of CD8+ T cell immunity is a key characteristic of an effective vaccine. For safety reasons, human vaccination strategies largely use attenuated nonreplicating or weakly replicating poxvirus-based vectors, but these often elicit poor CD8+ T cell immunity and might not result in optimal protection. Recent studies have suggested that virulence is directly linked to immunogenicity, but the molecular mechanisms underlying optimal CD8+ T cell responses remain to be defined. Here, using natural and recombinant vaccinia virus (VACV) strains, we have shown in mice that VACV strains of differing virulence induce distinct levels of T cell memory because of the differential use of TNF receptor (TNFR) family costimulatory receptors. With strongly replicating (i.e., virulent) VACV, the TNFR family costimulatory receptors OX40 (also known as CD134) and CD27 were engaged and promoted the generation of high numbers of memory CD8+ T cells, which protected against a lethal virus challenge in the absence of other mechanisms, including antibody and help from CD4+ T cells. In contrast, weakly replicating (i.e., low-virulence) VACV strains were poor at eliciting protective CD8+ T cell memory, as only the Ig family costimulatory receptor CD28 was engaged, and not OX40 or CD27. Our results suggest that the virulence of a virus dictates costimulatory receptor usage to determine the level of protective CD8+ T cell immunity.
Multiplier design utilizing improved column compression tree and optimized final adder in CMOS technology (2002)

The authors discuss improvements in bit reduction techniques and a final adder which is optimized for the uneven signal arrival profile in a CMOS multiplier. Different architectures of the column compression counters and carry propagate adders which take advantage of the speed of the carry signal are considered. The configuration of column compression counters is optimized in order to reduce the longest signal path. The final adder is designed for the uneven input arrival time of the signals originating from the multiplier tree. This results in more compact wiring and balanced delays yielding a faster multiplier.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Antitumor Polycyclic Acridines. 7. Synthesis and Biological Properties of DNA Affinic Tetra- and Pentacyclic Acridines (2000)

New synthetic routes to a series of tetra- and pentacyclic acridines related in structure to marine natural products are reported. The novel water-soluble agent dihydroindolizino[7,6,5-kl]acridinium chloride 14 has inhibitory activity in a panel of non-small-cell lung and breast tumor cell lines exceeding that of m-AMSA. The salt inhibited the release of minicircle products of kDNA confirming that disorganization of topoisomerase II partly underlies the activity of the compound. COMPARE analysis of the NCI mean graph profile of compound 14 at the GI(50) level corroborates this conclusion with Pearson correlation coefficients (>0.6) to clinical agents of the topoisomerase II class: however, this correlation was not seen at the LC(50) level. The inhibitory action of 14 on Saccharomyces cerevisiae transfected with human topoisomerase II isoforms showed a 3-fold selectivity against the IIalpha isoform over the IIbeta isoform. Unlike m-AMSA, 14 is not susceptible to P-glycoprotein-mediated drug efflux and retains activity in lung cells with derived resistance to the topoisomerase II inhibitor etoposide.
Achieving Out-of-Order Performance with Almost In-Order Complexity (2008)

There is still much performance to be gained by out-of-order processors with wider issue widths. However, traditional methods of increasing issue width do not scale; that is, they drastically increase design complexity and power requirements. This paper introduces the braid, a compile-time identified entity that enables the execution core to scale to wider widths by exploiting the small fanout and short lifetime of values produced by the program. Braid processing requires identification by the compiler, minor extensions to the ISA, and support by the microarchitecture. The result from processing braids is performance within 9% of a very aggressive conventional out-of-order microarchitecture with almost the complexity of an in-order implementation.
Die pathologische Wirkung verschiedener Mineralstaube im Tierversuch (1954)

ZusammenfassungSiliziumdioxyd hat bei Zimmertemperatur vier verschiedene Modifikationen, nämlich Quarz, Cristobalit, Tridymit und geschmolzene Kieselsäure. Die ersten drei sind kristallin aber geschmolzene Kieselsäure ist ein Glas. Tridymit, Cristobalit und Kieselglas sind metastabil, aber sie wandeln sich bei Zimmertemperatur in meßbarer Zeit nicht in Quarz um. Quarz ist die einzige bei Zimmertemperatur thermodynamisch stabile Modifikation.
Extrachromosomal recombination occurs efficiently in cells defective in various DNA repair systems (1996)

A series of different frameshift mutations of a firefly luciferase reporter plasmid was created so that no activity was obtained when they were transfected into mammalian cells. Co-transfection of these constructs with short fragments of the original sequence resulted in luciferase activity in different cell lines (A-549, NIH 3T3 and Jurkat). The level of this activity was dependent on the length of the fragment, regardless of cell line examined. Two different transfection techniques (lipofection and adenovirus-enhanced gene transfer) gave similar results. It was shown by polymerase chain reaction that expression of detectable luciferase required recombination of the transfected molecules. Cells with defined defects in DNA repair pathways were examined for their ability to perform this extrachromosomal recombination. Cells lacking normal Ku p80, (ADP-ribosyl)transferase, MLH1 or XP-C were all capable of restoring expression to the frameshifted constructs. Given the pivotal roles of the above molecules in the pathways of DNA repair, it seems that this recombination derives from a different activity.
Physical basis for wideband resonant reflectors (2008)

