gebhart/patrepeval huggingface dataset:
Crystal Structure of Human d-Dopachrome Tautomerase, a Homologue of Macrophage Migration Inhibitory Factor, at 1.54 Å Resolution, (1999)

D-Dopachrome tautomerase shares a low homologous amino acid sequence (33% homology) with the macrophage migration inhibitory factor (MIF) and possesses similar tautomerase activity as well. MIF is a cytokine involved in inflammatory reactions and immune responses. Whereas recent studies have identified MIF as a pituitary hormone and immunoregulator, much less is known about the structural basis of these physiological functions and the real significance of tautomerase activity. Therefore, interest in the structure-function relationship between D-dopachrome tautomerase and MIF has increased, especially with regard to inflammation and immune responses. We have determined the X-ray crystal structure of human D-dopachrome tautomerase at 1.54 A resolution. D-Dopachrome tautomerase folds to form a homotrimer that has extensive contact between subunits by intersubunit beta-sheets. Its overall topology and trimeric formations are similar to those of human MIF. The N-terminal proline is located at the bottom of a positively charged pocket in which the conformations of Lys32 and Ser63 are highly conserved. These positively charged properties are also seen in the active site pocket of human MIF, bacterial 5-(carboxymethyl)-2-hydroxymuconate isomerase (CHMI), and 4-oxalocrotonate tautomerase (4-OT). A detailed comparison of these structures revealed significant differences in the environment around the potential active site, the intersubunit contacts, and charge distribution on the molecular surface. It can be concluded that these features are related to the physiological role and tautomerase activity of MIF and D-dopachrome tautomerase. The present structural study could be helpful for designing effective inhibitors that modulate immunoregulatory and hormone-like effects.
Abnormal regulation of renal vitamin D catabolism by dietary phosphate in murine X-linked hypophosphatemic rickets. (1990)

Hyp mice exhibit increased renal catabolism of vitamin D metabolites by the C-24 oxidation pathway (1988. J. Clin. Invest. 81:461-465). To examine the regulatory influence of dietary phosphate on the renal vitamin D catabolic pathway in Hyp mice, we measured C-24 oxidation of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) in renal mitochondria isolated from Hyp mice and normal littermates fed diets containing 0.03% (low-Pi), 1% (control-Pi), and 1.6% (high-Pi) phosphate. In normal mice the low-Pi diet led to a rise in serum 1,25(OH)2D (22.2 +/- 1.8 to 48.1 +/- 6.8 pg/ml, P less than 0.05) and no change in C-24 oxidation products (0.053 +/- 0.006 to 0.066 +/- 0.008 pmol/mg protein per min) when compared with the control diet. In Hyp mice the low-Pi diet elicited a fall in serum 1,25(OH)2D (21.9 +/- 1.2 to 8.0 +/- 0.2 pg/ml, P less than 0.05) and a dramatic increase in C-24 oxidation products (0.120 +/- 0.017 to 0.526 +/- 0.053 pmol/mg protein per min, P less than 0.05) when compared with the control diet. The high-Pi diet did not significantly alter serum levels of 1,25(OH)2D or C-24 oxidation products in normal mice. Hyp mice on the high-Pi diet experienced a rise in serum 1,25(OH)2D (21.9 +/- 1.2 to 40.4 +/- 7.3, P less than 0.05) and a fall in C-24 oxidation products (0.120 +/- 0.017 to 0.043 +/- 0.007 pmol/mg protein per min, P less than 0.05). The present results demonstrate that the defect in C-24 oxidation of 1,25(OH)2D3 in Hyp mice is exacerbated by phosphate depletion and corrected by phosphate supplementation. The data suggest that the disorder in vitamin D metabolism in the mutant strain is secondary to the perturbation in phosphate homeostasis.
Continuous noninvasive monitoring of changes in human skin optical properties during oral intake of different sugars with optical coherence tomography (2014)

