gebhart/patrepeval huggingface dataset:
Quantitative Proteomics of the Thyroid Hormone Receptor-Coregulator Interactions (2004)

The thyroid hormone receptor regulates a diverse set of genes that control processes from embryonic development to adult homeostasis. Upon binding of thyroid hormone, the thyroid receptor releases corepressor proteins and undergoes a conformational change that allows for the interaction of coactivating proteins necessary for gene transcription. This interaction is mediated by a conserved motif, termed the NR box, found in many coregulators. Recent work has demonstrated that differentially assembled coregulator complexes can elicit specific biological responses. However, the mechanism for the selective assembly of these coregulator complexes has yet to be elucidated. To further understand the principles underlying thyroid receptor-coregulator selectivity, we designed a high-throughput in vitro binding assay to measure the equilibrium affinity of thyroid receptor to a library of potential coregulators in the presence of different ligands including the endogenous thyroid hormone T3, synthetic thyroid receptor beta-selective agonist GC-1, and antagonist NH-3. Using this homogenous method several coregulator NR boxes capable of associating with thyroid receptor at physiologically relevant concentrations were identified including ones found in traditional coactivating proteins such as SRC1, SRC2, TRAP220, TRBP, p300, and ARA70; and those in coregulators known to repress gene activation including RIP140 and DAX-1. In addition, it was discovered that the thyroid receptor-coregulator binding patterns vary with ligand and that this differential binding can be used to predict biological responses. Finally, it is demonstrated that this is a general method that can be applied to other nuclear receptors and can be used to establish rules for nuclear receptor-coregulator selectivity.
Characterization of the monocarboxylate transporter 1 expressed in Xenopus laevis oocytes by changes in cytosolic pH (1998)

Several laboratories have investigated monocarboxylate transport in a variety of cell types. The characterization of the cloned transporter isoforms in a suitable expression system is nevertheless still lacking. H+/monocarboxylate co-transport was therefore investigated in monocarboxylate transporter 1 (MCT1)-expressing Xenopus laevis oocytes by using pH-sensitive microelectrodes and [14C]lactate. Superfusion with lactate resulted in intracellular acidification of MCT1-expressing oocytes, but not in non-injected control oocytes. The basic kinetic properties of lactate transport in MCT1-expressing oocytes were determined by analysing the rates of intracellular pH changes under different conditions. The results were in agreement with the known properties of the transporter, with respect to both the dependence on the lactate concentration and the external pH value. Besides lactate, MCT1 mediated the reversible transport of a wide variety of monocarboxylic acids including pyruvate, D,L-3-hydroxybutyrate, acetoacetate, alpha-oxoisohexanoate and alpha-oxoisovalerate, but not of dicarboxylic and tricarboxylic acids. The inhibitor alpha-cyano-4-hydroxycinnamate bound strongly to the transporter without being translocated, but could be displaced by the addition of lactate. In addition to changes in the intracellular pH, lactate transport also induced deviations from the resting membrane potential.
Future Memory Technology Trends and Challenges (2006)

As memory market enters the Gigabit and GHz range with consumers demanding ever higher performance and diversified applications, new types of devices are being developed in order to keep up with the scaling requirements for cost reduction. Among these devices are well-known ones such as the recessed channel transistors, but also FinFET and vertically stacked transistors for DRAM and charge trap devices for Flash memory. The latter ones are still not at a manufacturable stage yet. Even more exotic memories implement new materials and stacked architectures on the cell, chip and package level. On the performance side, increasing speeds require higher time resolutions. The future difficulties of process control by far exceed those of conventional planar devices. Therefore device characteristics are expected to show ever increasing PVT variations. As these variations become more and more inevitable, especially as dimensions approach the atomic scale, negative effects on circuit and device performances have to be prevented by new, appropriate methods of 3D device modeling and circuit design which consider the mentioned parameter variations. In this talk such challenges will be discussed as well as some approaches to overcome them. An outlook will also be given about the memory technology trends in the next decades.
Calculations of Oxidation Potentials of Redox Shuttle Additives for Li-Ion Cells (2006)