In this paper, we address resonant leaky-mode reflectors made with a periodic silicon layer on an insulating substrate. Our objective is to explain the physical basis for their operation and to quantify the bandwidth provided by a single resonant layer by illustrative examples for both TE and TM polarized incident light. We find that the number of participating leaky modes and their excitation conditions affect the bandwidth. We show that recently reported experimental [1, 2] wideband reflectors operate under leaky-mode resonance. These compact reflectors are new elements with many potential applications in photonic systems. The results presented explaining their physical basis will aid in their continued development.
Surface acoustic wave characteristics based on c-axis (006) LiNbO3/diamond/silicon layered structure (2011)

The characteristics of surface acoustic wave (SAW) based on LiNbO3/diamond/silicon layered structure were investigated. The LiNbO3 film deposited on the diamond/silicon substrate by pulsed laser deposition exhibits highly c-axis (006) preferred orientation. Four samples with different wavelengths were fabricated on the same substrate to study the normalized LiNbO3 thickness dependence of SAW properties. It is shown that the measured phase velocities are in good agreement with the theoretical ones. In the case of 1st wave mode, the SAW device with a linewidth of 1.78 µm exhibits a very high phase velocity of 12 474 m/s in conjunction with a high electromechanical coupling coefficient of 4.85%.
Polarized Electroluminescence from Aligned Chromophores by the Friction Transfer Method (2000)

A new method for aligning light-emitting materials is reported here: The friction transfer technique was used to produce the poly(tetrafluoroethylene) surface shown in the Figure. The surface has a high density of ridges and grooves with height variations on the ten-nanometer scale, and thin films with high optical quality and controllable thickness were readily obtained. Polarized LEDs fabricated on such surfaces show high dichroic ratios.
Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy (2013)

Superresolution microscopy based on single-molecule centroid determination has been widely applied to cellular imaging in recent years. However, quantitative imaging of the mammalian nucleus has been challenging due to the lack of 3D optical sectioning methods for normal-sized cells, as well as the inability to accurately count the absolute copy numbers of biomolecules in highly dense structures. Here we report a reflected light-sheet superresolution microscopy method capable of imaging inside the mammalian nucleus with superior signal-to-background ratio as well as molecular counting with single-copy accuracy. Using reflected light-sheet superresolution microscopy, we probed the spatial organization of transcription by RNA polymerase II (RNAP II) molecules and quantified their global extent of clustering inside the mammalian nucleus. Spatiotemporal clustering analysis that leverages on the blinking photophysics of specific organic dyes showed that the majority (>70%) of the transcription foci originate from single RNAP II molecules, and no significant clustering between RNAP II molecules was detected within the length scale of the reported diameter of "transcription factories." Colocalization measurements of RNAP II molecules equally labeled by two spectrally distinct dyes confirmed the primarily unclustered distribution, arguing against a prevalent existence of transcription factories in the mammalian nucleus as previously proposed. The methods developed in our study pave the way for quantitative mapping and stoichiometric characterization of key biomolecular species deep inside mammalian cells.
Software Defect Prediction via Convolutional Neural Network (2017)

To improve software reliability, software defect prediction is utilized to assist developers in finding potential bugs and allocating their testing efforts. Traditional defect prediction studies mainly focus on designing hand-crafted features, which are input into machine learning classifiers to identify defective code. However, these hand-crafted features often fail to capture the semantic and structural information of programs. Such information is important in modeling program functionality and can lead to more accurate defect prediction. In this paper, we propose a framework called Defect Prediction via Convolutional Neural Network (DP-CNN), which leverages deep learning for effective feature generation. Specifically, based on the programs' Abstract Syntax Trees (ASTs), we first extract token vectors, which are then encoded as numerical vectors via mapping and word embedding. We feed the numerical vectors into Convolutional Neural Network to automatically learn semantic and structural features of programs. After that, we combine the learned features with traditional hand-crafted features, for accurate software defect prediction. We evaluate our method on seven open source projects in terms of F-measure in defect prediction. The experimental results show that in average, DP-CNN improves the state-of-the-art method by 12%.
When Good Components Go Bad: Formally Secure Compilation Despite Dynamic Compromise (2018)

We propose a new formal criterion for evaluating secure compilation schemes for unsafe languages, expressing end-to-end security guarantees for software components that may become compromised after encountering undefined behavior---for example, by accessing an array out of bounds. Our criterion is the first to model dynamic compromise in a system of mutually distrustful components with clearly specified privileges. It articulates how each component should be protected from all the others---in particular, from components that have encountered undefined behavior and become compromised. Each component receives secure compilation guarantees---in particular, its internal invariants are protected from compromised components---up to the point when this component itself becomes compromised, after which we assume an attacker can take complete control and use this component's privileges to attack other components. More precisely, a secure compilation chain must ensure that a dynamically compromised component cannot break the safety properties of the system at the target level any more than an arbitrary attacker-controlled component (with the same interface and privileges, but without undefined behaviors) already could at the source level. To illustrate the model, we construct a secure compilation chain for a small unsafe language with buffers, procedures, and components, targeting a simple abstract machine with built-in compartmentalization. We give a machine-checked proof in Coq that this compiler satisfies our secure compilation criterion. Finally, we show that the protection guarantees offered by the compartmentalized abstract machine can be achieved at the machine-code level using either software fault isolation or a tag-based reference monitor.