gebhart/patrepeval huggingface dataset:
Covalent immobilization of bovine serum albumin onto (maleic anhydride-alt-methyl vinyl ether) copolymers (1999)

The covalent immobilization of bovin serum albumin (BSA) onto maleic anhydride-alt-methyl vinyl ether copolymers (MAMVE) was successfully achieved under aqueous conditions. The grafting reaction was shown to be controlled by attractive electrostatic interactions and so took place at a low salt concentration. Under these conditions, the covalent binding reaction was quite efficient, reproducible, and complete within 20 min. The maximum loading capacity of the polymer was of 20 BSA molecules per polymer chain. This preliminary study demonstrated that the immobilization of proteins in an aqueous medium could be an efficient process, despite the existing hydrolysis of the functional polymer by water molecules. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 72: 1565–1572, 1999
Automating Software Testing Using Program Analysis (2008)

During the last 10 years, code inspection for standard programming errors has largely been automated with static code analysis. During the next 10 years, we expect to see similar progress in automating testing, and specifically test generation, thanks to advances in program analysis, efficient constraint solvers, and powerful computers. Three new tools from Microsoft combine techniques from static program analysis, dynamic analysis, model checking, and automated constraint solving while targeting different application domains.
Preparative Carbohydrate Chemistry (1997)

Detailing commonly used methods and procedures, this reference discusses the reactions and derivative forms of carbohydrates. Preparative Carbohydrate Chemistry covers the formation, cleavage, and reactions of derivatives and illustrates bond-forming reactions of SN2 types, free radicals, chain extensions, and branching. The contents include: sugar
Assessing long-distance RNA sequence connectivity via RNA-templated DNA–DNA ligation (2015)

Many RNAs, including pre-mRNAs and long non-coding RNAs, can be thousands of nucleotides long and undergo complex post-transcriptional processing. Multiple sites of alternative splicing within a single gene exponentially increase the number of possible spliced isoforms, with most human genes currently estimated to express at least ten. To understand the mechanisms underlying these complex isoform expression patterns, methods are needed that faithfully maintain long-range exon connectivity information in individual RNA molecules. In this study, we describe SeqZip, a methodology that uses RNA-templated DNA-DNA ligation to retain and compress connectivity between distant sequences within single RNA molecules. Using this assay, we test proposed coordination between distant sites of alternative exon utilization in mouse Fn1, and we characterize the extraordinary exon diversity of Drosophila melanogaster Dscam1.
Semi-imaging light pipe for collecting weakly scattered light (1998)

A simple reflective light pipe, formed from a cylindrical tube with an external reflective coating and a small central aperture, can be a highly efficient optical element for collecting light from molecular scattering processes along the path of a laser beam. When the laser beam is co-linear with the axis of the light pipe, scattered light from any location along the interaction region (near the pipe axis) re-images repeatedly to another location along the axis of the pipe. This semi-imaging property of the light pipe permits a large fraction of the total scattered light to re- image along the entire length of the interaction region. If one observes through the small central aperture, scattered light from the single segment of the laser beam in view appears to come from all the locations along the interaction length, as well as from the single segment. In this manner, one can have the advantage of collecting scattered light from a small segment (and thus onto a small detector), while observing an effective interaction length that is many times longer than the segment. Measurements from practical light pipes confirm effective gains of about 10X with light pipes a few centimeters long (Effective gain is defined as the ratio of light collected with the light pipe divided by the light collected from a direct image of the beam using the collection optics).
IL-12 Suppresses Vascular Endothelial Growth Factor Receptor 3 Expression on Tumor Vessels by Two Distinct IFN-γ–Dependent Mechanisms (2010)

IL-12 has been shown to be effective in enhancing antitumor responses. However, how IL-12 exerts its antiangiogenic effect is largely unknown. In this study, we elucidate this mechanism using B16 transfected to express IL-12 (B16/IL-12), a system that provides constant, local production of IL-12 within the tumor microenvironment. Intratumoral IL-12 resulted in a significant delay in tumor growth and phenotypic changes in the vasculature. Vessels found within B16 tumors are chaotic and poorly formed and express vascular endothelial growth factor receptor 3 (VEGFR3), a growth factor receptor not expressed on normal adult vessels. However, the vessels within B16/IL-12 tumors have a more normal morphology and do not express VEGFR3. We have shown that IFN-gamma is required for IL-12 to suppress the aberrant expression of VEGFR3. Indeed, the presence of intratumoral IL-12 stimulates the immune system resulting in more IFN-gamma-producing tumor-infiltrating lymphocytes per tumor when compared with parental B16 tumors, which may have a marked effect on control of tumor growth. Interestingly, within B16/IL-12 tumors, T cells are necessary to suppress VEGFR3 expression on tumor vessels. Finally, using IFN-gamma receptor knockout mice in a bone marrow chimera system, we show that the IFN-gamma produced within the tumor suppresses VEGFR3 expression in two ways: 1) acting directly on tumor vessel endothelial cells, and 2) acting on the tumor-infiltrating lymphocytes to indirectly alter endothelial cells' VEGFR3 expression. Our data indicate a mechanism in which tumor-infiltrating immune cells regulate tumor vessel phenotype.
A monoclonal antibody to the adherence-promoting leukocyte glycoprotein, CD18, reduces organ injury and improves survival from hemorrhagic shock and resuscitation in rabbits. (1988)

