gebhart/patrepeval huggingface dataset:
Model for the Interaction of T-cell Receptors with Peptide/MHC Complexes (1989)

The immune response against a viral infection is mediated by two different types of cells known as B and T lymphocytes. The receptor on the B cell is the well-characterized antibody molecule, which exists in a membrane-bound form and in a secreted form involved in the initiation of complement-mediated killing and the inactivation of viral particles by direct binding. The recognition molecule on T cells is the membrane-bound T-cell antigen receptor, which has specificity for a combination of foreign antigen with a molecule of the major histocompatibility complex (MHC), as first demonstrated by Zinkernagel and Doherty (1974). MHC proteins exist in two closely related forms called class I and class II MHC molecules, both of which are cell-surface glycoproteins that are highly polymorphic in the human population. In general, class II MHC molecules are involved in interactions with T-helper cells, which cooperate with B cells to make antibody.
Smoldering Combustion of Cellulosic Materials (1979)

In comparison to flaming combustion, the smoldering process seems more complex and is poorly understood. When heated by an ignition source, cellulosic materials decompose to volatile products and char. The volatile products fuel the flaming combustion which rapidly spreads in the gas phase. The slower oxidation of the char provides the heat flux required for propagation of the smoldering combustion. The initiation, propagation and termination of the latter process are controlled by several interrelated factors, including composition of the substrate, in organic additives, rates of heat release and heat flux and the combustibility of the char and volatile products, which are discussed.
Magnetic resonance imaging and the management of parapharyngeal space tumors (1996)

MRI, because of its superior soft-tissue resolution and ability to provide imaging in multiple planes, is the imaging modality of choice to diagnose neoplasms of the parapharyngeal space. Because most of these tumors are benign, MRI allows the surgeon to select the surgical approach with the least morbidity.
Scanning Nd:YAG laser system for industrially applicable processing in silicon solar cell manufacturing (2003)

In order to demonstrate different laser beam processes for solar cell manufacturing a state of the art high power scanning laser system has been installed at 'Fraunhofer ISE'. The high potential of laser beam techniques is mainly based on the contactless operation, making them suitable for fragile silicon wafers, and their in-line suitability. Besides, the laser process can be accurately controlled and hence, a perfect reproducibility is obtained even at high pulse repetition rates. Combined with the feed speed of the scanned laser beam of up to 10 m/s this allows short process times as necessary for industrial throughput. Laser beam applications that are presently under investigation are first the 'Laser-Fired Contacts' (called LFC), a technique for implementing the rear contact of dielectric passivated solar cells, and second 'Laser edge IS olation' (called LIS).
A Random Number Generator Based on Single-Photon Avalanche Photodiode Dark Counts (2009)

In this paper, a new physical random number generator is built. The generation concept is based on the dark pulses thermally generated in single photon avalanche photodiodes operating in the Geiger mode. Results show that the proposed random number generator produced nearly 50% zeros and 50% ones, which could be considered an acceptable suited for quantum cryptography systems.
Two-zone fluid bed combustion or gasification process. [fluidized bed] (1979)

A method of operating a fluidized bed system in a single vessel, typically as a combustor system for power or steam generation burning high-sulfur coal or as a gasifier for high-sulfur coal, which comprises forming an entrained fluidized bed in a first space region containing a first solid bed particle component, such as sand or hematite ore containing over 90% Fe/sub 2/O/sub 3/, forming in a limited space region partially within the first region a dense fluidized bed containing a second solid bed particle component, such as larger particles of the hematite, both first and second component particles, essentially comprising a material having long-term physical and chemical stability in the fluidized bed system so as to be substantially nonagglomerating and not subject to substantial attrition therein, effecting division of the dense fluidized bed into upper and lower zones, providing a recirculation path such as through a cyclone separator and particle reservoir for the first particle component from the first space region through the upper zone of the dense fluidized bed in the more limited space region, operating the fluidized bed system at a velocity such that the second component particles are effectively retained in the dense fluidized bed in themore » more limited space region, whereas the first component particles recirculate and interpenetrate through the upper zone thereof commingling with the second component particles, and maintaining different temperatures in the upper and lower zones of the dense fluidized bed. Typically, the temperature of the upper zone of the dense fluidized bed is conducive to capture of sulfur gases by a sorbent while a high temperature in the lower zone of the dense fluidized bed is maintained to be conducive to combustion of fuel and calcination of sorbent (for combustors) or gasification of fuel (for gasifiers).« less
Recent Developments in Novel Antidepressants Targeting α4β2-Nicotinic Acetylcholine Receptors (2014)

