gebhart/patrepeval huggingface dataset:
<i>Ab initio</i> computational modeling of loops in G‐protein‐coupled receptors: Lessons from the crystal structure of rhodopsin (2006)

With the help of the crystal structure of rhodopsin an ab initio method has been developed to calculate the three-dimensional structure of the loops that connect the transmembrane helices (TMHs). The goal of this procedure is to calculate the loop structures in other G-protein coupled receptors (GPCRs) for which only model coordinates of the TMHs are available. To mimic this situation a construct of rhodopsin was used that only includes the experimental coordinates of the TMHs while the rest of the structure, including the terminal domains, has been removed. To calculate the structure of the loops a method was designed based on Monte Carlo (MC) simulations which use a temperature annealing protocol, and a scaled collective variables (SCV) technique with proper structural constraints. Because only part of the protein is used in the calculations the usual approach of modeling loops, which consists of finding a single, lowest energy conformation of the system, is abandoned because such a single structure may not be a representative member of the native ensemble. Instead, the method was designed to generate structural ensembles from which the single lowest free energy ensemble is identified as representative of the native folding of the loop. To find the native ensemble a successive series of SCV-MC simulations are carried out to allow the loops to undergo structural changes in a controlled manner. To increase the chances of finding the native funnel for the loop, some of the SCV-MC simulations are carried out at elevated temperatures. The native ensemble can be identified by an MC search starting from any conformation already in the native funnel. The hypothesis is that native structures are trapped in the conformational space because of the high-energy barriers that surround the native funnel. The existence of such ensembles is demonstrated by generating multiple copies of the loops from their crystal structures in rhodopsin and carrying out an extended SCV-MC search. For the extracellular loops e1 and e3, and the intracellular loop i1 that were used in this work, the procedure resulted in dense clusters of structures with Calpha-RMSD approximately 0.5 angstroms. To test the predictive power of the method the crystal structure of each loop was replaced by its extended conformations. For e1 and i1 the procedure identifies native clusters with Calpha-RMSD approximately 0.5 angstroms and good structural overlap of the side chains; for e3, two clusters were found with Calpha-RMSD approximately 1.1 angstroms each, but with poor overlap of the side chains. Further searching led to a single cluster with lower Calpha-RMSD but higher energy than the two previous clusters. This discrepancy was found to be due to the missing elements in the constructs available from experiment for use in the calculations. Because this problem will likely appear whenever parts of the structural information are missing, possible solutions are discussed.
Regression of experimental Burkitt's lymphoma induced by Epstein-Barr virus-immortalized human B cells (1994)

Epstein-Barr virus (EBV)-immortalized human B cells survive only transiently when injected subcutaneously into athymic mice, whereas Burkitt's lymphoma cells give rise to progressively growing subcutaneous tumors. In this study, we tested whether these Burkitt's tumors could be induced to regress via a bystander effect induced by EBV-immortalized B cells. Simultaneous inoculation of EBV-immortalized B cells and Burkitt's lymphoma cells in the same subcutaneous site resulted in tumors that regressed with necrosis and scarring. Similarly, simultaneous inoculation of EBV-immortalized B cells and Burkitt's lymphoma cells in separate subcutaneous sites resulted in regression of a proportion of the Burkitt's tumors. Furthermore, most of the established human Burkitt's tumors regressed with necrosis and scarring after intratumor inoculations with EBV-immortalized B cells. The EBV-immortalized B cells continued to exert this antitumor effect even when killed with irradiation. The experimental approach to Burkitt's lymphoma treatment described here exploits the ability of athymic mice to reject EBV-immortalized B cells to target an effective antitumor response to malignant cells normally incapable of eliciting it.
A New Method for Transformation Techniques in Secure Information Systems (2016)

The transformation technique relies on the comparison of parity values computed in two ways. The fault detection structures are developed and they not only detected subsystem faults but also corrected faults introduced in the data processing system. Concurrent parity values techniques are very useful in detecting numerical error in the data processing operations, where a single fault can propagate to many output faults. Parity values are the most effective tools used to detect faults occurring in the code stream. In this paper, we present a methodology for redundant systems that allows to detect faults. Checkpointing is the typical technique to tolerate such faults. This paper presents a checkpointing approach to operate on encoded data. The advantage of this method is that it is able to achieve very low overhead according to the specific characteristic of an application. The numerical results of the multiple checkpointing technique confirm that the technique is more efficient and reliable by not only distributing the process of checkpointing over groups of processors. This technique has been shown to improve both the reliability of the computation and the performance of the checkpointing.
Efficacy of omeprazole in functional dyspepsia: double‐blind, randomized, placebo‐controlled trials (the Bond and Opera studies) (1998)

