gebhart/patrepeval huggingface dataset:
CYP72B1 Inactivates Brassinosteroid Hormones: An Intersection between Photomorphogenesis and Plant Steroid Signal Transduction (2003)

Active brassinosteroids, such as brassinolide (BL) and castasterone, are growth promoting plant hormones. An Arabidopsis cytochrome p450 monooxygenase encoded by CYP72B1 has been implicated in brassinosteroid catabolism as well as photomorphogenesis. We expressed CYP72B1 in yeast, coupled with brassinosteroid feeding, and established the biochemical function to be the hydroxylation of BL and castasterone, to give 26-hydroxybrassinolide and 26-hydroxycastasterone, respectively. Brassinosteroid feeding experiments with wild-type Arabidopsis, a CYP72B1 null mutant, and a CYP72B1 overexpression line demonstrated that carbon 26 hydroxylation of active brassinosteroids is an endogenous function of CYP72B1. Seedling growth assays demonstrated that 26-hydroxybrassinolide is an inactive brassinosteroid. Genetic and physiological analysis of the hypocotyl response to exogenous BL and varying intensities of white and monochromatic light suggested that CYP72B1 modulates photomorphogenesis primarily through far-red light and to a lesser extent through blue- and red-light pathways. CYP72B1 transcript accumulation in dark-grown seedlings was organ specific and down-regulated after 1 h of illumination in dim white, red, and blue light, but not far-red light. CYP72B1 translational fusions with the beta-glucuronidase reporter gene demonstrated that protein levels increased in the hypocotyl elongation zone when shifted from the dark to far-red light, but not blue or red light. We propose a model in which Arabidopsis seedling development switches from dark-grown development (skotomorphogenesis) to light-grown development (photomorphogenesis) in part by rapid modulation of brassinosteroid sensitivity and levels. CYP72B1 provides an intersection between the light and brassinosteroid pathways mainly by far-red-light-dependent modulation of brassinosteroid levels.
Periodicity in Al/Ti superconducting single electron transistors (2009)

We present experiments on single Cooper-pair transistors made of two different superconducting materials. We chose Ti and Al to create an energy gap profile such that the island has a higher gap than the leads, thereby acting as a barrier to quasiparticle tunneling. Our transport measurements demonstrate that quasiparticle poisoning is suppressed in all our TiAlTi structures (higher gap for the island) with clear 2e periodicity observed, whereas full quasiparticle poisoning is observed in all AlTiAl devices (higher gap for the leads) with e periodicity.
Ferric Ion Complexes of a DOPA-Containing Adhesive Protein from Mytilus edulis (1996)

Iron(III) binding to the DOPA-containing Mytilus edulis adhesive protein (Mefp1) has been studied by spectrophotometric titrations, electron paramagnetic resonance (EPR), and resonance Raman spectroscopies. At pH 7.0, two different forms of the iron−protein complex exist: one purple (λmax = 548 nm) and one pink (λmax = 500 nm). The pink form is favored at high DOPA:Fe ratios and the purple at low DOPA:Fe ratios. Resonance Raman spectroscopy of both forms demonstrates that the chromophores are ferric catecholate complexes. EPR spectra of both forms of the protein measured at the same iron concentration reveal a g ≈ 4.3 resonance of approximately 4 times the intensity in the spectrum of the pink complex compared with that of the purple form. On the basis of the collective evidence obtained here, a model for the purple form of the ferric Mefp1 involving bis(catecholato) coordination of ferric ions with most of the iron(III) complexed as EPR-silent μ-oxo- or μ-hydroxo-bridged binuclear clusters is suggested. In the pink form, in contrast, the ferric iron is EPR-active, mononuclear, and present in high-spin tris(catecholato) complexes. The biological implications of these complexes are discussed.
The Efficiency of Light-Directed Synthesis of DNA Arrays on Glass Substrates (1997)