The objective of this study was to evaluate the effects of blood glucose concentration (BGC) on in vivo human skin optical properties after oral intake of different sugars. In vivo optical properties of human skin were measured with a spectral domain optical coherence tomography (SD-OCT). Experimental results show that increase of BGC causes a decrease in the skin attenuation coefficient. And the maximum decrements in mean attenuation coefficient of skin tissue after drinking glucose, sucrose and fructose solution are 47.0%, 36.4% and 16.5% compared with that after drinking water, respectively (p < 0.05). The results also show that blood glucose levels of the forearm skin tissue are delayed compared with finger-stick blood glucose, and there are significant differences in the time delays after oral intake of different sugars. The time delay between mean attenuation coefficient and BGC after drinking glucose solution is evidently larger than that after drinking sucrose solution, and that after drinking sucrose solution is larger than that after drinking fructose solution. Our pilot studies indicate that OCT technique is capable of non-invasive, real-time, and sensitive monitoring of skin optical properties in human subjects during oral intake of different sugars.
Limited anti‐inflammatory efficacy of cyclo‐oxygenase‐2 inhibition in carrageenan‐airpouch inflammation (1999)

1. Cyclo-oxygenase-2 (COX-2) is expressed at sites of inflammation and is believed to be the major source of inflammation-associated prostaglandin synthesis. Selective inhibition of COX-2 has been suggested to produce anti-inflammatory effects with reduced toxicity in the gastrointestinal tract. We examined the extent to which suppression of COX-2 led to inhibition of various components of inflammation in the carrageenan-airpouch model in the rat. 2. Indomethacin (> or =0.3 mg kg(-1)), nimesulide (> or =3 mg kg(-1)) and the selective COX-2 inhibitor, SC-58125 (> or =0.3 mg kg(-1)), significantly suppressed the production of prostaglandin E2 at the site of inflammation. At higher doses, indomethacin (> or =1 mg kg(-1)) and nimesulide (30 mg kg(-1)), but not SC-58125 (up to 10 mg kg(-1)), significantly inhibited COX-1 activity (as measured by whole blood thromboxane synthesis). 3. All three test drugs significantly reduced the volume of exudate in the airpouch, but only at doses greater than those required for substantial (>90%) suppression of COX-2 activity. Similarly, reduction of leukocyte infiltration was only observed with the doses of indomethacin and nimesulide that caused significant suppression of COX-1 activity. 4. SC-58125 did not significantly affect leukocyte infiltration into the airpouch at any dose tested (up to 10 mg kg(-1)). A second selective COX-2 inhibitor, Dup-697, was also found to suppress exudate PGE2 levels without significant effects on leukocyte infiltration. 5. These results indicate that selective inhibition of COX-2 results in profound suppression of PGE2 synthesis in the carrageenan-airpouch, but does not affect leukocyte infiltration. Exudate volume was only reduced with the highly selective COX-2 inhibitor when a dose far above that necessary for suppression of COX-2 activity was used. Inhibition of leukocyte infiltration was observed with indomethacin and nimesulide, but only at doses that inhibited both COX-1 and COX-2.
Noncovalent Sidewall Functionalization of Single-Walled Carbon Nanotubes for Protein Immobilization (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNoncovalent Sidewall Functionalization of Single-Walled Carbon Nanotubes for Protein ImmobilizationRobert J. ChenRobert J. ChenDepartment of Chemistry, Stanford University Stanford, California 94305 More by Robert J. Chen, Yuegang ZhangYuegang ZhangDepartment of Chemistry, Stanford University Stanford, California 94305 More by Yuegang Zhang, Dunwei WangDunwei WangDepartment of Chemistry, Stanford University Stanford, California 94305 More by Dunwei Wang, and Hongjie Dai*Hongjie DaiDepartment of Chemistry, Stanford University Stanford, California 94305 Address correspondence to this author.More by Hongjie DaiCite this: J. Am. Chem. Soc. 2001, 123, 16, 3838–3839Publication Date (Web):April 18, 2001Publication History Published online18 April 2001Published inissue 1 April 2001https://pubs.acs.org/doi/10.1021/ja010172bhttps://doi.org/10.1021/ja010172brapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views20359Altmetric-Citations2235LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Carbon nanotubes,Functionalization,Immobilization,Molecules,Peptides and proteins Get e-Alerts
Identification of Bacillus anthracis by a simple protective antigen-specific mAb dot-ELISA (2002)