Omeprazole is modestly superior to placebo in functional dyspepsia at standard (20 mg) and low doses (10 mg) but not in patients with dysmotility-like dyspepsia.
A Novel Non-Iterative Method for the Prediction of the PVT Behavior of Reservoir Fluids (1999)

Abstract This paper presents a novel approach for the prediction of the complete PVT behavior of reservoir oils and gas condensates. The method uses key measurements that can be performed rapidly either in the lab or at the well site as input to an Artificial Neural Network (ANN) architecture. The ANN architecture has been trained by a PVT studies database of over 650 reservoir fluids originating from all parts of the world. Tests of the trained ANN architecture utilizing a validation set of PVT studies indicate that, for all fluid types, most PVT property estimates can be obtained with a very low mean relative error of 0.5–2.5%, with no data set having a relative error in excess of 5%. This level of error is considered better than that provided by tuned Equation of State (EOS) models, which are currently in common use for the estimation of reservoir fluid properties. In addition to improved accuracy, the proposed ANN architecture avoids the ambiguity and numerical difficulties inherent to EOS models and provides for continuous improvements by the enrichment of the ANN training database with additional data. The developed model has been named PVT Expert*, and is shown to be a robust, accurate and quick prediction tool that can be used for estimating reservoir fluid properties over the entire range of operating conditions and fluid types. The main application of the model is envisaged to be the rapid generation of PVT data based on field generated measurements. The results show that these reports will be of comparable accuracy to a full PVT study generated in the laboratory. In addition to this, other applications are seen in providing accurate estimates of physical properties for use in well test validation and reservoir/production engineering calculations as well as providing for the quality assurance of laboratory generated fluid property data.
Current status of pancreas transplantation for treatment of type I diabetes mellitus. (1998)

Pancreas transplantation is the only treatment of Type I diabetes that consistently establishes an insulin-independent, normoglycemic state. Currently long-term (> 1 year) insulin-independence is achieved in > 80% of recipients of pancreas grafts placed simultaneous with the kidney and > 70% in recipients of a pancreas after a kidney, and > 60% of non-uremic recipients of a pancreas alone. The penalty is immunosuppression, already obligatory for a kidney recipient, but the benefits are improvement in quality of life and the effect that perfect control of glycemia can have on secondary complications.
Radiant heater having formed filaments Patent (1963)

ramic and other high vapor pressure components are 3
Electrode reaction at fixed platinum film. Fixation of platinum film on stabilized-zirconia electrolyte and its effect on the electrode performance of the solid-electrolyte fuel cell. (1992)

Reliable polarization characteristics of noble metal or oxide electrodes in contact with solid oxide electrolyte are quite important. To obtain such characteristics, we fixed sputtered platinum electrodes on yttria stabilized-zirconia (YSZ) electrolyte by covering the electrode with a porous ceramic layer. As a result of the fixation, the Pt film was kept stable and the resistance of the electrodes was very small.Electrode impedance and potential-current curves were measured on the fixed electrodes. The effect of the oxygen partial pressure, PO2, on the electrode resistance, Ri, which was obtained from the impedance plots, was represented as Ri ∝ PO2–1 at high temperature and low oxygen partial pressure, and as Ri ∝ PO21/4 at low temperature and high oxygen partial pressure. Furthermore, effects of the thickness of the Pt film and the ceramic layer on the polarization characteristics were examined. The cathodic current increased as the Pt thickness decreased. The anodic current increased as the ceramic layer thickness decreased.
ChemInform Abstract: Synthesis and Diels—Alder Reactions of Prop‐1‐ene‐1,3‐sultone, and Chemical Transformations of the Diels—Alder Adducts. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Quantum interferometric generation of polarization entangled photons (2018)

Quantum interference, like Hong-Ou-Mandel interference, has played an important role to test fundamental concepts in quantum physics. We experimentally show that the multiple quantum interference effects enable the generation of high-performance polarization entangled photons. These photons have a high-emission rate, are degenerate, have a broadband distribution, and are postselection free. A quantum interferometric scheme, based on a round-trip configuration of a double-pass polarization Sagnac interferometer, makes it possible to use the large generation efficiency of polarization entangled photons in the process of parametric down-conversion and to separate degenerate photon pairs into different optical modes with no requirement of postselection. We demonstrate experimentally that multiple quantum interference is not only an interesting fundamental quantum optical phenomenon but can be used for novel photonic quantum information technologies.
A strict inter-domain anonymity attestation scheme (2010)

In this paper, we propose a strict inter-domain anonymity attestation scheme. We modify the original direct anonymous attestation protocol to provide strict anonymity attestation when the prover and the verifier are in different trusted domains. We introduce a new trusted party Trusted Auditor (TA). We show how to use the TA to prove the “trustworthiness” of an individual DAA Issuer and verify the signature from the prover in a different domain as well as to make the prover be able to join another trusted domain. We use the ideal-system/real-system model to prove the security of the protocol.
Intra/Inter Macroblock Mode Decision for Error-Resilient Transcoding (2007)

