gebhart/patrepeval huggingface dataset:
Glucose-induced conformational change in yeast hexokinase. (1978)

The A isozyme of yeast hexokinase (ATP:D-hexose 6-phosphotransferase, EC 2.7.1.1) crystallized as a complex with glucose has a conformation that is dramatically different from the conformation of the B isozyme crystallized in the absence of glucose. Comparison of the high-resolution structures shows that one lobe of the molecule is rotated by 12 degrees relative to the other lobe, resulting in movements of as much as 8 A in the polypeptide backbone and closing the cleft between the lobes into which glucose is bound. The conformational change is produced by the binding of glucose (R.C. McDonald, T.A. Steitz, and D.M. Engelman, unpublished data) and is essential for catalysis [Anderson, C.M., Stenkamp, R.E., McDonald, R.C. & Steitz, T.A. (1978) J. Mol. Biol. 123, 207-219] and thus provides an example of induced fit. The surface area of the hexokinase A-glucose complex exposed to solvent is smaller than that of native hexokinase B. By using the change in exposed surface area to estimate the hydrophobic contribution to the free energy changes upon glucose binding, we find that the hydrophobic effect alone favors the active conformation of hexokinase in the presence and absence of sugar. The observed stability of the inactive conformation of the enzyme in the absence of substrates may result from a deficiency of complementary interactions within the cavity that forms when the two lobes close together.
Fc gamma receptor II (CD32) on malignant B cells influences modulation induced by anti-CD19 monoclonal antibody (1994)

Antigenic modulation is one of many factors determining the effectiveness of monoclonal antibody (MoAb)-mediated therapy. To select the isotype of a CD19 MoAb most suitable for radioimmunotherapy of patients with B-cell malignancies, we studied the influence of MoAb isotype on modulation, after binding of the MoAb to different cell-line cells. The CD19-IgG1 MoAb was found to induce modulation of CD19 antigens on Daudi cell line cells more rapidly than did its IgG2a switch variant. We provide evidence that this difference in modulation rate is caused by the expression of Fc gamma receptor II (Fc gamma RII) on these cells. Experiments aimed at elucidating the mechanism of Fc gamma RII involvement in modulation induction by CD19-IgG1 showed that Fc gamma RII did not comodulate with CD19 MoAbs. However, cocrosslinking of CD19 and Fc gamma RII with CD19-IgG1 MoAb resulted in enhanced calcium mobilization in Daudi cells. This increased signal induction accompanies the enhanced capping and subsequent modulation of CD19 antigens. Because Fc gamma RII is expressed in varying densities on malignant B cells in all differentiation stages, our results have implications for the MoAb isotype most suitable for use in MoAb-based therapy of patients with B-cell malignancies.
Protective immunity following vaccination: How is it defined? (2008)

Vaccination represents an important medical breakthrough pioneered by Edward Jenner over 200 years ago when he developed the world's first vaccine against smallpox. To this day, vaccination remains the most effective means available for combating infectious disease. There are currently over 20 vaccines licensed for use within the US with many more vaccines in the R&D pipeline. Although vaccines must demonstrate clinical efficacy in order to receive FDA approval, the correlates of immunity vary remarkably between different vaccines and may be based primarily on animal studies, clinical evidence, or a combination of these sources of information. Correlates of protection are critical for measuring vaccine efficacy but researchers should know the history and limitations of these values. As vaccine technologies advance, the way in which we measure and define protective correlates may need to evolve as well. Here, we describe the correlates of protective immunity for vaccines against smallpox, tetanus, yellow fever and measles and compare these to a more recently introduced vaccine against varicella zoster virus, wherein a strict correlate of immunity has yet to be fully defined.
Wave-ray coupling for interactive sound propagation in large complex scenes (2013)