Nicotinic acetylcholine receptors (nAChRs) have been investigated for developing drugs that can potentially treat various central nervous system disorders. Considerable evidence supports the hypothesis that modulation of the cholinergic system through activation and/or desensitization/inactivation of nAChR holds promise for the development of new antidepressants. The introductory portion of this Miniperspective discusses the basic pharmacology that underpins the involvement of α4β2-nAChRs in depression, along with the structural features that are essential to ligand recognition by the α4β2-nAChRs. The remainder of this Miniperspective analyzes reported nicotinic ligands in terms of drug design considerations and their potency and selectivity, with a particular focus on compounds exhibiting antidepressant-like effects in preclinical or clinical studies. This Miniperspective aims to provide an in-depth analysis of the potential for using nicotinic ligands in the treatment of depression, which may hold some promise in addressing an unmet clinical need by providing relief from depressive symptoms in refractory patients.
Determination of Orthophosphate in Aqueous Solutions Containing Labile Organic and Inorganic Phosphorus Compounds (1977)

Abstract A simple and precise colorimetric method of determining orthophosphate in aqueous solutions containing labile organic and inorganic P compounds is described. It involves a rapid formation of molybdenum blue color by the reaction of orthophosphate with molybdate ions in the presence of ascorbic acid‐trichloroacetic acid and citrate‐arsenite reagents and complexation of the excess molybdate ions to prevent further formation of blue color from the phosphate derived from hydrolysis of the acid‐labile P compounds. The color is stable up to 24 hours. The method is sensitive and accurate, and it permits determination of microgram quantities of orthophosphate in samples containing large amounts of acid‐labile P compounds. Tests with a wide range of condensed phosphate and organic phosphate compounds showed that none of the P compounds studied interfered with this method. Results by this method are compared with those obtained by the method of Murphy and Riley.
Ex Vivo Treatment of Hematopoietic Stem Cells With 16,16-Dimethyl Prostaglandin E2 (FT1050) Improves Engraftment and Hematopoietic Reconstitution (2011)

Through an in vivo zebrafish screen for modulators of hematopoietic stem cell (HSC) development, a small molecule, 16,16-dimethyl prostaglandin E2 (FT1050) was identified (North, 2007). FT1050 was shown to enhance the engraftment potential of HSCs from murine bone marrow (mBM) or human umbilical cord blood (hCB) in murine engraftment models through an increase in proliferation, survival, migration and homing after a brief (1 to 2 hr) ex vivo treatment (North, 2007; North, 2009; Hoggatt, 2009; North, Goessling, Zon, unpublished data). We further optimized the ex vivo hCB incubation protocol using whole genome expression arrays and determined that HSC-containing cell products should be incubated with 10μM FT1050 for 2 hrs at 37°C to obtain the optimal response. In addition, we observed that FT1050 induces similar gene expression changes in hBM- and mobilized peripheral blood-derived CD34+ cells. Subsequent functional studies demonstrated that in keeping with increases of up to 18-fold in CXCR4 gene expression, cell surface CXCR4 protein expression was also significantly increased. One hour after treatment with10μM FT1050 for 2 hrs at 37°C, 48±1.9% of CB CD34+ cells expressed CXCR4 compared to 3.5±0.01% in DMSO control (p < 0.05). In vivo CFU-S12 analysis showed that treatment of mBM cells with 10μM FT1050 for 2 hrs at 37°C resulted in greater proliferation with a statistically significant increase in colony formation, 11.5±1.4, compared to 4±0.8 colonies with DMSO control (p < 0.001). This short-term ex vivo incubation protocol, 10μM FT1050 for 2 hrs at 37°C, has been introduced into an ongoing Phase Ib clinical trial in adults with hematologic malignancies receiving a nonmyeloablative conditioning (melphalan, fludarabine and ATG) followed by double hCB transplantation, in which one of the two hCBs is incubated with FT1050 prior to infusion. The primary objective of the study is to determine the safety of FT1050 treatment of hCB. Preliminary data demonstrate that this ex vivo incubation can be reliably performed at the clinical site on the day of infusion with good cell recovery and viability. 11 subjects with a median age of 44 years have been accrued to date, of which two have been treated using the optimized ex vivo incubation protocol. 10 of 11 patients have achieved an ANC > 500 before Day 42. Transplant related mortality has been low with one death at Day 53 from respiratory failure. 9 patients are alive, of which 7 are disease-free. Accrual is ongoing.
MODELING PROTOCOL FOR EARLY ENERGY DESIGN ASSISTANCE (2010)

