gebhart/patrepeval huggingface dataset:
Dominant negative mutants of transforming growth factor-beta 1 inhibit the secretion of different transforming growth factor-beta isoforms. (1992)

Transforming growth factor-beta (TGF-beta) is a secreted polypeptide factor that is thought to play a major role in the regulation of proliferation of many cell types and various differentiation processes. Several related isoforms have been structurally characterized, three of which, TGF-beta 1, -beta 2, and -beta 3, have been detected in mammalian cells and tissues. Each TGF-beta form is a homodimer of a 112-amino-acid polypeptide which is encoded as a larger polypeptide precursor. We have introduced several mutations in the TGF-beta 1 precursor domain, resulting in an inhibition of TGF-beta 1 secretion. Coexpression of these mutants with wild-type TGF-beta 1, -beta 2, and -beta 3 results in a competitive and specific inhibition of the secretion of different TFG-beta forms, indicating that these mutated versions act as dominant negative mutants for TGF-beta secretion. Overexpression of dominant negative mutants can thus be used to abolish endogenous secretion of TGF-beta and structurally related family members, both in vitro and in vivo, and to probe in this way the physiological functions of the members of the TGF-beta superfamily.
RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets (2014)

High-throughput RNA sequencing (RNA-seq) has become an instrumental assay for the analysis of multiple aspects of an organism's transcriptome. Further, the analysis of a biological specimen's associated microbiome can also be performed using RNA-seq data and this application is gaining interest in the scientific community. There are many existing bioinformatics tools designed for analysis and visualization of transcriptome data. Despite the availability of an array of next generation sequencing (NGS) analysis tools, the analysis of RNA-seq data sets poses a challenge for many biomedical researchers who are not familiar with command-line tools. Here we present RNA CoMPASS, a comprehensive RNA-seq analysis pipeline for the simultaneous analysis of transcriptomes and metatranscriptomes from diverse biological specimens. RNA CoMPASS leverages existing tools and parallel computing technology to facilitate the analysis of even very large datasets. RNA CoMPASS has a web-based graphical user interface with intrinsic queuing to control a distributed computational pipeline. RNA CoMPASS was evaluated by analyzing RNA-seq data sets from 45 B-cell samples. Twenty-two of these samples were derived from lymphoblastoid cell lines (LCLs) generated by the infection of naïve B-cells with the Epstein Barr virus (EBV), while another 23 samples were derived from Burkitt's lymphomas (BL), some of which arose in part through infection with EBV. Appropriately, RNA CoMPASS identified EBV in all LCLs and in a fraction of the BLs. Cluster analysis of the human transcriptome component of the RNA CoMPASS output clearly separated the BLs (which have a germinal center-like phenotype) from the LCLs (which have a blast-like phenotype) with evidence of activated MYC signaling and lower interferon and NF-kB signaling in the BLs. Together, this analysis illustrates the utility of RNA CoMPASS in the simultaneous analysis of transcriptome and metatranscriptome data. RNA CoMPASS is freely available at http://rnacompass.sourceforge.net/.
Double-stranded RNA induces sickle erythrocyte adherence to endothelium: a potential role for viral infection in vaso-occlusive pain episodes in sickle cell anemia (1995)

Vaso-occlusive pain episodes in sickle cell anemia are hypothesized to be precipitated by adherence of sickle erythrocytes to vascular endothelium in the microcirculation. Febrile episodes, thought to be viral in etiology, are frequently associated with vaso-occlusion; however, a direct link between viral infection and vascular occlusion has not yet been established. Many pathogenic viruses contain double-stranded RNA or replicate through double-stranded RNA intermediates. Double-stranded RNA has been shown to induce vascular cell adhesion molecule-1 (VCAM-1) protein expression on endothelial cells. Recently, a new adhesion pathway has been described between VCAM-1 expressed on cytokine stimulated endothelium and the alpha 4 beta 1 integrin complex expressed on sickle reticulocytes. Based on these observations, the hypothesis was developed that viral infection, through double-stranded RNA intermediates, increases endothelial VCAM-1 expression leading to sickle erythrocyte adhesion to endothelium via an alpha 4 beta 1-VCAM-1--dependent mechanism. In support of this hypothesis, endothelial cells exposed to the synthetic double-stranded RNA poly(I:C) or the RNA virus parainfluenza 1 (Sendai virus) express increased levels of VCAM-1 and support increased sickle erythrocyte adherence under continuous flow at 1.0 dyne/cm2 shear stress as compared with unstimulated endothelium. Blocking antibodies directed against either VCAM-1 on the endothelium or alpha 4 beta 1 on sickle erythrocytes inhibit nearly all of the increased sickle cell adherence caused by poly(I:C) or Sendai virus. These results support the hypothesis that viruses, through double-stranded RNA elements, can induce sickle erythrocyte adherence to endothelium through alpha 4 beta 1-VCAM-1--mediated adhesion and provide a potential link between viral infection and microvascular occlusion precipitating sickle cell pain episodes.
Eradication of Hepatitis C Virus Infection and the Development of Hepatocellular Carcinoma (2013)

