gebhart/patrepeval huggingface dataset:
Solvent Effects in Tandem Mass Spectrometry:  Mechanistic Studies Indicating How a Change in Solvent Conditions and pH Can Dramatically Alter CID Spectra (2002)

Dramatically different CID (collision-induced dissociation) spectra are obtained when the complex [Zn(dien-glucose)](+) is electrosprayed from acidic and basic solutions. To understand this peculiar phenomenon, an in-depth mechanistic study was performed on one of the product ions that is present when the initial complex is diluted in basic solution but absent when the complex is diluted with acidic solution. On the basis of the results of this study, the differences in the CID spectra can be rationalized by the fact that the complex electrosprayed from basic solution was kinetically trapped, with the deprotonation site distal from the metal center. Under acidic conditions, the deprotonation site is at a hydroxyl group coordinated to the metal ion. A variety of experiments support this hypothesis. The studies herein underscore the importance of using identical solvent conditions when comparing sets of CID spectra. The data also highlight a very interesting phenomenon involving deprotonation of a hydroxyl group, which was several atoms away from the Zn(II) metal center.
A Nonparametric Multidimensional IRT Approach with Applications to Ability Estimation and Test Bias. (1988)

Abstract : A determined case is made for the use of a nonparametric multidimensional monotonic IRT modeling framework with local independence replaced by the less restrictive assumption of essential independence. The concept of essential dimensionality is then introduced to count the number of dominant latent dimensions. Consequences of this more general approach include the consistent estimation of ability on a common scale using a natural class of estimators, uniqueness of the latent ability when essential unidimensionality holds, a theoretical treatment of test bias, an IRT based notion of validity, and a reassessment of the importance of the concept of item parameter invariance. Keywords: Local independence; Essential independence; Essential trait; Intrinsic ability scale; Marginal item response function; Latent dimensionality; Multidimensionality; Essential dimensionality; Essential unidimensionality; Item response theory; Latent trait theory; Ability estimation; Consistent estimation; Item parameter invariance; Validity; Linear formula scoring; Nonparametric.
Electronic Structures of LNA Phosphorothioate Oligonucleotides (2017)

Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e.g., energy and bonding, which make them distinguish or differentiate between the individual PS diastereoisomers determined by the position of sulfur atoms. Rules are derived from the electronic calculations of these molecules and include the effects of the phosphorothioate chirality and formation of electrostatic potential surfaces. Physical and electrochemical descriptors of the PS oligonucleotides are compared to the experiments in which chiral states on these molecules can be distinguished. The calculations demonstrate that electronic structure, electrostatic potential, and topology are highly sensitive to single PS configuration changes and can give a lead to understanding the activity of the molecules.
ChemInform Abstract: TRIQUINANE SESQUITERPENES. AN ITERATIVE, HIGHLY STEREOCONTROLLED SYNTHESIS OF (.+‐.)‐SILPHINENE (1984)

Abstract Der ausgehend von dem Cyclopentenon (I) erhältliche Bicyclus (Vl l) erweist sich im Gegensatz zu anderen, ebenfalls erprobten Bicyclen als geeigneter Synthesebaustein.
Programming for Non-Volatile Main Memory Is Hard (2017)

Using non-volatile memory as main memory (NVMM) can largely improve the performance of applications, but adds to the challenge of programming -- it turns out to be very error-prone to write real-world NVMM programs, especially with object-oriented programming. This paper presents a field study of erroneous NVMM programs written by programmers who are trained to use a general NVMM programming interface. We performed the field study in a training workshop of 30 participants. Our observations and derived best practices offer a reference for future NVMM programming techniques design. Toward that end, we propose a taxonomy of latest NVMM programming techniques and, accordingly, a set of paradigms that can reduce the risk of NVMM-specific bugs. The paradigms incorporate a minimal NVMM library interface design and a new design pattern inspired by the field study.
Optical Properties of Ru(dpp)<inf>3</inf> for Phosphorescence Biosensors (2007)

