gebhart/patrepeval huggingface dataset:
Rescue of functional replication origins from embedded configurations in a plasmid carrying the adenovirus genome. (1984)

A variant of the adenovirus type 5 genome which lacks EcoRI sites has been cloned in a bacterial plasmid after the addition of EcoRI oligonucleotide linkers to its ends. Closed circular forms of the recombinant viral genome were not infectious upon their introduction into permissive eucaryotic cells. The linear genome released by digestion of the 39-kilobase recombinant plasmid (pXAd) with EcoRI produced infectious virus at about 5% of the level of wild-type controls. The viruses which arose were indistinguishable from the parental strain, and the normal termini of the viral genome had been restored. Marker rescue experiments demonstrate that provision of a DNA fragment with a normal viral end improves infectivity. When a small fragment carrying a wild-type left end (the 0 to 2.6% ClaI-B fragment) was ligated to ClaI-linearized pXAd, virus was produced with efficiencies comparable to a similar reconstitution of the two ClaI fragments of the wild-type genome. These viruses stably carry the left-end fragment at both ends, leaving the normal right end embedded in 950 base pairs of DNA. The embedded right origin is inactive. The consensus of the analyses reported here is that a free end is a necessary configuration for the sequences which make up the adenovirus origin of replication.
Maximizing Energetic Efficiency in Flow Batteries Utilizing Non-Newtonian Fluids (2014)

High energy density flow batteries provide a potential solution to large-scale electrical energy storage needs. The high energy density fluid electrodes for such devices will typically have non-Newtonian rheology, especially when formulated as suspensions which increase electrical conductivity, energy density, or both [M. Duduta et al., Adv. Energy Mater., 1, 511 (2011); Z. Li et al., Phys. Chem. Chem. Phys., 15, 15833 (2013)]. A computational model that simulates electrochemical kinetics and flow is used to quantify coulombic and energetic efficiency under various flow conditions, taking as examples flow electrodes that contain suspensions of active materials (LiFePO4, LiCoO2) or conductive networks in redox solution (vanadium redox). Intermittent flow pulses of controlled volume and duration are found to incur less than half the electrochemical losses of continuous pumping. Increased slip and yield stress are shown to increase flow uniformity, energetic efficiency, and discharge energy. From these findings a general strategy is derived for the maximization of efficiency in energy-dense flow batteries applicable to arbitrary cell designs, suspension types, and operating conditions.
Transcription factors NF-IL6 and NF-kappa B synergistically activate transcription of the inflammatory cytokines, interleukin 6 and interleukin 8. (1993)

Single binding sites for transcription factors NF-IL6 and NF-kappa B are present in the promoter of the interleukin (IL) 6 gene. Previous studies of internally deleted promoter mutants demonstrated that these two sites are important for the transcriptional regulation of this gene. In this report, we describe the synergistic activation of the IL-6 promoter by transcription factors NF-IL6 and NF-kappa B. Cotransfection of NF-IL6 with the NF-kappa B p65 subunit resulted in strong synergistic activation of an IL-6 promoter-reporter construct. Both the NF-IL6 and NF-kappa B binding sites in the IL-6 promoter were required for synergistic activation. Similar synergistic activation was observed in the IL-8 promoter, which also contains both NF-IL6 and NF-kappa B binding sites. Furthermore, we demonstrated that NF-IL6 and the NF-kappa B p65 subunit directly associated via the basic leucine-zipper domain of NF-IL6 and the Rel homology domain of p65. Since the promoters of many other genes involved in the inflammatory and acute-phase responses also contain binding sites for NF-IL6 and NF-kappa B, the cooperation between these two factors may have an important role in these responses. We also discuss the possible interplay between various viral gene products and these two factors in the process of viral infection and constitutive cytokine production.
Stochastic Resonance in Biology How Noise Can Enhance Detection of Weak Signals and Help Improve Biological Information Processing (2002)

