gebhart/patrepeval huggingface dataset:
Multi-pulse CODEC using floating point signal processor. (1988)

On decrit les algorithmes et les implementations de deux codeurs-decodeurs utilisant le boitier NEC 77230. Le premier utilise un filtrage predictif («pitch prediction filter») et fonctionne a des debits binaires de 9,6 a 16 kbits/S. Le second, sans filtrage predictif, fonctionne de 8 a 96 kbits/S
Gene Expression Profiling of Archival Tumors from the Collaborative Ocular Melanoma Study: Association with Clinical Outcomes (2011)

From the Washington University Senior Honors Thesis Abstracts (WUSHTA), Volume 3, Spring 2011. Published by the Office of Undergraduate Research. Henry Biggs, Director, Office of Undergraduate Research / Associate Dean, College of Arts & Sciences; Joy Zalis Kiefer, Office of Undergraduate Research / Assistant Dean in the College of Arts & Sciences; E. Holly Tasker, Editor; Kristin Sobotka, Undergraduate Research Coordinator. Mentor: William Harbour
Activation Function 2 in the Human Androgen Receptor Ligand Binding Domain Mediates Interdomain Communication with the NH 2 -terminal Domain (2021)

Activation function 2 in the ligand binding domain of nuclear receptors forms a hydrophobic cleft that binds the LXXLL motif of p160 transcriptional coactivators. Here we provide evidence that activation function 2 in the androgen receptor serves as the contact site for the androgen dependent NH(2)- and carboxyl-terminal interaction of the androgen receptor and only weakly interacts with p160 coactivators in an LXXLL-dependent manner. Mutagenesis studies indicate that it is the NH(2)-/carboxyl-terminal interaction that is required by activation function 2 to stabilize helix 12 and slow androgen dissociation critical for androgen receptor activity in vivo. The androgen receptor recruits p160 coactivators through its NH(2)-terminal and DNA binding domains in an LXXLL motif-independent manner. The results suggest a novel function for activation function 2 and a unique mechanism of nuclear receptor transactivation.
Miniature, high performance, low-cost fiber optic microphone (2005)

A small, high performance fiber optic microphone has been designed, fabricated, and tested. The device builds on a previous design utilizing a thin, seven-fiber optical probe, but now adds a micromachined 1.5μm thick silicon diaphragm active element. The resulting sensor head is thin (several millimeters) and light, and the overall microphone system is less expensive than conventional microphones with comparable performance. Measurements in the laboratory using a standard free-field technique at high frequencies, an enclosed calibrator at lower frequencies, and pseudostatic pressure changes demonstrate uniform broadband response from near dc (0.01 Hz) up to near 20 kHz. The measured microphone internal noise is nearly flat over this band and does not exhibit noticeable levels of 1∕f noise. Over the audible portion of this band, the minimum detectable pressure is determined to be 680μPa per root Hz with further reductions possible using lower noise∕higher power light sources and∕or improvements in the diaphragm. In contrast to conventional high-performance microphones, there is no need for preamplifier packages close to the relatively small sensor head resulting in much lower acoustic scattering cross sections. This attribute, together with high performance, low cost, and immunity to emi, makes the microphone ideal for multielement array applications.
[A case report of chronic intestinal pseudo-obstruction with autoimmune autonomic ganglionopathy suspected from seropositive results for anti-ganglionic acetylcholine receptor antibody]. (2015)

A 37-year-old woman who had previously been diagnosed with idiopathic chronic intestinal pseudo-obstruction (CIPO) at another hospital was admitted to our institution with severe abdominal pain. She had a history of several abdominal surgeries to treat ileus at the previous hospital, and contrast-enhanced computed tomography on admission revealed subileus without any apparent causes of obstruction. Total parenteral nutrition, a gastrointestinal prokinetic agent, and opiates reduced persistent pain;however, breakthrough pain continued. A neurologist at our hospital suggested autoimmune autonomic ganglionopathy (AAG) as a potential cause of CIPO. The patient was diagnosed with suspected AAG on the basis of seropositive results for anti-ganglionic acetylcholine receptor antibody. Intravenous immunoglobulin administration and plasma exchange were performed in combination with immunosuppressive drugs;however, her symptoms barely improved. Although percutaneous endoscopic gastrostomy and enterostomy were subsequently performed to reduce internal intestinal pressure, her pain relief was insufficient.
A Comprehensive Study Over VLAD and Product Quantization in Large-Scale Image Retrieval (2014)