Sustained virologic response after treatment among HCV-infected persons at any stage of fibrosis is associated with reduced HCC. The evidence was determined to be of moderate quality.
MR imaging of intravoxel incoherent motions: application to diffusion and perfusion in neurologic disorders. (1986)

Molecular diffusion and microcirculation in the capillary network result in a distribution of phases in a single voxel in the presence of magnetic field gradients. This distribution produces a spin-echo attenuation. The authors have developed a magnetic resonance (MR) method to image such intravoxel incoherent motions (IVIMs) by using appropriate gradient pulses. Images were generated at 0.5 T in a high-resolution, multisection mode. Diffusion coefficients measured on images of water and acetone phantoms were consistent with published values. Images obtained in the neurologic area from healthy subjects and patients were analyzed in terms of an apparent diffusion coefficient (ADC) incorporating the effect of all IVIMs. Differences were found between various normal and pathologic tissues. The ADC of in vivo water differed from the diffusion coefficient of pure water. Results were assessed in relation to water compartmentation in biologic tissues (restricted diffusion) and tissue perfusion. Nonuniform slow flow of cerebrospinal fluid appeared as a useful feature on IVIM images. Observation of these motions may significantly extend the diagnostic capabilities of MR imaging.
Assembly of Metal−Organic Frameworks from Large Organic and Inorganic Secondary Building Units:  New Examples and Simplifying Principles for Complex Structures (2001)

The secondary building unit (SBU) has been identified as a useful tool in the analysis of complex metal-organic frameworks (MOFs). We illustrate its applicability to rationalizing MOF crystal structures by analysis of nine new MOFs which have been characterized by single-crystal X-ray diffraction. Tetrahedral SBUs in Zn(ADC)(2).(HTEA)(2) (MOF-31), Cd(ATC).[Cd(H(2)O)(6)](H2O)(5) (MOF-32), and Zn(2)(ATB)(H2O).(H2O)(3)(DMF)(3) (MOF-33) are linked into diamond networks, while those of Ni(2)(ATC)(H(2)O)(4).(H2O)(4) (MOF-34) have the structure of the Al network in SrAl(2). Frameworks constructed from less symmetric tetrahedral SBUs have the Ga network of CaGa(2)O(4) as illustrated by Zn(2)(ATC).(C(2)H(5)OH)(2)(H2O)(2) (MOF-35) structure. Squares and tetrahedral SBUs in Zn(2)(MTB)(H2O)(2).(DMF)(6)(H2O)(5) (MOF-36) are linked into the PtS network, which is the simplest structure type known for the assembly of these shapes. The octahedral SBUs found in Zn(2)(NDC)(3).[(HTEA)(DEF)(ClBz)](2) (MOF-37) form the most common structure for linking octahedral shapes, namely, the boron network in CaB(6). New structure types for linking triangular and trigonal prismatic SBUs are found in Zn(3)O(BTC)(2).(HTEA)(2) (MOF-38) and Zn(3)O(HBTB)(2)(H2O).(DMF)(0.5)(H2O)(3) (MOF-39). The synthesis, crystal structure, and structure analysis using the SBU approach are presented for each MOF.
Multicolor Far-Field Fluorescence Nanoscopy through Isolated Detection of Distinct Molecular Species (2008)

