gebhart/patrepeval huggingface dataset:
Reconstruction of MRI data encoded by multiple nonbijective curvilinear magnetic fields (2012)

Parallel imaging technique using localized gradients (PatLoc) uses the combination of surface gradient coils generating nonbijective curvilinear magnetic fields for spatial encoding. PatLoc imaging using one pair of multipolar spatial encoding magnetic fields (SEMs) has two major caveats: (1) The direct inversion of the encoding matrix requires exact determination of multiple locations which are ambiguously encoded by the SEMs. (2) Reconstructed images have a prominent loss of spatial resolution at the center of field-of-view using a symmetric coil array for signal detection. This study shows that a PatLoc system actually has a higher degree of freedom in spatial encoding to mitigate the two challenges mentioned above. Specifically, a PatLoc system can generate not only multipolar but also linear SEMs, which can be used to reduce the loss of spatial resolution at the field-of-view center. Here, we present an efficient and generalized image reconstruction method for PatLoc imaging using multiple SEMs without explicitly identifying the locations where SEM encoding is not unique. Reconstructions using simulations and empirical experimental data are compared with those using conventional linear gradients to demonstrate that the general combination of SEMs can improve image reconstructions.
Cloning of the Chicken Pituitary Receptor for Growth Hormone-Releasing Hormone (2006)

Details of the regulation of GH in birds are unclear. In this report, a receptor was cloned from chicken pituitary cDNA with 61% amino acid sequence identity to the human pituitary GHRH receptor. Phylogenies inferred from sequence alignments support that this is the chicken counterpart of the GHRH receptor known in mammals. Northern blotting shows that this receptor message is expressed in chicken pituitary, with lesser amounts seen in hypothalamus and brain but not in liver. The recombinant chicken receptor binds human GHRH with high affinity and specificity and signals cAMP accumulation. Surprisingly, available peptides synthesized to the published sequence for chicken GHRH-like peptide (cGHRH-LP) were inactive at this receptor. To address this we recloned the cDNA for this cGHRH-LP from chicken hypothalami. The revised sequence encodes lysine at position 21, which is consistent with all reported GHRH sequences from other species but different from the originally published chicken sequence. When this revised cGHRH-LP sequence was synthesized, it had improved but still weak potency at the cloned receptor. Consistent with the activity at the cloned receptor, human GHRH was potent when assayed in live chickens or on chicken pituitary membranes, but cGHRH-LP was not. We conclude that we have cloned a putative GHRH receptor that is homologous to mammalian GHRH receptors and functionally expressed in chicken pituitary, but that the identity of the endogenous ligand remains unclear. The chicken GHRH receptor cloned in this study can serve as a tool to identify its ligand and to clarify the evolutionary development of the regulation of GH.
Operational abstractions of model transforms (2014)

Model transforms convert a model to another model or text. Transforms play a key role in model-driven engineering; therefore, it is essential for a transform user to understand the transform semantics. However, examining the transform code to obtain such understanding can be cumbersome and impractical. To address this, we present an operational abstraction of model transforms. The abstraction captures the essential transformation semantics in terms of the structure of the output and the influence of input-model elements on output fragments. Thus, the abstraction supports the transform user's perspective, which is focused on inputs and outputs, and is unconcerned with implementation details. We present an automated approach that uses a combination of selective path enumeration, forced execution of enumerated paths, and an offline trace-merging analysis to synthesize operational abstractions. We discuss different applications of the abstraction. We implemented our approach for XSLT-based model transforms and conducted empirical studies. Our results indicate that selective path enumeration can be highly effective in reducing the scope of path exploration, while ensuring that the abstraction is complete. Our user study illustrates that the abstraction can improve user efficiency in debugging faulty input models. Our final study shows the feasibility of using abstractions for two metamodel management tasks.
Targeting Intracellular Pathogenic Bacteria Through N-Terminal Modification of Cationic Amphiphilic Polyproline Helices (2020)

