gebhart/patrepeval huggingface dataset:
Two small RNAs encoded by Epstein-Barr virus and complexed with protein are precipitated by antibodies from patients with systemic lupus erythematosus. (1981)

Primate cells harboring the Epstein-Barr virus (EBV) genome synthesize large amounts of two small RNAs:EBER 1 and EBER 2 (EBV-encoded RNA). These RNAs are approximately 180 nucleotides long, possess 5' pppA termini, and lack poly(A). They have different T1 and pancreatic RNase digestion fingerprints. They are not found in normal B lymphocytes, in transformed B lymphocytes that lack EBV DNA, in T lymphocytes transformed by Herpesvirus ateles, or in a variety of other nonlymphoid mammalian cells. Hybridization analyses indicate that EBER 1 and EBER 2 are encoded by the EcoRI-J fragment of EBV (B95-8) DNA. In vivo both RNAs are associated with protein(s), allowing their specific precipitation by the systemic lupus erythematosus-associated antibody anti-La. The La antigen in uninfected mammalian cells consists of a heterogeneous class of small ribonucleoprotein particles, some of whose RNA components exhibit sequence homology with a highly repetitive, interspersed class of human DNA designated the Alu family. Possible functions for EBER 1 and EBER 2 in infection and cell transformation by EBV and their potential relationship to the pathogenesis of systemic lupus erythematosus are discussed.
Practical Guidelines for the Surgical Treatment of Gallbladder Cancer (2014)

At present, surgical treatment is the only curative option for gallbladder (GB) cancer. Many efforts therefore have been made to improve resectability and the survival rate. However, GB cancer has a low incidence, and no randomized, controlled trials have been conducted to establish the optimal treatment modalities. The present guidelines include recent recommendations based on current understanding and highlight controversial issues that require further research. For T1a GB cancer, the optimal treatment modality is simple cholecystectomy, which can be carried out as either a laparotomy or a laparoscopic surgery. For T1b GB cancer, either simple or an extended cholecystectomy is appropriate. An extended cholecystectomy is generally recommended for patients with GB cancer at stage T2 or above. In extended cholecystectomy, a wedge resection of the GB bed or a segmentectomy IVb/V can be performed and the optimal extent of lymph node dissection should include the cystic duct lymph node, the common bile duct lymph node, the lymph nodes around the hepatoduodenal ligament (the hepatic artery and portal vein lymph nodes), and the posterior superior pancreaticoduodenal lymph node. Depending on patient status and disease severity, surgeons may decide to perform palliative surgeries.
A Pattern Description and Generation Method of Structural Characters (1986)

We report a pattern description and generation method of structural characters, and show some examples of Chinese and Korean character patterns actually generated. We also consider its educational and graphical applications. In this method, any character is regarded as a composite pattern constructed by several simpler subpatterns, and is described in terms of them by introducing three kinds of positional relationships among them. A composite pattern can become a subpattern, too. We call these patterns blocks. Syntactic grammar is defined to encode a pattern expression by two code strings, that is, a string of blocks and a string of production rules. They are used in generating patterns, namely, derivation of pattern expression from the code strings is defined as a process of pattern generation. By this description and generation method, we can encode structural characters without much memory, and generate natural shapes of patterns.
Linkage of Organic Anion Transporter-1 to Metabolic Pathways through Integrated “Omics”-driven Network and Functional Analysis (2011)

