gebhart/patrepeval huggingface dataset:
Ion-beam-induced amorphization and recrystallization in silicon (2004)

Ion-beam-induced amorphization in Si has attracted significant interest since the beginning of the use of ion implantation for the fabrication of Si devices. A number of theoretical calculations and experiments were designed to provide a better understanding of the mechanisms behind the crystal-to-amorphous transition in Si. Nowadays, a renewed interest in the modeling of amorphization mechanisms at atomic level has arisen due to the use of preamorphizing implants and high dopant implantation doses for the fabrication of nanometric-scale Si devices. In this paper we will describe the most significant experimental observations related to the ion-beam-induced amorphization in Si and the models that have been developed to describe the process. Amorphous Si formation by ion implantation is the result of a critical balance between the damage generation and its annihilation. Implantation cascades generate different damage configurations going from isolated point defects and point defect clusters in essentially crystalline Si to amorphous pockets and continuous amorphous layers. The superlinear trend in the damage accumulation with dose and the existence of an ion mass depending critical temperature above which it is not possible to amorphize are some of the intriguing features of the ion-beam-induced amorphization in Si. Phenomenological models were developed in an attempt to explain the experimental observations, as well as other more recent atomistic models based on particular defects. Under traditional models, amorphization is envisaged to occur through the overlap of isolated damaged regions created by individual ions (heterogeneous amorphization) or via the buildup of simple defects (homogeneous amorphization). The development of atomistic amorphization models requires the identification of the lattice defects involved in the amorphization process and the characterization of their annealing behavior. Recently, the amorphization model based on the accumulation and interaction of bond defects or IV pairs has been shown to quantitatively reproduce the experimental observations. Current understanding of amorphous Si formation and its recrystallization, predictive capabilities of amorphization models, and residual damage after regrowth are analyzed.
Molecular biology of the parathyroid hormone: biological actions (2004)

Parathyroid hormone (PTH); the principal parathyroid hormone
receptor (PTH1R); a G protein-linked heptahelical membrane
receptor; and a second heptahelical receptor, the calcium-
sensing receptor (CaR) through a tightly-regulated endocrine
feedback system together constitute the principal regulators
of calcium homeostasis. The effectors of the calcium
regulation are coordinated responses in target tissues.These
responses as well as hormone biosynthesis, secretion and
signaling are all under precise genetic control. Inactivatin gmutations in these genes controlling the multi-step process ofcalcium homeostasis lead to hypocalcemic disorders, as outlined in accompanying articles.
What Makes a Text Coherent? (1983)

Pedagogical interest in coherence has its roots in the nineteenth century, its probable beginnings in Alexander Bain's first rule of the paragraph: bearing of each sentence upon what precedes shall be explicit and unmistakeable.' By the end of the nineteenth century coherence, along with unity and emphasis, was an established canon of paragraph structure. The view of coherence in some of today's popular composition texts still closely resembles Bain's original formulation. For example, McCrimmon's Writing With a Purpose, one of the most widely used freshman composition texts, defines coherence as follows:
Independent Action of ELF3 and phyB to Control Hypocotyl Elongation and Flowering Time (2000)

Light regulates various aspects of plant growth, and the photoreceptor phytochrome B (phyB) mediates many responses to red light. In a screen for Arabidopsis mutants with phenotypes similar to those of phyB mutants, we isolated two new elf3 mutants. One has weaker morphological phenotypes than previously identified elf3 alleles, but still abolishes circadian rhythms under continuous light. Like phyB mutants, elf3 mutants have elongated hypocotyls and petioles, flower early, and have defects in the red light response. However, we found that elf3 mutations have an additive interaction with a phyB null mutation, with phyA or hy4 null mutations, or with a PHYB overexpression construct, and that an elf3 mutation does not prevent nuclear localization of phyB. These results suggest that either there is substantial redundancy in phyB and elf3 function, or the two genes regulate distinct signaling pathways.
New in-situ calibration of diode detectors used in six-port network analyzers (1990)