Intracellular pathogens can thrive within mammalian cells and are inaccessible to many antimicrobial agents. Herein, we present a facile method of enhancing the cell penetrating and antibacterial properties of cationic amphiphilic polyproline helices (CAPHs) with modifications to the hydrophobic moiety at the N-terminus. These altered CAPHs display superior cell penetration within macrophage cells, and in some cases, minimal cytotoxicity. Furthermore, one CAPH, <b>Pentyl-P14</b> exhibited excellent antibacterial activity against multiple strains of pathogenic bacteria and promoted the clearance of intracellular <i>Shigella</i> within macrophages.
Improved solid‐phase microextraction device for use in on‐line immunoaffinity capillary electrophoresis (2003)

A simple solid-phase microextraction device was fabricated for use in on-line immunoaffinity capillary electrophoresis (CE). The device, designed in the form of a four-part cross-shaped or cruciform configuration, includes a large-bore tube to transport samples and washing buffers and a small-bore fused-silica capillary for separation of analytes. At the intersection of the transport and separation tubes, a small cavity was fabricated, termed the analyte concentrator-microreactor, which contains four porous walls or semipermeable membranes (one for each inlet and outlet of the tubes) permitting the confinement of beads or suitable microstructures. The surface of the beads in the analyte concentrator carried a molecular recognition adsorbing chemical or affinity ligand material. The improved cruciform configuration of the analyte concentrator-microreactor device, designed for use in on-line immunoaffinity CE, enables it to specifically trap, enrich, and elute an analyte from any biological fluid or tissue sample extract without any sample pretreatment except filtration, centrifugation, and/or dilution allowing the separation and characterization of target analyte(s) with improved speed, sensitivity, and lower cost than existing techniques. As a model system, Fab' fragments derived from a purified immunoglobulin G (IgG) antibody were covalently bound to controlled-porosity glass and used as constituents of the analyte-microreactor device. The high-specificity polyclonal antibodies employed in these experiments were individually raised against the acidic nonsteroidal anti-inflammatory drugs ibuprofen and naproxen, and the neuropeptides angiotensin II, and neurotensin. These compounds, which were present in simple and complex matrices were captured by and eluted from the analyte concentrator-microreactor using a 50 mM sodium tetraborate buffer solution, pH 9.0, followed by a 100 nL plug of 300 mM glycine buffer, pH 3.4. Two analyte concentrators were tested independently: one containing Fab' fragments derived from antibodies raised against ibuprofen and naproxen; the other containing Fab' fragments derived from antibodies raised against angiotensin II and neurotensin. Each resulting electropherogram demonstrated the presence of two eluted materials in less than 20 min. Immunoaffinity CE performed in a cruciform structure was simpler and faster than previously reported in the literature using on-line microextraction devices designed in a linear format. The new concentration-separation system operated consistently for many runs, maintaining reproducible migration times and peak areas for every analyte studied.
<title>Two Fixed, Evacuated, Glass, Solar Collectors Using Nonimaging Concentration</title> (1984)

Two fixed, evacuated, glass solar thermal collectors have been designed. The incorporation of nonimaging concentration, selective absorption and vacuum insulation into their design is essential for obtaining high efficiency through low heat loss, while operating at high temperatures. Nonimaging, approximately ideal concentration with wide acceptance angle permits solar radiation collection without tracking the sun, and insures collection of much of the diffuse radiation. It also minimizes the area of the absorbing surface, thereby reducing the radiation heat loss. Functional integration, where different parts of these two collectors serve more than one function, is also important in achieving high efficiency, and it reduces cost.
Delimiting subterritories of the human subthalamic nucleus by means of microelectrode recordings and a Hidden Markov Model (2009)