When transmitting the precoded bitstream over an error-prone network, error-resilient transcoding is adopted to convert the bitstream to a resilient format for robust delivery. Intra refreshment is an efficient tool to reduce the dependency between frames and stop the channel error propagation. In the conventional scheme, the rate-distortion optimized macroblock mode decision is employed to adaptively determine the coding mode of each macroblock. However, this scheme only considers the channel error propagated from the previous frames to the current frame. As opposed to this traditional algorithm, this paper proposes a method which considers consecutive two frames in a sequence, thus taking the error propagation to the following frame into account. This enhances the overall robustness of the transcoded bitstream against the packet loss. Considering the availability of the next frame information, two cases are discussed respectively. Experimental results show that the proposed methods present quality improvement when compared with the conventional rate-distortion optimized error-resilient coding scheme under different test environments, and the PSNR improvement can reach as high as 0.9 dB.
Leukocyte, Rather than Tumor-produced SPARC, Determines Stroma and Collagen Type IV Deposition in Mammary Carcinoma (2003)

Secreted protein, acidic and rich in cysteine (SPARC), also known as osteonectin or BM-40, is a Ca2+-binding matricellular glycoprotein involved in development, wound healing, and neoplasia. However, the role of SPARC in tumors is ill defined mostly because it is expressed by both tumor and stromal cells, especially inflammatory cells. We analyzed the respective roles of host- and tumor-derived SPARC in wild-type and congenic SPARC knockout (SPARC-/-) mice on a BALB/c genetic background injected into the mammary fat pad with SPARC-producing mammary carcinoma cells derived from c-erB2 transgenic BALB/c mice. Reduced tumor growth but massive parenchyma infiltration, with large areas of necrosis and impaired vascularization were observed in SPARC-/- mice. Immunohistochemical analysis showed a defect in collagen type IV deposition in the stroma of lobular tumors from SPARC-/- mice. Chimeric mice expressing SPARC only in bone marrow-derived cells were able to organize peritumoral and perilobular stroma, whereas reciprocal chimeras transplanted with bone marrow from SPARC-/- mice developed tumors with less defined lobular structures, lacking assembled collagen type IV and with a parenchyma heavily infiltrated by leukocytes. Together, the data indicate that SPARC produced by host leukocytes, rather than the tumor, determines the assembly and function of tumor-associated stroma through the organization of collagen type IV.
Dietary fibers as functional ingredients in meat products and their role in human health (2011)

The article evaluates the effect of dietary fibers as functional ingredient in meat products and their physiological role in human health. Fibers are naturally occurring compounds present in variety of vegetables, fruits, cereal flours etc in abundance, and act through their solubility, viscosity, gel forming ability, water-binding capacity, oil adsorption capacity, fermentability, and mineral and organic molecule binding capacity which affect product quality and characteristics. Beside these, high-fiber intake tends to reduce risk of colon cancer, obesity, cardiovascular diseases, and several other disorders. Moreover, based on their physiochemical properties, many fibers can help to improve colour, texture and sensorial characteristics instead of nutritional benefits. Fiber inclusions could help in diminution of calorie content in foods.

	 

	Key words: Dietary fiber, functional food, colour, texture, health.
Selection and characterization of MUC1‐specific CD8<sup>+</sup> T cells from MUC1 transgenic mice immunized with dendritic‐carcinoma fusion cells (2000)

Mice transgenic for the human MUC1 carcinoma-associated antigen (MUC1.Tg) are tolerant to immunization with MUC1 antigen. Recent studies, however, have demonstrated that immunization of MUC1.Tg mice with fusions of MUC1-positive tumour and dendritic cells (FC/MUC1) reverses MUC1 unresponsiveness and results in rejection of established MUC1-positive pulmonary metastases. Here we demonstrate that lymph node cells from MUC1.Tg mice immunized with the FC/MUC1 fusion cells proliferate in response to MUC1 antigen by a mechanism dependent on the function of CD4, major histocompatibility complex (MHC) class II, B7-1, B7-2, CD28, CD40 and CD40 ligand. The findings demonstrate that stimulation of lymph node cells with MUC1 results in selection of MUC1-specific CD8+ T cells. We show that the CD8+ T cells exhibit MUC1-specific cytotoxic T lymphocyte (CTL) activity by recognition of MUC1 peptides presented in the context of MHC class I molecules Kb and Db. The MUC1-specific CD8+ T cells also exhibit antitumour activity against MUC1-positive metastases, but with no apparent reactivity against normal tissues. These results indicate that immunization of MUC1.Tg mice with FC/MUC1 reverses immunological unresponsiveness to MUC1 by presentation of MUC1 peptides in the presence of costimulatory signals and generates MHC-restricted MUC1-specific CD8+ T cells.
A comparison of the effectiveness and patient tolerance of oral sodium phosphate, castor oil, and standard electrolyte lavage for colonoscopy or sigmoidoscopy preparation. (1993)