The saturation intensity and photobleaching lifetime of tris(4,7-diphenyl-1,10-phenanthroline) ruthenium(II) chloride (Ru(dpp) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ) are measured and applied to the design of oxygen sensitive optodes for enzymatic biosensors. Photobleaching limits the excitation intensity in practical sensor systems.
Sensor plane processing for multiplex imaging (2002)

Digital imaging systems are fundamentally different from analog ones because they differentiate the measurement space and the reconstruction space. Multiplex systems use this separation to optimize source reconstruction. We consider the requirements imposed on sensor plane processors by multiplex imaging systems. We consider system flexibility, analog/digital split, A/D dynamic range, bandwidth, and sensitivity.
Video Object Segmentation with 3D Convolution Network (2019)

We explore a novel method to realize semi-supervised video object segmentation with special spatiotemporal feature extracting structure. Considering 3-dimension convolution network can convolute a volume of image sequence, it is a distinct way to get both spatial and temporal information. Our network is composed of three parts, the visual module, the motion module and the decoder module. The visual module learns object appearance feature from object in the first frame for network to detect specific object in following image sequences. The motion module aims to get spatiotemporal information of image sequences with 3-dimension convolution network, which learns diversities of object temporal appearance and location. The purpose of decoder module is to get foreground object mask from output of visual module and motion module with concatenation and upsampling structure. We evaluate our model on DAVIS segmentation dataset[15]. Our model doesn't need online training compared with most detection-based methods because of visual module. As a result, it takes 0.14 second per frame to get mask which is 71 times faster than the state-of-art method-OSVOS[2]. Our model also shows better performance than most methods proposed in recent years and its meanIOU accuracy is comparable with state-of-art methods.
Microdiagnostic Lab on a Chip - LDRD Final Report (2002)

Polycrystalline silicon (polysilicon) surface micromachining is a new technology for building micrometer ({micro}m) scale mechanical devices on silicon wafers using techniques and process tools borrowed from the manufacture of integrated circuits. Sandia National Laboratories has invested a significant effort in demonstrating the viability of polysilicon surface micromachining and has developed the Sandia Ultraplanar Micromachining Technology (SUMMiT V{trademark} ) process, which consists of five structural levels of polysilicon. A major advantage of polysilicon surface micromachining over other micromachining methods is that thousands to millions of thin film mechanical devices can be built on multiple wafers in a single fabrication lot and will operate without post-processing assembly. However, if thin film mechanical or surface properties do not lie within certain tightly set bounds, micromachined devices will fail and yield will be low. This results in high fabrication costs to attain a certain number of working devices. An important factor in determining the yield of devices in this parallel-processing method is the uniformity of these properties across a wafer and from wafer to wafer. No metrology tool exists that can routinely and accurately quantify such properties. Such a tool would enable micromachining process engineers to understand trends and thereby improve yield of micromachined devices. In this LDRD project, we demonstrated the feasibility of and made significant progress towards automatically mapping mechanical and surface properties of thin films across a wafer. The MEMS parametrics measurement team has implemented a subset of this platform, and approximately 30 wafer lots have been characterized. While more remains to be done to achieve routine characterization of all these properties, we have demonstrated the essential technologies. These include: (1) well-understood test structures fabricated side-by-side with MEMS devices, (2) well-developed analysis methods, (3) new metrologies (i.e., long working distance interferometry) and (4) a hardware/software platform that integrates (1), (2) and (3). In this report, we summarize the major focus areas of our LDRD project. We describe the contents of several articles that provide the details of our approach. We also describe hardware and software innovations we made to realize a fully automatic wafer prober system for MEMS mechanical and surface property characterization across wafers and from wafer-lot to wafer-lot.
Monazite Coatings on SiC Fibers I: Fiber Strength and Thermal Stability (2006)