This paper deals with content-based large-scale image retrieval using the state-of-the-art framework of VLAD and Product Quantization proposed by Jegou as a starting point. Demonstrating an excellent accuracy-efficiency trade-off, this framework has attracted increased attention from the community and numerous extensions have been proposed. In this work, we make an in-depth analysis of the framework that aims at increasing our understanding of its different processing steps and boosting its overall performance. Our analysis involves the evaluation of numerous extensions (both existing and novel) as well as the study of the effects of several unexplored parameters. We specifically focus on: a) employing more efficient and discriminative local features; b) improving the quality of the aggregated representation; and c) optimizing the indexing scheme. Our thorough experimental evaluation provides new insights into extensions that consistently contribute, and others that do not, to performance improvement, and sheds light onto the effects of previously unexplored parameters of the framework. As a result, we develop an enhanced framework that significantly outperforms the previous best reported accuracy results on standard benchmarks and is more efficient.
Phosphorus Diffusion Mechanisms and Deep Incorporation in Polycrystalline and Single-Crystalline CdTe (2016)

CdTe solar-cell technology could provide a levelized cost of electricity (LCOE) below that of $a\phantom{\rule{0}{0ex}}n\phantom{\rule{0}{0ex}}y$ conventional source, including silicon photovoltaics and fossil fuels---if only the open-circuit voltage could be increased. The key is to raise the density of holes, for which phosphorus doping seems promising. A combination of experiment and theory reveals the atomistic mechanisms of P diffusion in CdTe, including fast grain-boundary and bulk diffusion paths. This strong physical insight is needed for next-generation applications, even beyond photovoltaics.
A Novel Design of Grooved Fibers for Fiber-Optic Localized Plasmon Resonance Biosensors (2009)

Bio-molecular recognition is detected by the unique optical properties of self-assembled gold nanoparticles on the unclad portions of an optical fiber whose surfaces have been modified with a receptor. To enhance the performance of the sensing platform, the sensing element is integrated with a microfluidic chip to reduce sample and reagent volume, to shorten response time and analysis time, as well as to increase sensitivity. The main purpose of the present study is to design grooves on the optical fiber for the FO-LPR microfluidic chip and investigate the effect of the groove geometry on the biochemical binding kinetics through simulations. The optical fiber is designed and termed as U-type or D-type based on the shape of the grooves. The numerical results indicate that the design of the D-type fiber exhibits efficient performance on biochemical binding. The grooves designed on the optical fiber also induce chaotic advection to enhance the mixing in the microchannel. The mixing patterns indicate that D-type grooves enhance the mixing more effectively than U-type grooves. D-type fiber with six grooves is the optimum design according to the numerical results. The experimental results show that the D-type fiber could sustain larger elongation than the U-type fiber. Furthermore, this study successfully demonstrates the feasibility of fabricating the grooved optical fibers by the femtosecond laser, and making a transmission-based FO-LPR probe for chemical sensing. The sensor resolution of the sensor implementing the D-type fiber modified by gold nanoparticles was 4.1 × 10(-7) RIU, which is much more sensitive than that of U-type optical fiber (1.8 × 10(-3) RIU).
Osteogenic Protein-1 and Insulin-Like Growth Factor I Synergistically Stimulate Rat Osteoblastic Cell Differentiation and Proliferation (1997)