Using energy modeling to drive design decisions earlier in the design process has long been recognized as an effective way to increase the energy performance of building design. With this in mind, several utility- sponsored Design Assistance programs in the Midwest region expanded their scope to provide comparative energy analysis of design options as early as the building programming portion of the design process. These utility programs attempt to influence decisions that significantly impact the energy performance of the designed building. To be effective for market transformation, these programs need to provide incentives for more energy-efficiency decisions that occur in the conceptual stages of design. To calculate savings in a utility program and provide incentives that can be defensible, a fair and consistent baseline protocol is needed. Appendix G to ASHRAE/IESNA Standard 90.1-2007 is currently the most robust energy modeling protocol that can be used by such incentive programs and rating systems. However, this protocol does not provide adequate baseline criteria to evaluate early design decisions, such as building shape, glazing and skylight area and programmatic efficiency. To enable the calculation of savings and incentives, Appendix G needs to be expanded to provide additional baseline criteria. This paper explores where Appendix G falls short of providing baseline criteria for decisions made early in the design process, and proposes changes to Appendix G that would allow these savings to be captured.
Pressure Aided Low Temperature Direct Bonding of Silicon Wafers with High Surface Roughness (2006)

It has been widely accepted that the threshold of surface roughness for low temperature hydrophilic wafer bonding is 0.5nm. However, we have proven that wafers with higher surface roughness can be bonded. By the aid of proper contact pressure, we have bonded the wafers with roughness of 1.0nm successfully and found that thinner wafers were easier to be bonded than thick ones whereas wafers with thickness of 525mum couldn't be bonded and maximum bonding strength has been obtained for wafers with thickness of 300mum in our tensile test. In a word, low temperature hydrophilic bonding can be realized for wafers with high surface roughness if thickness and contact pressure are chosen properly
Solid–Vapor Sorption of Xylenes: Prioritized Selectivity as a Means of Separating All Three Isomers Using a Single Substrate (2012)

A Werner complex is highly selective for o-xylene in a vapor mixture containing all three isomers. However, in the absence of o-xylene, the substrate shows similar selectivity for m-xylene over p-xylene. Kinetic studies show a different trend whereby m-xylene is absorbed most rapidly, implying that thermodynamic factors must be responsible for the selectivity.
Resveratrol Prevents Estrogen-DNA Adduct Formation and Neoplastic Transformation in MCF-10F Cells (2008)