The oxidation potentials of seventeen molecules used as candidate shuttle additives in Li-ion cells were calculated using density functional theory and compared with experiment. The root-mean-square deviation between the calculated and measured oxidation potentials of these seventeen molecules is with the maximum deviation being , indicating that the ab initio calculation is in good agreement with the experiment. Neglecting thermal contributions in the calculation of standard oxidation potentials at ambient conditions does not lead to significant errors. An empirical relation between the oxidation potentials and the orbital energies of these molecules in solution is presented. The oxidation potential of a molecule could be estimated based on the orbital energy of the molecule's highest occupied molecular orbital or its cation's lowest unoccupied molecular orbital in solution with an error less than for most molecules reported.
Respiratory mechanics and timing during sleep in occlusive sleep apnea (1980)

Six human obese subjects with the sleep apnea hypersomnolence syndrome associated with upper airway occlusion (UAO) were studied during sleep to characterize respiration. Measurements included the timing components of ventilation, pulmonary resistance, flow, and esophageal and gastric pressures before and during UAOs. During the period between UAOs, the resistance progressively increased (9.4-18.1 cmH2O/l(-1) . s, P less than 0.05) as the ventilation decreased (1.82-0.77 l/s, P less than 0.05), but without changes in esophageal pressure swings. During this period, inspiratory time-to-total cycle time decreased (0.42-0.25 s, P less than 0.05) due to expiratory phase prolongation. The apnea began after expiration and terminated on inspiration with the maximal swings in esophageal and gastric pressure near the termination. During the UAO, the respiratory cycle time decreased slightly, but the expiratory pause time was significantly shortened immediately before ventilation. We suggest that the UAO is but one aspect of this syndrome and that a decrease in central nervous system activity diminishes the respiratory drive before the onset of the UAO.
Gearbox Reliability Collaborative Project Report: Findings from Phase 1 and Phase 2 Testing (2011)

This report describes the Gearbox Reliability Collaborative's work at NREL to increase the reliability of wind turbine gearboxes.
High-performance application-specific networking (1997)

Experience with parallel and distributed systems has shown that different application domains require different communication models in order to perform efficiently and be programmed conveniently [37, 57, 60]. Unfortunately, programmers traditionally have had to choose between inflexible but efficient inkernel protocols and flexible but inefficient user-level protocols. This thesis presents application-specific safe handlers (ASHs), a new technique that provides a protected, efficient, and flexible communication interface. ASHs make user-level protocols more efficient and usable by enabling application-specific communication protocols to be dynamically yet safely downloaded into the kernel and tightly integrated with the communication system. ASHs eliminate kernel crossings and scheduling delays for common, time-critical events by decoupling network processing from application execution; they also provide the capability for eliminating extraneous data copying and integrating necessary data copying with other data
BRCA1/2‐negative hereditary triple‐negative breast cancers exhibit BRCAness (2016)

BRCA1/2-associated breast cancers are sensitive to poly(ADPribose) polymerase (PARP) inhibitors and platinum compounds mainly due to their deficiency in DNA repair via homologous recombination (HR). However, approximately only 15% of triple-negative breast cancers (TNBCs) are BRCA1/2-associated. TNBCs that exhibit BRCAness (a phenotype reflecting impaired HR in BRCA1/2-negative tumors) are also regarded sensitive to PARP inhibitors and platinum compounds. Thus, we hypothesized that hereditary BRCA1/2-negative TNBCs may exhibit BRCAness. To find a subset of hereditary BRCA1/2-negative TNBCs among 360 TNBCs, we first identified a group of 41 hereditary TNBCs by analyzing the family histories of the patients. Next, we tested this group for the presence of germline BRCA1/2 mutations, and finally, we compared the expression levels of 120 genes involved in HR and five other major mechanisms of DNA damage repair between BRCA1/2-associated and BRCA1/2-negative subgroups of hereditary TNBCs using real-time PCR arrays. Approximately 73% of the hereditary TNBCs were BRCA1/2-associated and 27% were BRCA1/2-negative. The expression levels of the analyzed genes showed no significant differences between these two subgroups indicating the BRCAness of the BRCA1/2-negative hereditary TNBCs and thereby distinguishing a novel subset of TNBCs as a potential target for PARP inhibitors or platinum-based therapy. The results show the significance of family history in selecting patients with TNBC for therapies directed at incompetent DNA repair (e.g., PARP inhibitors and/or platinum-based therapies) and indicate that a relatively simple strategy for broadening the target group for these modes of treatment is to identify patients with hereditary TNBCs.
462. The third isomeric (cis-trans-) muconic acid (1950)

