gebhart/patrepeval huggingface dataset:
Activation and Repression by Nuclear Hormone Receptors: Hormone Modulates an Equilibrium between Active and Repressive States (1996)

Transactivation-defective retinoid X and thyroid hormone receptors have been used to examine mechanisms of hormonal activation. Activation and repression of transcription by retinoid X and thyroid hormone receptors are shown to be mediated by physically distinct and functionally independent regions of the hormone binding domain. Nevertheless, the ability of receptors to respond to hormone requires communication between both functional domains. Deletion of the hormone-dependent transactivation function of the retinoid X receptor, the common subunit of heterodimeric nuclear receptors, significantly impairs hormone-dependent transcription by retinoic acid, thyroid hormone, and vitamin D receptors. The results indicate that receptors do not exist in static off and on conformations but that hormone alters an equilibrium between inactive and active states.
Cancer pain management. (1993)

Pain can be adequately relieved in most cancer patients through the application of widely accepted management approaches. Current therapeutic guidelines emphasize ongoing patient assessment and optimal pharmacotherapy with opioid and nonopioid analgesics.
Intra-abdominal Pressures during Voluntary and Reflex Cough (2008)

The induced LCR is the involuntary rapid and repeated synchronous expiratory muscle activation that causes and sustains an elevated IAP over time, sufficient for airway protection. VC and LCR have different neurophysiological functions. Quantification of the LCR using AUC values and mean or peak IAP values may be useful as a clinical tool for determining neurophysiological airway protection status and provide a quantitative assessment of changes in a patient's functional recovery or decline.
Development and Testing of a Multilevel Chevron Actuator-Based Positioning System (2011)

We present the design, fabrication, and testing of a microscale positioning system. The system was designed in the SUMMiT V process to produce in-plane, bidirectional, micrometer-scale linear motion of a shuttle using a ratcheting mechanism and multilayered chevron actuators. A single latching system with oppositely faced ratchet teeth on either side of the shuttle is used for achieving the bidirectional actuation. The device has a smaller footprint and fewer electrical connections compared to similar devices, without compromising performance. Moreover, this device is capable of generating more force compared to previous devices. A LabVIEW-based optical characterization setup was developed for automated testing of the device. The device produced a maximum displacement of <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\sim \!\!180\ \mu\hbox{m}$</tex></formula> with a step size of 9 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\mu\hbox{m}$</tex></formula> . <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$\hfill$</tex> </formula> [2011-0151]
Molecular Neurosurgery: Using Plant Toxins to Make Highly Selective Neural Lesions (1999)

Ribosome inactivating proteins found in many plants can be used to make targeted cytotoxins that selectively destroy specific types of cells. Ricin and volkensin have been used to make anatomically selective neural lesions. Immunotoxins consisting of monoclonal anti-neuronal antibodies armed with saporin (from Saponaria officinalis) can selectively destroy specific types of neurons such as the cholinergic neurons of the basal forebrain. This approach is valuable for animal modeling of neurodegenerative diseases such as Alzheimer's and Parkinson's disease. Recently, neuropeptides, such as substance P, have been armed with saporin and used to selectively destroy neurons expressing the appropriate neuropeptide receptors. This approach holds great promise for research in the neurobiology of pain and for treatment of chronic, intractable pain.
Synthesis of an interactive haptic dancing partner (2010)

This paper studies dancing as a haptic interaction task with the aim of replacing one of the human dancing partners by an interactive robot. Starting from haptic recordings of human dancing couples, the interactive behavior of a male dancing partner is synthesized. For this purpose recorded dancing steps are approximated using multiple vector fields and faded into each other by simply switching between them. Adaptation to the female style of dancing is realized by implementing an adaptation law which changes the step size of the robot. Experimental results performed on a mobile haptic interface show the validity of the presented approach.
Case‐control association testing in the presence of unknown relationships (2009)