Commercially available SiC fibers were coated with monazite (LaPO 4 ) using a continuous vertical coater at 1100°C. Coated fibers were heat treated in dry air, argon, and laboratory air at 1200°C for 1–20 h. The tensile strengths of uncoated and coated fibers were measured and evaluated before and after heat treatment. Fiber coating did not degrade SiC fiber strength, but heat treatment afterwards caused significant degradation that correlated with silica scale thickness. Possible strength degradation mechanisms for the coated fibers are discussed. Coating morphology, microstructure, and SiC oxidation were observed with scanning electron microscopy and transmission electron microscopy. Monazite reacted with SiC to form lanthanum silicate (La 2 Si 2 O 7 ) in argon, but was stable with SiC in air. Despite the large coefficient of thermal expansion difference between monazite and SiC, micron thick monazite coatings did not debond from most types of SiC fibers. Possible explanations for the thermomechanical stability of the monazite fiber coatings are discussed.
Scattering of electromagnetic waves from a slightly random surface—reciprocal theorem, cross-polarization and backscattering enhancement (1995)

Abstract The present paper deals with the electromagnetic (EM) scattering from a perfectly conductive, random surface by means of the stochastic functional approach and aims to study the backscattering enhancement associated with co-polarized and cross-polarized scattering. The treatment is based on the stochastic functional theory where the random EM field is represented in terms of a Wiener-Hermite functional of the homogeneous Gaussian random surface. To obtain more precise solutions than the previous works (Nakayama J et al 1981 Radio Sci. 16 831-53), we first establish the reciprocal theorem for vector Wiener kernels which describe the stochastic functional representation of the EM field and, using this, we derive the reciprocal relations for the co-polarized and cross-polarized scattering distribution relative to TE and TM polarizations of incident wave. Solutions for the vector Wiener kernels up to the second are obtained so precisely as to satisfy the reciprocal relations and are expressed in terms of generating matrices, so that complex EM scattering processes described by the vector Wiener kernels are given dear physical interpretations. Compact operator representations are introduced to reformulate the hierarchical kernel equations, the mass operator equation and higher-order kernel solutions. It is shown that the second vector Wiener kernel physically describes a ‘dressed double-scattering’ process, similar to the scalar theory (Ogura H and Takahashi N 1995 Waves Random Media 5 223-42), and that the ‘dressed double scattering’, which involves anomalous scattering in the intermediate scattering processes, creates the backscattering enhancement in both co- and cross-polarized scattering for both TE and TM wave incidence. Additional informationNotes on contributorsZ L Wang§ §On leave from: National Key Laboratory of Optical Fiber Communications, University of Electronics, Science and Technology of China, Chengdu 610054, People's Republic of China
Abstract 405: Kindlin-2 regulates integrin function and sensitivity to docetaxel in prostate cancer cells (2015)

Abstract Over the past decade, many lines of evidence have emerged to implicate the three members of the kindlin family of FERM domain proteins as important regulators of integrin adhesion receptors. Specifically, kindlins appear to cooperate with talin to be essential regulators of the ligand binding function of integrins and thereby enhance the adhesive and migratory responses of cells. Kindlin-2 (FERMT2) is the most broadly distributed of the kindlins. To explore the relationship between integrin activation and kindlin-2, prostate cancer cell lines were screened and LNCaP prostate cancer cells were found to express relatively low levels of kindlin-2 and endogenous levels of beta-1 integrin on their surface. A portion of this integrin was expressed in an activated state as detected with an activation specific antibody, HUTS-4. These cells were transfected with vectors for kindlin-2, with or without talin-head domain, a combination that leads to activation of β3 integrins in model cells. Transfections with kindlin-2 suppressed β1 integrin activation on the surface of the LNCaP cells. This inhibitory effect was abolished by mutation of kindlin-2 that prevented its binding to integrin cytoplasmic tail. This inhibitory response to kindlin-2 on β1 integrin was in stark contract to the effects of kindlin-2 plus talin-head expression on β3 function, where co-expression of the same constructs enhanced integrin activation. A mutation in kindlin-2, deletion of its last 15 amino acids, that blocks activation of β3 integrins without preventing its binding to the integrin, also prevents its inhibition of β1 function. We next looked at the effects of kindlin-2 on docetaxel induced apoptosis as monitored with Annexin V staining and cell death as monitored by propidium iodide staining (both by flow cytometry). Compared to LNCaP cells expressing EGFP alone, cells overexpressing EGFP-kindlin-2 were protected against apoptosis and cell death. This effect was dependent upon binding of kindlin-2 to the cytoplasmic tail of integrins. Hence, the capacity of kindlin-2 to influence integrin function depends upon the integrin subfamily and can range from activation to suppression of function. Kindlin-2, which is often overexpressed in transformed cells, may desensitize cells towards chemotherapeutic agents. Citation Format: Edward F. Plow, Mitali Das, Jamila Hirbawi, Khalid Sossey-Alaoui. Kindlin-2 regulates integrin function and sensitivity to docetaxel in prostate cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 405. doi:10.1158/1538-7445.AM2015-405
A review: Photonics devices, architectures, and algorithms for optical neural computing (2021)