Noise is usually thought of as the enemy of order rather than as a constructive influence. In nonlinear systems that possess some sort of threshold, random noise plays a beneficial role in enhancing the detection of weak information-carrying signals. This phenomenon, termed stochastic resonance, does find useful applications in physical, biological, and biomedical contexts. Certain biological systems may even use this effect for optimizing function and behavior.
Simultaneous determination of the constituent azimuthal and radial mode indices for light fields possessing orbital angular momentum (2012)

A wide array of diffractive structures such as arrays of pinholes, triangular apertures, slits, and holograms have all recently been used to measure the azimuthal index of individual Laguerre-Gaussian beams. Here, we demonstrate a powerful approach to simultaneously measure both the radial and azimuthal indices of pure Laguerre-Gaussian light fields using the method of principal component analysis. We find that the shape of the diffracting element used to measure the mode indices is in fact of little importance and the crucial step is training any diffracting optical system and transforming the observed pattern into uncorrelated variables. The method is generic and may be extended to other families of light fields such as Bessel or Hermite-Gaussian beams.
Formation of High-Affinity C5 Convertases of the Alternative Pathway of Complement (2001)

Cleavage of C5 by C5 convertase is the last enzymatic step in the complement activation cascade leading to the formation of the cytolytic proteolytically activated form of C5 (C5b)-9 complex. In the present study, we examined the effect of the density of C3b (the proteolytically activated form of C3) on the function of the noncatalytic subunit of natural surface-bound forms of the enzyme. A comparison of the kinetic parameters of C5 convertases assembled on three surfaces (zymosan, rabbit erythrocytes, and sheep erythrocytes) were similar and revealed that the average K:(m) decreased approximately 28-fold (5.2-0.18 microM) when the density of C3b was increased from approximately 18,000 to 400,000 C3b/cell. Very-high-affinity C5 convertases were generated when preformed C3 convertases were allowed to self amplify by giving them excess C3. These convertases exhibited K(m) from 0.016 to 0.074 microM, well below the normal plasma concentration of C5 in blood (0.37 microM). The results suggest that in serum convertases formed with monomeric C3b will be relatively inefficient in capturing C5 but will continue to cleave C3 opsonizing the cell surface for phagocytosis, whereas convertases formed with C3b-C3b complexes in areas of high C3b density will primarily cleave C5. The catalytic rate of these convertases approaches maximum velocity, thereby switching the enzyme from cleavage of C3 to cleavage of C5, and production of the cytolytic C5b-9 complex.
Identification of a 69-kilodalton nonfimbrial protein as an agglutinogen of Bordetella pertussis (1988)

Cells of Bordetella pertussis BP353, a nonfimbriated Eldering serotype 1.3 strain, were used as an immunogen to produce three monoclonal antibodies, BPE3, BPD8, and BPE8, that agglutinated the immunizing cells, as well as certain other nonfimbriated and fimbriated serotype 3-containing B. pertussis strains. The antibodies did not agglutinate serotype 1 or nontypable B. pertussis cells. These monoclonal antibodies specifically detected a 69-kilodalton (kDa) band on Western blots (immunoblots) containing whole B. pertussis cell lysates of Eldering agglutinogen serotypes 1.3, 1.3.6, 1.2.3.4, and 1.2.3.4.6. This 69-kDa antigen was released from the bacteria by cell incubation for 60 min at 60 degrees C, and it was purified by affinity chromatography with a BPE3-agarose affinity matrix. Purified material was used to produce a polyclonal antiserum that agglutinated all nonfimbriated and fimbriated B. pertussis cells containing serotype 3 agglutinogen. Immunogold electron microscopy and indirect immunofluorescence studies demonstrated that it is an outer membrane constituent but nonfimbrial in appearance. BPE3 did not detect purified fimbriae on Western blots, and antibodies to these fimbriae did not bind to the 69-kDa component. Although B. bronchiseptica and B. parapertussis cells were not agglutinated by the monoclonal antibodies, antigenically similar proteins were detected in extracts of the bacteria. These results identify the 69-kDa protein as a nonfimbrial agglutinogen present on all virulent strains of B. pertussis. The monoclonal antibodies described here should be useful for further studies on the structure and function of this protein.
Protection against Autoimmunity in Nonlymphopenic Hosts by CD4+CD25+ Regulatory T Cells Is Antigen-Specific and Requires IL-10 and TGF-β (2005)

