gebhart/patrepeval huggingface dataset:
Substrate Specificities and Inhibition Pattern of the Solute Carrier Family 10 Members NTCP, ASBT and SOAT (2021)

Three carriers of the solute carrier family SLC10 have been functionally characterized so far. Na<sup>+</sup>/taurocholate cotransporting polypeptide NTCP is a hepatic bile acid transporter and the cellular entry receptor for the hepatitis B and D viruses. Its intestinal counterpart, apical sodium-dependent bile acid transporter ASBT, is responsible for the reabsorption of bile acids from the intestinal lumen. In addition, sodium-dependent organic anion transporter SOAT specifically transports sulfated steroid hormones, but not bile acids. All three carriers show high sequence homology, but significant differences in substrate recognition that makes a systematic structure-activity comparison attractive in order to define the protein domains involved in substrate binding and transport. By using stably transfected NTCP-, ASBT-, and SOAT-HEK293 cells, systematic comparative transport and inhibition experiments were performed with more than 20 bile acid and steroid substrates as well as different inhibitors. Taurolithocholic acid (TLC) was identified as the first common substrate of NTCP, ASBT and SOAT with <i>K</i> <sub>m</sub> values of 18.4, 5.9, and 19.3 µM, respectively. In contrast, lithocholic acid was the only bile acid that was not transported by any of these carriers. Troglitazone, BSP and erythrosine B were identified as pan-SLC10 inhibitors, whereas cyclosporine A, irbesartan, ginkgolic acid 17:1, and betulinic acid only inhibited NTCP and SOAT, but not ASBT. The HBV/HDV-derived myr-preS1 peptide showed equipotent inhibition of the NTCP-mediated substrate transport of taurocholic acid (TC), dehydroepiandrosterone sulfate (DHEAS), and TLC with IC<sub>50</sub> values of 182 nM, 167 nM, and 316 nM, respectively. In contrast, TLC was more potent to inhibit myr-preS1 peptide binding to NTCP with IC<sub>50</sub> of 4.3 µM compared to TC (IC<sub>50</sub> = 70.4 µM) and DHEAS (IC<sub>50</sub> = 52.0 µM). Based on the data of the present study, we propose several overlapping, but differently active binding sites for substrates and inhibitors in the carriers NTCP, ASBT, SOAT.
Energy demand in mechanical recycling of glass fibre reinforced thermoset plastic composites (2016)

Increased demand of fibre reinforced plastic (FRP) composites has led to high volumes of manufacturing scrap and end-of-life waste. Restrictions on landfill disposal and the high energy for virgin material production call for cost effective composite recycling technology. Unfortunately there is limited high integrity environmental related data in literature, to help assess the life cycle benefits of composite recycling, particularly glass fibre reinforced plastic (GFRP). In this work new approaches based on bottom-up unit process modelling were used to model and experimentally validate the energy demand in mechanical recycling of GFRP. Total energy requirement was classified into sources by machine functions (basic energy) and for actual cutting process (tip energy) as modelled from material specific cutting energy for GFRP. The mechanics of cutting was utilised to model the specific energy from orthogonal tests. The model was then extended and validated to cater for mechanical recycling with a milling based granulator recycling machine. Energy demand was modelled and validated for a number of industrial granulators. This paper provides valuable information on the impact of processing rate and granulator capacity in relation to reducing the energy demand in recycling of thermoset based glass fibre (GFRPT). The bottom-up approach is an important framework that can be used to model the energy and environmental footprint of other recycling unit processes. This information provides vital data for life cycle analysis, enabling the assessment of resource hot spots and quantifying the environmental benefits of end-of-life options.
Estrogen-Dependent in Vitro Transcription from the Vitellogenin Promoter in Liver Nuclear Extracts (1988)

One approach to analyzing the molecular mechanisms of gene expression in vivo is to reconstitute these events in cell-free systems in vitro. Although there is some evidence for tissue-specific transcription in vitro, transcriptionally active extracts that mimic a steroid hormone-dependent enhancement of transcription have not been described. In the study reported here, nuclear extracts of liver from the frog Xenopus laevis were capable of estrogen-dependent induction of a homologous vitellogenin promoter that contained the estrogen-responsive element.
Corrosion and Heat Resistant Materials. Development of High Performance Heat Resistant Near-Alpha Titanium Alloy Compressor Disk. (1996)