A simple protective antigen (PA)-reactive mAb dot-ELISA was standardized for confirmation of toxin-producing strains of Bacillus anthracis. Twenty-seven clinical isolates were collected from patients clinically suspected of having anthrax. PA was elaborated from these isolates using Casamino acids medium and the culture medium was boiled to kill the cells. PA in boiled culture supernatants was detected using a dot-ELISA. Of the 27 clinical isolates tested, PA was detected in 24 isolates. This was further confirmed by amplifying the PA gene by PCR. This testing procedure is simple to perform, specific and safer than existing procedures, which are added advantages over existing methods of identification of B. anthracis. This test system could be a valuable tool in confirming clinical and environmental isolates of B. anthracis.
Experimental Nonlocality Proof of Quantum Teleportation and Entanglement Swapping (2001)

Quantum teleportation strikingly underlines the peculiar features of the quantum world. We present an experimental proof of its quantum nature, teleporting an entangled photon with such high quality that the nonlocal quantum correlations with its original partner photon are preserved. This procedure is also known as entanglement swapping. The nonlocality is confirmed by observing a violation of Bell's inequality by 4.5 standard deviations. Thus, by demonstrating quantum nonlocality for photons that never interacted, our results directly confirm the quantum nature of teleportation.
Semiconductor laser insert with uniform illumination for use in photodynamic therapy (2005)

A low-cost semiconductor red laser light delivery system for esophagus cancer treatment is presented. The system is small enough for insertion into the patient's body. Scattering elements with nanoscale particles are used to achieve uniform illumination. The scattering element optimization calculations, with Mie theory, provide scattering and absorption efficiency factors for scattering particles composed of various materials. The possibility of using randomly deformed spheres and composite particles instead of perfect spheres is analyzed using an extension to Mie theory. The measured radiation pattern from a prototype light delivery system fabricated using these design criteria shows reasonable agreement with the theoretically predicted pattern.
RNase H Active Site Inhibitors of Human Immunodeficiency Virus Type 1 Reverse Transcriptase: Design, Biochemical Activity, and Structural Information (2009)

Pyrimidinol carboxylic acids were designed as inhibitors of HIV-1 RNase H function. These molecules can coordinate to two divalent metal ions in the RNase H active site. Inhibition of enzymatic activity was measured in a biochemical assay, but no antiviral effect was observed. Binding was demonstrated via a solid state structure of the isolated p15-Ec domain of HIV-1 RT showing inhibitor and two Mn(II) ions bound to the RNase H active site.
Notes on Red-Winged Parrots, Corellas and Galahs Feeding on Pods and Seeds of Acacia Species (2010)

A paper on Red-winged Parrots, Little and Long-billed Corellas, and Galahs feeding on the pods and seeds of various Acacia species is presented. The unique structure of the birds' bill and mandible enables them to forage for and feed on Acacia seeds. Observations of the feeding habits of the three parrot species at Surprise Creek and Engine Hole are presented.
Microglia in brain tumors (2002)