Genome-wide association studies result in inflated false-positive results when unrecognized cryptic relatedness exists. A number of methods have been proposed for testing association between markers and disease with a correction for known pedigree-based relationships. However, in most case-control studies, relationships are generally unknown, yet the design is predicated on the assumption of at least ancestral relatedness among cases. Here, we focus on adjusting cryptic relatedness when the genealogy of the sample is unknown, particularly in the context of samples from isolated populations where cryptic relatedness may be problematic. We estimate cryptic relatedness using maximum-likelihood methods and use a corrected chi(2) test with estimated kinship coefficients for testing in the context of unknown cryptic relatedness. Estimated kinship coefficients characterize precisely the relatedness between truly related people, but are biased for unrelated pairs. The proposed test substantially reduces spurious positive results, producing a uniform null distribution of P-values. Especially with missing pedigree information, estimated kinship coefficients can still be used to correct non-independence among individuals. The corrected test was applied to real data sets from genetic isolates and created a distribution of P-value that was close to uniform. Thus, the proposed test corrects the non-uniform distribution of P-values obtained with the uncorrected test and illustrates the advantage of the approach on real data.
Northienamycin and 8-epi-thienamycin, new carbapenems from Streptomyces cattleya. (1983)

Two new carbapenem antibiotics, northienamycin and 8-epi-thienamycin have been isolated from culture broth of Streptomyces cattleya grown under conditions for thienamycin production. The isolation, structure elucidation and in vitro antibacterial spectra of the new carbapenems are reported. In addition, comparison of the in vitro potency of the corresponding formamidine derivatives to that of MK787 is presented.
AlGaN/GaN HEMTs with an InGaN-based back-barrier (2005)

In this work, we use an ultra-thin InGaN layer below the GaN channel to increase the confinement of the electrons. In this novel approach, the polarization induced electric field in the InGaN layer is used to raise the conduction band energy in the buffer layer with respect to the channel. With this technique, a double-heterojunction transistor can be formed without the need of a high bandgap or p-doped buffer. Poisson-Schrodinger simulations (Wu, et.al.) have confirmed the increased electron confinement at electron temperatures as high as 3000 K
Carotenoids and Retinoids: A Review of Research, Clinical, and Public Health Applications (1997)

Traditionally, the carotenoids and retinoids have been regarded as dietary sources of vitamin A and have been evaluated regarding their respective physiologic roles in vision, growth, immune system integrity, and prevention of vitamin A deficiency. In the 1990s, however, vitamin A deficiency is no longer widespread in Western countries. Therefore, the role of carotenoids and retinoids is evolving to encompass treatment and prevention of conditions such as cancer and cardiovascular disease, which are prevalent in Western societies. This review summarizes current research concerning the therapeutic utility of vitamin A and its analogues and their roles in the prevention of cancer and cardiovascular disease.
Efficacy of a Bioreactor Filled with Porcine Hepatocytes Immobilized on Nonwoven Fabric for Ex Vivo Direct Hemoperfusion Treatment of Liver Failure in Pigs (1998)

We developed a new bioreactor for a bioartificial liver filled with porcine hepatocytes immobilized on polyester nonwoven fabric (NWF) and in our previous study showed that this NWF bioreactor has promising in vitro efficiency. In the present study, we investigated the efficacy of the NWF bioreactor in a direct hemoperfusion experiment conducted to treat pigs with liver failure. Porcine hepatocytes were isolated from the whole liver of a Sangen strain pig. They were immobilized in a 200 ml column containing NWF via perfusion in a closed circuit for 24 h to prepare a NWF bioreactor. The following day an operative liver failure model was produced by creating a portocaval shunt and ligating the entire hepatoduodenal ligament in the porta hepatis. Perfusion treatment was initiated 4 h after operative induction of liver failure and continued for about 1 h. The pigs which underwent perfusion treatment showed significant improvements in survival and blood data, including ammonia, total bile acid, glucose, and prothrombin time, attributed to significant improvements in the post- as compared to the prebioreactor levels in the perfused blood of the treated pigs. These beneficial effects of the NWF bioreactor were based on its excellent composition which allows the accommodation of adequate numbers of hepatocytes and direct contact between hepatocytes and perfused blood.
Recovering lossy multiconductor transmission line parameters from impedance or scattering representations (2002)