Positive therapeutic response without adverse side effects to subthalamic nucleus deep brain stimulation (STN DBS) for Parkinson's disease (PD) depends to a large extent on electrode location within the STN. The sensorimotor region of the STN (seemingly the preferred location for STN DBS) lies dorsolaterally, in a region also marked by distinct beta (13-30 Hz) oscillations in the parkinsonian state. In this study, we present a real-time method to accurately demarcate subterritories of the STN during surgery, based on microelectrode recordings (MERs) and a Hidden Markov Model (HMM). Fifty-six MER trajectories were used, obtained from 21 PD patients who underwent bilateral STN DBS implantation surgery. Root mean square (RMS) and power spectral density (PSD) of the MERs were used to train and test an HMM in identifying the dorsolateral oscillatory region (DLOR) and nonoscillatory subterritories within the STN. The HMM demarcations were compared to the decisions of a human expert. The HMM identified STN-entry, the ventral boundary of the DLOR, and STN-exit with an error of -0.09 +/- 0.35, -0.27 +/- 0.58, and -0.20 +/- 0.33 mm, respectively (mean +/- standard deviation), and with detection reliability (error < 1 mm) of 95, 86, and 91%, respectively. The HMM was successful despite a very coarse clustering method and was robust to parameter variation. Thus, using an HMM in conjunction with RMS and PSD measures of intraoperative MER can provide improved refinement of STN entry and exit in comparison with previously reported automatic methods, and introduces a novel (intra-STN) detection of a distinct DLOR-ventral boundary.
Managing Credit Lines and Prices for Bank One Credit Cards (2003)

We developed a method for managing the characteristics of a bank's card holder portfolio in an optimal manner. The annual percentage rate (APR) and credit line of an account influence card use and bank profitability. Consumers find low APRs and high credit lines attractive. However, low APRs may reduce bank profitability, while indiscriminate increases in credit lines increase the bank's exposure to credit loss. We designed the PORTICO (portfolio control and optimization) system using Markov decision processes (MDP) to select price points and credit lines for each card holder that maximize net present value (NPV) for the portfolio. PORTICO uses account-level historical information on purchases, payments, profitability, and delinquency risk to determine pricing and credit-line changes. In competitive benchmark tests over more than a year, the PORTICO model outperforms the bank's current method and may increase annual profits by over $75 million.
Improvement of immunoassay detection system by using alternating current magnetic susceptibility (2016)

A major goal with this research was to develop a low-cost and highly sensitive immunoassay detection system by using alternating current (AC) magnetic susceptibility. We fabricated an improved prototype of our previously developed immunoassay detection system and evaluated its performance. The prototype continuously moved sample containers by using a magnetically shielded brushless motor, which passes between two anisotropic magneto resistance (AMR) sensors. These sensors detected the magnetic signal in the direction where each sample container passed them. We used the differential signal obtained from each AMR sensor's output to improve the signal-to-noise ratio (SNR) of the magnetic signal measurement. Biotin-conjugated polymer beads with avidin-coated magnetic particles were prepared to examine the calibration curve, which represents the relation between AC magnetic susceptibility change and polymer-bead concentration. For the calibration curve measurement, we, respectively, measured the magnetic signal caused by the magnetic particles by using each AMR sensor installed near the upper or lower part in the lateral position of the passing sample containers. As a result, the SNR of the prototype was 4.5 times better than that of our previous system. Moreover, the data obtained from each AMR sensor installed near the upper part in the lateral position of the passing sample containers exhibited an accurate calibration curve that represented good correlation between AC magnetic susceptibility change and polymer-bead concentration. The conclusion drawn from these findings is that our improved immunoassay detection system will enable a low-cost and highly sensitive immunoassay.
Oxidative Dehydrogenation of Propane to Propylene over VO<sub><i>x</i></sub> on Mixed θ-Al<sub>2</sub>O<sub>3</sub>/Alkaline Earth Metal Oxide Supports (2019)

The oxidative dehydrogenation of propane to propylene with solid-phase oxygen of VOx-based mixed-oxide catalysts is investigated. The catalysts are prepared by depositing VOx species on alkaline-oxide-modified θ-Al2O3 supports. X-ray diffraction and X-ray photoelectron spectroscopy reveal the nature and variations of the crystalline phases. The surface area, acidity, and reduction properties of the catalysts are functions of the innate properties of bare θ-Al2O3 and the characteristic properties of each alkaline oxide. The multistage reduction of VOx on mixed-oxide supports indicates the reduction of various VOx species. The catalysts are evaluated in a fluidized CREC Riser Simulator by injecting a known amount of propane at different reaction temperatures. All catalysts show excellent propane conversion and plausible selectivity to olefins. VOx on θ-Al2O3/CaO minimizes the formation of COx species, whereas VOx θ-Al2O3/BaO displays the highest olefin yields (49%).
Genetic engineering of onco/lentivirus hybrids results in formation of infectious but not of replication-competent viruses (2004)