J. A. Elvidge, R. P. Linstead, P. Sims and B. A. Orkin, J. Chem. Soc., 1950, 2235 DOI: 10.1039/JR9500002235
Application of the Border Gateway Protocol in the Internet (1991)

This protocol is being developed by the Border Gateway Protocol Working Group (BGP) of the Internet Engineering Task Force (IETF). This RFC specifies an IAB standards track protocol for the Internet community, and requests discussion and suggestions for improvements. Please refer to the current edition of the "IAB Official Protocol Standards" for the standardization state and status of this protocol.
Photocrosslinking of polyethylene. II. Properties of photocrosslinked polyethylene (1989)

Abstract Some properties of photocrosslinked high density polyethylene (2 mm thick sheets) have been studied. The homogeneity of the network is greatly improved by the application of triallylcyanurate (TAC) as crosslinking agent. The role of TAC in promoting the crosslinking is discussed. The crosslinked PE is found to be durable towards immersion in boiling water. Oxygen permeability increases while density and melting point decrease with increasing degree of crosslinking. The network chain density is obtained using conventional swelling method in boiling xylene, which together with data from melting point depression show that contribution of chain entanglement is insignificant to the gel formation of PE in this work.
The Role of the Vagus Nerve in Cytokine‐to‐Brain Communication (1998)

Peripheral interleukin-1 beta (IL-beta) and inflammatory stimuli that induce the synthesis and release of IL-1 beta produce a variety of central nervous system responses. Most proposals designed to explain how peripheral IL-1 beta influences the CNS have focused on blood-borne routes of communication. We will review data that indicate that at least some of the CNS response to peripheral IL-1 beta are instead mediated by a neural route of communication between the periphery and the CNS. IL-1 beta activates afferent vagal fibers that terminate in the nucleus tractus solitarius, and communication via the vagus is responsible for much of the hyperalgesia, fever, anorexia, taste aversions, increased levels of plasma corticosteroid, and brain norepinephrine changes produced by intraperitoneal injections of IL-1 beta and LPS. Data extending this analysis to TNF-alpha and intravenous routes will be described.
Capillary zone electrophoresis in agarose gels using absorption imaging detection (1996)

A simple home-built electrophoretic unit and a commercially available charge-coupled device (CCD) camera with image acquisition and analysis software were used to study the separation process in zone electrophoresis experiments in 4 cm long, round capillaries (inside diameter 0.2 mm). Several capillaries could be investigated simultaneously. The absorption imaging system was used not only to follow the course of the separation but also to study the interaction between biologically active substances (proteins, detergents, enzymes and-substrate). Since the system allows visual on-line observation of the separation one can rapidly decide when the analysis is finished, which often shortens the analysis time. The electrophoresis method presented is suitable also for preparative runs, since direct visualizations of a solute zone allows it to be excised and then used for further studies.
An Algorithm for the Concave Minimization Problem under 0-1 Knapsack Constraint (1993)