In this paper, we present a generalization of the simultaneous diagonalization technique by means of congruence transformations to the general reciprocal lossy multiconductor transmission line case. The method paves the way to solving the inverse problem, i.e., given a lossy multiconductor transmission line system of a given length, recover the transmission line parameters from the impedance or scattering descriptions.
Proteolytically Processed Soluble Tumor Endothelial Marker (TEM) 5 Mediates Endothelial Cell Survival during Angiogenesis by Linking Integrin αvβ3 to Glycosaminoglycans (2006)

Tumor endothelial marker (TEM) 5 is a member of the adhesion family of G-protein-coupled receptors and up-regulated in endothelial cells during tumor and physiologic angiogenesis. Here, we report that TEM5 is expressed on the surface of endothelial cells. A soluble TEM5 (sTEM5) fragment is shed by endothelial cells during capillary-like network formation and upon growth factor stimulation. We found that sTEM5 binds to several glycosaminoglycans. Furthermore, sequence analysis and functional and biochemical studies revealed that sTEM5 contains a cryptic RGD-binding site for integrin alpha(v)beta3. Matrix metalloprotease 9-processed, but not full-length, sTEM5 mediated endothelial cell adhesion by direct interaction with integrin alpha(v)beta3. Adhesion to proteolytically processed sTEM5 (ppsTEM5) or glycosaminoglycan-bound ppsTEM5 promoted survival of growth factor deprived endothelial cells. ppsTEM5-mediated cell survival was inhibited by a function blocking integrin alpha(v)beta3 antibody. Based on our results we conclude that sTEM5 is shed by endothelial cells during angiogenesis and binds to glycosaminoglycans present on extracellular matrix and cell surface proteoglycans. Further proteolytic processing of sTEM5 leads to exposure of its RGD motif mediating endothelial cell survival by linking integrin alpha(v)beta3 to glycosaminoglycans.
Determination of cardiac output by Doppler echocardiography. (1984)

Cardiac output determined by Doppler echocardiography was compared with that determined by thermodilution at rest and during dobutamine infusion in 10 patients (group A) and by the Fick method at rest in 11 patients (group B). All patients had angina pectoris without valvular heart disease. Maximum spatial blood velocity and cross sectional aortic area were estimated by the Doppler technique and echocardiography. Cardiac output was calculated by multiplying blood velocity by aortic area at various levels in the ascending aorta. The best correlation of cardiac output between the invasive and non-invasive methods was obtained when maximum velocity in the aortic root and the aortic orifice area were used in the calculations. Cardiac output was considerably overestimated when area measurements in the aortic root were used.
Tumor-Associated CD8+ T Cell Tolerance Induced by Bone Marrow-Derived Immature Myeloid Cells (2005)

T cell tolerance is a critical element of tumor escape. However, the mechanism of tumor-associated T cell tolerance remains unresolved. Using an experimental system utilizing the adoptive transfer of transgenic T cells into naive recipients, we found that the population of Gr-1+ immature myeloid cells (ImC) from tumor-bearing mice was able to induce CD8+ T cell tolerance. These ImC accumulate in large numbers in spleens, lymph nodes, and tumor tissues of tumor-bearing mice and are comprised of precursors of myeloid cells. Neither ImC from control mice nor progeny of tumor-derived ImC, including tumor-derived CD11c+ dendritic cells, were able to render T cells nonresponsive. ImC are able to take up soluble protein in vivo, process it, and present antigenic epitopes on their surface and induce Ag-specific T cell anergy. Thus, this is a first demonstration that in tumor-bearing mice CD8+ T cell tolerance is induced primarily by ImC that may have direct implications for cancer immunotherapy.
A Hydrophobic Stretch of 12 Amino Acid Residues in the Middle of α-Synuclein Is Essential for Filament Assembly (2001)