Microglia have long been ignored by neurooncologists. This has changed with the realization that microglial cells not only occur within and around brain tumors but also contribute significantly to the actual tumor mass, notably in astrocytic gliomas. In addition, it has been speculated that microglia could play a role in the defense against neoplasms of the nervous system. However, the biological success of these tumors, i.e., their highly malignant behavior, indicates that natural microglial defense mechanisms do not function properly in astrocytomas. In fact, there is evidence that microglial behavior is controlled by tumor cells, supporting their growth and infiltration. This unexpected "Achilles heel" of microglial immune defense illustrates the risk of generalizing on the basis of a single aspect of microglial biology. Microglia are highly plastic cells, capable of exerting cytotoxic functions under conditions of CNS infections, but not necessarily during glioma progression. Thus, the suggestion that microglial activation through stimulation by cytokines (e.g., interferon-gamma) will benefit patients with brain tumors could prove fatally wrong. Therapeutic recruitment of microglia to treat such diffusely infiltrative brain tumors as astrocytic gliomas must be considered premature.
A comparative dose–response study of cartilage‐derived morphogenetic protein (CDMP)‐1, ‐2 and ‐3 for tendon healing in rats (2003)

Cartilage-derived morphogenetic proteins (CDMPs), belonging to the bone morphogenetic protein (BMP) family, are known to be cartilage and bone inducers as well as to induce tendon and ligament-like tissue. In this study we investigated the influence of CDMP-1, -2 or -3 at four different doses (0, 0.4, 2 and 10 microg) on tendon healing in a rat model, as well as differences in osteogenesis between the different CDMPs and doses.In 110 rats, a 3 mm segment of the Achilles tendon was removed via a 2 mm skin incision. CDMP-1, -2 or -3 was injected into the defect 6 h postoperative. The rats were killed 8 days after operation. The tendon regenerates were tested biomechanically. There was a significant dose-related increase in strength and stiffness with all three CDMPs, but no difference between the CDMPs was found. Another 50 rats were used to compare the highest dose of the CDMPs with controls and osteogenic protein 1 (OP-1), as regards cartilage or bone formation after 4 weeks. Cartilage occurred in all groups, including the controls. Some specimens in all groups contained bone, except the controls. No difference between the CDMPs could be demonstrated. The CDMP-1, CDMP-3 and OP-1 groups contained significantly more calcium than controls. Only the CDMP-2 group and the controls contained significantly less calcium than the OP-1 group.In conclusion, the three CDMPs appeared similar as regards improvement of tendon repair and osteogenicity in this setting.
Personal neoantigen cancer vaccines (2014)

Neoantigen-based cancer vaccines designed to target the unique immunogenic mutations arising in each patient's tumor are breathing new life into a struggling approach. Data continue to demonstrate the importance of neoantigens in immune control of cancer. Despite manufacturing complexity, outstanding questions and desired further improvements, neoantigen vaccines are currently undergoing clinical evaluation.
Image segmentation using temporal-spatial information in dynamic scenes (2004)

The goal of image segmentation is to identify homogeneous regions in images. A common method for segmentation of moving regions in image sequences involves "background subtraction", namely, thresholding the error between an estimate of the image without moving objects and the current image. The numerous approaches to this problem differ in the type of background model used and the procedure used to update the model. One possible approach to this problem is to model the attributes of the pixels. In order to segment a larger image in reasonable time and obtain better results, an algorithm of segmenting background based on temporal spatial information of pixels is proposed in this paper. Firstly, adaptive pixel models are modeled to describe the recent history of color at each observed pixel. Then each pixel is classified as background or foreground according to pixel models and the spatial relation between pixels. Finally, parameters of pixel models are updated using on-line EM algorithm. Experimental results show that our approach is suitable for segmenting foreground from background in dynamic environments.
CD137 ligand mediates opposite effects in human and mouse NK cells and impairs NK-cell reactivity against human acute myeloid leukemia cells (2009)