The main kidney transporter of many commonly prescribed drugs (e.g. penicillins, diuretics, antivirals, methotrexate, and non-steroidal anti-inflammatory drugs) is organic anion transporter-1 (OAT1), originally identified as NKT (Lopez-Nieto, C. E., You, G., Bush, K. T., Barros, E. J., Beier, D. R., and Nigam, S. K. (1997) J. Biol. Chem. 272, 6471-6478). Targeted metabolomics in knockouts have shown that OAT1 mediates the secretion or reabsorption of many important metabolites, including intermediates in carbohydrate, fatty acid, and amino acid metabolism. This observation raises the possibility that OAT1 helps regulate broader metabolic activities. We therefore examined the potential roles of OAT1 in metabolic pathways using Recon 1, a functionally tested genome-scale reconstruction of human metabolism. A computational approach was used to analyze in vivo metabolomic as well as transcriptomic data from wild-type and OAT1 knock-out animals, resulting in the implication of several metabolic pathways, including the citric acid cycle, polyamine, and fatty acid metabolism. Validation by in vitro and ex vivo analysis using Xenopus oocyte, cell culture, and kidney tissue assays demonstrated interactions between OAT1 and key intermediates in these metabolic pathways, including previously unknown substrates, such as polyamines (e.g. spermine and spermidine). A genome-scale metabolic network reconstruction generated some experimentally supported predictions for metabolic pathways linked to OAT1-related transport. The data support the possibility that the SLC22 and other families of transporters, known to be expressed in many tissues and primarily known for drug and toxin clearance, are integral to a number of endogenous pathways and may be involved in a larger remote sensing and signaling system (Ahn, S. Y., and Nigam, S. K. (2009) Mol. Pharmacol. 76, 481-490, and Wu, W., Dnyanmote, A. V., and Nigam, S. K. (2011) Mol. Pharmacol. 79, 795-805). Drugs may alter metabolism by competing for OAT1 binding of metabolites.
Ultrasensitive detections in atomic and molecular physics: demonstration in molecular overtone spectroscopy (1998)

We consider several highly sensitive techniques commonly used in detection of atomic and molecular absorptions. Their basic operating principles and corresponding performances are summarized and compared. We then present our latest results on the ultrasensitive detection of molecular overtone transitions to illustrate the principle and application of the cavity-enhanced frequency-modulation (FM) spectroscopy. An external cavity is used to enhance the molecular response to the light field, and an FM technique is applied for shot-noise-limited signal recovery. A perfect match between the FM sideband frequency and the cavity free spectral range makes the detection process insensitive to the laser-frequency noise relative to the cavity, and, at the same time, overcomes the cavity bandwidth limit. Working with a 1.064-μm Nd:YAG laser, we obtained sub-Doppler overtone resonances of C2HD,C2H2, and CO2 molecules. A detection sensitivity of 5×10-13 of integrated absorption (1×10-14/cm) over 1-s averaging time has been achieved.
Nanoscale domain patterns in ultrathin polymer ferroelectric films (2009)

High-resolution studies of domain configurations in Langmuir-Blodgett films of ferroelectric polymer poly(vinylidene fluoride-trifluoroethylene), P(VDF-TrFE), have been carried out by means of piezoresponse force microscopy (PFM). Changes in film thickness and morphology cause significant variations in polarization patterns. In continuous films and nanomesas with relatively low thickness/grain aspect ratio (<1/10), the relationship between the average domain size and thickness follows the Kittel law. Nanomesas with high aspect ratio (>1/5) exhibit significant deviations from this law, suggesting additional surface-energy-related mechanisms affecting the domain patterns. Polarization reversal within a single crystallite has been demonstrated and local switching parameters (coercive voltage and remnant piezoresponse) have been measured by monitoring the local hysteresis loops. Reliable control of polarization at the sub-grain level demonstrates a possibility of studying the mechanism of the intrinsic switching behavior down to the molecular scale.
Symmetry X system and method for absolute measurements of reflectance and transmittance of specular samples (2003)

A symmetry X system that has been constructed for the absolute measurements of reflectance and transmittance of specular samples in the infrared region is described. The system has been designed so that it can be incorporated into commercial Fourier-transform infrared spectrometers. Although ten mirrors were used in this system, it is disclosed that the geometric mean of two reflectance values is independent of the reflectance difference of the individual mirrors and the optical loss at each mirror. This system achieves spectral measurements with high accuracy and within a short period of time. In particular, the system affords us the self-diagnostic ability for measured spectra, and the simultaneous measurements of reflectance and transmittance under the same geometry enable us to evaluate measurement uncertainties. Although the symmetry X system is used for infrared spectral measurements, the measurement method, design principles, and features are generally applicable to other wavelengths as well.
The strong WCD property for Banach spaces (1995)