Neuronal and oligodendrocytic aggregates of fibrillar alpha-synuclein define several diseases of the nervous system. It is likely that these inclusions impair vital metabolic processes and compromise viability of affected cells. Here, we report that a 12-amino acid stretch ((71)VTGVTAVAQKTV(82)) in the middle of the hydrophobic domain of human alpha-synuclein is necessary and sufficient for its fibrillization based on the following observations: 1) human beta-synuclein is highly homologous to alpha-synuclein but lacks these 12 residues, and it does not assemble into filaments in vitro; 2) the rate of alpha-synuclein polymerization in vitro decreases after the introduction of a single charged amino acid within these 12 residues, and a deletion within this region abrogates assembly; 3) this stretch of 12 amino acids appears to form the core of alpha-synuclein filaments, because it is resistant to proteolytic digestion in alpha-synuclein filaments; and 4) synthetic peptides corresponding to this 12-amino acid stretch self-polymerize to form filaments, and these peptides promote fibrillization of full-length human alpha-synuclein in vitro. Thus, we have identified key sequence elements necessary for the assembly of human alpha-synuclein into filaments, and these elements may be exploited as targets for the design of drugs that inhibit alpha-synuclein fibrillization and might arrest disease progression.
Dynamic Taint Tracking in Managed Runtimes (2012)

This paper provides a taxonomy of runtime taint tracking approaches for managed code, such as code written in Java, C#, PHP, Perl, or Ruby. It covers main applications of data tainting such as prevent-ing web application vulnerabilities including cross-site scripting and SQL injection attacks, along with disallowing privacy-sensitive data leaks. In addition to giving an overview of related literature from the last decade, this paper provides guidance and describes the trade-offs of different instrumentation approaches. Lastly, we provide a list of open problems whose solu-tions would aid practical adaption of runtime tainting on a wider scale. 2 Abstract—This paper provides a taxonomy of run-time taint tracking approaches for managed code, such as code written in Java, C#, PHP, Perl, or Ruby. It covers main applications of data tainting such as pre-venting web application vulnerabilities including cross-site scripting and SQL injection attacks, along with disallowing privacy-sensitive data leaks. In addition to giving an overview of related literature from the last decade, this paper provides guidance and describes the trade-offs of different instrumentation approaches. Lastly, we provide a list of open problems whose solu-tions would aid practical adaption of runtime tainting on a wider scale. I.
DNA Methylation-Related Chromatin Remodeling in Activity-Dependent <i>Bdnf</i> Gene Regulation (2003)

In conjunction with histone modifications, DNA methylation plays critical roles in gene silencing through chromatin remodeling. Changes in DNA methylation perturb neuronal function, and mutations in a methyl-CpG-binding protein, MeCP2, are associated with Rett syndrome. We report that increased synthesis of brain-derived neurotrophic factor (BDNF) in neurons after depolarization correlates with a decrease in CpG methylation within the regulatory region of the Bdnf gene. Moreover, increased Bdnf transcription involves dissociation of the MeCP2-histone deacetylase-mSin3A repression complex from its promoter. Our findings suggest that DNA methylation-related chromatin remodeling is important for activity-dependent gene regulation that may be critical for neural plasticity.
Interaction of nucleolar protein B23 with peptides related to nuclear localization signals and its modulation by phosphorylation (1995)

Nucleolar protein B23 is a putative ribosome assembly factor with a high affinity for peptides containing nuclear localization signals (NLSs). The interactions of various NLS-containing peptides with two B23 isoforms (B23.1 and B23.2) were examined using equilibrium dialysis and Scatchard analyses. The KD for protein B23 binding to a peptide containing the SV40 T-antigen NLS sequence was approximately 1 microM with a stoichiometry of 1:1 (peptide:protein). No significant differences were seen between the two B23 isoforms in their affinities for any of the peptides tested. Binding by a reverse sequence SV40 T-NLS peptide showed a nonlinear Scatchard plot: this peptide was unable displace the correct sequence peptide, suggesting that the reverse sequence peptide binds to a different site on the protein. A peptide containing the sequence required for nucleolar localization of the HIV-1 Rev protein had an affinity for B23 approximately 10-fold greater than that of the SV40 T-NLS. However, with a sequence sufficient only for Rev location in the nucleoplasm, the affinity for B23 was diminished to a level between that of the longer Rev sequence and the SV40 T-NLS. In competition binding assays, the Rev NLS peptide was able to displace the SV40 T NLS, indicating that both peptides bind to the same site on protein B23. There was no detectable binding to protein B23 by a peptide containing the bipartite NLS of nucleoplasmin. Phosphorylation of protein B23 by casein kinase II enhanced its affinity for the SV40 T- and Rev-derived peptides approximately 2-fold.(ABSTRACT TRUNCATED AT 250 WORDS)
Correlation of Anti-HIV Potency with Lipophilicity in a Series of Cosalane Analogs Having Normal Alkenyl and Phosphodiester Chains as Cholestane Replacements (1996)