For near-alpha DAT54, Ti-5.8Al-4Sn-3.5Zr-2.8Mo-0.7Nb-0.4Si-0.06C, designed as a compressor disk alloy, the optimum primary alpha was defined 17vol.% in the transformed beta. The full-scale disks in the alloy were successfully manufactured through the melting by PPC-VAR-VAR and the thermomechanical processing by GFM press- die forge. The solution treatment for the above structure, at beta transus-25 °C, contributed to the proper balance of the LCF life with the creep strength of the disks up to 540 °C.
Hybrid-Ion (2006)

This communication describes the performance characteristics of a graphite/ electrolyte/ hybrid-ion cell. The properties of this system compare favorably with commercial lithium ion cells. During the initial charging of this cell, sodium ions are extracted from the fluorophosphate while concurrent lithium ion intercalation occurs at the graphite counter electrode. During subsequent cell cycling the cathode reaction is likely based on a mixed insertion mechanism. Importantly we find that highly lithiated graphite is electrochemically stable in the presence of in the electrolyte phase, presumably due to the presence of the carbon passivation layer.
Compact ultrasound-guided diffuse optical tomography system for breast cancer imaging (2018)

Near-infrared diffuse optical tomography (DOT) has demonstrated a great potential as an adjunct modality for differentiation of malignant and benign breast lesions and for monitoring treatment response in patients with locally advanced breast cancers. The path toward commercialization of DOT techniques depends upon the improvement of robustness and user-friendliness of this technique in hardware and software. In this study, we introduce our recently developed ultrasound-guided DOT system, which has been improved in system compactness, robustness, and user-friendliness by custom-designed electronics, automated data preprocessing, and implementation of a new two-step reconstruction algorithm. The system performance has been tested with several sets of solid and blood phantoms and the results show accuracy in reconstructed absorption coefficients as well as blood oxygen saturation. A clinical example of a breast cancer patient, who was undergoing neoadjuvant chemotherapy, is given to demonstrate the system performance.
Polarization-Preserving Light Guide Plate for a Linearly Polarized Backlight (2014)

We analyze the polarization-preserving property of two conventional edge-lit light guide plates (LGPs) based on scattering dots and refractive microgrooves and find that these two structures almost completely depolarize the incident linearly polarized light. We then propose a new edge-lit LGP based on total internal reflection (TIR). Simulation results show that such a TIR-based LGP can largely preserve the polarization state of the incident linearly polarized light. The polarization efficiency is 77.2%. By incorporating a linearly polarized LED to our proposed LGP, the overall optical gain is 1.54 compared with the backlight system with an unpolarized LED. At on-axis, the luminance is 2.4× higher. Because the output light is concentrated near the surface normal direction, no additional brightness enhancement film is needed. This polarization-preserving LGP enables a polarized or partially polarized LED backlight to be used, which in turn greatly enhances the optical efficiency of a LCD.
Glucocorticoid deficiency increases phospholipase A2 activity in rats. (1993)