Leukocytes have been shown to play an important role in the development of isolated organ injury after experimental ischemia and reperfusion. To examine the role of leukocytes in generalized ischemia-reperfusion injury we used the MAb 60.3 (directed to the human leukocyte adherence glycoprotein, CD18) to block leukocyte adherence functions in a rabbit model of hemorrhagic shock and resuscitation. In control animals subjected to 1 h of shock (mean blood pressure 45 torr and mean cardiac output 30% of baseline) followed by resuscitation, only 29% survived 5 d. All had gross and histologic evidence of injury to lungs, liver, and gastrointestinal mucosa. In contrast, 100% of the MAb 60.3-treated animals survived 5 d (P less than 0.01) and organ injury was absent or markedly attenuated. The control animals also had a persistent acidosis, lost more weight, and had evidence of continued gastrointestinal bleeding in contrast to MAb 60.3-treated animals. We conclude that increased leukocyte adhesiveness plays an important role in the development of multiple organ injury and death after generalized ischemia-reperfusion and that this injury may be significantly reduced by blocking leukocyte adherence functions with the MAb 60.3.
Synthesis of Supercritical Carbon Dioxide Soluble Perfluorinated Dendrons for Surface Modification (2007)

The rational design, synthesis, and characterization of a series of novel perfluorinated dendrons 14a,b, 25a,b, 26a,b, and 18 are described. The dendrimers were designed to have a thiol at the focal point for attachment to a gold surface to enable the fabrication of self-assembled monolayers (SAMs). Perfluorinated tails were attached to the periphery to provide solubility in supercritical carbon dioxide, and to increase the hydrophobicity and the stability of self-assembled monolayers formed. Mitsunobu reactions were utilized to provide high-yielding steps allowing large-scale production of the novel dendrimers.
A Definition of Advanced Types of Atherosclerotic Lesions and a Histological Classification of Atherosclerosis (1995)

This report is the continuation of two earlier reports that defined human arterial intima and precursors of advanced atherosclerotic lesions in humans. This report describes the characteristic components and pathogenic mechanisms of the various advanced atherosclerotic lesions. These, with the earlier definitions of precursor lesions, led to the histological classification of human atherosclerotic lesions found in the second part of this report. The Committee on Vascular Lesions also attempted to correlate the appearance of lesions noted in clinical imaging studies with histological lesion types and corresponding clinical syndromes. In the histological classification, lesions are designated by Roman numerals, which indicate the usual sequence of lesion progression. The initial (type 1) lesion contains enough atherogenic lipoprotein to elicit an increase in macrophages and formation of scattered macrophage foam cells. As in subsequent lesion types, the changes are more marked in locations of arteries with adaptive intimal thickening. (Adaptive thickenings, which are present at constant locations in everyone from birth, do not obstruct the lumen and represent adaptations to local mechanical forces). Type II lesions consist primarily of layers of macrophage foam cells and lipid-laden smooth muscle cells and include lesions grossly designated as fatty streaks. Type III is the intermediate stage between type II and type IV (atheroma, a lesion that is potentially symptom-producing). In addition to the lipid-laden cells of type II, type III lesions contain scattered collections of extracellular lipid droplets and particles that disrupt the coherence of some intimal smooth muscle cells. This extracellular lipid is the immediate precursor of the larger, confluent, and more disruptive core of extracellular lipid that characterizes type IV lesions. Beginning around the fourth decade of life, lesions that usually have a lipid core may also contain thick layers of fibrous connective tissue (type V lesion) and/or fissure, hematoma, and thrombus (type VI lesion). Some type V lesions are largely calcified (type Vb), and some consist mainly of fibrous connective tissue and little or no accumulated lipid or calcium (type Vc).
A large family of bacterial activator proteins. (1988)

At least nine different bacterial proteins belong to the LysR family. The gene sequence for one of these proteins is presented here. Six others (Escherichia coli LysR, IlvY, CysB; Salmonella typhimurium MetR; Rhizobium NodD; and Enterobacter cloacae AmpR) are known to activate other genes. Based on sequence alignments, each member of this family is predicted to have a helix-turn-helix DNA binding motif near its amino terminus. The combined evidence indicates that all nine proteins are related by common ancestry, are similarly folded, and are not detectably related to other known bacterial regulatory proteins. The DNA database searching procedure and other methods used in this study should be useful in detecting other groups of related proteins.
A general theory of bibliometric and other cumulative advantage processes (1976)