In order to define the role of the cholestane moiety in the anti-HIV agent cosalane, a series of cosalane analogs was synthesized in which the cholestane ring system was replaced by normal alkenyl and phosphodiester substituents having varied chain lengths and lipophilicities. The compounds containing simple alkenyl substituents were found to be more potent as inhibitors of the cytopathic effect of HIV-1 in cell culture than the phosphodiesters. In addition, the potencies of the alkene congeners correlated positively with chain length and lipophilicity of the alkene. The results indicate that the cholestane moiety of cosalane functions as a lipophilic accessory appendage to escort the dichlorodisalicylmethane pharmacophore to a lipid environment.
Olfaction and Taste XI (1994)

In this compendium of current studies on olfaction and taste - the most comprehensive yet to appear in this series - the chemical senses are elucidated from points of view ranging from anatomy, electr
Diversity and Prevalence of PorA Types in<i>Neisseria meningitidis</i>Serogroup B in the United States, 1992–1998 (2000)

Two hundred eighty-one sporadic Neisseria meningitidis serogroup B isolates, collected through active laboratory-based surveillance, were selected to be analyzed by PorA variable region (VR) typing to determine the prevalence of PorA types in the United States. A substantial number of distinct VR types were identified, 31 in VR1 and 41 in VR2. A total of 73 different PorA types were found, and 76. 7% of these types comprise nonprototype sequences in VR1, VR2, or both. The most prevalent PorA types were P1.7,16-20 (previously P1.7, 16i), P1.22,14, P1.22-1,14 (previously P1.22a,14), P1.7,16, P1.7-1,1 (previously P1.7d,1), P1.19,15, and P1.17,16-3 (previously P1.B,16d). No correlation was observed between the PorA types and geographic origin of the isolates. These data may aid in the design of an efficacious outer membrane protein-based vaccine by identifying the most appropriate PorA types for vaccine formulation. Studies are needed to fully evaluate the extent of cross-protection in humans among the variants and prototypes in each PorA VR family.
Luminescence Centers of MgS, CaS and CaSe Phosphors Activated with Eu<sup>2+</sup> Ion (1980)

Emission and excitation spectra of Eu 2+ ions incorporated in MgS, CaS and CaSe were measured at temperatures 300, 80 and 6 K. Both spectra are interpreted as due to the allowed transition between the Eu 2+ ion's ground state ( 8 S 7/2 ) of 4f 7 configuration and the excited states of 4f 6 5d configuration, together with the forbidden transition arising from the configuration interaction between 4f 6 5d and4f 6 6s. From the observed excitation spectra for CaS: Eu 2+ and CaSe: Eu 2+ phosphors, \(^{8}\varGamma_{4}(t_{\text{2g}})\)-, \(^{8}\varGamma_{3}(e_{\text{g}})\)-bands were assigned for lower concentrations of Eu 2+ ion; besides these bands \(^{8}\varGamma_{1}(6s)\)- and \(^{6}\varGamma_{4}(t_{\text{2g}})\)-bands were assigned for higher concentrations of Eu 2+ ion. From the assigned \(^{8}\varGamma_{4}(t_{\text{2g}})\)- and \(^{8}\varGamma_{3}(e_{\text{g}})\)-bands, it has been found that 10 D q for MgS, CaS and CaSe are 19500 cm -1 , 18750 cm -1 and 17300 cm -1 , respectively.