An important mechanism for the antiinflammatory effect of pharmacological doses of glucocorticoids is the inhibition of arachidonic acid release from phospholipids by phospholipase A2 (PLA2). As a corollary, one might predict that low endogenous concentrations of glucocorticoids favor inflammatory disease states. Indeed, clinical and experimental observations revealed an association between glucocorticoid deficiency and disease states caused by immunological and/or inflammatory mechanisms. The purpose of the present investigation was to study the regulation of PLA2 mRNA, protein, and enzyme activity in adrenalectomized (ADX) rats where glucocorticoid concentrations were below physiological levels. The mRNA of group I and II PLA2 were measured by PCR. Group II PLA2 mRNA was increased by 126 +/- 9% in lung tissue of ADX rats, whereas group I PLA2 was increased only by 27 +/- 1.5%. The increase in group II mRNA in ADX rats was reflected by a corresponding increase of group II PLA2 protein (70-100%) in lung, spleen, liver, and kidney. This increase was reversed by the administration of exogenous corticosterone. After ADX, the percentage increase in total PLA2 activity was higher than that of mRNA or PLA2 protein, suggesting that the activity of the enzyme was modulated by inhibitors or activators. The concentration of lipocortin-I, an inhibitor of PLA2 enzyme was strongly correlated with the activity of PLA2 in the tissues (lung, spleen, liver, and kidney). In all these tissues, the concentrations of lipocortin-I declined after ADX. Thus upregulation of PLA2 enzyme and downregulation of lipocortin-I might account for the enhanced inflammatory response in hypoglucocorticoid states.
Therapeutic Efficacy of Adoptive Cell Transfer on Survival of Patients with Glioblastoma Multiforme: Case Reports (2010)

Glioblastoma multiforme (GBM), which occurs mostly in individuals over the age of 40, accounts for 12-15% of all primary brain tumors. Patients with GBM have a poor prognosis, even after aggressive upfront therapies. The present study documents that in 5 of these patients, the use of a novel immunotherapeutic approach combined with standard initial therapies resulted in a prolonged survival of over 3 years, which is significantly longer than the expected survival time with conventional therapies. During the course of intravenous cell-transfer immunotherapy, axial magnetic resonance images of the tumor region were monitored for over 5 years. The discontinuation of adoptive transfer regimens resulted in the rapid deterioration of patients with development of Gd-enhancing regions, indicating the initiation of tumor recurrence. Among patients with recurrence, the reinstatement of adoptive cell regimens with more frequent cell-transfers resulted in an apparent re-regression of tumors. Significantly longer survival times were seen in patients receiving transferred autologous lymphoid cells which were expanded in vitro, and which had a considerable proportion of gammadeltaT cells. We conclude that immunotherapy, combined with standard treatment, plays a significant role in the management of GBM patients and provides patients with a better prognosis.
Design of a Programmable Gain, Temperature Compensated Current-Input Current-Output CMOS Logarithmic Amplifier (2014)

This paper presents the design of a programmable gain, temperature compensated, current-mode CMOS logarithmic amplifier that can be used for biomedical signal processing. Unlike conventional logarithmic amplifiers that use a transimpedance technique to generate a voltage signal as a logarithmic function of the input current, the proposed approach directly produces a current output as a logarithmic function of the input current. Also, unlike a conventional transimpedance amplifier the gain of the proposed logarithmic amplifier can be programmed using floating-gate trimming circuits. The synthesis of the proposed circuit is based on the Hart's extended translinear principle which involves embedding a floating-voltage source and a linear resistive element within a translinear loop. Temperature compensation is then achieved using a translinear-based resistive cancelation technique. Measured results from prototypes fabricated in a 0.5 μm CMOS process show that the amplifier has an input dynamic range of 120 dB and a temperature sensitivity of 230 ppm/°C (27 °C- 57°C), while consuming less than 100 nW of power.
The Inter-relationship Between Mandibular Autorotation and Maxillary LeFort I Impaction Osteotomies (2006)