New methods based on photolithography and surface fluorescence were used to determine photodeprotection rates and stepwise yields for light-directed oligonucleotide synthesis using photolabile 5‘-(((α-methyl-2-nitropiperonyl)oxy)carbonyl)(MeNPOC)-2‘-deoxynucleoside phosphoramidites on planar glass substrates. Under near-UV illumination (primarily 365 nm) from a mercury light source, the rate of photoremoval of the MeNPOC protecting group was found to be independent of both the nucleotide and length of the growing oligomer (t1/2 = 12 s at 27.5 mW/cm2). A moderate dependence on solvent polarity was observed, with photolysis proceeding most rapidly in the presence of nonpolar solvents or in the absence of solvent (e.g., t1/2 = 10−13 s at 27.5 mW/cm2). In solution, the photolysis rate was linearly dependent on light intensity over the range 5−50 mW/cm2. Average stepwise yields for the synthesis of dodecamer oligonucleotides were in the range of 92−94%, using monomers based on N6-(phenoxyacetyl)-2‘-deoxyadenosine, N2-isobutyryl-2‘-deoxyguanosine, N4-isobutyryl-2‘-deoxycytidine, and thymidine. By comparison, an efficiency of 98%/step was obtained using a conventional 5‘-dimethoxytrityl monomer with acid deprotection on the same support. The lower yields associated with the photochemical process appears to be due to incomplete recovery of free 5‘-hydroxyl groups after photolysis on the support, although high yields of 5‘-OH nucleosides (≥96%) are consistently observed when 5‘-MeNPOC monomers are photolyzed in solution.
Differences and Similarities in DNA-Binding Preferences of MyoD and E2A Protein Complexes Revealed by Binding Site Selection (1990)

A technique was developed for studying protein-DNA recognition that can be applied to any purified protein, partially purified protein, or cloned gene. From oligonucleotides in which particular positions are of random sequence, that subset to which a given protein binds is amplified by the polymerase chain reaction and sequenced as a pool. These selected and amplified binding site (SAAB) "imprints" provide a characteristic set of preferred sequences for protein binding. With this technique, it was shown that homo- and heterooligomers of the helix-loop-helix proteins MyoD and E2A recognize a common consensus sequence, CA--TG, but otherwise bind to flanking and internal positions with different sequence preferences that suggest half-site recognition. These findings suggest that different combinations of dimeric proteins can have different binding sequence preferences.
Repeated primed in situ labeling: formation and labeling of specific DNA sequences in chromosomes and nuclei (1993)

A new version of our previously published PRINS (PRimed IN Situ labeling) method is presented. It represents a significant improvement in the detection of specific DNA sequences in situ. The idea is to perform the reaction repeatedly, rather than just once. This change of strategy results in a localized accumulation of sequence-specific labeled DNA, resulting in up to a 15-fold amplification of the signal as compared to the standard PRINS method. Interestingly, the retention of the labeled DNA is so good that it stays within the chromosomal band where it is synthesized, provided that the reaction is not performed an excessive number of times. The key trick is the performance of the procedure on small glass slides in PCR tubes, thereby avoiding the use of cover slips. In addition, use of the small glass slides seems to give less variance when the signals are quantified in a fluorescence microscope.
Delineation of mRNA Export Pathways by the Use of Cell-Permeable Peptides (2001)

The transport of messenger RNAs (mRNAs) from the nucleus to the cytoplasm involves adapter proteins that bind the mRNA as well as receptor proteins that interact with the nuclear pore complex. We demonstrate the utility of cell-permeable peptides designed to interfere with interactions between potential adapter and receptor proteins to define the pathways accessed by particular mRNAs. We show that HuR, a protein implicated in the stabilization of short-lived mRNAs containing AU-rich elements (AREs), serves as an adapter for c-fos mRNA export through two pathways. One involves the HuR shuttling domain, HNS, which exhibits a heat shock-sensitive interaction with transportin 2 (Trn2); the other involves two protein ligands of HuR-pp32 and APRIL-which contain leucine-rich nuclear export signals (NES) recognized by the export receptor CRM1. Heterokaryon and in situ hybridization experiments reveal that the peptides selectively block the nucleocytoplasmic shuttling of their respective adapter proteins without perturbing the overall cellular distribution of polyadenylated mRNAs.
Lymphocyte proliferation modulated by glutamine: involved in the endogenous redox reaction (1999)