By combining the photoswitching and localization of individual fluorophores with spectroscopy on the single molecule level, we demonstrate simultaneous multicolor imaging with low crosstalk and down to 15 nm spatial resolution using only two detection color channels. The applicability of the method to biological specimens is demonstrated on mammalian cells. The combination of far-field fluorescence nanoscopy with the recording of a single switchable molecular species at a time opens up a new class of functional imaging techniques.
Autofluorescence characteristics of healthy oral mucosa at different anatomical sites (2003)

No relevant systematic spectral differences have been observed between most locations, allowing the use of one large reference database. For DST and VB separate databases are required.
Chemical Properties of Water-soluble Porphyrins. 5. Reactions of Some Manganese (III) Porphyrins with the Superoxide and Other Reducing Radicals (1986)

Solution properties of three manganese porphyrins, in monomeric form, were investigated. These were the 'picket-fence-like' porphyrin Mn(III)-alpha,alpha,alpha,beta- tetra-ortho(N-methylisonicotinamidophenyl)porphyrin (Mn(III)PFP) and two 'planar unhindered' porphyrins, the Mn(III)TMPyP (tetrakis (4-N-methylpyridyl)porphyrin) and Mn(III)TAP (tetra(4-N,N,N-trimethylanilinium)porphyrin). The porphyrin properties studied were: the absorption spectra in their manganic and manganous forms; acid/base properties of the aquo complexes; the effect of potential axial ligands (up to a concentration of 0.1 mol dm-3) and their one electron reduction potentials. Knowing these properties, the reaction of the Mn(III) porphyrins with the superoxide radical and other reducing radicals were studied using the pulse radiolysis technique. The second-order reaction rate constant of O2- with the Mn(III) porphyrins, which governs the catalytic efficiency of the metalloporphyrins upon the disproportionation of the superoxide radical, was 5.1 X 10(7) to 4.0 X 10(5) dm3 mol-1 s-1, depending on the pH and the nature of the metalloporphyrin. These values are at least one order of magnitude lower than found for Fe(III)TMPyP. One electron reduction of the three Mn(III) porphyrins by eaq-, CO2-, CH2OH and (CH3)2COH had similar second-order rate constants (10(9)-10(10) dm3 mol-1 s-1). That for (CH3)2(CH2)COH was about 10(5) dm3 mol-1 s-1. Reduction in all cases produced the corresponding Mn(II) porphyrin and no intermediate was found. The oxidation reaction of the Mn(II) porphyrins by O2- was approximately two orders of magnitude faster when compared to the reduction of Mn(III) porphyrins with the same radical. Since the reactivities of O2- towards the three manganese (III) compounds follow their reduction potentials, it is suggested that these reactions are governed by an outer-sphere mechanism. This suggestion is corroborated by the finding that water molecules acting as axial ligands, in these aqueous solution systems, are not replaced by another potential ligand when the latter is in the concentration range of 100 mM or less.
Polyoxazoline: Chemistry, Properties, and Applications in Drug Delivery (2011)

Polyoxazoline polymers with methyl (PMOZ), ethyl (PEOZ), and propyl (PPOZ) side chains were prepared by the living cationic polymerization method and purified by ion-exchange chromatography. The following properties of polyoxazoline (POZ) were measured: apparent hydrodynamic radius by aqueous size-exclusion chromatography, relative lipophilicity by reverse-phase chromatography, and viscosity by cone-plate viscometry. The PEOZ polymers of different molecular weights were first functionalized and then conjugated to model biomolecules such as bovine serum albumin, catalase, ribonuclease, uricase, and insulin. The conjugates of catalase, uricase, and ribonuclease were tested for in vitro activity using substrate-specific reaction methods. The conjugates of insulin were tested for glucose lowering activity by injection to naïve Sprague-Dawley rats. The conjugates of BSA were injected into New Zealand white rabbits and serum samples were collected periodically and tested for antibodies to BSA. The safety of POZ was also determined by acute and chronic dosing to rats. The results showed that linear polymers of POZ with molecular weights of 1 to 40 kDa can easily be made with polydispersity values below 1.10. Chromatography results showed that PMOZ and PEOZ have a hydrodynamic volume slightly lower than PEG; PEOZ is more lipophilic than PMOZ and PEG; and PEOZ is significantly less viscous than PEG especially at the higher molecular weights. When PEOZ was attached to the enzymes catalase, ribonuclease, and uricase, the in vitro activity of the resultant bioconjugates depended on the extent of protein modification. POZ conjugates of insulin lowered blood glucose levels for a period of 8 h when compared to 2 h for insulin alone. PEOZ, like PEG, was also able to successfully attenuate the immunogenic properties of BSA. The POZ polymers (10 and 20 kDa) are safe when administered intravenously to rats, and the maximum tolerated dose (MTD) was greater than 2 g/kg. Blood counts, serum chemistry, organ weights, and the histopathology of key organs were normal. These results conclude that POZ has the desired drug delivery properties for a new biopolymer.
Comparison of the two techniques for measurement of the density of Demodex folliculorum: standardized skin surface biopsy and direct microscopic examination (2010)