To achieve specific gene transfer into human CD4(+) cells, murine leukaemia virus (MLV)-based pseudotype vector particles were generated employing Env variants derived from human or simian immunodeficiency virus (HIV-1 or SIVagm). Here, we describe the generation of full-length onco/lentivirus hybrid genomes comprising components of MLV and HIV-1 or SIVagm, respectively, to assess the possibility of replication-competent hybrid virus formation. The env reading frame of an infectious molecular clone of MLV was replaced with the analogous coding regions of HIV-1 or SIVagm encompassing the env gene and accessory genes. Resulting MLV/HIV-1 or MLV/SIVagm hybrid genomes were transfected into 293T cells. Expression of viral proteins and budding of retroviral particles was shown by specific immunostaining and electron microscopy. The viral particles mediated CD4- and co-receptor-specific infection of human cells as demonstrated by PCR and immunostaining in the respective target cells. However, no productive infection resulting in the generation of infectious virus was detected in these cells. Thus, these onco/lentivirus hybrids, although able to initiate single-round infection, were not replication competent. Thus, MLV-based pseudotype vectors carrying Env variants of HIV-1 or SIVagm are not prone to form replication-competent retroviruses, suggesting a favourable safety profile for MLV-based CD4-specific pseudotype vectors.
Luminescent Solar Concentrators: An Overview (1983)

The Luminescent Solar Concentrator (LSC) offers the possibility of reducing the cost of photovoltaic solar energy conversion through the use of light pipe trapping of luminescence. Three concepts govern the performance of an LSC: light concentration, light pipe trapping of luminescence, and photovoltaic conversion. We present prototype performance data as well as a simple model which predicts the light intensity gain and efficiency from molecular parameters.
Controlled Formation and Mechanical Characterization of Metallic Glassy Nanowires (2009)

Extraordinary flexible, very long, and individual amorphous nanowires composed of metallic glasses are produced by the drawing process based on superplastic deformation above the glass transition temperature. The outstanding mechanical properties of metallic glasses including low Young's modulus and high strength can be inherited in nanowire.
Electronic musical instrument having a portamento function utilizing whole and half transformations (1995)

First Page
Focus improvement with NIR absorbing underlayer attenuating substructure reflectivity (2012)

Process dependent focus leveling errors occur in photolithography when there is unpredicted reflectivity originating from multilayer structures on the fully integrated process wafer. The typical wavelength used in optical focus sensors is in the near infrared (NIR) range which is highly transparent to most dielectric materials. Consequently, the reflected light from underlying structures perturbs the accuracy of the leveling signal reflected from resist surface. To alleviate this issue, air-gauge focus sensors have been used to measure the wafer surface topography for an in-situ calibration to correct the focus leveling error. Using an air-gauge sensor is a slow process and a throughput detractor. Therefore, an NIR-absorbing underlayer has been developed for easy insertion into existing resist coating processes. It has been demonstrated that the air-gauge sensor can be turned off without showing any degradation in leveling data or litho performance on back end of line (BEOL) integrated wafers.
Dedicated Protection for Survivable Virtual Network Embedding (2016)

Network virtualization is enabling infrastructure providers (InPs) to offer new services to service providers (SPs). InPs are usually bound by service level agreements to ensure various levels of resource availability for different SPs' virtual networks (VNs). They provision redundant backup resources while embedding an SP's VN request to conform to the SLAs during physical failures in the infrastructure. An extreme backup resource provisioning is to reserve a mutually exclusive backup of each element in an SP's VN request. Such dedicated protection scheme can enable an InP to ensure fast VN recovery, thus, providing high uptime guarantee to the SPs. In this paper, we study the 1 + 1-Protected Virtual Network Embedding (1 + 1-ProViNE) problem. We propose Dedicated Protection for Virtual Network Embedding (DRONE), a suite of solutions to the 1 + 1-ProViNE problem. DRONE includes an integer linear programming formulation for optimal solution (OPT-DRONE) and a heuristic (FAST-DRONE) to tackle the computational complexity of the optimal solution. Trace driven simulations show that FAST-DRONE allocates only 14.3% extra backup resources on average compared to the optimal solution, while executing 200-1200 times faster. Simulation results also show that FAST-DRONE can accept four times more VN requests on average compared to the state-of-the-art solution for providing dedicated protection to VNs.
Thermoelectric Ceramics for Energy Harvesting (2012)