We present a novel hybrid approach that couples geometric and numerical acoustic techniques for interactive sound propagation in complex environments. Our formulation is based on a combination of spatial and frequency decomposition of the sound field. We use numerical wave-based techniques to precompute the pressure field in the near-object regions and geometric propagation techniques in the far-field regions to model sound propagation. We present a novel two-way pressure coupling technique at the interface of near-object and far-field regions. At runtime, the impulse response at the listener position is computed at interactive rates based on the stored pressure field and interpolation techniques. Our system is able to simulate high-fidelity acoustic effects such as diffraction, scattering, low-pass filtering behind obstruction, reverberation, and high-order reflections in large, complex indoor and outdoor environments and Half-Life 2 game engine. The pressure computation requires orders of magnitude lower memory than standard wave-based numerical techniques.
Highly Tunable Self-Assembled Nanostructures from a Poly(2-vinylpyridine-b-dimethylsiloxane) Block Copolymer (2011)

An extraordinarily large degree of tunability in geometry and dimension is demonstrated in films of a self-assembled block copolymer. A poly(2-vinylpyridine-b-dimethylsiloxane) block copolymer with highly incompatible blocks was spun-cast on patterned substrates and treated with various solvent vapors. The degree of selective swelling in the poly(2-vinylpyridine) matrix block could be controlled over an extensive range, leading to the formation of various microdomain morphologies such as spheres, cylinders, hexagonally perforated lamellae, and lamellae from the same block copolymer. The systematic control of swelling ratio and the choice of solvent vapors offer the unusual ability to control the width of very well-ordered linear features within a range between 6 and 31 nm. This methodology is particularly useful for nanolithography based on directed self-assembly in that a single block copolymer film can form microdomains with a broad range of geometries and sizes without the need to change molecular weight or volume fraction.
L1-Mediated Branching Is Regulated by Two Ezrin-Radixin-Moesin (ERM)-Binding Sites, the RSLE Region and a Novel Juxtamembrane ERM-Binding Region (2005)

We investigated how the neural cell adhesion molecule L1 mediates neurite outgrowth through L1-L1 homophilic interactions. Wild-type L1 and L1 with mutations in the cytoplasmic domain (CD) were introduced into L1 knock-out neurons, and transfected neurons were grown on an L1 substrate. Neurite length and branching were compared between wild-type L1 and L1CD mutations. Surprisingly, the L1CD is not required for L1-mediated neurite outgrowth but plays a critical role in neurite branching, through both the juxtamembrane region and the RSLE region. We demonstrate that both regions serve as ezrin-moesin-radixin-binding sites. A truncation mutant that deletes 110 of 114 amino acids of the L1CD still supports neurite outgrowth on an L1 substrate, suggesting that a coreceptor binds to L1 in cis and mediates neurite outgrowth and that L1-ankyrin interactions are not essential for neurite initiation or outgrowth. These data are consistent with a model in which L1 can influence L1-mediated neurite outgrowth and branching through both the L1CD and a coreceptor.
Confined Excitons in GaN-AlGaN Quantum Wells (1999)

We calculate the original properties of excitons in GaN–AlGaN quantum wells by a variational approach in the envelope function formalism. The separation of electrons and holes by huge internal electric fields induces an enhanced dependence of exciton binding energy and oscillator strength on the well width. We demonstrate the necessity to perform excitonic calculations for obtaining, in particular, reliable values of oscillator strengths (thus radiative lifetimes), which are extremely sensitive to the well width.
A digital micro‐mirror device‐based system for the microfabrication of complex, spatially patterned tissue engineering scaffolds (2006)