The authors present a novel method for calibrating the diode detectors used in six-port network analyzers without disconnecting the diodes. The method uses either a precision variable attenuator at the six-port input or a power meter connected to the six-port test port. No actual measurement of power is required to calibrate the diode detectors when an attenuator is used. The method is very well suited to in situ calibration of the diode detection circuits for the operation of the six-port with pulsed signals when the average power detected by the power meter drops to very low levels for low duty cycles. In these cases. The precision variable attenuator method is required.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Trench doping conformality by plasma immersion ion implantation (PIII) (1994)

Plasma immersion ion implantation (PIII) is a technique which can be used to conformally dope sidewalls of Si trenches. Using junction staining techniques and subsequently calibrating the observed stained depth to measured dose, dopant distributions inside Si trenches with aspect ratios ranging from 1 to 12 are studied for various bias voltages from 5 to 20 kV. Unlike conventional collimated beam implantation, PIII was able to conformally dope all aspect ratios studied with no evidence of abrupt discontinuities in the dopant distribution along the trench surface as a result of beam shadowing by trench geometry. Furthermore, it is shown that the higher implant biases results in more directional trajectories. Thus, dopant distributions along irregular geometries can be controlled by PDIII process conditions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Example-Based Regularization Deployed to Super-Resolution Reconstruction of a Single Image (2007)

In super-resolution (SR) reconstruction of images, regularization becomes crucial when insufficient number of measured low-resolution images is supplied. Beyond making the problem algebraically well posed, a properly chosen regularization can direct the solution toward a better quality outcome. Even the extreme case—a SR reconstruction from a single measured image—can be made successful with a well-chosen regularization. Much of the progress made in the past two decades on inverse problems in image processing can be attributed to the advances in forming or choosing the way to practice the regularization. A Bayesian point of view interpret this as a way of including the prior distribution of images, which sheds some light on the complications involved. This paper reviews an emerging powerful family of regularization techniques that is drawing attention in recent years—the example-based approach. We describe how examples can and have been used effectively for regularization of inverse problems, reviewing the main contributions along these lines in the literature, and organizing this information into major trends and directions. A description of the state-of-the-art in this field, along with supporting simulation results on the image scale-up problem are given. This paper concludes with an outline of the outstanding challenges this field faces today.
Efficient and Robust Music Identification With Weighted Finite-State Transducers (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We present an approach to music identification based on weighted finite-state transducers and Gaussian mixture models, inspired by techniques used in large-vocabulary speech recognition. Our modeling approach is based on learning a set of elementary music sounds in a fully unsupervised manner. While the space of possible music sound sequences is very large, our method enables the construction of a compact and efficient representation for the song collection using finite-state transducers. This paper gives a novel and substantially faster algorithm for the construction of <emphasis emphasistype="boldital">factor transducers</emphasis>, the key representation of song snippets supporting our music identification technique. The complexity of our algorithm is linear with respect to the size of the suffix automaton constructed. Our experiments further show that it helps speed up the construction of the weighted suffix automaton in our task by a factor of 17 with respect to our previous method using the intermediate steps of determinization and minimization. We show that, using these techniques, a large-scale music identification system can be constructed for a database of over 15 000 songs while achieving an identification accuracy of 99.4% on undistorted test data, and performing robustly in the presence of noise and distortions. </para>
The antiepileptic drug valproic acid and other medium-chain fatty acids acutely reduce phosphoinositide levels independently of inositol in <i>Dictyostelium</i> (2011)

Valproic acid (VPA) is the most widely prescribed epilepsy treatment worldwide, but its mechanism of action remains unclear. Our previous work identified a previously unknown effect of VPA in reducing phosphoinositide production in the simple model Dictyostelium followed by the transfer of data to a mammalian synaptic release model. In our current study, we show that the reduction in phosphoinositide [PtdInsP (also known as PIP) and PtdInsP(2) (also known as PIP(2))] production caused by VPA is acute and dose dependent, and that this effect occurs independently of phosphatidylinositol 3-kinase (PI3K) activity, inositol recycling and inositol synthesis. In characterising the structural requirements for this effect, we also identify a family of medium-chain fatty acids that show increased efficacy compared with VPA. Within the group of active compounds is a little-studied group previously associated with seizure control, and analysis of two of these compounds (nonanoic acid and 4-methyloctanoic acid) shows around a threefold enhanced potency compared with VPA for protection in an in vitro acute rat seizure model. Together, our data show that VPA and a newly identified group of medium-chain fatty acids reduce phosphoinositide levels independently of inositol regulation, and suggest the reinvestigation of these compounds as treatments for epilepsy.
Deckschichtbildung und Korrosionsverhalten des hochsiliciumlegierten austenitischen Sonderstahls X 2 CrNiSi 18 15 in Salpetersäuren (1982)