Decreased glutamine concentrations are found during catabolic stress and are related to susceptibility to infections. However, little is known about the mechanism of glutamine modulation of lymphocyte functions. Glutamine is not only an important energy source in mitochondria, but is also a precursor of glutamate, which is used for cellular glutathione (GSH) biosynthesis in lymphocytes. In this study, we investigated the effects of glutamine on the redox reaction during lymphocyte proliferation. Peripheral blood mononuclear cells, obtained from healthy adult volunteers, were cultured and stimulated by phytohaemagglutinin (PHA) in the presence of different glutamine concentrations. Cells were harvested and prepared for analysis of lymphocyte proliferation, cell cycle propagation, intracellular glutathione levels and reactive oxygen species (ROS) production. We found that glutamine supplementation significantly enhanced PHA-stimulated lymphocyte proliferation and propagation of the cell cycle from the G1 to S and G2/M phases. Glutamine also enhanced production of both intracellular ROS and GSH levels in PHA-stimulated lymphocytes. Flow cytometric analysis by the mercury orange staining method showed that glutamine significantly enhanced intracellular non-protein thiols in PHA-stimulated CD4+, but not CD8+ lymphocyte subsets. Furthermore, intracellular GSH detected by monochlorobimane dye probe showed that glutamine enhanced GSH both in PHA-stimulated CD4+ and CD8+ lymphocyte subsets. Inadequate glutamine supplementation resulted in decreased lymphocyte proliferation in association with decreased levels of intracellular GSH. Addition of exogenous GSH significantly enhanced lymphocyte proliferation, whereas blockade of GSH synthesis enhanced ROS production and suppressed lymphocyte proliferation. These results suggest that the modulation of PHA-stimulated lymphocyte proliferation by glutamine is closely related to the maintenance of appropriate intracellular redox status.
Optimization of Anti-Rh D Immunoglobulin Stability in the Lyophilization Processes (2008)

Objective
Anti-Rh D IgG is used for the prevention of anti-D antibody production in Rh- individuals who have been exposed to Rh+ red blood cells. The stability of IgG preparations as a solution is low, with a shelf life of a year or more. Formulation of anti-Rh D IgG as a lyophilized preparation would decrease its degradation rate and increases its shelf life. The objective of this study was to formulate the anti-Rh D as a lyophilized preparation using different formulations and optimize the lyophilization processes.
Materials and Methods
The effect of various formulations on the stability of anti-Rh D was evaluated using accelerated stability test.  In this method the amount of transmittance (T %) at 585 nm for the lyophilized preparations had inverse relationship with aggregation of anti-Rh D. To improve stability, the most stable formulation was selected and different concentrations of sucrose in the presence of sodium-potassium phosphate buffer 25 mM pH 7.5. Then, the bioactivity was determined, using the ELAT test and also, the amount of moisture measured in this formulation.
Results
Among different formulations, the one with anti-Rh D 5 mg/ml, tween 80 0.1%, glycine 0.15 M, manitol 7% and sucrose 60 mM in sodium-potassium phosphate buffer 25 mM pH 7.5 was the most stable formulation (P<0.05). The result of biological test of ELAT showed that bioactivity of more than 93% meets the requirement set by British Pharmacopoeia. The amount of moisture measured in this formulation was less than 3%.   
Conclusion
It was concluded that this formulation could be introduced as a candidate for the formulation of anti-Rh D in a lyophilized dosage form.
加固服务应用程序 为软件创建其使用的用户账号，并赋予它最低的权限 (2007)

也许作为系统管理员的您正在使用第三方软件作为Web、FTP、邮件服务器，如何加固这些服务应用程序，保证系统环境的安全一定是您比较关心的问题。本文作者从应用程序的安装、专用用户账号的建立和权限的分配等几个方面帮您出谋划策，并替您总结出一些较为通用的保障安全的步骤和措施。
Reduced electromigration of Cu wires by surface coating (2002)

Electromigration in on-chip Cu interconnections with a selective electroless metal coating, CoWP, CoSnP, or Pd, on the top surface of Cu damascene lines has been investigated. The 10–20 nm thick metal cap significantly improves electromigration lifetime by providing protection against interface diffusion of Cu which has been the leading contributor to metal line failure by electromigration.
Miniaturization of Mass Spectrometry Analysis Systems (2010)

The key concepts and technologies developed in our laboratories in Purdue University for the miniaturization of mass spectrometry analysis systems are introduced. Mass analyzers of simple geometries with a novel atmospheric pressure interface were employed allowed reduction in the size of the ion trap mass spectrometer. Ambient ionization methods were developed and coupled to miniature mass spectrometers to allow direct MS analysis of complex samples without sample preparation and chemical separation. The performance of desorption electrospray ionization, low temperature plasma probe, paper spray as well as two handheld MS systems, Mini 10 and Mini 11, are described with demonstrations of capabilities for chemical analysis.
Enhanced endothelial cytopathogenicity induced by a cytomegalovirus strain propagated in endothelial cells (1989)