Our ability to create precise, pre-designed, spatially patterned biochemical and physical microenvironments inside polymer scaffolds could provide a powerful tool in studying progenitor cell behavior and differentiation under biomimetic, three-dimensional (3D) culture conditions. We have developed a simple and fast, layer-by-layer microstereolithography system consisting of an ultra-violet light source, a digital micro-mirror masking device, and a conventional computer projector, that allows fabrication of complex internal features along with precise spatial distribution of biological factors inside a single scaffold. Photo-crosslinkable poly(ethylene glycol) diacrylates were used as the scaffold material, and murine bone marrow-derived cells were successfully encapsulated or seeded on fibronectin-functionalized scaffolds. Fluorescently-labeled polystyrene microparticles were used to show the capability of this system to create scaffolds with complex internal architectures and spatial patterns. We demonstrate that precisely controlled pore size and shapes can be easily fabricated using a simple, computer-aided process. Our results further indicate that multi-layered scaffolds with spatially distributed factors in the same layer or across different layers can be efficiently manufactured using this technique. These microfabricated scaffolds are conducive for osteogenic differentiation of marrow-derived stem cells, as indicated by efficient matrix mineralization.
Synthesis and Amyloid Binding Properties of Rhenium Complexes:  Preliminary Progress Toward a Reagent for SPECT Imaging of Alzheimer's Disease Brain (1999)

The definitive diagnosis of Alzheimer's disease (AD) requires the detection of amyloid plaques in postmortem brain. Although the amount of fibrillar amyloid roughly correlates with the severity of symptoms at the time of death, the temporal relationship between amyloid deposition, neuronal loss, and cognitive decline is unclear. To elucidate this relationship, a noninvasive, practical method for the quantitation of brain amyloid deposition is required. We describe herein the initial stages of a strategy to accomplish this goal by single photon computed tomographic imaging. The amyloid-binding dye Congo Red was modified to allow its conjugation to the monoamine-monoamide bis(thiol) ligand. This ligand complexes technetium(V) in its neutral oxo form. A biphenyl-containing building block was conjugated to the protected ligand, and the product was coupled to the relevant aromatic compounds. Rhenium oxo complexes, which are isosteric, but nonradioactive, analogues of the potential imaging agent technetium oxo complexes, were synthesized. These complexes bound to Abeta amyloid fibrils produced in vitro and stained amyloid plaques and vascular amyloid in AD brain sections.
Differentiation and long-term survival of C2C12 myoblast grafts in heart. (1993)

We have assessed the ability of skeletal myoblasts to form long-term, differentiated grafts in ventricular myocardium. C2C12 myoblasts were grafted directly into the heart of syngeneic mice. Viable grafts were observed as long as 3 mo after implantation. Immunohistological analyses revealed the presence of differentiated myotubes that stably expressed the skeletal myosin heavy chain isoform. Thymidine uptake studies indicated that virtually all of the grafted skeletal myocytes were withdrawn from the cell cycle by 14 d after grafting. Graft myocytes exhibited ultrastructural characteristics typical of differentiated myotubes. Graft formation and the associated myocardial remodeling did not induce overt cardiac arrhythmia. This study indicates that the myocardium can serve as a stable platform for skeletal myoblast grafts. The long-term survival, differentiated phenotype, and absence of sustained proliferative activity observed in myoblast grafts raise the possibility that similar grafting approaches may be used to replace diseased myocardium. Furthermore, the genetic tractability of myoblasts could provide a useful means for the local delivery of recombinant molecules to the heart.
CD2 is functionally linked to the ζ‐natural killer receptor complex (1991)

Natural killer (NK) cells express two distinct surface receptors capable of triggering cytolytic effector function. The first is CD16, an immunoglobulin Fc receptor that allows NK cells to mediate antibody-dependent killing (ADCC). NK cells express CD16 in association with zeta, a signal-transducing subunit that is also a component of the T cell receptor complex. Activation of NK cells via CD16 results in tyrosine phosphorylation of zeta. The second NK cell triggering receptor is CD2, a 50-55-kDa cell surface molecule that is also expressed on T cells. Here we show that NK cell activation induced by mAb reactive with CD2 (either anti-T11.1 alone or with anti-T11.2 in combination) also results in the tyrosine phosphorylation of zeta. Our results indicate that CD2 is functionally linked to the CD16-zeta complex and suggest that the zeta subunit plays a central role in the signal transduction pathways utilized by NK cells.
Cerebral blood flow in patients with normal-pressure hydrocephalus before and after shunting (1987)