One hundred thirteen patients were randomized to receive either oral sodium phosphate (Fleet Phospho-Soda), lemon-flavored castor oil (Purge), or standard polyethylene glycol-based lavage solution (GoLYTELY) before elective colonoscopy. The study purpose was to confirm the efficacy of oral sodium phosphate and extend observations to include castor oil. Overall, patients reported that sodium phosphate and castor oil were easier to complete (p < 0.05). Scores for cleansing the entire colon as determined by endoscopists who were blinded to the cathartic agent were highest in patients receiving sodium phosphate (p < 0.02). Scores of left-colon cleansing for flexible sigmoidoscopy were equally high for the three methods. Scores for taste and symptom side effects were similar for each preparation. There were no recognized signs or symptoms of hypocalcemia in the sodium phosphate group. Because of the low cost of oral sodium phosphate combined with the lowest repeat endoscopy rate for inadequate cleansing, patient savings were projected to be $5000 per 100 patients at this center. Oral sodium phosphate is a cost-effective colonoscopy preparation that is better tolerated and more effective than the polyethylene glycol-electrolyte lavage solution or castor oil.
A New Differential P-Channel Logic-Compatible Multiple-Time Programmable (MTP) Memory Cell With Self-Recovery Operation (2011)

This letter presents a novel differential p-channel logic-compatible multiple-time programmable (MTP) memory cell. This MTP cell has a pair of floating gates, and performs differential read to increase the on/off window. Additionally, a novel self-recovery operation is implemented to boost the floating gate level, thus avoiding the charge-loss problem due to the thin gate oxide requirement in advance logic nonvolatile memory applications. This differential cell with its self-recovery operation is a very promising MTP solution for gate oxide layer with a 70 Å thickness, and can be implemented by 3.3 V I/O in 90 nm and the advanced CMOS logic processes such as 45 nm and beyond.
Security Primitive Design with Nanoscale Devices (2016)

Inherent stochastic physical mechanisms in emerging nonvolatile memories (NVMs), such as resistive random-access-memory (RRAM), have recently been explored for hardware security applications. Unlike the conventional silicon Physical Unclonable Functions (PUFs) that are solely based on manufacturing process variation, RRAM has some intrinsic randomness in its physical mechanisms that can be utilized as entropy sources; for instance, resistance variation, random telegraph noise, and probabilistic switching behaviors. This paper reviews the challenges and opportunities in building security primitives with emerging devices. In particular, it presents research progress of RRAM-based hardware security primitives, including PUF and True Random Number Generator (TRNG).
Rationale and study design of the Prospective comparison of Angiotensin Receptor neprilysin inhibitor with Angiotensin receptor blocker MEasuring arterial sTiffness in the eldERly (PARAMETER) study (2014)

EUDract number 2012-002899-14 and ClinicalTrials.gov NCT01692301.
Self-priming of reverse transcriptase impairs strand-specific detection of dengue virus RNA (2009)

Dengue virus infection is the most frequent arthropod-borne infection affecting humans in the world. Our understanding of the pathophysiological events leading to mild or severe outcomes of the disease remains limited by the fact that viral target cells in the human body are poorly characterized. One of the most sensitive strategies for detecting cells supporting active replication of this positive-strand RNA virus is the search for the replicative intermediate, an antigenome of negative polarity, by RT-PCR. However, a phenomenon described as 'false priming' of the reverse transcriptase (RT) prevents strand-specific detection. The results of the current study showed that this event corresponds to cDNA synthesis that is independent of any primer addition. This property was general to all RNAs tested and was not associated with small free nucleic acids, such as tRNAs and microRNAs. Rather, it corresponded to initiation of cDNA synthesis from the 3' end of the RNA template, and a model is proposed in which the template RNA snaps back upon itself and creates a transient RNA primer suitable for the RT. Such a property would explain why many assays proposed for detection of a replicative intermediate are not specific, and may help in the development of a molecular biology protocol that could allow replication studies of RNA viruses of human interest, such as dengue virus, hepatitis C virus and enteroviruses.
Reducing Student Prejudice in Diversity-Infused Core Psychology Classes (2010)

The current quasi-experimental study compared two sections of a course, one that included diversity content and one that did not. The authors obtained pretest and posttest data on students’ attitudes toward a number of different minority groups and on their levels of course content knowledge. The authors also examined two questions: first, whether exposure to diversity would reduce prejudice, and second, whether inclusion of diversity content would reduce the amount of core course content learned by students. At posttest, significant differences were found in terms of positive attitude change; infusing diversity into course content did not affect content knowledge.