Endothelial involvement has been implicated in cytomegalovirus (CMV) infection, a source of major complications in immunosuppressed individuals (e.g., those with acquired immune deficiency syndrome [AIDS] and organ transplants). Traditionally, CMV has been grown in fibroblasts; however, propagation in these cells may alter characteristics of the virus. In developing an in vitro model system of CMV/endothelial cell interaction, we have addressed this issue by propagating a clinical isolate, CMV VHL 1, in human umbilical vein endothelial (HUVE) cells by serial cocultivation of heavily infected cultures with fresh HUVE monolayers and have compared its infectious properties with those of the fibroblast-raised strain, CMV AD169. In situ hybridization using a biotinylated DNA probe, as well as immunofluorescent staining for CMV-specific antigen, has confirmed infection of HUVE cells inoculated with either strain of the virus. Infection of HUVE by VHL was accompanied by dramatic cytopathology not observed in AD169-infected cells. Plaque assay of culture supernatants revealed greater virus production in VHL-infected HUVE as compared with equivalently inoculated fibroblasts. In contrast, AD169 production in inoculated fibroblasts exceeded that in HUVE. These studies demonstrate the suitability of cultured endothelial cells as a substrate for CMV propagation and suggest that a strain of virus thus propagated may offer an accurate model of CMV/endothelial cell interaction in human disease.
Increased surface expression of a newly identified 150-kDa dimer early after human T lymphocyte activation (1992)

Lymphocyte activation induces or increases the expression of several surface structures, some of which are directly involved in cell growth such as receptors for IL-2 or transferrin. In order to identify new structures characteristic of activated lymphocytes, we developed a series of mAb against functionally defined human T cell clones. In the present study we report the isolation of a mAb termed BB18 recognizing, at the cell surface, a novel 150-kDa glycoprotein dimer whose expression on T lymphocytes increases readily after their activation with various stimuli including lectins. In contrast, in the presence of PMA, cell-surface expression of this 150-kDa structure is down-regulated even earlier than CD3 molecules. Biochemical studies as well as phenotypic analysis revealed that this structure is different from all previously identified molecules on the lymphocyte cell surface. Furthermore, functional studies showed that triggering this disulfide-linked dimer through BB18 epitope in the presence of submitogenic concentrations of PMA induced strong lymphocyte proliferation. This proliferative response require E+ cells and accessory cells, and this even after immobilization of BB18 mAb.
Sonochemical Synthesis of Trigonal Selenium Nanowires (2003)

This paper describes a solution-based method for the large-scale synthesis of selenium nanowires. Sonication was used as the driving force for both nucleation and dispersion. The trigonal Se seeds were formed during sonication and grew over the course of hours at the expense of the amorphous Se colloids in a process similar to Ostwald ripening. The resultant nanowires were typically single crystals of trigonal Se whose morphologies could be tuned by adjusting the reaction conditions. A variety of solvents are demonstrated for use with this process. We also demonstrate patterned growth of these nanowires on substrates to form extensive 2D networks and isolated clusters. The morphologies of the products were examined with a combination of microscopic and spectroscopic techniques.
Broad-band erbium-doped fiber amplifier flattened beyond 40 nm using long-period grating filter (1997)

Broad-bandwidth amplification is essential for the construction of high-capacity multichannel communication systems. We describe a silica-based erbium doped fiber amplifier (EDFA) with a flat gain bandwidth exceeding 40 nm. The dual-stage EDFA includes a precisely designed inter-stage long-period fiber grating filter with more than 14-dB peak attenuation. By careful choice of the filter spectrum and fiber lengths, this EDFA is flat to within 1 dB over 40 nm while producing a noise figure below 4.0 dB and nearly +15-dBm output power.
Cell positioning and sorting using dielectrophoresis. (2002)