The purposes of the present investigation were to: 1)locate the instantaneous rotation center of mandible autorotation during maxillary surgical impaction; 2) identify the discrepancies between the resultant mandibular position following by maxillary surgical impaction and presurgical predictions, which use the radiographic condylar center as the rotation center for mandibular autorotation; and 3)find the interrelation between the magnitude of maxillary surgical impaction and the sagittal change of mandible. Ten patients underwent maxillary LeFort I impaction without concomitant major mandibular ramus split osteotomies were included. The preoperative (T0) and postoperative (T1) lateral cephalograms were used to evaluate the surgical changes and locate the center of rotation of mandibular autorotation with Reuleaux method. Prediction errors were measured by comparing the predicted (Tp) and postoperative (T1) cephalometric tracings. The magnitude of the maxillary surgical impaction was compared to the positional changes of mandible after mandibular autorotation with correlation and regression analysis. The results demonstrated that the centers of mandibular autorotation located 2.5 mm behind and 19.6 mm below the radiographic condylar center of the mandible in average with large individual variations. By using the radiographic condylar center of the mandible to predict the mandibular autorotation would overestimate the horizontal position of chin by 2 mm and underestimate the vertical position of chin by 1.3 mm following an average of 5 mm surgical maxillary impaction. The magnitude of maxillary impaction was highly and positively correlated to the horizontal displacement of chin position. The rotation centers of mandibular autorotation following by maxillary LeFort I impaction osteotomies might not usually locate at the radiographic condylar center of the mandible also with large individual variations in their positions. Surgeons and orthodontists should be aware of the horizontal and vertical discrepancies of chin positions while planning a two-jaw surgery by using the radiographic center of mandibular condyle as the rotation center in mandibular autorotation.
Overexpression of RAD51 suppresses recombination defects: a possible mechanism to reverse genomic instability (2009)

RAD51, a key protein in the homologous recombinational DNA repair (HRR) pathway, is the major strand-transferase required for mitotic recombination. An important early step in HRR is the formation of single-stranded DNA (ss-DNA) coated by RPA (a ss-DNA-binding protein). Displacement of RPA by RAD51 is highly regulated and facilitated by a number of different proteins known as the 'recombination mediators'. To assist these recombination mediators, a second group of proteins also is required and we are defining these proteins here as 'recombination co-mediators'. Defects in either recombination mediators or co-mediators, including BRCA1 and BRCA2, lead to impaired HRR that can genetically be complemented for (i.e. suppressed) by overexpression of RAD51. Defects in HRR have long been known to contribute to genomic instability leading to tumor development. Since genomic instability also slows cell growth, precancerous cells presumably require genomic re-stabilization to gain a growth advantage. RAD51 is overexpressed in many tumors, and therefore, we hypothesize that the complementing ability of elevated levels of RAD51 in tumors with initial HRR defects limits genomic instability during carcinogenic progression. Of particular interest, this model may also help explain the high frequency of TP53 mutations in human cancers, since wild-type p53 represses RAD51 expression.
Critical paths in circuits with level-sensitive latches (1995)

This paper extends the classical notion of critical paths in combinational circuits to the case of synchronous circuits that use level-sensitive latches. Critical paths in such circuits arise from setup, hold, and cyclic constraints on the data signals at the inputs of each latch and may extend through one or more latches. Two approaches are presented for identifying these critical paths and verifying their timing. The first implicitly checks all paths using a relaxation-based solution procedure. Results of this procedure are used to calculate slack values, which in turn identify satisfied and violated critical paths. The second approach is based on a constructive algorithm which generates all the critical paths in a circuit and then verifies that their timing constraints are satisfied. Algorithms are evaluated and compared using circuits from the ISCAS89 sequential benchmark suite and the Michigan High Performance Microprocessor Project.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Partial Cox regression analysis for high-dimensional microarray gene expression data (2004)

R codes are available upon request.
Receptor‐<scp>L</scp>ike Kinases in Plant Innate Immunity (2013)

Plants employ a highly effective surveillance system to detect potential pathogens, which is critical for the success of land plants in an environment surrounded by numerous microbes. Recent efforts have led to the identification of a number of immune receptors and components of immune receptor complexes. It is now clear that receptor-like kinases (RLKs) and receptor-like proteins (RLPs) are key pattern-recognition receptors (PRRs) for microbe- and plant-derived molecular patterns that are associated with pathogen invasion. RLKs and RLPs involved in immune signaling belong to large gene families in plants and have undergone lineage specific expansion. Molecular evolution and population studies on phytopathogenic molecular signatures and their receptors have provided crucial insight into the co-evolution between plants and pathogens. [Figure: see text] Jian-Min Zhou (Corresponding author).
An Evolutionary Approach to Slim-Hole Drilling, Evaluation, and Completion (1992)