We recommend the use of SSSB for the measurement of Dd as more patients with demodicosis can be diagnosed with this method compared with the DME method.
One-way functions are necessary and sufficient for secure signatures (1990)

Article Free AccessOne-way functions are necessary and sufficient for secure signatures Author: J. Rompel Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, MA Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, MAView Profile Authors Info & Claims STOC '90: Proceedings of the twenty-second annual ACM symposium on Theory of ComputingApril 1990 Pages 387–394https://doi.org/10.1145/100216.100269Published:01 April 1990Publication History 433citation1,331DownloadsMetricsTotal Citations433Total Downloads1,331Last 12 Months122Last 6 weeks33 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Estimation of three‐phase relative permeability by simulating fluid dynamics directly on rock‐microstructure images (2016)

Abstract Given the world's growing demand for energy, a combination of geological CO 2 sequestration and enhanced oil recovery (EOR) technologies is currently regarded as a promising solution, as it would provide a means of reducing carbon emissions into the atmosphere while also leading to the economic benefit of simultaneously recovering oil. The optimization of injection strategies to maximize CO 2 storage and increase the oil recovery factors requires complicated pore‐scale flow information within a reservoir system consisting of coexisting oil, water, and CO 2 phases. In this study, an immiscible three‐phase lattice‐Boltzmann (LB) model was developed to investigate the complicated flow state with interaction between water, oil, and CO 2 systems in porous media. The two main mechanisms of oil remobilization, namely, double‐drainage and film flow, can be captured by our model. The estimation of three‐phase relative permeability is proposed using the digital rock physics (DRP) simulations. The results indicate that the relative permeability of CO 2 as calculated using our steady state method is not sensitive to the initial oil fraction if the oil distribution is originally uniform. Baker's (1988) empirical model was tested and found to be able to provide a good prediction of the three‐phase relative permeability data. Our numerical method provides a new tool for accurately predicting three‐phase relative permeability data directly based on micro‐CT rock images.
ChemInform Abstract: Thiazolidine Derivatives: A New Source of α‐Aminoalkyl Radicals for Carbon—Carbon Bond Formation in Synthesis. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Improving web search ranking by incorporating user behavior information (2006)

We show that incorporating user behavior data can significantly improve ordering of top results in real web search setting. We examine alternatives for incorporating feedback into the ranking process and explore the contributions of user feedback compared to other common web search features. We report results of a large scale evaluation over 3,000 queries and 12 million user interactions with a popular web search engine. We show that incorporating implicit feedback can augment other features, improving the accuracy of a competitive web search ranking algorithms by as much as 31% relative to the original performance.
Multilayer White Light-Emitting Organic Electroluminescent Device (1995)

Organic electroluminescent devices are light-emitting diodes in which the active materials consist entirely of organic materials. Here, the fabrication of a white light-emitting organic electroluminescent device made from vacuum-deposited organic thin films is reported. In this device, three emitter layers with different carrier transport properties, each emitting blue, green, or red light, are used to generate white light. Bright white light, over 2000 candelas per square meter, nearly as bright as a fluorescent lamp, was successfully obtained at low drive voltages such as 15 to 16 volts. The applications of such a device include paper-thin light sources, which are particularly useful for places that require lightweight illumination devices, such as in aircraft and space shuttles. Other uses are a backlight for liquid crystal display as well as full color displays, achieved by combining the emitters with micropatterned color filters.
Chemical Sensors Based on Immobilized Indicators and Fiber Optics (1988)