Abstract The explosive growth of data and information has motivated various emerging non-von Neumann computational approaches in the More-than-Moore era. Photonics neuromorphic computing has attracted lots of attention due to the fascinating advantages such as high speed, wide bandwidth, and massive parallelism. Here, we offer a review on the optical neural computing in our research groups at the device and system levels. The photonics neuron and photonics synapse plasticity are presented. In addition, we introduce several optical neural computing architectures and algorithms including photonic spiking neural network, photonic convolutional neural network, photonic matrix computation, photonic reservoir computing, and photonic reinforcement learning. Finally, we summarize the major challenges faced by photonic neuromorphic computing, and propose promising solutions and perspectives.
Measurement of SOA α factor using AM-induced FM laser operation in a fiber ring cavity (2009)

We present a new method for measuring the semiconductor optical amplifier (SOA) linewidth enhancement factor, employing a configuration wherein the SOA is placed within a loss modulated fiber ring cavity operated in the FM laser regime. This allows an easy phase-index measurement in lasing operation at small modulation frequencies. A comparison with the conventional FM/AM technique enables independent measurement of the two underlying phase modulation mechanisms: thermal effects from the current modulation and gain-to-refractive index coupling.
Field Implementation of "Squeeze Matrix-Access Reservoir-Targeting" Water Reduction System (2006)

Abstract For many years, bullhead systems to reduce water production have received a great deal of attention from the oil- and gas-production industry. Water production becomes a major problem as fields mature, leading to higher levels of scale, greater lift requirements, more load on fluid-handling facilities, and increased environmental concerns. Because of the completion techniques used in many wells, protecting the hydrocarbon producing interval effectively during a water-control treatment is not always practical or cost-effective. Bullhead systems offer treatments that do not require zonal isolation and are designed to reduce water production with little or no reduction in oil or gas production. Previous papers have discussed the laboratory development of a new water reduction system based on the use of a hydrophobically modified polymer. This paper will outline the field implementation of this squeeze-matrix access reservoir-targeting (SMART) water reduction system and will describe some of the successes (and failures) in its implementation. Even though bullhead systems such as this do not seal off water zones and, therefore, do not have the capability to completely stop water production, it will be demonstrated that SMART treatments can be economically attractive. While field-wide, multiwell treatments are attractive from the viewpoint of fully assessing system capabilities, single-well treatments can be beneficial to small and large operators alike.
Volunteering Versus Work for Pay: Incentives and Tradeoffs in Crowdsourcing (2013)

Paid and volunteer crowd work have emerged as a means for harnessing human intelligence for performing diverse tasks. However, little is known about the relative performance of volunteer versus paid crowd work, and how financial incentives influence the quality and efficiency of output. We study the performance of volunteers as well as workers paid with different monetary schemes on a difficult real-world crowdsourcing task. We observe that performance by unpaid and paid workers can be compared in carefully designed tasks, that financial incentives can be used to trade quality for speed, and that the compensation system on Amazon Mechanical Turk creates particular indirect incentives for workers. Our methodology and results have implications for the ideal choice of financial incentives and motivates further study on how monetary incentives influence worker behavior in crowdsourcing.
Modelling, Analysis and Control of DC-connected Wind Farms to Grid (2006)