Cerebral blood flow (CBF) was measured by xenon-133 inhalation and single photon emission tomography in 17 demented patients with normal-pressure hydrocephalus before and after shunt treatment. All patients had a decreased conductance to outflow (C out) of cerebrospinal fluid as measured by lumboventricular perfusion (C out less than 0.12 ml X mm Hg-1 X min-1). Computerized tomography (CT) scanning, clinical assessment, and neuropsychological grading were performed pre- and postoperatively. The preoperative CBF studies revealed abnormal flow patterns in all patients. Fourteen patients showed moderate-sized, large, or very large central low-flow areas, and four patients had reduced flow bilaterally in the occipital and contiguous temporoparietal regions. After shunting, six patients had a significant reduction in the size of the central low-flow area on the CBF map, agreeing well with the changes of ventricular size on the CT scan. All six patients showed an improvement in either clinical or neuropsychological grading. In 10 of the remaining 11 patients flow patterns were essentially unchanged; one patient deteriorated further. Four of these 11 patients improved on postoperative clinical or neuropsychological testing. Thus, a positive correlation was found between the changes in CBF and the reduction of the ventricular size on the CT scan, but changes in CBF as measured by the present technique did not accompany improvement in the functional state in all patients.
An Alkynylpyrimidine-Based Covalent Inhibitor That Targets a Unique Cysteine in NF-κB-Inducing Kinase (2021)

NF-κB-inducing kinase (NIK) is a key enzyme in the noncanonical NF-κB pathway, of interest in the treatment of a variety of diseases including cancer. Validation of NIK as a drug target requires potent and selective inhibitors. The protein contains a cysteine residue at position 444 in the back pocket of the active site, unique within the kinome. Analysis of existing inhibitor scaffolds and early structure-activity relationships (SARs) led to the design of C444-targeting covalent inhibitors based on alkynyl heterocycle warheads. Mass spectrometry provided proof of the covalent mechanism, and the SAR was rationalized by computational modeling. Profiling of more potent analogues in tumor cell lines with constitutively activated NIK signaling induced a weak antiproliferative effect, suggesting that kinase inhibition may have limited impact on cancer cell growth. This study shows that alkynyl heterocycles are potential cysteine traps, which may be employed where common Michael acceptors, such as acrylamides, are not tolerated.
Prospective Validation of Rapid Plasma Genotyping for the Detection ofEGFRandKRASMutations in Advanced Lung Cancer (2016)

Plasma ddPCR detected EGFR and KRAS mutations rapidly with the high specificity needed to select therapy and avoid repeat biopsies. This assay may also detect EGFR T790M missed by tissue genotyping due to tumor heterogeneity in resistant disease.
ChemInform Abstract: 1‐Azaribofuranoside Analogues as Designed Inhibitors of Purine Nucleoside Phosphorylase. Synthesis and Biological Evaluation. (1999)

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.
Reduced Chlorhexidine Tooth Stain Coverage by Sequential Administration of Monoperoxyphthalic Acid in the Beagle Dog (1997)

Extrinsic tooth stain is sometimes a side-effect observed with the chronic use of chlorhexidine-containing oral care products. This chlorhexidine (CHX)-induced tooth staining is observed both in humans as well as in experimental animals. The present study tested the hypothesis that the sequential administration of monoperoxyphthalic acid (MPA) will reduce the development of chlorhexidine-induced tooth stain coverage in a beagle dog. For this study, dogs were treated with 30 mL of mouthrinse b.i.d. for 28 days. The following treatment groups ( = 12 dogs/group) were tested: water (negative control), 1.0% MPA rinse, 0.12% CHX rinse, and 1.0% MPA rinse followed by 0.12% CHX rinse. The sequential dosing of 1.0% MPA followed by 0.12+ CHX resulted in significantly (p < or = 0.05) less tooth stain than when dogs were dosed with 0.12% CHX alone. Additionally, the sequential dosing of MPA followed by chlorhexidine resulted in a 75% reduction in plaque formation in this model, which was significantly different (p < or = 0.05) from results with either treatment alone. A further study demonstrated that similar results could be obtained when MPA plus CHX treatment alone. A further study demonstrated that similar results could be obtained when MPA plus CHX treatments were separated by approximately a five-hour period in an AM and PM schedule. We conclude that the oxidizer, MPA, can significantly reduce tooth stain induced by CHX while enhancing its antiplaque and antigingivitis activity.
Multivariate Matching Methods That are Equal Percent Bias Reducing, I: Some Examples (1976)