Previous studies have shown that osteogenic protein-1 (OP-1; also known as BMP-7) alters the steady state levels of messenger RNA (mRNA) encoding insulin-like growth factor I (IGF-I), IGF-II, and IGF-binding proteins (IGFBPs) in primary cultures of fetal rat calvaria (FRC) cells. In the present study, the effects of exogenous IGF-I on bone cell differentiation and mineralized bone nodule formation induced by OP-1 were examined. Exogenous IGF-I synergistically and dose dependently enhanced OP-1 action in stimulating[ 3H]thymidine incorporation, alkaline phosphatase activity, PTH-dependent cAMP level, and bone nodule formation. Maximal synergism between OP-1 and IGF-I was observed when both factors were added simultaneously. Synergism was not observed when FRC cells were pretreated with IGF-I for 24 h, followed by OP-1 treatment. These findings suggest that IGF-I acted on OP-1-sensitized FRC cells. To examine the mechanism(s) by which this sensitization may occur, levels of mRNA encoding OP-1 receptor, IGF-I receptor, and IGFBPs were measured. The mRNA levels of both type I and II OP-1 receptors were elevated by OP-1, but were not changed further by combined OP-1 and IGF-I treatment. IGF-I receptor gene expression was not changed by OP-1, IGF-I, or a combination of both factors. OP-1 alone or together with IGF-I increased the steady state IGFBP-3 mRNA level and reduced the steady state mRNA levels of IGFBP-4, -5, and -6. IGF-I alone did not change the steady state mRNA levels of IGFBP-3, -4, and -6, but elevated that of IGFBP-5. Des(1–3)-IGF-I, which has a lower affinity for IGFBPs, was more effective than the full-length IGF-I in enhancing the OP-1-induced alkaline phosphatase activity. Exogenous IGFBP-5 inhibited the OP-1-induced alkaline phosphatase activity and reduced the synergistic stimulatory effect of IGF-I and OP-1. These findings strongly suggest that the OP-1-induced down-regulation of IGFBPs, especially that of IGFBP-5, is an important mechanism by which OP-1 and IGF-I synergize to stimulate FRC cell differentiation.
Novobiocin Induces a Distinct Conformation of Hsp90 and Alters Hsp90−Cochaperone−Client Interactions (2004)

Hsp90 functions to facilitate the folding of newly synthesized and denatured proteins. Hsp90 function is modulated through its interactions with cochaperones and the binding and hydrolysis of ATP. Recently, novobiocin has been shown to bind to a second nucleotide binding site located within the C-terminal domain of Hsp90. In this report, we have examined the effect of novobiocin on Hsp90 function in reticulocyte lysate. Novobiocin specifically inhibited the maturation of the heme-regulated eIF2alpha kinase (HRI) in a concentration-dependent manner. Novobiocin induced the dissociation of Hsp90 and Cdc37 from immature HRI, while the Hsp90 cochaperones p23, FKBP52, and protein phosphatase 5 remained associated with immature HRI. Proteolytic fingerprinting of Hsp90 indicated that novobiocin had a distinct effect on the conformation of Hsp90, and molybdate lowered the concentration of novobiocin required to alter Hsp90's conformation by 10-fold. The recombinant C-terminal domain of Hsp90 adopted a proteolytic resistant conformation in the presence of novobiocin, indicating that alteration of Hsp90/cochaperone interactions was not the cause of the novobiocin-induced protease resistance within Hsp90's C-terminal domain. The concentration dependence of this novobiocin-induced conformation change correlated with the dissociation of Hsp90 and Cdc37 from immature HRI and novobiocin-induced inhibition of Hsp90/Cdc37-dependent activation of HRI's autokinase activity. The data suggest that binding of novobiocin to the C-terminal nucleotide binding site of Hsp90 induces a change in Hsp90's conformation leading to the dissociation of bound kinase. The unique structure and properties of novobocin-bound Hsp90 suggest that it may represent the "client-release" conformation of the Hsp90 machine.
Salidroside Improves Behavioral and Histological Outcomes and Reduces Apoptosis via PI3K/Akt Signaling after Experimental Traumatic Brain Injury (2012)

Post-injury salidroside improved long-term behavioral and histological outcomes and reduced brain edema and apoptosis following TBI, at least partially via the PI3K/Akt signaling pathway.
Co-designing for NFC and ATMs (2013)

This paper addresses the field of mobile payment through Near Field Communication (NFC) and Automated Teller Machines (ATMs). We report how we used the Inspirational Bits method to inspire the design of novel NFC usage scenarios and application ideas for ATMs in a joint industry and academia project. We describe a set of small applications exposing different properties of NFC (henceforth, referred to as NFC-Bits) and how they informed and inspired collaborative design ideas for different use cases. The NFC-Bits reveal a broad range of NFC characteristics in a playful manner. We outline some of the developed use cases and describe features of MyPocketATM, an application stemmed from these ideas.
EDEN: an integrated computer-aided software engineering environment (2003)