INTRODUCTION: In this paper we describe a micro-fabricated cell separation and positioning system based on the AC electrokinetic technique, dielectrophoresis (DEP). The system uses nonuniform electric fields produced by arrays of microelectrodes to manipulate cells held in suspension. Depending upon the mode of operation one can either concentrate a single cell type from a heterogeneous mixture (with all other cell types passing through the device); or alternatively separate different cell types along the length of the device. In the second mode of operation the position at which a cell ends up is based on its size and the dielectric properties of its cellular membrane.
Msx1 controls inductive signaling in mammalian tooth morphogenesis (1996)

Members of the Msx homeobox family are thought to play important roles in inductive tissue interactions during vertebrate organogenesis, but their precise developmental function has been unclear. Mice deficient for Msx1 exhibit defects in craniofacial development and a failure of tooth morphogenesis, with an arrest in molar tooth development at the E13.5 bud stage. Because of its potential for experimental manipulation, the murine molar tooth germ provides a powerful system for studying the role of Msx genes in inductive signaling during organogenesis. To further analyze the role of Msx1 in regulating epithelial-mesenchymal interactions during tooth morphogenesis, we have examined the expression of several potential Msx1 downstream genes in Msx1 mutant tooth germs and we have performed functional experiments designed to order these genes into a pathway. Our results show that expression of Bone Morphogenetic Protein 4 (BMP4), the HMG box gene Lef1 and the heparan sulfate proteoglycan syndecan-1 is specifically reduced in Msx1 mutant dental mesenchyme, while expression of the extracellular matrix protein tenascin is unaffected. BMP4 soaked beads can induce Bmp4 and Lef1 expression in explanted wild-type dental mesenchymes, but only Lef1 expression in Msx1 mutant dental mesenchyme. We thus conclude that epithelial BMP4 induces its own expression in dental mesenchyme in a manner that requires Msx1. In turn, we show that addition of BMP4 to Msx1 deficient tooth germs bypasses the requirement for Msx1 and rescues epithelial development from the bud stage to the E14.5 cap stage. Lastly, we show that FGFs induce syndecan-1 expression in dental mesenchyme in a manner that also requires Msx-1. These results integrate Msx1 into a regulatory hierarchy in early tooth morphogenesis and demonstrate that Msx1 is not only expressed in dental mesenchyme in response to epithelial signals, but also in turn regulates the reciprocal expression of inductive signals in the mesenchyme which then act back upon the dental epithelium. We propose that Msx genes function repetitively during vertebrate organogenesis to permit inductive signaling to occur back and forth between tissue layers.
A Novel Mechanism for Regulating Transforming Growth Factor β (TGF-β) Signaling (2001)

Transforming growth factor beta (TGF-beta) mediates its biological effects through three high-affinity cell surface receptors, the TGF-beta type I, type II, and type III receptors, and the Smad family of transcription factors. Although the functions of the type II and type I receptors are well established, the precise role of the type III receptor in TGF-beta signaling remains to be established. While expression cloning signaling molecules downstream of TGF-beta, we cloned GIPC (GAIP-interacting protein, C terminus), a PDZ domain-containing protein. GIPC binds a Class I PDZ binding motif in the cytoplasmic domain of the type III receptor resulting in regulation of expression of the type III receptor at the cell surface. Increased expression of the type III receptor mediated by GIPC enhanced cellular responsiveness to TGF-beta both in terms of inhibition of proliferation and in plasminogen-activating inhibitor (PAI)-based promoter gene induction assays. In all cases, deletion of the Class I PDZ binding motif of the type III receptor prevented the type III receptor from binding to GIPC and abrogated the effects of GIPC on type III receptor expressing cells. These results establish, for the first time, a protein that interacts with the cytoplasmic domain of the type III receptor, determine that expression of the type III receptor is regulated at the protein level and that increased expression of the type III receptor is sufficient to enhance TGF-beta signaling. These results further support an essential, non-redundant role for the type III receptor in TGF-beta signaling.
Development of a disease activity score based on judgment in clinical practice by rheumatologists. (1993)

In a prospective study of up to 3 years' duration of 113 patients with early rheumatoid arthritis a disease activity score (DAS) was developed based on the clinical judgment of 6 rheumatologists. The patients were divided in groups with high and low disease activity according to explicit rules. By various statistical methods, including discriminant analysis and multiple regression analysis, a DAS could be defined. This DAS is a continuous measure consisting of the variables Ritchie articular index, number of swollen joints, erythrocyte sedimentation rate and general health measured on a visual analog scale.