Multivariate matching methods are commonly used in the behavioral and medical sciences in an attempt to control bias when randomization is not feasible. Some examples of multivariate matching methods are discussed in Althauser and Rubin (1970) and Cochran and Rubin (1973), but otherwise seem to have received little attention in the literature. Here, we present examples of multivariate matching methods that will yield the same percent reduction in bias for each matching variable for a variety of underlying distributions. Eleven distributional cases are considered, and for each one, matching methods are defined which are equal percent bias reducing. Methods discussed in Section 8, which are based on the values of the estimated best linear discriminant or which define distance by a sample based inner-product, will probably be the most generally applicable in practice.
Before and After Treatment Quantitative Assessment of Hepatic Steatosis in a Romanian Population Using Magnetic Resonance Liver Spectroscopy. (2019)

Non-alcoholic fatty liver disease (NAFLD) is currently the most common liver disease that progressively develops in four stages (steatosis, non-alcoholic steatohepatitis-NASH, fibrosis, cirrhosis). In order to accurately evaluate the amount of fat content inside the hepatocytes, non-invasive imaging studies such as magnetic resonance spectroscopy (MRS) of the liver can be used as an alternative method to the traditional invasive liver biopsy. The main objective of our study was to quantitatively assess hepatic steatosis before and after treatment using liver MRS. The study group included 35 patients diagnosed with NAFLD who freely expressed their agreement to take part in this study. The treatment lasted 6 months and consisted of administering a local commercially available liver protection supplement combined with dietary and lifestyle adjustments. The initial quantitative assessment of the liver fat content using MRS revealed a hepatic lipid accumulation ranging from 15.70% to 68.03%, with a mean value of 41.26%. The subsequent liver MRS performed after 6 months of proper treatment indicated a fat content inside the liver parenchyma ranging from 15.47% to 58.98%, with a mean value of 36.07%. The therapeutic measures that were applied to the patients managed to reduce the amount of fat content inside the liver parenchyma in 24 patients (68.57%), while in 11 patients (31.43%) the results revealed an increase in hepatic lipid content. In conclusion, the current study reached its initial objective and offered a modern approach regarding the pre and post-treatment evaluation of hepatic steatosis using MRS.
Strategies for Mutagenesis and Gene Cloning Using Transposon Tagging and T-DNA Insertional Mutagenesis (1992)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
Unsupervised induction of stochastic context-free grammars using distributional clustering (2001)

An algorithm is presented for learning a phrase-structure grammar from tagged text. It clusters sequences of tags together based on local distributional information, and selects clusters that satisfy a novel mutual information criterion. This criterion is shown to be related to the entropy of a random variable associated with the tree structures, and it is demonstrated that it selects linguistically plausible constituents. This is incorporated in a Minimum Description Length algorithm. The evaluation of unsupervised models is discussed, and results are presented when the algorithm has been trained on 12 million words of the British National Corpus.
INHIBITION OF COMPLEMENT-MEDIATED IMMUNE HEMOLYSIS BY PEPTIDES DERIVED FROM THE CONSTANT DOMAIN OF IMMUNOGLOBULIN1 (1999)

High-dose administration of intravenous immunoglobulin is reported to be useful for inhibiting complement-dependent immune cytolysis. We have found that, among the proposed C1q-binding sites of the Fc portion of human IgG1, only residues 282-292 inhibited pig red blood cell lysis by human serum. Moreover, a hexadecemeric multiple antigen peptide of residues 282-292 from IgG showed significantly greater activity in suppressing complement-mediated immune cytolysis and can be used in place of high-dose intravenous immunoglobulin, which is extracted from donors and thus is expensive.