EDEN, a computer-aided software engineering (CASE) environment, is currently being developed. The objective of this project is to integrate structure design methodologies, software module libraries, and rigorous testing through the entire software life-cycle. In addition to supporting each phase of the life-cycle, EDEN will provide project management tools such as metrics analysis, configuration management, and quality assurance compliance. An important concept inherent in this research is that an effective CASE environment cannot be achieved without completely integrating the different phases through a common database system. An interactive graphics interface to shelter the EDEN user from the complexity of the system will also be developed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Substrate specificity of porcine renin: P1', P1, and P3 residues of renin substrates are crucial for activity (1994)

Renin, the rate-limiting enzyme in the formation of angiotensin II, is well-known for its stringent substrate specificity. In this study, the biochemical basis for the unusual specificity of renin was investigated by replacing individual amino acids in the octapeptide substrate of renin with Ala. Kinetic analyses of Ala-substituted substrates revealed that the substitutions did not cause significant changes in the Km values, but did cause variable changes in the kcat and kcat/Km values. Ala substitutions at the P1', P1, and P3 sites decreased the kcat/Km values by 400-700-fold. Similar substitutions at the P3', P2, P4, and P5 sites only reduced the kcat/Km values by 2-7-fold. Interestingly, Ala substitution for the P2' Val produced a substrate with an approximately 3-fold increase in activity. These results indicate that the P1', P1, and P3 residues are crucial in determining the substrate specificity of renin. The findings also suggest that the specificity of renin is achieved mainly through substrate discrimination in the transition state, rather than in the ground state. Further studies on the effects of amino acid substitutions at the P2' site revealed that non-branched-chain amino acids (e.g., Ala and alpha-aminobutyric acid) are preferred at this site. Only P1' substitution demonstrated any significant change in Km, presumably due to the decreased hydrophobic interactions in the S1' site upon Ala substitution. The species specificity of renin presumably arises from differing P1'-P3' residues in angiotensinogens. For example, the P1'-P3' residues from human and porcine angiotensinogens are Ile-Val-His and Leu-Val-Tyr, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Phantom Breathing in Monitored Infants (1973)

Excessive fluctuations of power line voltage can result in defective performance of some commercially available electronic medical monitoring devices. Transient decreases in electrical outlet voltage were found to explain malfunctioning of apnea monitors which failed to alarm when infants stopped breathing. This report suggests that specifications should be established for performance of monitoring equipment and that electrical outlet voltage should be carefully maintained within known limits in areas in which monitoring of critically ill patients is necessary.
Assessing the Effects of Acupuncture by Comparing Needling the Hegu Acupoint and Needling Nearby Nonacupoints by Spectral Analysis of Microcirculatory Laser Doppler Signals (2010)

We aimed to assess the effects of acupuncture by analyzing the frequency content of skin blood-flow signals simultaneously recorded at the Hegu acupoint and two nearby nonacupoints following acupuncture stimulation (AS). Laser Doppler flowmetry (LDF) signals were measured in male healthy volunteers in two groups of experiments: needling the Hegu acupoint (n = 13) and needling a nearby nonacupoint (control experiment; n = 10). Each experiment involved recording a 20 min baseline-data sequence and two sets of effects data recorded 0-20 and 50-70 min after stopping AS. Wavelet transform with Morlet mother wavelet was applied to the measured LDF signals. Needling the Hegu acupoint significantly increased the blood flow, significantly decreased the relative energy contribution at 0.02-0.06 Hz and significantly increased the relative energy contribution at 0.4-1.6 Hz at Hegu, but induced no significant changes at the nonacupoints. Also, needling a nearby nonacupoint had no effect in any band at any site. This is the first time that spectral analysis has been used to investigate the microcirculatory blood-flow responses induced by AS, and has revealed possible differences in sympathetic nerve activities between needling the Hegu acupoint and its nearby nonacupoint. One possible weakness of the present design is that different De-Qi feelings following AS could lead to nonblind experimental setup, which may bias the comparison between needling Hegu and its nearby nonacupoint. Our results suggest that the described noninvasive method can be used to evaluate sympathetic control of peripheral vascular activity, which might be useful for studying the therapeutic effects of AS.
Contributions of Cell Metabolism and H+ Diffusion to the Acidic pH of Tumors (2003)