Abstract A Cumulative Advantage Distribution is proposed which models statistically the situation in which success breeds success. It differs from the Negative Binomial Distribution in that lack of success, being a non‐event, is not punished by increased chance of failure. It is shown that such a stochastic law is governed by the Beta Function, containing only one free parameter, and this is approximated by a skew or hyperbolic distribution of the type that is widespread in bibliometrics and diverse social science phenomena. In particular, this is shown to be an appropriate underlying probabilistic theory for the Bradford Law, the Lotka Law, the Pareto and Zipf Distributions, and for all the empirical results of citation frequency analysis. As side results one may derive also the obsolescence factor for literature use. The Beta Function is peculiarly elegant for these manifold purposes because it yields both the actual and the cumulative distributions in simple form, and contains a limiting case of an inverse square law to which many empirical distributions conform.
Comparison of Replication-Competent, First Generation, and Helper-Dependent Adenoviral Vaccines (2009)

All studies using human serotype 5 Adenovirus (Ad) vectors must address two major obstacles: safety and the presence of pre-existing neutralizing antibodies. Helper-Dependent (HD) Ads have been proposed as alternative vectors for gene therapy and vaccine development because they have an improved safety profile. To evaluate the potential of HD-Ad vaccines, we compared replication-competent (RC), first-generation (FG) and HD vectors for their ability to induce immune responses in mice. We show that RC-Ad5 and HD-Ad5 vectors generate stronger immune responses than FG-Ad5 vectors. HD-Ad5 vectors gave lower side effects than RC or FG-Ad, producing lower levels of tissue damage and anti-Ad T cell responses. Also, HD vectors have the benefit of being packaged by all subgroup C serotype helper viruses. We found that HD serotypes 1, 2, 5, and 6 induce anti-HIV responses equivalently. By using these HD serotypes in heterologous succession we showed that HD vectors can be used to significantly boost anti-HIV immune responses in mice and in FG-Ad5-immune macaques. Since HD vectors have been show to have an increased safety profile, do not possess any Ad genes, can be packaged by multiple serotype helper viruses, and elicit strong anti-HIV immune responses, they warrant further investigation as alternatives to FG vectors as gene-based vaccines.
Synthesis and study of a spin-labeled cyclophosphamide analog 3-(1-oxy-2,2,6,6-tetramethyl-4-piperidinyl)cyclophosphamide (1982)

3-(1-Oxy-2,2,6,6-tetramethyl-4-piperidinyl)cyclophosphamide (7) was isolated in 36% yield following H2O2-Na2WO4 oxidation of 3-(2,2,6,6-tetramethyl-4-piperidinyl)cyclophosphamide (6), which was synthesized in three steps (25% yield) starting with 4-amino-2,2,6,6-tetramethylpiperidine. Binding of 7 to mouse liver microsomes was investigated by optical and electron spin resonance spectroscopy. Compared with the mouse liver microsomal metabolism of 1, separate incubations of 6 and an ca. 1:1 mixture of 1 and 6 gave approximately 90 and 60% less acrolein, respectively. A spin-labeled metabolite of 7, viz., N-(1-oxy-2,2,6,6-tetramethyl-4-piperidinyl)phosphoramide mustard (9), was synthesized and its intramolecular O-alkylation at pH 7.4, 37 degrees C, was studied by 31P NMR spectroscopy. Compounds 7 and 9 were inactive in screening tests against L1210 lymphoid leukemia in mice.
Vaccination with autoantigen protects against aggregated β‐amyloid and glutamate toxicity by controlling microglia: effect of CD4+CD25+ T cells (2004)

Neurodegenerative diseases differ in etiology but are propagated similarly. We show that neuronal loss caused by intraocular injection of aggregated beta-amyloid was significantly greater in immunodeficient mice than in normal mice. The neurodegeneration was attenuated or augmented by elimination or addition, respectively, of naturally occurring CD4(+)CD25(+) regulatory T cells (Treg). Vaccination with retina-derived antigens or with the synthetic copolymer glatiramer acetate (Copolymer-1, Cop-1), but not with beta-amyloid, reduced the ocular neuronal loss. In mouse hippocampal slices, microglia encountering activated T cells overcame the cytotoxicity of aggregated beta-amyloid. These findings support the concept of "protective autoimmunity", show that a given T cell-based vaccination is protective at a particular site irrespective of toxicity type, and suggest that locally activated T cells induce a microglial phenotype that helps neurons withstand the insult. Alzheimer's and other neurodegenerative diseases might be arrested or retarded by vaccination with Cop-1 or related compounds or by treatment with compounds that weaken Treg suppression.
Butyrate derivatives. New agents for stimulating fetal globin production in the beta-globin disorders. (1994)

