gebhart/patrepeval huggingface dataset:
Use of the Phase Diagram Method to Analyze the Protein Unfolding-Refolding Reactions:  Fishing Out the “Invisible” Intermediates (2004)

Partially folded conformations are important players in protein self-organization, function, and misfolding, thus attracting the intensive and constant attention of researchers. Different conformational states of proteins can be easily discriminated from one another using the multiparametric approach, which usually involves the application of several physicochemical methods sensitive to the various structural levels of a protein molecule. This approach gives the most complete information about the structural changes in protein during its de- and renaturation. However, in many cases researches are interested in a brief and simple test for the appearance of an intermediate state. The binding of the hydrophobic fluorescent probe ANS represents one of the well-established techniques, allowing the retrieval of such information. We are introducing another approach, based on the analysis of the spectroscopic data in a form of spectral diagrams. The essence of this method is to build the Ilambda1, versus Ilambda2 dependence, where Ilambda1 and Ilambda2 are the spectral intensity values (e.g., fluorescence, CD, FTIR, absorbance, etc.) measured on wavelengths lambda1 and lambda2. We are showing that this approach gives the detailed description of the protein unfolding pathway, detects the numerous partially folded species, and even fishes out the hidden intermediates. An application of this method for the analysis of the equilibrium and kinetic unfolding/refolding of several proteins under the variety of conditions is described. Advantages and disadvantages of the technique suggested are also discussed.
β‐<i>Catenin</i> mutations in a mouse model of inflammation‐related colon carcinogenesis induced by 1,2‐dimethylhydrazine and dextran sodium sulfate (2005)

In a previous study, we developed a novel mouse model for colitis-related carcinogenesis, utilizing a single dose of azoxymethane (AOM) followed by dextran sodium sulfate (DSS) in drinking water. In the present study, we investigated whether colonic neoplasms can be developed in mice initiated with a single injection of another genotoxic colonic carcinogen 1,2-dimethylhydrazine (DMH), instead of AOM and followed by exposure of DSS in drinking water. Male crj: CD-1 (ICR) mice were given a single intraperitoneal administration (10, 20 or 40 mg/kg body weight) of DMH and 1-week oral exposure (2% in drinking water) of a non-genotoxic carcinogen, DSS. All animals were killed at week 20, histological alterations and immunohistochemical expression of beta-catenin, cyclooxygenase (COX-2) and inducible nitric oxide synthase (iNOS) were examined in induced colonic epithelial lesions (colonic dysplasias and neoplasms). Also, the beta-catenin gene mutations in paraffin-embedded colonic adenocarcinomas were analyzed by the single strand conformation polymorphism method, restriction enzyme fragment length polymorphism and direct sequencing. The incidences of colonic neoplasms with dysplastic lesions developed were 100% with 2.29+/-0.95 multiplicity, and 100% with 10.38+/-4.00 multiplicity in mice given DMH at doses of 10 mg/kg or 20 mg/kg and 2%DSS, respectively. Although approximately half of the mice given DMH at a dose of 40 mg/kg bodyweight were dead after 2-3 days after the injection, mice who received DMH 40 mg/kg and 2%DSS had 100% incidence of colonic neoplasms with 9.75+/-6.29 multiplicity. Immunohistochemical investigation revealed that adnocarcinomas, induced by DMH at all doses and 2%DSS, showed positive reactivities against beta-catenin, COX-2 and iNOS. In DMH/DSS-induced adenocarcinomas, 10 of 11 (90.9%) adenocacrcinomas had beta-catenin gene mutations. Half of the mutations were detected at codon 37 or 41, encoding serine and threonine that are direct targets for phosphorylation by glycogen synthase kinase-3beta. The present results suggests that, as in the previously reported model (AOM/DSS) our experimental protocol, DMH initiation followed by DSS, may provide a novel and useful mouse model for investigating inflammation-related colon carcinogenesis and for identifying xenobiotics with modifying effects.
Publishing in the Journal Literature of Library and Information Science: A Survey of Manuscript Review Processes and Acceptance (1996)

