gebhart/patrepeval huggingface dataset:
Solution structure of the N‐terminal amphitropic domain of <i>Escherichia coli</i> glucose‐specific enzyme IIA in membrane‐mimetic micelles (2003)

The N-terminal domain of enzyme IIA(Glc) of the Escherichia coli phosphoenolpyruvate:sugar phosphotransferase system confers amphitropism to the protein, allowing IIA(Glc) to shuttle between the cytoplasm and the membrane. To further understand this amphitropic protein, we have elucidated, by NMR spectroscopy, the solution structure of a synthetic peptide corresponding to the N-terminal domain of IIA(Glc). In water, this peptide is predominantly disordered, consistent with previous data obtained in the absence of membranes. In detergent micelles of dihexanoylphosphatidylglycerol (DHPG) or sodium dodecylsulfate (SDS), however, residues Phe 3-Val 10 of the peptide adopt a helical conformation in the ensemble of structures calculated on the basis of NOE-derived distance restraints. The root mean square deviations for superimposing the backbone atoms of the helical region are 0.18 A in DHPG and 0.22 A in SDS. The structure, chemical shifts, and spin-spin coupling constants all indicate that, of the four lysines in the N-terminal domain of IIA(Glc), only Lys 5 and Lys 7 in the amphipathic helical region interact with DHPG. In addition, the peptide-detergent interactions were investigated using intermolecular NOESY experiments. The aliphatic chains of anionic detergents DHPG, SDS, and 2,2-dimethyl-2-silapentane-5-sulfonate sodium salt (DSS) all showed intermolecular NOE cross-peaks to the peptide, providing direct evidence for the putative membrane anchor of IIA(Glc) in binding to the membrane-mimicking micelles.
Recombinant T cell receptor molecules can prevent and reverse experimental autoimmune encephalomyelitis: dose effects and involvement of both CD4 and CD8 T cells (1997)

Autoimmune diseases are often characterized by spontaneous remission followed by relapses. Although the mechanism(s) controlling pathogenic self-reactive T cells are not fully understood, recent data in experimental autoimmune encephalomyelitis (EAE), a prototype for CD4 T cell-mediated autoimmune diseases, indicate that spontaneous recovery is mediated by regulatory T cells (Treg) specific for peptides derived from the beta-chain of the TCR. Here we have tested whether recombinant single-chain TCRs (scTCRs) containing Vbeta domains can be used as vaccines for efficient priming of Treg. A single injection of mice with these recombinant proteins leads to efficient in vivo priming of Treg and almost complete protection from Ag-induced EAE. Significantly, administration of scTCRs during ongoing disease at a 10-fold lower dose than that required for prophylactic treatment also reverses established EAE. However, if a higher dose of scTCR is administered during ongoing disease, paralytic symptoms become exacerbated and the majority of treated animals die from severe and chronic EAE. Furthermore, we demonstrate that regulatory determinants are processed and presented from scTCRs resulting in the recruitment of both CD4 and CD8 regulatory T cells which are required for efficient regulation induced by scTCR. Reversal of established disease following an optimum dose of recombinant TCRs suggests that proteins expressing appropriate Vbeta domains could be used for the treatment of a variety of T cell-mediated pathologic conditions.
Visual media retargeting (2009)

The increasing variety of commonly used display devices, especially mobile devices, requires adapting visual media to different resolutions and aspect ratios - a process called "retargeting." The media retargeting problem is further accentuated by the explosion of image and video content on the web. This course presents a comparative overview of the latest research in visual-media retargeting. It focuses on content-aware approaches, which, contrary to traditional scaling and cropping, adapt to the salient information within the image or video and rescale the content while preserving visually important information.
Overcoming 5G PRACH Capacity Shortfall by Combining Zadoff-Chu and M-Sequences (2018)