Udgivelsesdato: Februar
iPS Cell-Based Model for MAPT Haplotype as a Risk Factor for Human Tauopathies Identifies No Major Differences in TAU Expression (2021)

The H1 haplotype of the microtubule-associated protein tau (<i>MAPT</i>) gene is a common genetic risk factor for some neurodegenerative diseases such as progressive supranuclear palsy, corticobasal degeneration, and Parkinson's disease. The molecular mechanism causing the increased risk for the named diseases, however, remains unclear. In this paper, we present a valuable tool of eight small molecule neural precursor cell lines (smNPC) homozygous for the <i>MAPT</i> haplotypes (four H1/H1 and four H2/H2 cell lines), which can be used to identify <i>MAPT</i>-dependent phenotypes. The employed differentiation protocol is fast due to overexpression of <i>NEUROGENIN-2</i> and therefore suitable for high-throughput approaches. A basic characterization of all human cell lines was performed, and their TAU and α-SYNUCLEIN profiles were compared during a differentiation time of 30 days. We could identify higher levels of conformationally altered TAU in cell lines carrying the H2 haplotype. Additionally, we found increased expression levels of α-SYNUCLEIN in H1/H1 cells. With this resource, we aim to fill a gap in neurodegenerative disease modeling with induced pluripotent stem cells (iPSC) for sporadic tauopathies.
The role of bladder-to-urethral reflexes in urinary continence mechanisms in rats (2004)

Urethral closure mechanisms during passive increments in intravesicular pressure (P(ves)) were investigated using microtip transducer catheters in urethane-anesthetized female rats. After a block of reflex bladder contractions by spinal cord transection at T8-T9, abruptly raising P(ves) to 20, 40, or 60 cmH(2)O for 2 min induced a bladder pressure-dependent contractile response in a restricted portion of the middle urethra (12.5-15 mm from the urethral orifice) that was abolished by cutting the pelvic nerves bilaterally. In pelvic nerve-intact rats, the bilateral transection of either the pudendal nerves, the nerves to the iliococcygeous/pubococcygeous muscles, or the hypogastric nerves significantly reduced (49-74%) the urethral reflex response induced by passive P(ves) increases, and combined transection of these three sets of nerves totally abolished the urethra-closing responses. In spinal cord-intact rats, similar urethral contractile responses were elicited during P(ves) elevation (20 or 40 cmH(2)O) and were also eliminated by bilateral pelvic nerve transection. After spinal cord and pelvic nerve transection, leak point pressures, defined as the pressure inducing fluid leakage from the urethral orifice during passive P(ves) elevation by either bladder pressure clamping in 2.5-cmH(2)O steps or direct compression of the bladder, were significantly lowered by 30-35% compared with sham-operated (spinal cord-transected and pelvic nerve-intact) rats. These results indicate that 1) passive elevation of P(ves) can elicit pelvic afferent nerve-mediated contractile reflexes in the restricted portion of the urethra mediated by activation of sympathetic and somatic nerves and 2) bladder-to-urethral reflexes induced by passive P(ves) elevation significantly contribute to the prevention of stress urinary incontinence.
Twist Sense Bias Induced by Chiral Side Chains in Helically Folded Oligomers (2000)

Kooperative Wechselwirkungen zwischen den Seitenketten von helicalen Phenylen-Ethinylen-Oligomeren (siehe Bild; n=2, 4, 6, 8, 10, 12, 14, 16, 18) können zur Bevorzugung einer Helixgängigkeit führen. Dies zeigt, dass die Seitenketten mehr als nur eine Hilfsfunktion in diesen konformativ geordneten Oligomeren erfüllen. Die Bevorzugung einer Helixgängigkeit erfolgt signifikant später als das Auftreten von helicalen Konformationen, möglicherweise deshalb, weil zunächst ein großes Ensemble von „kollabierten”︁ Konformationen gebildet wird.