The journal literature of library and information science is important because it not only enhances the ability of librarians to do their work, but also provides a major part of the scholarly underpinnings, both theoretical and applied, for the field. Many academic librarians are expected to publish in the journal literature as part of their faculty responsibilities. There is keen interest on the part of academic librarians in assessing the quality of library and information science journals, the methods used to review unsolicited manuscripts, and the acceptance rates for those manuscripts. This article reports on a survey of library and information science journal editors. The survey results show that thirty-four of the sixty-eight journals covered by the survey utilize some form of blind review for unsolicited manuscripts. The proliferation of new journal titles in the field has meant that there are many more publishing outlets for potential authors. This survey shows that the acceptance rates reported in earlier studies in 1978 and 1988 have risen for a majority of the journals reported in this study.
The state of DNA methylation in the promoter and exon 1 regions of the human gene for the interleukin-2 receptor α chain (IL-2Rα) in various cell types (1993)

The gene for the human interleukin-2 receptor alpha chain (IL-2R alpha) is expressed only in stimulated, not in resting, human T lymphocytes. This gene, in conjunction with others, plays a pivotal role in eliciting the T cell-mediated immune response. We have investigated the promoter and exon 1 region, the nucleotide -300 to +300 region of this gene relative to the position of transcriptional initiation at nucleotide +1, particularly with respect to the extent of DNA methylation at the 5'-CG-3' sequences and its changes upon induction. By using RNA transfer analyses and the in vivo footprinting technique, we have confirmed the previously reported finding that, upon stimulation of lymphocytes by phytohemagglutinin (PHA) plus interleukin-2 (IL-2), the IL-2R alpha gene can be induced to be transcribed. The region of the IL-2R alpha gene analyzed for 5'-CG-3' methylation by the genomic sequencing method or a polymerase chain reaction-based method subsequent to HpaII or HhaI cleavage of the DNA does not seem to be significantly methylated in most cell types tested, except for the cytidine residue in position +198 which is partly methylated. In the DNA of cells from a chronic B cell lymphatic leukemia 5'-CCGG-3' sequences in the exon 1 region are almost completely unmethylated. These results suggest that the promoter of a gene that is crucial in promoting the immune response and may have to be activated momentarily, will not be silenced by a long-term mechanism like DNA methylation. It is striking that the absence of DNA methylation in this promoter and exon 1 segment also extends to cell types not directly associated with the immune response and even to continuous cell lines.
Based on the analysis of mobile terminal application software performance test (2017)

With the rapid development of mobile terminal, mobile applications are gradually penetrated into all aspects of people's life and work. Mobile games, mobile streaming media, location services, mobile Internet news, instant messaging, mobile music and other rich and colorful information era are changing the social life. In view of this, we propose the application software performance test based on the mobile terminal, and analyze the performance test technology and method of the mobile application. Experimental results show that the performance test of the application system can predict the pressure in real environment, the system will be applied in the problems exposed, through the analysis of the data of the test, it will provide help for performance optimization of application system.
LUMBAR CSF 5- HYDROXYINDOLEACETIC ACID AND HOMOVANILLIC ACID IN AFFECTIVE SYNDROMES (1974)

Lumbar cercbrospinal fluid (CSF) 5-hydroxyindoleacetic acid (5-HIAA) and homovanillic acid (HVA) have been measured following probenccid administration in psychiatric patients. Values obtained probably reflect composite rates of formation of these acid monoamine metabolites at various sites within the central nervous system. Both absolute values for 5-HIAA and HVA and the 5-HIAA to HVA ratio are helpful in the interpretation of results. There seems to be an increase in the absolute level of baseline or probenecid-induced concentrations of these metabolites in older subjects which may be due to an increase in monoamine oxidasc activity with age.In a group of unipolar depressives (no history of mania) prctreatment values for CSF 5-HIAA were not different from controls while CSF HVA was increased leading to a somewhat decreased 5-HIAA to HVA ratio.Treatment with amitryptyline led to significant reductions in 5-HIAA and the 5-HIAA to HVA ratio.In a group of bipolar patients (history of mania) pretrcatment values for both metabolites were decreased compared to controls. The values for the 5-HIAA to HVA ratio were somewhat elevated.In a group of atypical depressives treated with phenclzinc, CSF 5-HIAA and HVA values were consistent with the presence of central monoamine oxidase inhibition.
Radiation properties of microstrip array antennas fed by radial line (1993)