In this study, we develop a B & B type algorithm for the concave minimization problem with 0-1 knapsack constraint. Our algorithm reformulates the original problem into the singly linearly constrained concave minimization problem by relaxing 0-1 integer constraint in order to get a lower bound. But this relaxed problem is the concave minimization problem known as NP-hard. Thus the linear function that underestimates the concave objective function over the given domain set is introduced. The introduction of this function bears the following important meanings. Firstly, we can efficiently calculate the lower bound of the optimal object value using the conventional convex optimization methods. Secondly, the above linear function like the concave objective function generates the vertices of the relaxed solution set of the subproblem, which is used to update the upper bound. The fact that the linear underestimating function is uniquely determined over a given simplex enables us to fix underestimating function by considering the simplex containing the relaxed solution set. The initial containing simplex that is the intersection of the linear constraint and the nonnegative orthant is sequentially partitioned into the subsimplices which are related to subproblems.
Surface-emitting, distributed-feedback diode lasers with uniform near-field intensity profile (1998)

Theoretical analysis of second-order surface-emitting, complex-coupled distributed feedback diode lasers with first-order distributed Bragg reflectors (DBR) is presented. The DBR reflectors are shown to insure simultaneous operation in a virtually uniform near-field profile with high efficiency and adequate intermodal discrimination. Such devices display symmetric-mode (single-lobe) surface emission with relatively high external differential quantum efficiency (30%), low gain threshold (18 cm−1), and &amp;lt;8% near-field intensity profile variations (in the longitudinal direction). The devices have the potential to provide &amp;gt;100 mW of stable, single-mode cw power, significantly higher than it is possible with vertical-cavity surface-emitting lasers. It is also shown that the device studied here can be combined with a resonant optical waveguide array device to produce a 2D uniform near-field surface-emitting source capable of providing greater than 1 W cw power in a stable, single-lobed beam.
Evaluation of Clipping Based Iterative PAPR Reduction Techniques for FBMC Systems (2014)

This paper investigates filter bankmulticarrier (FBMC), a multicarrier modulation technique exhibiting an extremely low adjacent channel leakage ratio (ACLR) compared to conventional orthogonal frequency division multiplexing (OFDM) technique. The low ACLR of the transmitted FBMC signal makes it especially favorable in cognitive radio applications, where strict requirements are posed on out-of-band radiation. Large dynamic range resulting in high peak-to-average power ratio (PAPR) is characteristic of all sorts of multicarrier signals. The advantageous spectral properties of the high-PAPR FBMC signal are significantly degraded if nonlinearities are present in the transceiver chain. Spectral regrowth may appear, causing harmful interference in the neighboring frequency bands. This paper presents novel clipping based PAPR reduction techniques, evaluated and compared by simulations and measurements, with an emphasis on spectral aspects. The paper gives an overall comparison of PAPR reduction techniques, focusing on the reduction of the dynamic range of FBMC signals without increasing out-of-band radiation. An overview is presented on transmitter oriented techniques employing baseband clipping, which can maintain the system performance with a desired bit error rate (BER).
Biology and predator use of cisco (Coregonus artedi) in Fort Peck Reservoir, Montana (2015)

Selected biological parameter of the cisco (Coregonus artedi) and its use by predators in Fort Peck Reservoir were examined during 1989 and 1990.The average length of cisco was approximately 144, 210, and 273 mm at ages 1, 2, and 3, respectively.The average size of spawners was approximately 240 mm and mean condition factors for size groups ranged from 0.75 to 0.91.Comparisons indicated that average size, growth, and condition factors have declined from previous years.Fecundity ranged from 1,119 to 13,956 for spawners with most gonadal development occurring during the fall months for both males and females.Qualitative analysis of stomach contents showed that the cisco utilized primarily Daphnia spp.and copepods and appeared to select the larger zooplankton types.Densities of reservoir zooplankton have not changed from pre-cisco (1984) introduction densities, but the zooplankton community composition has shifted towards smaller species.Examination of fish predator stomach contents showed that cisco were the most frequent prey species.
Comparative Effects of Interferon-Consensus 1, Interferon-α 2a , and Interferon-/β lb on HLA Expression and Lymphoproliferation: A Preclinical Model for Treatment of Multiple Sclerosis (1996)