Abstract Mit Hilfe von ESCA‐ und AAS‐Messungen wurde die Ausbildung der Deckschicht auf dem austenitischen Stahl X 2 CrNiSi 18 15 in Salpetersäuren untersucht. Es entsteht eine chromoxidreiche Deckschicht, über der sich eine SiO 2 ‐Schicht befindet. Nickel und Mangan sind am Aufbau der Oxidschichten nicht beteiligt. Unter der Oxidschicht wurde eine Chromanreicherung bzw. Eisenverarmung im Stahl nachgewiesen. Um die teilweise sehr geringen (bis 5 · 10 −5 mm · a −1 ) Abtragungsraten reproduzierbar erfassen zu können, wurde in Lösung gegangenes Eisen, Chrom und Nickel in Abhängigkeit von der Beanspruchungsdauer mittels AAS bestimmt. Für ruhende Werkstoffproben ergaben sich scheinbare Aktivierungsenergien von 65,2 kJ/Mol (azeotrope Salpetersäure) bzw. 37,5 kJ/Mol (hochkonzentrierte Salpetersäure); diese Werte bestätigen die Annahme einer geschwindigkeitsbestimmenden Phasengrenzreaktion. Ein nennenswerter Einfluß der Fließgeschwindigkeit auf die Korrosion war nicht nachweisbar.
Novel Tubing Microreactor for Monitoring Chemical Reactions (2002)

There is an expanding interest in small-scale methods to evaluate catalysts and chemical reactions at a variety of conditions, ranging up to 6.9 MPa (1000 psig) and 300 degrees C. Multiwell parallel batch techniques are most commonly applied in high-throughput screening systems. In contrast, we describe here a rapid, serial, highly controllable method based on LC-type steel tubing rated for high pressures. The tube, containing a variety of flowing ingredients, such as carrier solvents, catalyst formulations, and reactants, is self-heated ohmically using electrical current from a power supply monitored and regulated with a precision of 0.01%. An array of voltage taps arranged along its length serves to sense the real-time temperature profile of the tube. Reactions are seen as temperature pulses progressing through the reactor, in zones of 200 microL each, and tracked with a temperature precision of 0.1 degrees C. A unique pressure controller was devised to maintain constant reactor pressures despite effluent viscosity fluctuations due to polymerization. Several chemical reaction systems have been characterized to date, including decomposition reactions of di-tert-butyl peroxide, polymerizations of styrene, formation of polyethylene from ethylene, and copolymerization of ethylene with 1-octene. For ethylene polymerization, the amount of mass of polymer formed is proportional to the responses observed.
Small Molecule Transcription Factor Mimic (2004)

Regulation of gene expression by transcription factors touches many aspects of eukaryotic biology, and its systematic, external control by organic molecules represents a challenge in chemistry. Here we report the design of a completely organic, nonpeptidic compound that mimics a transcription factor. The design takes advantage of the specific DNA-binding affinity of a hairpin polyamide molecule and the ability of wrenchnolol to bind to the Sur-2 subunit of human mediator complex. The hybrid compound of these two molecules activates transcription of a reporter gene in vitro in a promoter-dependent manner through simultaneous contacts with DNA and Sur-2. Our results indicate that it is possible to generate a transcription factor out of nonpeptidic components.
Synthesis of the <i>C</i><sub>2</sub>-Symmetric, Macrocyclic Alkaloid, (+)-Xestospongin A and Its C(9)-Epimer, (−)-Xestospongin C:  Impact of Substrate Rigidity and Reaction Conditions on the Efficiency of the Macrocyclic Dimerization Reaction (1996)