Exposure to estrogens is a risk factor for breast cancer. Specific estrogen metabolites may initiate breast cancer and other cancers. Genotoxicity may be caused by cytochrome P450 (CYP)-mediated oxidation of catechol estrogens to quinones that react with DNA to form depurinating estrogen-DNA adducts. CYP1B1 favors quinone formation by catalyzing estrogen 4-hydroxylation, whereas NAD(P)H quinone oxidoreductase 1 (NQO1) catalyzes the protective reduction of quinones to catechols. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) induces CYP1B1 expression through the aryl hydrocarbon receptor (AhR). Resveratrol has anticancer effects in diverse in vitro and in vivo systems and is an AhR antagonist that decreases CYP expression but induces NQO1 expression. The chemopreventive effect of resveratrol on breast cancer initiation was investigated in MCF-10F cells. Its effects on estrogen metabolism and formation of estrogen-DNA adducts were analyzed in culture medium by high-performance liquid chromatography, whereas its effects on CYP1B1 and NQO1 were determined by immunoblotting and immunostaining. The antitransformation effects of resveratrol were also examined. TCDD induced expression of CYP1B1 and its redistribution in the nucleus and cytoplasm. Concomitant treatment with resveratrol dose-dependently suppressed TCDD-induced expression of CYP1B1, mainly in the cytoplasm. Resveratrol dose- and time-dependently induced expression of NQO1. NQO1 is mainly in the perinuclear membrane of control cells, but resveratrol induced NQO1 and its intracellular redistribution, which involves nuclear translocation of nuclear factor erythroid 2-related factor 2. Resveratrol decreased estrogen metabolism and blocked formation of DNA adducts in cells treated with TCDD and/or estradiol. Resveratrol also suppressed TCDD and/or estradiol-induced cell transformation. Thus, resveratrol can prevent breast cancer initiation by blocking multiple sites in the estrogen genotoxicity pathway.
Control architecture for a robot with visual and tactile capabilities skilled in sorting dishes (2003)

The goal of the Cooperating Robot project is to build a robot with visual and tactile skills that is able to work in unstructured environments cooperating with a human operator. The basic idea is to employ the robot for laborious, repetitive, or dangerous work whereas the human acts as a supervisor and handles exceptions. One benchmark problem chosen for the Cooperating Robot (COR) is to remove dishes from trays and put them into a dishwasher. The layout of the controller for the COR, which has to deal with a variety of sensor information and derive appropriate commands for the actuators (more than 20 different ones in the case considered) is described. The controller consists of several finite state machines running in parallel. Each state machine correspond to a task associated with a specific priority. The state machines are synchronized by means of signals. A multiprocessor multitasking development system makes implementation of such a control structure easy. The presented control strategy was proved to deal effectively with the information provided by more than 40 sensors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Neuroprotection by the PGE<sub>2</sub> EP2 receptor in permanent focal cerebral ischemia (2005)

Recent studies suggest a neuroprotective function of the PGE2 EP2 receptor in excitotoxic neuronal injury. The function of the EP2 receptor was examined at time points after excitotoxicity in an organotypic hippocampal model of N-methyl-D-aspartate (NMDA) challenge and in a permanent model of focal forebrain ischemia. Activation of EP2 led to significant neuroprotection in hippocampal slices up to 3 hours after a toxic NMDA stimulus. Genetic deletion of EP2 resulted in a marked increase in stroke volume in the permanent middle cerebral artery occlusion model. These findings support further investigation into therapeutic strategies targeting the EP2 receptor in stroke.
Generation, representation and flow of phase information in structure determination: recent developments in and around <i>SHARP</i> 2.0 (2003)

The methods for treating experimental data in the isomorphous replacement and anomalous scattering methods of macromolecular phase determination have undergone considerable evolution since their inception 50 years ago. The successive formulations used are reviewed, from the most simplistic viewpoint to the most advanced, including the exploration of some blind alleys. A new treatment is proposed and demonstrated for the improved encoding and subsequent exploitation of phase information in the complex plane. It is concluded that there is still considerable scope for further improvements in the statistical analysis of phase information, which touch upon numerous fundamental issues related to data processing and experimental design.
Noninvasive assessment of myocardial viability by measuring adenosine triphosphate degradation product in coronary sinus effluent of preserved dog heart. (1987)