I. INTRODUCTION I. INTRODUCTION In recent years, there has been increasing interest in the development of optically based chemical sensors. While a large variety of devices are possible, they share as a common feature an immobilized reagent phase which changes the optical properties in some way upon interaction with an analyte on either a continuous or a reusable basis. Factors stimulating this interest include the following:
A Quantum-Mechanical Description of Macrocyclic Ring Rotation in Benzylic Amide [2]Catenanes (2001)

Catenanes can undergo rotation of one ring through the cavity of the other. Since macroscopic and molecular properties must clearly vary with the relative positions and orientations of the interlocked components, a complete understanding of the way that the rings rotate is of considerable importance. Here we show that low-dimensional quantum-mechanical modeling can yield rate constants and barriers similar to those obtained by temperature-dependent nuclear magnetic resonance experiments. Data from both non-hydrogen bond disrupting (e.g. CDCl3) and hydrogen bond disrupting (e.g. [D6]DMSO) solvents are well reproduced demonstrating the validity of the model. The successful simulation of the rates of circumrotations by entirely harmonic transition state theory originates from the description of the anharmonic levels of the systems through an effective harmonic frequency, not very different from twice the zero point energy. The nature of the model makes it extendable, in principle, to the calculation of properties dependent upon circumrotational activity.
Studying protein–protein interactions using peptide arrays (2011)

Screening of arrays and libraries of compounds is well-established as a high-throughput method for detecting and analyzing interactions in both biological and chemical systems. Arrays and libraries can be composed from various types of molecules, ranging from small organic compounds to DNA, proteins and peptides. The applications of libraries for detecting and characterizing biological interactions are wide and diverse, including for example epitope mapping, carbohydrate arrays, enzyme binding and protein-protein interactions. Here, we will focus on the use of peptide arrays to study protein-protein interactions. Characterization of protein-protein interactions is crucial for understanding cell functionality. Using peptides, it is possible to map the precise binding sites in such complexes. Peptide array libraries usually contain partly overlapping peptides derived from the sequence of one protein from the complex of interest. The peptides are attached to a solid support using various techniques such as SPOT-synthesis and photolithography. Then, the array is incubated with the partner protein from the complex of interest. Finally, the detection of the protein-bound peptides is carried out by using immunodetection assays. Peptide array screening is semi-quantitative, and quantitative studies with selected peptides in solution are required to validate and complement the screening results. These studies can improve our fundamental understanding of cellular processes by characterizing amino acid patterns of protein-protein interactions, which may even develop into prediction algorithms. The binding peptides can then serve as a basis for the design of drugs that inhibit or activate the target protein-protein interactions. In the current review, we will introduce the recent work on this subject performed in our and in other laboratories. We will discuss the applications, advantages and disadvantages of using peptide arrays as a tool to study protein-protein interactions.
A2B Adenosine Receptor Antagonists with Picomolar Potency (2019)

The A<sub>2B</sub> adenosine receptor (A<sub>2B</sub>AR) was proposed as a novel target for the (immuno)therapy of cancer since A<sub>2B</sub>AR blockade results in antiproliferative, antiangiogenic, antimetastatic, and immunostimulatory effects. In this study, we explored the structure-activity relationships of xanthin-8-yl-benzenesulfonamides mainly by introducing a variety of linkers and substituents attached to the sulfonamide residue. A new, convergent strategy was established, which facilitated the synthesis of the target compounds. Many of the new compounds exhibited subnanomolar affinity for the A<sub>2B</sub>AR combined with high selectivity. Functional groups were introduced, which will allow the attachment of dyes and other reporter groups. 8-(4-((4-(4-Bromophenyl)piperazin-1-yl)sulfonyl)phenyl)-1-propylxanthine (34, PSB-1901) was the most potent A<sub>2B</sub>-antagonist ( K<sub>i</sub> 0.0835 nM, K<sub>B</sub> 0.0598 nM, human A<sub>2B</sub>AR) with >10 000-fold selectivity versus all other AR subtypes. It was similarly potent and selective at the mouse A<sub>2B</sub>AR, making it a promising tool for preclinical studies. Computational studies predicted halogen bonding to contribute to the outstanding potency of 34.