In this paper, we introduce weakly compact version of the weakly countably determined (WCD) property, the strong WCD (SWCD) property. A Banach space X is said to be SWCD if there s a sequence ( A n ) of weak ∗ compact subsets of X ∗∗ such that if K ⊂ X is weakly compact, there is an ( n m ) ⊂ N such that . In this case, ( A n ) is called a strongly determining sequence for X . We show that SWCG⇒SWCD and that the converse does not hold in general. In fact, X is a separable SWCD space if and only if ( X , weak) is an ℵ 0 ‐space. Using c 0 for an example, we show how weakly compact structure theorems may be used to construct strongly determining sequences.
Microisolation of Biologically Active Polypeptides by Reverse-Phase Liquid Chromatography (1986)

The development of new, high-sensitivity methods in protein chemistry (microisolation, amino acid microanalysis, and microse-quencing) has permitted the characterization of a large number of previously unknown polypeptides with regulatory functions. After decades of research devoted to the metabolism of the individual cell, this new methodology has sparked investigation into the presence and functional significance of polypeptides that govern the communication between cells within the multicellular organism. The technology is presently developing in two directions: (1) initial studies were done with small peptides, then progressed to medium-size polypeptides, and are now more and more utilized for proteins, and (2) less and less material is becoming necessary for structural characterization by amino acid analysis and sequencing, i.e., whereas initially several nanomoles of purified material were necessary, picomolar amounts are now required for partial or complete structural characterization. Over the years, reverse-phase liquid chromatography (RPLC) has evolved as the dominant tool for the isolation and characterization of polypeptides. Recently, however, alternative modes of chromatography, such as high-performance ion exchange, gel filtration, and chromatofocusing techniques, have been further developed, thus becoming integral parts of isolation programs.
Geminin is essential for the development of preimplantation mouse embryos (2006)

Replication of DNA is strictly controlled to ensure that it occurs only once per cell cycle. Geminin has been thought to serve as a central mediator of this licensing mechanism by binding to and antagonizing the function of Cdt1 and thereby preventing re-replication during S and G2 phases. We have now generated mice deficient in geminin to elucidate the physiologic role of this protein during development. Lack of geminin was shown to result in preimplantation mortality. A delay in the development of homozygous mutant embryos was first apparent at the transition from the four- to eight-cell stages, concomitant with the disappearance of maternal geminin protein, and development was arrested at the eight-cell stage. The mutant embryos manifest morphological abnormalities such as dispersed blastomeres with nuclei that are irregular both in size and shape as well as impaired cell-cell adhesion. DNA replication occurs but mitosis was not detected in the mutant embryos. The abnormal blastomeres contain damaged DNA and undergo apoptosis, likely as a consequence of the deregulation of DNA replication. Our results suggest that geminin is essential for cooperative progression of the cell cycle through S phase to M phase during the preimplantation stage of mouse development.
High-efficiency infrared light emitting diodes made in liquid phase epitaxy and molecular beam epitaxy HgCdTe layers (1991)

We report in this article, for the first time the performance of light emitting diodes (LEDs) made in HgCdTe (MCT) epilayers on CdZnTe (CZT) lattice-matched substrates grown either by liquid phase epitaxy (LPE) or molecular beam epitaxy (MBE). Diodes are n/p homojunctions made by ion implantation. The MCT composition was chosen in order to get the emission wavelength between 3 and 5 μm. Electroluminescence spectra were recorded between 20 K and 300 K. A comparison of the two materials is made, demonstrating that they exhibit similar performances. Internal quantum efficiencies as high as 25% (λ peak=4.1 μm at 77 K) and 6% (λ peak=3.5 μm at 300 K) were obtained on both LPE and MBE materials and they reach a maximum for a temperature of about 90 K. For a material with λ peak=5.5 μ at 77 K, internal quantum efficiency remains as high as 5%. The external quantum efficiency is considerably increased using backside emission through the CZT substrate and optical coupling with a CZT lens: in such conditions 20% of the emitted light could be extracted from the structure. These results show that MCT can already be used for LEDs in the 3–5 μm region.
Can haptic feedback improve the perception of self-motion in virtual reality? (2004)