The tumor microenvironment is hypoxic and acidic. These conditions have a significant impact on tumor progression and response to therapies. There is strong evidence that tumor hypoxia results from inefficient perfusion due to a chaotic vasculature. Consequently, some tumor regions are well oxygenated and others are hypoxic. It is commonly believed that hypoxic regions are acidic due to a stimulation of glycolysis through hypoxia, yet this is not yet demonstrated. The current study investigates the causes of tumor acidity by determining acid production rates and the mechanism of diffusion for H(+) equivalents through model systems. Two breast cancer cell lines were investigated with divergent metabolic profiles: nonmetastatic MCF-7/s and highly metastatic MDA-mb-435 cells. Glycolysis and acid production are inhibited by oxygen in MCF-7/s cells, but not in MDA-mb-435 cells. Tumors of MDA-mb-435 cells are significantly more acidic than are tumors of MCF-7/s cells, suggesting that tumor acidity is primarily caused by endogenous metabolism, and not the lack of oxygen. Metabolically produced protons are shown to diffuse in association with mobile buffers, in concordance with previous studies. The metabolic and diffusion data were analyzed using a reaction-diffusion model to demonstrate that the consequent pH profiles conform well to measured pH values for tumors of these two cell lines.
The Diagnostic Value of Cytokeratin 5/6, 14, 17, and 18 Expression in Human Non-Small Cell Lung Cancer (2011)

Our data suggest that CK5/6, CK7, CK14, CK17, and CK18 have diagnostic value in the subclassification of NSCLC.
The foliar fungal endophytes of the Amazonian palm<i>Euterpe oleracea</i> (1994)

A survey of the fungal endophytes in leaves of trees and saplings of Euterpe oleracea was carried out over two years. An average of 25% of the leaf discs taken from 10 trees and 10 saplings over four samplings were colonized by endophytic fungi. Overall fungal colonization was positively correlated with leaf age, plant growth stages, site, and the interactive effects of growth stage × season and growth stage × site. Fewer isolates were recovered from younger than from older leaves, and from trees than from saplings. Fifty-seven species and six familial taxa assigned mainly to the Ascomycotina and Deuteromycotina were isolated. Xylaria cubensis and Letendraeopsis palmarum were the most common species. Significant differences in the number of isolates of the 21 most frequent species were observed with respect to plant growth stages, season and site. A community ordination analysis showed that depending upon the host tissue, vein or intervein, trees and saplings located at different sites were characterized by distinct endophytic communities.
Macrophages Release Tumor Necrosis Factor Alpha and Interleukin-12 in Response to Intracellular <i>Bacillus anthracis</i> Spores (2004)

Herein we report that infection of a murine macrophage cell line with Bacillus anthracis results in the production of tumor necrosis factor alpha and interleukin-12 (IL-12). When infected with B. anthracis spores in combination with lipopolysaccharide, macrophages release increased amounts of IL-12. We found no evidence of inhibition of cytokine responses in macrophages infected with B. anthracis spores.
Circulating CD8 T Lymphocytes in Human Immunodeficiency Virus-Infected Individuals Have Impaired Function and Downmodulate CD3ζ, the Signaling Chain of the T-Cell Receptor Complex (1998)

Although human immunodeficiency virus (HIV)-infected subjects without acquired immunodeficiency syndrome have a high frequency of HIV-specific CD8 T lymphocytes, freshly isolated lymphocytes frequently lack detectable HIV-specific cytotoxicity. However, this effector function becomes readily apparent after overnight culture. To investigate reasons for T-cell dysfunction, we analyzed T-cell expression of the cytolytic protease granzyme A and of CD3ζ, the signaling component of the T-cell receptor complex. An increased proportion of CD4 and CD8 T cells from HIV-infected donors contain granzyme A, consistent with the known increased frequency of activated T cells. In 28 HIV-infected donors with mild to advanced immunodeficiency, a substantial fraction of circulating T cells downmodulated CD3ζ (fraction of T cells expressing CD3ζ, 0.74 ± 0.16 v 1.01 ± 0.07 in healthy donors; P < .0000005). CD3ζ expression is downregulated more severely in CD8 than CD4 T cells, decreases early in infection, and correlates with declining CD4 counts and disease stage. CD3ζ expression increases over 6 to 16 hours of culture in an interleukin-2–dependent manner, coincident with restoration of viral-specific cytotoxicity. Impaired T-cell receptor signaling may help explain why HIV-specific cytotoxic T lymphocytes fail to control HIV replication.