Xestospongin A [also known as araguspongine D (1)], a C2-symmetric macrocyclic alkaloid isolated from the sponge Xestospongia exigua (Xestospongia sp.), and its C(9) epimer xestospongin C [also known as araguspongine E (2)] have been synthesized. The route capitalizes on the facile condensation between 5-halovaleraldehydes and 1,3-aminoalcohols to produce an oxaquinolizidine ring system in which all proper relative stereochemical relationships are controlled by equilibration. A linchpin synthesis was used to construct one key monomeric precursora 2,5-disubstituted thiophene derivative 26 [N≡CCH2CH(OH)-2-Th-5-CH2CH2CH(CH(OMe)2)CH2CH2CH2Cl]. A second precursor lacking the thiophene ring 38 [N≡CCH2CH(OH)(CH2)6CH(CH(OMe)2)CH2CH2CH2Cl] was assembled in a similar fashion. The carbinol center in each of these precursors was efficiently resolved enzymatically; lipase (PS-30) hydrolysis of the racemic acetate derivative of the thiophenemethanol derivative 26 and SP-435-catalyzed esterification of the β-hydroxynitrile 38 proved effective. The initial macrocyclization strategy involved (i) hydrolysis of a portion of monomer (+)-26 to the corresponding aldehyde, (ii) reduction of the nitrile to a 1,3-aminoalcohol derivative with a second portion of the monomer, (iii) condensation of these two, end-differentiated monomers to give the “half-cyclized” oxaquinolizidine 30 that bears pendant nitrile and acetal groups, (iv) sequential reduction and acid-catalyzed hydrolysis to give the corresponding aldehyde ammonium ion 31, and v) dilution and elevation of pH leading to the macrocyclic bis-thiophene (−)-32. Final reductive removal of both thiophenes with Raney nickel proceeded smoothly to give (+)-xestospongin A/(+)-araguspongine D (1). The impact of pH-control, concentration effects, and monomer rigidity on the macrocyclic dimerization event are discussed. A more direct strategy involved sequential nitrile reduction and acetal hydrolysis within (+)-26 and direct, two-stage macrocyclic dimerization to (−)-32. Control of pH is important to the success of this cyclization. In an analogous fashion the non-thiophene monomer (−)-38 was converted to the ammonium ion/aldehyde S-41. This could be used to probe the effect of substrate rigidity on the efficiency of macrocycle formation. Substrate S-41 spontaneously dimerized to produce a mixture of xestospongin A (1) and xestospongin C (2) with similar efficiency to the thiophene-containing 33.
Unified architecture level energy-efficiency metric (2002)

The development of power-efficient microprocessors presents the need to consider power consumption at early stages of design, particularly at the ISA and microarchitecture definition stages, where the potential for power savings is more significant than at lower-level stages, and the opportunity for making power-performance tradeoffs is the largest. Design modifications to the ISA and microarchitecture, however, affect most (if not all) parameters of the design, including architectural speed, code density, clocking rate and power. A reliable metric is required to make knowledgeable power-performance tradeoffs in this multi-dimensional space. This paper derives a unified energy-efficiency metric for evaluating ISA and microarchitecture features, which subsumes other commonly used power-performance metrics as special cases of a more general equation. This new metric is derived based on an analysis of a multi-dimensional power optimization problem, and the resulting formula involves only relative changes in the characteristics of a processor, enabling its application at the early stages of the design.
Anisotropic MRI Contrast Reveals Enhanced Ionic Transport in Plastic Crystals (2014)