This paper describes an experiment which was conducted to evaluate the influence of haptic feedback on the perception of self-motion in virtual reality. Participants were asked to estimate the angles of turns made during a passive visual navigation. Sometimes, during a turn, a haptic feedback was sent to the dominant hand of the participants. This haptic feedback consisted in rotating the participants' fist by the same angular value as the visual turn. The presence of haptic feedback globally influenced the performances of the participants. On average, with haptic feedback, the participants less under-estimated the angles the turns made in the visual navigation. These results suggest that the perception of self-motion could be improved in virtual reality by using an appropriate haptic feedback. Haptic stimulation during navigation could partially substitute for the missing information provided by proprioception and vestibular system.
Two‐dimensional electrophoresis of proteins in an immobilized pH 4–12 gradient (1998)

For checking theoretical two-dimensional (2-D) maps derived from sequenced genomes, indicating that nonnegligible amounts of proteins up to pH 12 are to be expected, a wide-range immobilized pH 4-12 gradient was generated. Depending on the extraction method of sample preparation, proteins with pls up to pH 12 are detected in a single gel. Highly reproducible protein patterns focused to the steady state with round-shaped spots up to pH 12 are obtained with the standard protocol originally described in 1988 (Görg et al., Electrophoresis 1988, 9, 531-546).
Counteracting Effects Operating on Src Homology 2 Domain-containing Protein-tyrosine Phosphatase 2 (SHP2) Function Drive Selection of the Recurrent Y62D and Y63C Substitutions in Noonan Syndrome* (2012)

Activating mutations in PTPN11 cause Noonan syndrome, the most common nonchromosomal disorder affecting development and growth. PTPN11 encodes SHP2, an Src homology 2 (SH2) domain-containing protein-tyrosine phosphatase that positively modulates RAS function. Here, we characterized functionally all possible amino acid substitutions arising from single-base changes affecting codons 62 and 63 to explore the molecular mechanisms lying behind the largely invariant occurrence of the Y62D and Y63C substitutions recurring in Noonan syndrome. We provide structural and biochemical data indicating that the autoinhibitory interaction between the N-SH2 and protein-tyrosine phosphatase (PTP) domains is perturbed in both mutants as a result of an extensive structural rearrangement of the N-SH2 domain. Most mutations affecting Tyr(63) exerted an unpredicted disrupting effect on the structure of the N-SH2 phosphopeptide-binding cleft mediating the interaction of SHP2 with signaling partners. Among all the amino acid changes affecting that codon, the disease-causing mutation was the only substitution that perturbed the stability of the inactive conformation of SHP2 without severely impairing proper phosphopeptide binding of N-SH2. On the other hand, the disruptive effect of the Y62D change on the autoinhibited conformation of the protein was balanced, in part, by less efficient binding properties of the mutant. Overall, our data demonstrate that the selection-by-function mechanism acting as driving force for PTPN11 mutations affecting codons 62 and 63 implies balancing of counteracting effects operating on the allosteric control of the function of SHP2.
Erratum: “Perfect spatial ordering of self-organized InGaAs/AlGaAs box-like structure array on GaAs (311)<b> <i>B</i> </b> substrate with silicon nitride dot array” [Appl. Phys. Lett. <b>71</b>, 1655 (1997)] (1997)

First Page
Google TV search (2008)