Metal oxides (Ca 3 Co 4 O 9 , CaMnO 3 , SrTiO 3 , In 2 O 3 ), Ti sulfides, and Mn silicides are promising thermoelectric (TE) material candidates for cascade‐type modules that are usable in a temperature range of 300–1200 K in air. In this paper, we review previous studies in the field of TE materials development and make recommendations for each material regarding future research. Furthermore, the R&D of TE modules composed of metal oxide materials and the prospect of their commercialization for energy harvesting is demonstrated.
Autoantibodies recognizing carbamylated proteins are present in sera of patients with rheumatoid arthritis and predict joint damage (2011)

Autoimmune responses against posttranslationally modified antigens are a hallmark of several autoimmune diseases. For example, antibodies against citrullinated protein antigens (ACPA) have shown their relevance for the prognosis and diagnosis of rheumatoid arthritis (RA), and have been implicated in disease pathogenesis. It is conceivable that other autoantibody systems, recognizing other posttranslationally modified proteins, are also present in RA. Here, we describe the presence of an autoantibody system that discriminates between citrulline- and homocitrulline-containing antigens in the sera of RA-patients. IgG antibodies recognizing carbamylated (homocitrulline-containing) antigens were present in sera of over 45% of RA-patients. Likewise, anticarbamylated protein (anti-CarP) IgA antibodies were observed in 43% of RA-sera. ACPA and anti-CarP antibodies are distinct autoantibodies because, in selected double-positive patients, the anti-CarP antibody binding to carbamylated antigens could be inhibited by carbamylated antigens, but not by control or citrullinated antigens. Similarly, ACPA-binding to citrullinated antigens could only be inhibited by citrullinated antigens. In line with this observation, 16% of ACPA-negative RA-patients, as measured by a standard ACPA assay, harbored IgG anti-CarP antibodies, whereas 30% of these patients tested positive for IgA anti-CarP antibodies. The presence of anti-CarP antibodies was predictive for a more severe disease course in ACPA-negative patients as measured by radiological progression. Taken together, these data show the presence of a unique autoantibody system recognizing carbamylated, but not citrullinated, protein antigens. These antibodies are predictive for a more severe clinical course in ACPA-negative RA-patients, indicating that anti-CarP antibodies are a unique and relevant serological marker for ACPA-negative RA.
Trace: time reservation using adaptive control for energy efficiency (2003)

Time reservation using adaptive control for energy efficiency (TRACE) is a time frame based media access control (MAC) protocol designed primarily for energy-efficient reliable real-time voice packet broadcasting in a peer-to-peer, single-hop infrastructureless radio network. Such networks have many application areas for various scenarios that obey a strongly connected group mobility model, such as interactive group trips, small military or security units, and mobile groups of hearing impaired people. TRACE is a centralized MAC protocol that separates contention and data transmission, providing high throughput, bounded delay, and stability under a wide range of data traffic. Furthermore, TRACE uses dynamic scheduling of data transmissions and data summarization prior to data transmission to achieve energy efficiency, which is crucial for battery operated lightweight radios. In addition, energy dissipation is evenly distributed among the nodes by switching network controllers when the energy from the current controller is lower than other nodes in the network, and reliability is achieved through automatic controller backup features. TRACE can support multiple levels of quality-of-service, and minimum bandwidth and maximum delay for voice packets are guaranteed to be within certain bounds. In this paper, we describe TRACE in detail and evaluate its performance through computer simulations and theoretical analysis.