5G physical random access channel (PRACH) will use several new preamble formats in order to enable new use cases. These new formats, however, results in a PRACH capacity shortfall. In this paper, we propose a solution based on an extension of the LTE PRACH sequence set. Cell-specific sequences are derived from single-root Zadoff-Chu (ZC) sequences with a zero-correlation zone, and if necessary, different m-sequence covers instead of multiple roots as in LTE. While this construction is shown to preserve a similar low-correlation zone as with the LTE design, it does not consume the other ZC roots which can then be used to support more cells. The proposed PRACH design is evaluated by 5G link-level simulations to verify the expected good detection performance and low PAPR.
Dynamic atomic force microscopy operation based on high flexure modes of the cantilever (2006)

We show the interest of the high flexure modes of vibration for amplitude-controlled atomic force microscopy (AFM). In connection with AFM working conditions, we define the stabilization time threshold of the oscillating sensor. We show experimentally that, in both air and vacuum, the stabilization time decreases appreciably when the order of the flexure mode of the cantilever increases. Under ambient conditions, this increases the possible scan speeds by about one order of magnitude. Under vacuum and using standard sensors, the amplitude-controlled conditions are satisfied for harmonics equal to or higher than the second. Morphology imaging is then obtained. Thus, high flexure mode AFM easily extends the well known amplitude-controlled operations from ambient to vacuum environment, which allows new AFM applications.
Accelerated Racemization of Aspartic Acid and Asparagine Residues via Succinimide Intermediates:  An ab Initio Theoretical Exploration of Mechanism (1996)

Aspartic acid and asparagine residues racemize rapidly relative to other amino acid residues in proteins and peptides. This has been attributed to the increased acidity of the α-carbons of succinimide residues derived from the spontaneous cyclizations of these residues. To understand the basis of this effect, the acidities of model compounds were calculated using ab initio quantum mechanics (RHF/6-31+G*). The results were also checked with DFT (Becke3LYP/6-31+G*) and solvent cavity models (IPCM and SCIPCM). The geometries of succinimide, 2-pyrrolidinone, and the derived enolate anions were optimized, and the gas phase deprotonation energies were calculated. The imide is more acidic than the amide by 18 kcal/mol in the gas phase. Since there is a qualitative correlation between gas phase and aqueous acidities, this result provides an explanation for the experimental observations that the rate of peptidyl succinimide racemization can be ∼105 times greater than that of unmodified aspartic acid residues. To quantitate the source of the succinimide acidity, the geometries and CH acidities of various conformations of N-formylacetamide and acetamide, acyclic models of succinimide and 2-pyrrolidinone, and 3-oxobutanal and acetone, acyclic models lacking the nitrogen atom, were studied. The importance of resonance effects for increasing the acidity of the α-carbon of succinimide was established, but electrostatic and inductive effects also have an important influence on acidities. The acidity of succinimide is compared to the acidities of several peptide models. Isosuccinimide, an alternative degradation product of aspartic acid and asparagine residues, is also be expected to be racemization prone by similar mechanisms.
Creating Interaction Techniques by Demonstration (1987)

When creating highly interactive, direct-manipulation interfaces, one of the most difficult design and implementation tasks is handling the mouse and other input devices. Peridot, a new user interface management system, addresses this problem by allowing the designer of the user interface to demonstrate how the input device should be handled by giving an example of the interface in action. The designer uses sample values for parameters, and the system automatically infers the general operation and creates the code. After an interaction is specified, it can be executed rapid prototyping, since it is very easy to design, implement, and modify mouse-based interfaces. Perudit also supports such additional input devices as touch tablets, as well as multiple input devices operating in parallel (for example, one in each hand) in a natural, easy-to-specify manner. All interaction techniques are implemented using active values, which are like variables except that the objects that depend on active values are updated immediately whenever they change. Active values are a straightforward and efficient mechanism for implementing dynamic interactions.
Maternal Monoclonal Antibody to the V3 Loop Alters Specificity of the Response to a Human Immunodeficiency Virus Vaccine (1996)