ABSTRACT Shell and Eastman Teleco have developed a Slim Hole Drilling system appropriate for hole sizes less than 6 1/4″ in diameter. Since the project was started in 1987 the system has been used in 46 wells. Nine wells contained 4 1/8″ hole, one down to 5382 meters. Overall progress per day no longer decreases in smaller hole sizes enabling the total well design to be downsized. Cost reduction of up to a quarter (or more in some cases) are thus possible. The smaller scale of operations reduces environmental impact. Extensions such as horizontal, high pressure / high temperature, and floating drilling are underway. Complementary evaluation and completion technology allows Oil Companies to downsize production wells, potentially reducing field (re)development costs. There remain significant opportunities for the service industry to develop complementary "Slim" rigs, equipment, and services.
A line integration based method for depth recovery from surface normals (2003)

A method for constructing a depth map from surface normals is described. In this depth recovery method, an arbitrary depth must first be preset for a point somewhere in the image, and then path-independent line integrals are computed to get the relative depths at every point in the image. The validity of the proposed method is discussed and its efficiency is tested using surface normals obtained by shape from the shading algorithm. A comparison to previous methods is made. Theoretical analysis and experimental results show that the present method is both powerful and easy to implement.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Partitioning techniques for fine-grained indexing (2011)

Many data-intensive websites use databases that grow much faster than the rate that users access the data. Such growing datasets lead to ever-increasing space and performance overheads for maintaining and accessing indexes. Furthermore, there is often considerable skew with popular users and recent data accessed much more frequently. These observations led us to design Shinobi, a system which uses horizontal partitioning as a mechanism for improving query performance to cluster the physical data, and increasing insert performance by only indexing data that is frequently accessed. We present database design algorithms that optimally partition tables, drop indexes from partitions that are infrequently queried, and maintain these partitions as workloads change. We show a 60× performance improvement over traditionally indexed tables using a real-world query workload derived from a traffic monitoring application.
Evaluation of cation-exchanged zeolite adsorbents for post-combustion carbon dioxide capture (2012)

A series of zeolite adsorbents has been evaluated for potential application in post-combustion CO2 capture using a new high-throughput gas adsorption instrument capable of measuring 28 samples in parallel. Among the zeolites tested, Ca-A exhibits the highest CO2 uptake (3.72 mmol g−1 and 5.63 mmol cm−3) together with an excellent CO2 selectivity over N2 under conditions relevant to capture from the dry flue gas stream of a coal-fired power plant. The large initial isosteric heat of adsorption of −58 kJ mol−1 indicates the presence of strong interactions between CO2 and the Ca-A framework. Neutron and X-ray powder diffraction studies reveal the precise location of the adsorption sites for CO2 in Ca-A and Mg-A. A detailed study of CO2 adsorption kinetics further shows that the performance of Ca-A is not limited by slow CO2 diffusion within the pores. Significantly, Ca-A exhibited a higher volumetric CO2 uptake and CO2/N2 selectivity than Mg2(dobdc) (dobdc4− = 1,4-dioxido-2,5-benzenedicarboxylate; Mg-MOF-74, CPO-27-Mg), one of the best performing adsorbents. The exceptional performance of Ca-A was maintained in CO2 breakthrough simulations.
Interval Estimation for Reinforcement-Learning Algorithms in Continuous-State Domains (2010)

The reinforcement learning community has explored many approaches to obtaining value estimates and models to guide decision making; these approaches, however, do not usually provide a measure of confidence in the estimate. Accurate estimates of an agent’s confidence are useful for many applications, such as biasing exploration and automatically adjusting parameters to reduce dependence on parameter-tuning. Computing confidence intervals on reinforcement learning value estimates, however, is challenging because data generated by the agentenvironment interaction rarely satisfies traditional assumptions. Samples of valueestimates are dependent, likely non-normally distributed and often limited, particularly in early learning when confidence estimates are pivotal. In this work, we investigate how to compute robust confidences for value estimates in continuous Markov decision processes. We illustrate how to use bootstrapping to compute confidence intervals online under a changing policy (previously not possible) and prove validity under a few reasonable assumptions. We demonstrate the applicability of our confidence estimation algorithms with experiments on exploration, parameter estimation and tracking. 1