Interferon-consensus 1 (IFN-Con 1) is a novel synthetic protein generated from codons for the most frequent amino acids in different type 1 IFNs. Compared with natural IFNs, IFN-Con 1 has been shown to have higher specific activity and antiproliferative activity and a higher ability to induce natural killer cells. In this study, the effects of IFN-Con 1 were compared with those of IFN-β1b and IFN-α2a on HLA expression and lymphoproliferation. Human umbilical vein endothelial cells (HUVEC) express HLA class I but not class II molecules; however, both class I and class II molecules can be upregulated by IFN-γ. IFN-Con-1 shared with IFN-β1b and IFN-α2a the capacity to enhance HLA class I expression on HUVEC, alone and in combination with IFN-γ. Although IFN-Con 1 had no effect on the basal expression of HLA class II molecules, it inhibited the IFN-γ-induced class II expression on the HUVEC in a dose-dependent fashion. When this effect was compared among the three IFNs on mass basis, IFN-Con 1 activity was intermediate between that of IFN-β1b and IFN-α2a. IFN-Con 1 also demonstrated an inhibitory effect on mitogen-driven lymphoproliferation similar to that of IFN-α2a and exceeded that of IFN-β1b. The results indicate that IFN-Con 1 has immunomodulatory effects similar to those of IFN-β1b and IFN-α2a, which could be relevant to the treatment of autoimmune and virus-mediated diseases.
Weighted low-rank approximations (2003)

We study the common problem of approximating a target matrix with a matrix of lower rank. We provide a simple and efficient (EM) algorithm for solving weighted low-rank approximation problems, which, unlike their unweighted version, do not admit a closed-form solution in general. We analyze, in addition, the nature of locally optimal solutions that arise in this context, demonstrate the utility of accommodating the weights in reconstructing the underlying low-rank representation, and extend the formulation to non-Gaussian noise models such as logistic models. Finally, we apply the methods developed to a collaborative filtering task.
Role of thrombospondin in platelet aggregation. (1984)

Thrombospondin (TSP), the major alpha-granule protein of human platelets, binds to the activated platelet surface upon platelet stimulation. TSP has hemagglutinating (lectin-like) activity and forms a specific complex with fibrinogen. Based on these observations, it was postulated that the interaction of TSP and fibrinogen on the activated platelet surface may be an important step in the platelet aggregation process. To test this hypothesis, monospecific, affinity-purified anti-TSP Fab fragments were prepared and their effects on platelet aggregation and platelet fibrinogen binding were studied. Anti-TSP Fab caused significant interference with thrombin- and collagen-induced platelet aggregation, as monitored by both turbidometric aggregometry and particle counting measuring the disappearance of single platelets. Phase-contrast microscopy revealed that anti-TSP Fab caused a marked decrease in platelet macroaggregates and an increase in microaggregates and nonaggregated single platelets. Anti-TSP Fab did not affect the initial phase of ADP-induced platelet aggregation but caused rapid platelet disaggregation with the abolition of the secondary phase of aggregation. The effect of anti-TSP Fab was not mediated by a direct inhibition of platelet secretion. The effect of anti-TSP Fab on specific binding of labeled fibrinogen to thrombin-stimulated platelets was also studied. Anti-TSP Fab caused a marked decrease in the affinity of fibrinogen binding to the receptors on the activated platelet surface. Kinetic analyses revealed significant displacement of labeled fibrinogen by unlabeled fibrinogen in the presence of anti-TSP Fab, suggesting that TSP serves to stabilize fibrinogen binding to the activated platelet surface and reinforces the strength of interplatelet interactions. It is proposed that platelet aggregation is a dynamic, multistep process, governed initially by the platelet membrane glycoprotein IIb/IIIa-fibrinogen interaction, with the TSP-fibrinogen interaction playing an important role in determining the size and reversibility of platelet aggregates.