Isolated dog hearts (n = 19) were preserved in cold Collins solution at 4 degrees C for 1 to 26 hours. At the end of preservation the coronary system was flushed out by cold cardioplegic solution, and the hearts were reperfused with supporting dogs. Myocardial biopsies at the end of preservation and coronary sinus effluents at the time of flush-out were analyzed for adenosine 5'-triphosphate and inosine. Both the degree of depletion in adenosine triphosphate content and the accumulation of inosine in the myocardium during preservation correlated significantly to the preservation time (correlation coefficient = -0.85 and 0.86, respectively). There was a significant correlation between the myocardial inosine level and total amount of inosine released into coronary sinus effluent (correlation coefficient = 0.91, p less than 0.001). Also, a significant correlation between the total amount of inosine in coronary sinus effluent and cellular level of adenosine triphosphate was found (correlation coefficient = -0.86, p less than 0.001). Five hearts that failed to resume beating showed significantly higher amounts of released inosine than the other hearts (3.3 +/- 0.9 versus 1.5 +/- 0.5 mumol, p less than 0.005). These results indicate that the inosine level in the coronary sinus effluent reflects the myocardial energy state, and it is suggested that the measurement of inosine level in the effluent may be applicable as a noninvasive method for assessment of myocardial viability in heart preservation.
Human immunodeficiency virus-1 Rev protein activates hepatitis C virus gene expression by directly targeting the HCV 5′-untranslated region (2011)

Coinfection with human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) accelerates hepatitis C disease progression; however, the mechanism underlying this effect is unknown. Here, we investigated the role of HIV-1 in HCV gene expression and the mechanism involved in this regulation. We discovered that HIV-1 Rev protein activates HCV gene expression. We further revealed that Rev binds to the internal loop of the HCV 5'-untranslated region (5'-UTR) to stimulate HCV IRES-mediated translation.
Design and performance of hybrid constructed wetland systems for high-content wastewater treatment in the cold climate of Hokkaido, northern Japan (2013)

The performance of six multistage hybrid constructed wetland systems was evaluated. The systems were designed to treat four kinds of high-content wastewater: dairy wastewater (three systems, average inflow content 2,400-5,000 mg·COD l(-1), 3-6 years of operation); pig farm wastewater, including liquid food washing wastewater (one system, 9,500 mg·COD l(-1), 3 years); potato starch processing wastewater (one system, 20,000-60,000 mg·COD l(-1), 3 years); and wastewater containing pig farm swine urine (one system, 6,600 mg·COD l(-1), 2.8 years) (COD = chemical oxygen demand). The systems contained three or four vertical (V) flow beds with self-priming siphons and surface partitions and no or one horizontal (H) flow bed (three to five beds). In some V flow beds, treated effluents were recirculated (Vr) through the inlet to improve performance. Mean annual temperature was 5-8 °C at all locations. To overcome clogging due to the high load in a cold climate, we applied a safety bypass structure and floating cover material to the V flow beds. Calculated average oxygen transfer rates (OTRs) increased proportionally with the influent load, and the OTR value was Vr > V> H. The relations of load-OTR, COD-ammonium, and a Arrhenius temperature-dependent equation enable the basic design of a reed bed system.
Pressureless Sintering of High‐Density ZrB <sub>2</sub> –SiC Ceramic Composites (2006)

Ultra‐high‐temperature ceramic composites of ZrB 2 20 wt%SiC were pressureless sintered under an argon atmosphere. The starting ZrB 2 powder was synthesized via the sol–gel method with a small crystallite size and a large specific surface area. Dry‐pressed compacts using 4 wt% Mo as a sintering aid can be pressureless sintered to ∼97.7% theoretical density at 2250°C for 2 h. Vickers hardness and fracture toughness of the sintered ceramic composites were 14.82±0.25 GPa and 5.39±0.13 MPa·m 1/2 , respectively. In addition to the good sinterability of the ZrB 2 powders, X‐ray diffraction and scanning electron microscopy results showed that Mo formed a solid solution with ZrB 2 , which was believed to be beneficial for the densification process.
Portable telephone for personal digital cellular system (1993)

A pocket-size portable telephone for a digital cellular system is described. The telephone's design basis, the configuration of the portable phone radio unit, software configuration, major parameters and interfaces for G3 facsimile transmission and MNP modem (V.42 ANNEX) transmission are presented. This portable telephone features small size, high speech quality, long stand-by time, high quality data communication and an excellent man-machine interface.