CD4+ CD25+ regulatory T cells (T(Reg)) play a critical role in the control of autoimmunity. However, little is known about how T(Reg) suppress self-reactive T cells in vivo, thus limiting the development of T(Reg)-based therapy for treating autoimmune diseases. This is in large part due to the dependency on a state of lymphopenia to demonstrate T(Reg)-mediated suppression in vivo and the unknown Ag specificity of T(Reg) in most experimental models. Using a nonlymphopenic model of autoimmune pneumonitis and T(Reg) with known Ag specificity, in this study we demonstrated that these T(Reg) can actively suppress activation of self-reactive T cells and protect mice from fatal autoimmune pneumonitis. The protection required T(Reg) with the same Ag specificity as the self-reactive T cells and depended on IL-10 and TGF-beta. These results suggest that suppression of autoimmunity by T(Reg) in vivo consists of multiple layers of regulation and advocate for a strategy involving Ag-specific T(Reg) for treating organ-specific autoimmunity, because they do not cause generalized immune suppression.
Solubility of Cyclodextrins and Drug/Cyclodextrin Complexes (2018)

Cyclodextrins (CDs), a group of oligosaccharides formed by glucose units bound together in a ring, show a promising ability to form complexes with drug molecules and improve their physicochemical properties without molecular modifications. The stoichiometry of drug/CD complexes is most frequently 1:1. However, natural CDs have a tendency to self-assemble and form aggregates in aqueous media. CD aggregation can limit their solubility. Through derivative formation, it is possible to enhance their solubility and complexation capacity, but this depends on the type of substituent and degree of substitution. Formation of water-soluble drug/CD complexes can increase drug permeation through biological membranes. To maximize drug permeation the amount of added CD into pharmaceutical preparation has to be optimized. However, solubility of CDs, especially that of natural CDs, is affected by the complex formation. The presence of pharmaceutical excipients, such as water-soluble polymers, preservatives, and surfactants, can influence the solubilizing abilities of CDs, but this depends on the excipients' physicochemical properties. The competitive CD complexation of drugs and excipients has to be considered during formulation studies.
In Vitro and In Vivo Activities of Chios Mastic Gum Extracts and Constituents against <i>Helicobacter pylori</i> (2006)

The extracts and pure major constituents of Chios mastic gum (resin of Pistacia lentiscus var. chia) were tested for their activities against Helicobacter pylori. A total mastic extract without polymer (TMEWP) was prepared after removal of the contained insoluble polymer in order to ameliorate solubility and enhance in vivo activity. Administration of TMEWP to H. pylori SS1-infected mice over the period of 3 months with an average dose of 0.75 mg/day led to an approximately 30-fold reduction in the H. pylori colonization (1.5 log CFU/g of tissue). However, no attenuation in the H. pylori-associated chronic inflammatory infiltration and the activity of chronic gastritis was observed. To further characterize potential active mastic constituents, the TMEWP was separated into an acidic and a neutral fraction. Both were extensively characterized by nuclear magnetic resonance and mass spectroscopy to elucidate the structure of the components contained within each fraction. After chromatographic separation, the acid fraction gave the major triterpenic acids, while the neutral fraction gave several triterpenic alcohols and aldehydes. Mastic extracts and isolated pure triterpenic acids were tested for in vitro activity against a panel of 11 H. pylori clinical strains. The acid fraction was found to be the most active extract (minimum bactericidal concentration [MBC], 0.139 mg/ml), and the most active pure compound was isomasticadienolic acid (MBC, 0.202 mg/ml [0.443 mM]). Our results show that administration of TMEWP may be effective in reducing H. pylori colonization and that the major triterpenic acids in the acid extract may be responsible for such an activity.
Formal verification of digital systems (2002)