Natural killer (NK) cells play an important role in the immunosurveillance of leukemia. Their reactivity is governed by a balance of activating and inhibitory receptors including various members of the tumor necrosis factor receptor (TNFR) family. Here we report that human NK cells acquire expression of the TNFR family member CD137 upon activation, and NK cells of acute myeloid leukemia (AML) patients display an activated phenotype with substantial CD137 expression. CD137 ligand (CD137L) was detectable on leukemic cells in 35% of 65 investigated AML patients, but not on healthy CD34(+) cells, and expression was associated with monocytic differentiation. Bidirectional signaling following CD137-CD137L interaction induced the release of the immunomodulatory cytokines interleukin-10 and TNF by AML cells and directly diminished granule mobilization, cytotoxicity, and interferon-gamma production of human NK cells, which was restored by blocking CD137. Cocultures of NK cells with CD137L transfectants confirmed that human CD137 inhibits NK-cell reactivity, while activating signals were transduced by its counterpart on NK cells in mice. Our data underline the necessity to study the function of seemingly analog immunoregulatory molecules in mice compared with men and demonstrate that CD137-CD137L interaction enables immune evasion of AML cells by impairing NK-cell tumor surveillance in humans.
Negative Regulation of the Nuclear Factor κB-inducing Kinase by a cis-Acting Domain (2000)

Nuclear factor kappaB (NF-kappaB)-inducing kinase (NIK) participates in the activation of NF-kappaB, a family of eukaryotic transcription factors that mediate cell growth and transformation. NIK activates the IkappaB kinase both in vivo and in vitro, although how the activity of NIK is regulated has remained unclear. Here we show that the N-terminal region of NIK contains a negative-regulatory domain (NRD), which is composed of a basic motif and a proline-rich repeat motif. Deletion of these motifs leads to a marked enhancement of NIK function. We further demonstrate that the N-terminal NRD interacts with the C-terminal region of NIK, thereby inhibiting the binding of NIK to its substrate IkappaB kinase. Consistently, when expressed alone, the NRD potently inhibits NIK-mediated NF-kappaB signaling. These results provide a new insight into the mechanism of NIK regulation.
Current biosensor technologies in drug discovery (2006)

Over the past two decades the benefits of biosensor analysis have begun to make an impact in the market, and systems are beginning to be used as mainstream research tools in many laboratories1,2. Biosensors are devices that use biological or chemical receptors to detect analytes in a sample.They give detailed information on the binding affinity, and in many cases also the binding kinetics of an interaction.Typically, the receptor molecule must be connected in some way to a transducer that produces an electrical signal in real-time. Labelfree biosensors do not require the use of reporter elements (fluorescent, luminescent, radiometric, or colorimetric) to facilitate measurements. Detailed information on an interaction can be obtained during analysis while minimising sample processing requirements and assay run times3. Unlike label- and reporter-based technologies that simply confirm the presence of the detector molecule, label-free techniques can provide direct information on analyte binding to target molecules typically in the form of mass addition or depletion from the surface of the sensor substrate, or measuring changes in the heat capacity of a sample4. However, these technologies have failed to gain widespread acceptance due to technical constraints, low throughput, high user expertise requirements, and cost.While they can be powerful tools in the hands of a skilled user evaluating purified samples, they are not readily adapted to every day lab use where simple to understand results on high numbers of samples are the norm.This article seeks to address some of the issues surrounding the un-met needs in the market place, and the difficulties faced by technology developers in meeting these needs with innovative products. It also reviews recent entries from newer technology developers who are in the race to release products for primary and secondary drug screening, mode of action studies, and screening of pharmacokinetic properties.
Recent Advances in Production of Bioethanol from Lignocellulosic Biomass (2009)

Abstract Ethanol is considered the most potential next generation automotive fuel because it is carbon‐neutral and could be produced from renewable resources like lignocellulosic biomass. There are some technological barriers such as pretreatment, saccharification of cellulose and hemicellulose matrix, and simultaneous fermentation of hexose and pentose sugars which needs to be addressed for efficient conversion of lignocellulosic biomass to bioethanol. This paper reviews the various process options and kinetic models adopted towards resolving the technological challenges to develop a low‐cost commercial process.
Structure of the CaMKIIδ/Calmodulin Complex Reveals the Molecular Mechanism of CaMKII Kinase Activation (2010)

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