The effect of maternally transferred monoclonal antibody (MAb) on the offspring antibody response to rgp120SF2 was examined in a murine model. Two MAbs were studied: MAb 83.1, which recognizes a determinant in the V3 loop of gp120 from human immunodeficiency virus-1 (HIV-1) SF2, and MAb 26.2D3, which recognizes a conserved N-terminal region of gp120 from HIV-1SF2. Offspring were immunized at 18-21 days of age with 100 micrograms of rgp120SF2 in complete Freund's adjuvant. Offspring immunized in the presence of preexisting MAb 83.1 but not MAb 26.2D3 demonstrated inhibition of the IgG anti-V3 response. The total IgG anti-rgp120SF2 response was not affected by preexisting MAb. Since newborns at risk for HIV may be immunized in the presence of maternal or administered anti-HIV antibody, alternative strategies may be required to circumvent inhibition of the infant's epitope-specific response to HIV immunization by preexisting antibody.
Anti-Obesity and Antioxidative Effects of Purple Sweet Potato Extract in 3T3-L1 Adipocytes <i>In Vitro</i> (2011)

The purpose of the current study was to determine the anti-obesity and anti-inflammatory effects of an extract of purple sweet potatoes (PSPs) on 3T3-L1 adipocytes. For this purpose, differentiated 3T3-L1 adipocytes were treated with a PSP extract at concentrations of 1,000, 2,000, and 3,000 μg/mL for 24 hours. Then, we measured the changes in the sizes of the adipocytes, the secretion of leptin, and the mRNA/protein expression of lipogenic, inflammatory, and lipolytic factors after the treatment with the PSP extract. The PSP extract diminished leptin secretion, indicating that growth of fat droplets was suppressed. The extract also suppressed the expression of mRNAs of lipogenic and inflammatory factors and promoted lipolytic action. The antioxidative activity of the PSP extract was also measured using three different in vitro methods: 1,1-diphenyl-2-picrylhydrazyl free radical scavenging activity, ferric reducing ability potential assay, and chelating activity of transition metal ions. Taken together, our study shows that PSP extract has antilipogenic, anti-inflammatory, and lipolytic effects on adipocytes and has radical scavenging and reducing activity.
Memory Augmented Neural Networks with Wormhole Connections (2017)

Recent empirical results on long-term dependency tasks have shown that neural networks augmented with an external memory can learn the long-term dependency tasks more easily and achieve better generalization than vanilla recurrent neural networks (RNN). We suggest that memory augmented neural networks can reduce the effects of vanishing gradients by creating shortcut (or wormhole) connections. Based on this observation, we propose a novel memory augmented neural network model called TARDIS (Temporal Automatic Relation Discovery in Sequences). The controller of TARDIS can store a selective set of embeddings of its own previous hidden states into an external memory and revisit them as and when needed. For TARDIS, memory acts as a storage for wormhole connections to the past to propagate the gradients more effectively and it helps to learn the temporal dependencies. The memory structure of TARDIS has similarities to both Neural Turing Machines (NTM) and Dynamic Neural Turing Machines (D-NTM), but both read and write operations of TARDIS are simpler and more efficient. We use discrete addressing for read/write operations which helps to substantially to reduce the vanishing gradient problem with very long sequences. Read and write operations in TARDIS are tied with a heuristic once the memory becomes full, and this makes the learning problem simpler when compared to NTM or D-NTM type of architectures. We provide a detailed analysis on the gradient propagation in general for MANNs. We evaluate our models on different long-term dependency tasks and report competitive results in all of them.
CONDICIONES, IMAGINARIOS Y PRÁCTICAS DOCENTES PARA UNA GEOGRAFÍA EN CAMBIO (2011)