A formal verifier is an automated decision procedure that can prove or disprove a set of statements in some logical system of reasoning. Problems informal verification have been posed and studied in a variety of disciplines for many years. However the last ten years have produced significant advances in both the theory and practical art of building formal verifiers. Various formal proof techniques available today include language containment, model checking, equivalence checking, symbolic simulation and theorem proving. In this tutorial, we will be restricting ourselves to the formal finite state machine based techniques: language containment, model checking and equivalence checking. A brief introduction to the technologies that underly these techniques will be presented as well. The tutorial will conclude with some examples of how formal methods can be employed in the verification of hardware systems.
MagIC System: a New Textile-Based Wearable Device for Biological Signal Monitoring. Applicability in Daily Life and Clinical Setting (2005)

The paper presents a new textile-based wearable system for the unobtrusive recording of cardiorespiratory and motion signals during spontaneous behavior along with the first results concerning the application of this device in daily life and in a clinical environment. The system, called MagIC (Maglietta Interattiva Computerizzata), is composed of a vest, including textile sensors for detecting ECG and respiratory activity, and a portable electronic board for motion detection, signal preprocessing and wireless data transmission to a remote monitoring station. The MagIC system has been tested in freely moving subjects at work, at home, while driving and cycling and in microgravity condition during a parabolic flight. Applicability of the system in cardiac in-patients is now under evaluation. Preliminary data derived from recordings performed on patients in bed and during physical exercise showed 1) good signal quality over most of the monitoring periods, 2) a correct identification of arrhythmic events, and 3) a correct estimation of the average beat-by-beat heart rate. These positive results supports further developments of the MagIC system, aimed at tuning this approach for a routine use in clinical practice and in daily life.
Facial component features for facial expression identification using Active Appearance Models (2009)

Statistical methods of shape and appearance are powerful tools used in computer vision for near-correct interpretation of images. In this paper, we present a method for classifying facial expressions based on the extracted features of facial components. The face, the window to the inner self of an individual can be analyzed for outright expressions like sadness, happiness, anger, surprise, disgust and fear. The facial region is detected; pre-processing is done on the image by using Active Appearance Model (AAM) to extract the vital feature on the facial components. Six classes are formed based on the different expressions and the model from the AAM procedure used to compare with the query image/face. Mahalanobis distance algorithm is used to classify the image in question into the best-fit class. Japanese Female Facial Expression (JAFFE) public database is used to evaluate our method with over 200 images of still images used in our experiment. A higher classification rate observed.
Polysilicon resistor trimming for packaged integrated circuits (2002)

Pulse current trimming to adjust values of polysilicon resistors has been investigated for use in full scale IC production. The technique is remarkably accurate, layout efficient, quick and inexpensive from a test perspective, and requires no additional process complexity. The trim process is shown to be reversible to a small, but usable extent for n-type polysilicon. A new physical model consistent with all observations for resistance trim and recovery is presented. Finally, reliability results from extensive burn-in show the trimmed resistors to be exceptionally robust.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Novel Histology-directed Strategy for MALDI-MS Tissue Profiling That Improves Throughput and Cellular Specificity in Human Breast Cancer (2006)