Abstract This paper proposes a new type of radial line microstrip antenna and studies both the design method and radiation characteristics. The following conclusions are obtained. (1) The relationship between the basic design parameters of this new type of planar antenna and the radiation characteristics was demonstrated, and the essential design data of this type of antenna were obtained. (2) A boresight antenna was fabricated based on the design data obtained in the foregoing, and it was shown clearly that such a type of antenna system offers an aperture efficiency of above 90 percent, ranging from the small‐aperture (low‐gain) type to the large‐aperture (high‐gain) type. (3) A beam‐tilt type antenna also was studied theoretically as well as experimentally, and the relationship of its radiation characteristics with the tilt angle and aperture efficiency was explained. It was demonstrated that such an antenna system may be considered to be effectively applicable as a high‐efficiency circularly polarized planar antenna.
Some conditions under which hierarchical verification is O(N) (2003)

Before manufacturing, each chip design must be inspected for possible errors. For example, design rule checking is used to check for adherence to the physical manufacturing rules, and static timing analysis is used to verify that the design has adequate performance. Although modern chip designs are invariably specified hierarchically, verification algorithms can treat this hierarchy in different ways. The most straightforward way to verify a hierarchical design is to expand (or flatten) the hierarchy, then do the test. Since most verification algorithms involve at least sorting the data, such algorithms are at least O(N log N), where N is the size of the flattened hierarchy. Alternatively, a verification tool can try to use the hierarchy rather than flattening it. One form of hierarchical verification involves verifying each cell, generating a model (also called an abstract) for each cell, and then checking all interactions between cells by using their abstracts. Under some conditions, this may be more efficient than flattening the hierarchy and then verifying. In particular, if the size of the abstract is O(n/sup a/) for a cell containing n primitives, and the time to verify a cell and generate the abstract is O(n/sup b/), then the complete verification of all levels of the hierarchy is O(N), provided ab<1.
An introduction to the properties of carbon nano-particle enhanced polymers. (2010)

This data sheet introduces and quantifies the enhancement obtained in electrical properties from nano-particle modification of polymers, for both thermoset (epoxy) and thermoplastic (polypropylene and PEEK). The nano-particles considered are nanoscale carbon-based fillers considered are single walled carbon nanotubes (SWNTs), multiwalled carbon nanotubes (MWNTs) and carbon black (CB).
Influence of Salts on the Covalent Immobilization of Proteins to Modified Copolymers of 2‐Hydroxyethyl Methacrylate with Ethylene Dimethacrylate (1988)

In the study of the covalent immobilization of aminoacylase, thermitase, pepsin, trypsin, chymotrypsin, elastase, subtilisin, penicillinamidohydrolase, carboxypeptidase A, cystathionine-beta-synthase, and anticathepsin D-IgG to copolymers of 2-hydroxyethyl methacrylate and ethylene dimethacrylate (Separon HEMA) containing epoxy groups a marked influence of added salts on the immobilization efficiency was observed. Yields in covalently bound active enzymes were dependent on the concentrations and type of ions added, which can be arranged according to the Hofmeister series. At a distinct concentration, the salting-out ions cause a protein-matrix hydrophobic interaction which is a prerequisite for the covalent bond formation.
Using a Hypervisor to Migrate Running Operating Systems to Secure Virtual Machines (2010)