En Argentina, los procesos de renovacion de ensenanza de la Geografia y las transformaciones de los temarios escolares en la escuela media, comenzaron a cobrar impulso a partir de la decada de 1990. Dichas transformaciones se explican por la combinacion de una serie de factores: cambios en el enfoque disciplinar y didactico de los disenos curriculares, mayor proximidad entre los saberes escolares y la agenda de temas de relevancia academica, renovados libros de texto y necesidad de los profesores por incorporar perspectivas, tematicas y metodologias adaptadas a los nuevos desafios de la ensenanza de la Geografia. Sin embargo, los alcances de la renovacion no estuvieron exentos de dificultades, expresandose en discursos y practicas que combinaron diferentes tradiciones didactico-pedagogicas y disciplinares. Esto revela el peso que adquiere muchas veces una epistemologia practica, en la que confluyen los saberes de referencia, las creencias personales, las representaciones sociales sobre contenidos geograficos considerados valiosos,  tambien el entorno sociocultural, las condiciones materiales e institucionales en las que se desarrolla la profesion. El proposito de este trabajo consiste en mostrar los resultados alcanzados en una investigacion realizada entre 2006-2009, sobre los logros y dificultades existentes en torno a la renovacion del temario escolar. Nos interrogamos sobre como dialogan saberes y herramientas del campo academico con las practicas docentes en la escuela y con la imagen publica de la disciplina.
Developing Quality Online Dialogue: Dialogical Inquiry (2010)

Dialogue is “at the heart of the e-learning experience” (Littleton & Whitelock 2004, p.173). It is the means to building mutual understanding, encouraging the construction of personal meaning and ensuring engagement. Inquiry requires dialogue. If we value processes of inquiry, then it is at our peril that we ignore the complex issues and aspects of designing and facilitating in online environments for inquiry processes. How do we design online learning experiences that encourage dialogue and a process of inquiry? A phenomenological inquiry using student postings, student interviews and survey data from an online undergraduate course is undertaken to explore the dynamic interrelation between design, facilitation, tools and learning. As part of the analysis, a heuristic device was developed – the Map of aspects of dialogical inquiry. In this article, this device and the dynamic interrelation between design, facilitation, tools and learning are discussed, and implications for practitioners teaching in online environments are explored.
High speed nanofluidic protein accumulator (2009)

Highly efficient preconcentration is a crucial prerequisite to the identification of important protein biomarkers with extremely low abundance in target biofluids. In this work, poly(dimethylsiloxane) microchips integrated with 10 nm polycarbonate nanopore membranes were utilized as high-speed protein accumulators. Double-sided injection control of electrokinetic fluid flow in the sample channel resulted in highly localized protein accumulation at a very sharp point in the channel cross point. This greatly enhanced the ability to detect very low levels of initial protein concentration. Fluorescein labeled human serum albumin solutions of 30 and 300 pM accumulated to 3 and 30 microM in only 100 s. Initial solutions as low as 0.3 and 3 pM could be concentrated within 200 s to 0.3 and 3 microM, respectively. This demonstrates a approximately 10(5)-10(6) accumulation factor, and an accumulation rate as high as 5000/sec, yielding a >10x improvement over most results reported to date.
Phasenanalyse mit Röntgenstrahlen (1989)

Liegen bei heterogenen Werkstoffen Phasen mit unterschiedlichen Gitterstrukturen und hinreichend großen Volumenanteilen vor, so lassen sich die einzelnen Phasenanteile röntgènographisch ermitteln. Das dabei angewandte Prinzip beruht auf der Registrierung der phasenspezifischen Interferenzlinien nach dem Debye-Scherrer-Verfahren (vgl. V 2) und auf der quantitativen Ermittlung sowie dem Vergleich der Röntgenintensitäten, die einzelnen Interferenzen der Phasen zukommen. Dabei kann davon ausgegangen werden, daß die Intensitäten der Röntgeninterferenzen den Volumenanteilen der Phasen in den bestrahlten Werkstoffbereichen proportional sind.
Design and implementation of video DAC in 0.13&amp;mu;m CMOS technology (2003)

This paper presents the design and implementation of video digital-to-analog converter (DAC) in CMOS 0.13μm technology on 8 bits resolution, 500 MS/s, with good performances, smaller area, low glitch energy, which makes it suitable for RAMDAC (Random Memory Access Digital to Analog Converter) application. The proposed current steering DAC is a fully thermometer architecture which assumes a smaller area for a single DAC unit with a new deglitching circuit architecture added to improve the dynamic performances. In this way the interface between the digital part, which operates at low power supply 1.2V, and the analog part operating at 3.3V supply is made possible.
Evaluating the effect of last-level cache sharing on integrated GPU-CPU systems with heterogeneous applications (2016)