We describe a novel tissue profiling strategy that improves the cellular specificity and analysis throughput of protein profiles obtained by direct MALDI analysis. The new approach integrates the cellular specificity of histology, the accuracy and reproducibility of robotic liquid dispensing, and the speed and objectivity of automated spectra acquisition. Traditional methodologies for preparing and analyzing tissue samples rely heavily on manual procedures, which for various reasons discussed, restrict cellular specificity and sample throughput. Here, a robotic spotter deposits micron-sized droplets of matrix precisely onto foci of normal mammary epithelium, ductal carcinoma in situ, invasive mammary cancer, and peritumoral stroma selected by a pathologist from high resolution histological images of sectioned human breast cancer samples. The location of each matrix spot was then determined and uploaded into the instrument to facilitate automated profile acquisition by MALDI-TOF. In the example shown, the different lesions were clearly differentiated using mass profiling. Further, the workflow permits a visual projection of any information produced from the profile analyses directly on the histological image for a unique combination of proteomic and histological assessment of sample regions. The higher performance characteristics offered by the new workflow promises to be a significant advancement toward the next generation of tissue profiling studies.
Quality Assurance for Blood Glucose Monitoring in Health-Care Facilities (1991)

When survey results are compared with regulatory and accreditation standards, it is evident that a wide gap exists. Resources to bridge this gap may be scarce in many facilities. Further research is needed to determine minimal QA standards for CBGM that provide for optimal patient outcomes.
Magnetic resonance–coupled fluorescence tomography scanner for molecular imaging of tissue (2008)

A multichannel spectrally resolved optical tomography system to image molecular targets in small animals from within a clinical MRI is described. Long source/detector fibers operate in contact mode and couple light from the tissue surface in the magnet bore to 16 spectrometers, each containing two optical gratings optimized for the near infrared wavelength range. High sensitivity, cooled charge coupled devices connected to each spectrograph provide detection of the spectrally resolved signal, with exposure times that are automated for acquisition at each fiber. The design allows spectral fitting of the remission light, thereby separating the fluorescence signal from the nonspecific background, which improves the accuracy and sensitivity when imaging low fluorophore concentrations. Images of fluorescence yield are recovered using a nonlinear reconstruction approach based on the diffusion approximation of photon propagation in tissue. The tissue morphology derived from the MR images serves as an imaging template to guide the optical reconstruction algorithm. Sensitivity studies show that recovered values of indocyanine green fluorescence yield are linear to concentrations of 1 nM in a 70 mm diameter homogeneous phantom, and detection is feasible to near 10 pM. Phantom data also demonstrate imaging capabilities of imperfect fluorophore uptake in tissue volumes of clinically relevant sizes. A unique rodent MR coil provides optical fiber access for simultaneous optical and MR data acquisition of small animals. A pilot murine study using an orthotopic glioma tumor model demonstrates optical-MRI imaging of an epidermal growth factor receptor targeted fluorescent probe in vivo.
Fabrication of a Micro-omnifluidic Device by Omniphilic/Omniphobic Patterning on Nanostructured Surfaces (2014)

We integrate the adhesive properties of marine mussels, the lubricating properties of pitcher plants, and the nonfouling properties of diatoms into nanostructured surfaces to develop a device called a micro-omnifluidic (μ-OF) system to solve the existing challenges in microfluidic systems. Unlike conventional poly(dimethylsiloxane)-based fluidic systems that are incompatible with most organic solvents, the μ-OF system utilizes a variety of solvents such as water, ethanol, dimethyl sulfoxide, dimethylformamide, tetrahydrofuran, n-hexane, 1,2-dichloroethane, acetic acid, 2-propanol, acetone, toluene, diesel oil, dioxane, gasoline oil, hexadecane, and xylene. The μ-OF system is based on a phenomenon called microchannel induction that spontaneously occurs when virtually all droplets of solvents are applied on omniphilically micropatterned regions of a slippery liquid-infused porous surface. Any solvents with surface tension greater than that of the lubricant (17.1 mN/m, Fluorinert FC-70) are able to repel the infused lubricant located on top of the omniphilic microlines, triggering controlled movement of the droplet by gravity along the microlines. We also demonstrated that the μ-OF system is reusable by the nonadsorption properties of the silicified layer. Due to the organic solvent compatibility, we were able to perform organic reactions with high portability and energy efficiency in operation.