In 2006 Google designed and implemented a TV Show search system which featured a dual-navigation control combining a powerful search system with an interactive, personalize-able TV listings grid. The dual-control system allowed users to move fluidly between explicit search and general discovery, obtain detailed information without leaving the global context and construct a personal channel for easy access and recommendations. As a complete system, TV Search integrated with Google's general search page through a mini-listings onebox and also exported information out to Google calendar, Gmail and TiVo. Building this TV Search system as a large-scale product meant addressing many technological, business and fine-grained user experience details. This paper describes the design process including the early designs, the user studies and the details of the final system including the mini-guide, main page dual-control and the integrated services on the detail pages.
ADIBEAM: Design and experimental validation of a robust beamforming platform for Galileo reference ground stations (2010)

The increase in navigation accuracy demanded by EGNOS and Galileo and their future evolution encourages the study and design of advance receiver architectures. In that direction, the ADIBEAM project focuses on the design of high accuracy ground stations, specifically GNSS Reference Stations, in order to improve its robustness in front of multipath and interference errors with the goal of achieving centimeter level tracking accuracy. The adoption of antenna arrays and digital beamforming at the ground reference station receivers is one of the most promising approaches to cope with errors induced by multipath and interference. This paper proposes an innovative design of a ground based tracking station. In particular, the architecture proposed is based on the use of an antenna array and digital beamforming techniques, considering both adaptive and deterministic methods. The work carried out here considers the ground based tracking system, including the characterization of the system components (antennas, RF chains, calibration techniques, GNSS software receiver and digital beamforming), and the development of a software based experimentation platform representative of the proposed design for a hardware prototype. The sensitivity to perturbations and the extreme difficulty to perfectly control and calibrate all the components of the system, especially regarding the antenna array implementation, requires that the proposed design take into consideration not only the benefits of the possible solutions but also their feasibility for a real implementation. In summary, this paper will present the design proposed and the Experimentation Platform used for its validation.
Surface Properties of Porous Carbon Obtained from Polystyrene Sulfonic Acid-Based Organic Salts (2004)

Pyrolysis ofpolysterene sulfonic acid-co-maleic acid salts at 800 degrees C resulted in formation of new materials consisting of porous carbon and metal species dispersed on the surface. After hydrochloric acid treatment, the metal oxides/salts were removed. Obtained materials were characterized using adsorption of nitrogen, thermogravimetric analysis, Raman spectroscopy, and scanning electron microscopy with energy dispersive analysis of X-rays. The results showed highly developed porous structures in the range of micro- and mesopores. The porous features of new materials resemble those characteristics for carbon foams. The differences in the porous structure are linked to the type of transition metal used for the modification of the initial polymer and the chelation process. Macro- and mesopores are spherical/cylindrical in shape, and they are likely formed when release of pyrolysis gases, such as CO2, NO2, SO2, H2S, and CxHy, occurs. Moreover, reduction of metal, its migration to the surface, and agglomeration contribute to development of porosity. Depending on the reactivity of the metal used for cation exchange (Fe, Co, or Ni) either sulfides (nickel and cobalt) or oxides (cobalt and iron) are formed on the carbon surface.
The subgoal learning model: Creating better examples so that students can solve novel problems. (1998)

Learners have great difficulty solving problems requiring changes to solutions demonstrated in examples. However, if the solution procedures learners form are organized by subgoals, then they are more successful. Subgoal learning is hypothesized to be aided by cues in example solutions that indicate that certain steps go together. These cues may induce a learner to attempt to self-explain the purpose of the steps, resulting in the formation of a subgoal. Across 4 experiments it was found that a label for a group of steps in examples helped participants form subgoals as assessed by measures such as problem-solving performance and talk aloud protocols. Abstract labels were more likely than superficial labels to lead participants to form subgoals with fewer ties to surface features. Subgoals guide problem solving by helping learners focus on the steps to modify in novel problems that involve the same subgoals but require new steps to achieve them.