Heterogeneous systems are ubiquitous in the field of High- Performance Computing (HPC). Graphics processing units (GPUs) are widely used as accelerators for their enormous computing potential and energy efficiency; furthermore, on-die integration of GPUs and general-purpose cores (CPUs) enables unified virtual address spaces and seamless sharing of data structures, improving programmability and softening the entry barrier for heterogeneous programming. Although on-die GPU integration seems to be the trend among the major microprocessor manufacturers, there are still many open questions regarding the architectural design of these systems. This paper is a step forward towards understanding the effect of on-chip resource sharing between GPU and CPU cores, and in particular, of the impact of last-level cache (LLC) sharing in heterogeneous computations. To this end, we analyze the behavior of a variety of heterogeneous GPU-CPU benchmarks on different cache configurations. We perform an evaluation of the popular Rodinia benchmark suite modified to leverage the unified memory address space. We find such GPGPU workloads to be mostly insensitive to changes in the cache hierarchy due to the limited interaction and data sharing between GPU and CPU. We then evaluate a set of heterogeneous benchmarks specifically designed to take advantage of the finegrained data sharing and low-overhead synchronization between GPU and CPU cores that these integrated architectures enable. We show how these algorithms are more sensitive to the design of the cache hierarchy, and find that when GPU and CPU share the LLC execution times are reduced by 25% on average, and energy-to-solution by over 20% for all benchmarks.
A comprehensive analysis and design of a single phase active power filter with unified constant-frequency integration control (2002)

In this paper, an analysis and design for a single-phase active power filter (APF) with unified constant-frequency integration (UCI) control method is presented. The proposed control method eliminates the need of sensing the load current, a nontrivial task of calculating the harmonics and reactive current components, as well as the use of multipliers, as reported by many previous reported control methods. In addition, the switching loss is reduced by employing unipolar operation mode. The design methodology including electromagnetic interference (EMI) filter is also discussed in detail. The theoretical analysis is verified by experiments.
No Meeting of Minds on XMRV's Role in Chronic Fatigue, Cancer (2010)

Many hoped a workshop last week would help resolve the controversy over reports linking a new retrovirus to some cases of prostate cancer and, more recently—and more controversially—the mysterious illness chronic fatigue syndrome. Instead, the field remains mired in "a zone of chaos," organizers concluded.
Family Encouragement and Life Experiences: The Road to the Monastic Life (2016)

Twenty-two Cistercian monks from a suburban Atlanta, Georgia monastery participated in ninety-minute personal interviews. The monks were asked specific questions about their families, life experiences, monastic vocations, and prayer lives. They came from diverse family backgrounds and life experiences. The main research question that guided this paper was: What role did family encouragement and life experiences play in their road to the monastic life? The overwhelming majority of the monks’ parents supported their son’s monastic vocations. All but two of the monks were raised in Catholic families and most were raised in what they considered to be religious households. Prior to entering the monastery, the monks had been gainfully employed in a variety of occupations and endeavors such as the military, education, retail, construction, the diocesan priesthood, and as a member of a religious order. Keywords: monastic life, Cistercian monks, monastic vocations, Roman Catholics, family encouragement, life experiences
Quality of life issues in chronic wound management (1999)

As a result of improvements in health care, patients are living for many years with chronic disabling diseases. For these people quality of life may be as or even more important than quantity of life. Health-related quality of life (HRQoL) measures attempt to evaluate the patients' perceived mental and social health, not merely their physical problems. Wound care is an ideal area in which to evaluate HRQoL, since the problems are rarely life threatening, but may have a major impact on the way patients live their lives. While there have been preliminary studies to develop disease-specific tools for leg ulceration and chronic venous insufficiency, other types of wound have not received similar attention. Generic tools have been used extensively, not only as indicators of the impact of ulceration on patients but also as outcome measures in both observational studies and clinical trials. The evidence suggests that chronic wounds have an important impact on patients' perceived health particularly in relation to bodily pain, mobility and psychiatric morbidity which are relieved on healing.