We propose HyperShield, which is a hypervisor that can be inserted into and removed from a running operating system, for improving security. While many existing security-oriented hypervisors require modifying or rebooting an overlying operating system, HyperShield does not require this. HyperShield is intended to be a general framework for various security mechanisms. The current implementation provides two mechanisms for preventing kernel-level buffer overflow. One detects the execution of user code with the kernel privilege, and the other detects malicious modification of a return address in a control stack. HyperShield is implemented on Linux as a loadable kernel module. When the module is inserted, it places itself under the operating system and executes as a hypervisor. The operating system is migrated into a virtual machine and managed by the hypervisor. HyperShield detects attacks by combining virtualization of memory management with a hardware-assisted execution-bit feature. We have confirmed through experiments that HyperShield successfully prevented kernel-level buffer overflow attacks.
T Lymphocyte Transduction with Herpes Simplex VirusThymidine Kinase (HSV-tk) Gene: Comparison of Four Different Infection Protocols (1999)

In this study, we assessed the efficiency of T lymphocyte transduction with a retroviral vector carrying the herpes simplex virus thymidine kinase (HSV-tk) and neomycin phosphotransferase (neo) genes by four different protocols: standard supernatant infection, supernatant infection plus centrifugation steps, supernatant infection on fibronectin fragment-coated wells, and cocultivation. After retrovirus-mediated gene transfer of tk-neo in PHA/IL-2-stimulated primary T lymphocytes and G418 selection, T cells retained their proliferative activity, alloresponsiveness, ability to produce and to respond to IL-2, and ganciclovir (gcv)-specific sensitivity. When the four different transduction techniques were compared, no significant differences were seen in terms of cellular viability, proliferation capacity, and immunophenotyping. tk gene expression was the same in all transduced selected populations, as indicated by gcv sensitivity. Transduction efficiency was evaluated by semiquantitative PCR. Using the standard supernatant infection method, the rate of infection was extremely low (<5%). After adding the centrifugation step or performing supernatant infection on fibronectin fragment-coated wells, PCR analysis showed a 30%-40% rate of transduced cells. After infection by cocultivation, the rate of transduced cells was 30%-40%. These results demonstrate that supernatant infection plus centrifugation, supernatant infection on fibronectin fragment-coated wells, and cocultivation methods provide equivalent rates of transduced cells. The lack of reproducibility and safety indicates that cocultivation is not suitable for clinical studies. In our view, supernatant infection plus centrifugation is easier to perform than using fibronectin fragments, and it is currently the optimal method for clinical studies when large quantities of T lymphocytes are being processed.
Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D):  Evaluation of Performance (2004)

A molecular similarity searching technique based on atom environments, information-gain-based feature selection, and the naive Bayesian classifier has been applied to a series of diverse datasets and its performance compared to those of alternative searching methods. Atom environments are count vectors of heavy atoms present at a topological distance from each heavy atom of a molecular structure. In this application, using a recently published dataset of more than 100000 molecules from the MDL Drug Data Report database, the atom environment approach appears to outperform fusion of ranking scores as well as binary kernel discrimination, which are both used in combination with Unity fingerprints. Overall retrieval rates among the top 5% of the sorted library are nearly 10% better (more than 14% better in relative numbers) than those of the second best method, Unity fingerprints and binary kernel discrimination. In 10 out of 11 sets of active compounds the combination of atom environments and the naive Bayesian classifier appears to be the superior method, while in the remaining dataset, data fusion and binary kernel discrimination in combination with Unity fingerprints is the method of choice. Binary kernel discrimination in combination with Unity fingerprints generally comes second in performance overall. The difference in performance can largely be attributed to the different molecular descriptors used. Atom environments outperform Unity fingerprints by a large margin if the combination of these descriptors with the Tanimoto coefficient is compared. The naive Bayesian classifier in combination with information-gain-based feature selection and selection of a sensible number of features performs about as well as binary kernel discrimination in experiments where these classification methods are compared. When used on a monoaminooxidase dataset, atom environments and the naive Bayesian classifier perform as well as binary kernel discrimination in the case of a 50/50 split of training and test compounds. In the case of sparse training data, binary kernel discrimination is found to be superior on this particular dataset. On a third dataset, the atom environment descriptor shows higher retrieval rates than other 2D fingerprints tested here when used in combination with the Tanimoto similarity coefficient. Feature selection is shown to be a crucial step in determining the performance of the algorithm. The representation of molecules by atom environments is found to be more effective than Unity fingerprints for the type of biological receptor similarity calculations examined here. Combining information prior to scoring and including information about inactive compounds, as in the Bayesian classifier and binary kernel discrimination, is found to be superior to posterior data fusion (in the datasets tested here).
Physical simulation for monocular 3D model based tracking (2011)