Organic ionic plastic crystals (OIPCs) are attractive as solid-state electrolytes for electrochemical devices such as lithium-ion batteries and solar and fuel cells. OIPCs offer high ionic conductivity, nonflammability, and versatility of molecular design. Nevertheless, intrinsic ion transport behavior of OIPCs is not fully understood, and their measured properties depend heavily on thermal history. Solid-state magnetic resonance imaging experiments reveal a striking image contrast anisotropy sensitive to the orientation of grain boundaries in polycrystalline OIPCs. Probing triethyl(methyl)phosphonium bis(fluorosulfonyl)imide (P1222FSI) samples with different thermal history demonstrates vast variations in microcrystallite alignment. Upon slow cooling from the melt, microcrystallites exhibit a preferred orientation throughout the entire sample, leading to an order of magnitude increase in conductivity as probed using impedance spectroscopy. This investigation describes both a new conceptual window and a new characterization method for understanding polycrystalline domain structure and transport in plastic crystals and other solid-state conductors.
New technologies in scanning probe microscopy for studying molecular interactions in cells (2000)

Atomic force microscopy (AFM) is a specialised form of scanning probe microscopy, which was invented by Binnig and colleagues in 1986. Since then, AFM has been increasingly used to study biomedical problems. Because of its high resolution, AFM has been used to examine the topography or shape of surfaces, such as during the molecular imaging of proteins. This, combined with the ability to operate under known force regimes, makes AFM technology particularly useful for measuring intermolecular bond forces and assessing the mechanical properties of biological materials. Many of the constraints (e.g. complex instrumentation, slow acquisition speeds and poor vertical range) that previously limited the use of AFM in cell biology are now beginning to be resolved. Technological advances will enable AFM to challenge both confocal laser scanning microscopy and scanning electron microscopy as a method for carrying out three-dimensional imaging. Its use as both a precise micro-manipulator and a measurement tool will probably result in many novel and exciting applications in the future. In this article, we have reviewed some of the current biological applications of AFM, and illustrated these applications using studies of the cell biology of bone and integrin-mediated adhesion.
Biological Pathways Contributing to Organ-Specific Phenotype of Brain Metastatic Cells (2008)

Secondary to the increased survival following chemotherapy, brain metastases have recently become a significant clinical problem for breast cancer patients. The aim of this study was to characterize those functional phenotypes that might enhance brain metastasis in breast cancer cells. We first analyzed by two-dimensional electrophoresis (2DE-DIGE) differences in protein expression between parental MDA-MB 435 cells and the brain metastatic variant 435-Br1, obtaining 19 identified proteins by peptide mass fingerprinting, 11 under-expressed (<2-fold) and 8 overexpressed (>2-fold) in 435-Br1. We created and analyzed protein interaction networks with a bioinformatic program (PIANA) from protein data, and it allowed us to associate 34/67-laminin receptor functionally with HSP 27, through a chaperone glucose-regulated protein GRP 94. Moreover, HSP 27 had the largest amount of direct and indirect protein interactions, forming a cluster of chaperones and cochaperones, associated through kinases to a set of intermediated filament proteins. In addition, functional groups of proteins identified were peptidase, DNA binding transcription factors, ATP synthase complex, anion transporters, and carbohydrate metabolism. Further functional analyses in cells, expression analyses in experimental tissues, and in human brain metastasis were addressed to validate the biological pathways contributing to organ-specific phenotype of brain metastasis.
Radio test performance of a narrowband TDMA system (1987)

Using TDMA transmission in digital cellular radio gives several advantages over conventional FDMA systems. However, TDMA implies a higher bitrate at each carrier and hence the multi-path fading will appear as frequency selective fading. This type of distortion destroys the function of a conventional demodulator. In this paper it is shown that a decision feedback equalizer can remove the intersymbol interference created by the frequency selective fading. The paper gives a description of the design of a narrowband TDMA experimental system, DMS 90. Experimental results from CEPT trials in Paris and from field measurements in Stockholm are also given for transmission rates of 340 and 170 kbps.
Comparative epidemiology of oral cancer in Brazil and India. (1991)

A comparison of the risk factors and occurrence of oral cancer in Brazil and India is presented. These two countries have among the highest incidence rates for such cancer in the world. A distinct pattern of risk factors was observed for each country: in India, tobacco chewing was the predominant risk factor: in Brazil, the major risk factor was the combination of tobacco smoking and alcohol consumption. Observations by descriptive epidemiology reveal high age-standardized incidence rates of oral cancer along with some distinctive differences associated with age distribution, sex ratios, and trends in each country. The desirability of additional oral cancer prevention research is also emphasized.