The problem of model-based object tracking in three dimensions is addressed. Most previous work on tracking assumes simple motion models, and consequently tracking typically fails in a variety of situations. Our insight is that incorporating physics models of object behaviour improves tracking performance in these cases. In particular it allows us to handle tracking in the face of rigid body interactions where there is also occlusion and fast object motion. We show how to incorporate rigid body physics simulation into a particle filter. We present two methods for this based on pose and force noise. The improvements are tested on four videos of a robot pushing an object, and results indicate that our approach performs considerably better than a plain particle filter tracker, with the force noise method producing the best results over the range of test videos.
Polyubiquitin Binding to Optineurin Is Required for Optimal Activation of TANK-binding Kinase 1 and Production of Interferon β (2011)

TANK-binding kinase (TBK1) is essential for transcription of the interferon (IFN) β gene in response to lipopolysaccharide (LPS) and double-stranded RNA, but the molecular mechanisms that underlie the activation of TBK1 are incompletely understood. Previously, we identified the NF-κB essential modulator (NEMO)-related polyubiquitin-binding protein, optineurin (OPTN), as a novel binding partner of TBK1. To determine whether the ubiquitin-binding function of OPTN is involved in regulating TBK1 and IFNβ production, we generated a mouse in which wild-type optineurin was replaced by the polyubiquitin binding-defective mutant, OPTN(D477N/D477N). In this study, we found that LPS or poly(I:C)-induced TBK1 activity was significantly reduced in bone marrow-derived macrophage (BMDM) from OPTN(D477N/D477N) mice. Consistent with this, the phosphorylation of IFN regulatory factor 3 (IRF3) and the production of IFNβ mRNA and secretion were reduced. Stimulation of BMDMs with LPS triggered the phosphorylation of OPTN, which was reversed by phosphatase treatment and prevented by pharmacological inhibition of both the canonical IκB kinases (IKKα/β) and the IKK-related kinases (TBK1/IKKε). In contrast, LPS-stimulated phosphorylation of OPTN(D477N) was markedly reduced in BMDMs from OPTN(D477N/D477N) mice, and inhibition of the canonical IKKs alone prevented phosphorylation, providing further evidence that ubiquitin binding to OPTN contributes to LPS-induced TBK1 activation. TBK1 and IKKβ phosphorylated OPTN preferentially at Ser-177 and Ser-513, respectively, in vitro. In conclusion, our results suggest that OPTN binds to polyubiquitylated species formed in response to LPS and poly(I:C), enhancing the activation of TBK1 that is required for optimal phosphorylation of IRF3 and production of IFNβ.
A Convenient Synthesis of 3,3-Dimethylcyclohexanone (1981)

Abstract An interest in the boll weevil sex attractants1 prompted an investigation into alternative syntheses of the starting material, 3,3-dimethylcyclohexanone (1). Despite its relatively simple structure, the available synthetic approaches to this comnound are often indirect and usually involve expensive or exotic reagents and starting materials. For example, 3,3-dimethyl-cyclohexanone (1) may be obtained from conjugate addition of lithium dimethylcuprate,2 methylmagnesium iodide,3 or trimethyl-aluminum4 to 3-methyl-2-cyclohexen-l-one. Similarly, reaction of lithium dimethylcuprate with 3-t-butylthio-2-cyclohexen-l-one also yields ketone 1.5 Other preparations have involved hydrogenations of 5,5-dimethyl-2-cyclohexen-l-one6 and 5,5-dimethyl-3-chloro-2-cyclohexen-l-one7 and pyrolysis of β,β-dimethylpimelic anhydride.8 Ketone 1 was also obtained, albeit as a minor product, in the dichlorotris (triphenylphosphine) ruthenium catalyzed transfer hydrogenation of 5,5-dimethyl-l,3-cyclohexanedione.9