These agents may provide a new and specific approach for ameliorating the clinical manifestations of sickle cell disease and beta-thalassemia.
Antibacterial Activity of Nitric Oxide-Releasing Hyperbranched Polyamidoamines (2017)

Hyperbranched polyamidoamines (h-PAMAM) were prepared using a one-pot reaction to have similar molecular weight to third generation PAMAM (G3-PAMAM) dendrimers, and then functionalized with N-diazeniumdiolate nitric oxide (NO) donors. A wide range of NO storage capacities (∼1-2.50 μmol mg<sup>-1</sup>) and NO-release kinetics (t<sub>1/2</sub> ∼30-80 min) were achieved by changing the extent of propylene oxide (PO) modification. The therapeutic potential of these materials was evaluated by studying their antibacterial activities and toxicity against common dental pathogens and human gingival fibroblast cells, respectively. Our results indicate that the combination of NO release and PO modification is necessary to yield h-PAMAM materials with efficient bactericidal action without eliciting unwarranted cytotoxicity. Of importance, NO-releasing PO-modified h-PAMAM polymers exhibited comparable biological properties (i.e., antibacterial action and cytotoxicity) to defect-free G3-PAMAM dendrimers, but at a substantially lower synthetic burden.
Role of Glutamate and NMDA Receptors in Alzheimer’s Disease (2016)

Excitatory glutamatergic neurotransmission via N-methyl-d-aspartate receptor (NMDAR) is critical for synaptic plasticity and survival of neurons. However, excessive NMDAR activity causes excitotoxicity and promotes cell death, underlying a potential mechanism of neurodegeneration occurred in Alzheimer's disease (AD). Studies indicate that the distinct outcomes of NMDAR-mediated responses are induced by regionalized receptor activities, followed by different downstream signaling pathways. The activation of synaptic NMDARs initiates plasticity and stimulates cell survival. In contrast, the activation of extrasynaptic NMDARs promotes cell death and thus contributes to the etiology of AD, which can be blocked by an AD drug, memantine, an NMDAR antagonist that selectively blocks the function of extrasynaptic NMDARs.
Reaction of octacarbonyldicobalt with organo-silanes, -germanes, and -stannanes: formation, properties, and vibrational spectra of trimethylgermyltetracarbonylcobalt and related complexes (1974)

The hydrides R3MH (R = Me, M = Si, Ge, or Sn; R = Et, M = Ge) react exothermically with Co2(CO)8 at 20 °C affording in high yield the complexes R3MCo(CO)4[R = Me, M = Si (I); M = Ge (II); M = Sn (III); and R = Et, M = Ge (IV)]. Conversion of (I) to (II) or (III) and of (II) to (III) occurs on reaction with Me3MH (M = Ge or Sn), and (II) can also be prepared from (I) with Me3GeBr. The Ge–Co bond in (II) is cleaved by HCl or HgCl2; (II) with Et3N or piperidine forms tetracarbonylcobaltate adducts. The vibrational spectra of (II)–(IV) are reported, with ν(M–Co) assigned to polarised Raman shifts respectively at 192,177, and 188 cm–1. Variation with M of the vapour-phase i.r.-intensity of one of the two a1 CO stretching fundamentals expected for C3v symmetry points to a significant out-of-plane displacement of equatorial carbonyl groups in the direction of the silicon atom in (I), but with no analogous effect in (II) or (III). Deviations from C3v selection rules observed in the solid state for (II) and (III) are also discussed.
Statistical models for automatic video annotation and retrieval (2004)

We apply a continuous relevance model (CRM) to the problem of directly retrieving the visual content of videos using text queries. The model computes a joint probability model for image features and words using a training set of annotated images. The model may then be used to annotate unseen test images. The probabilistic annotations are used for retrieval using text queries. We also propose a modified model - the normalized CRM - which substantially improves performance on a subset of the TREC video dataset.
Hidden Variable Fractal Interpolation Functions (1989)

Interpolation functions $f:[0,1] \to \mathbb{R}$ of the following nature are constructed. Given data \[ \left\{ {\left( {t_n ,x_n } \right) \in [0,1] \times \mathbb{R}:n = 0,1,2, \cdots ,N} \right\}\] with $0 = t_0 < t_1 < \cdots <' t_N = 1$, f obeys \[ f(t_n ) = x_n ,\qquad n = 0,1,2, \cdots ,N.\] Furthermore, the graph of f is the projection of a set G in $\mathbb{R}^M $ (M an integer greater than or equal to 2) that is homeomorphic to $[0,1]$ and is the attractor for an iterated function system consisting of afflne maps in $\mathbb{R}^M $. The latter characterization ensures that f can be computed rapidly while possessing many ”hidden” variables, on which its values continuously depend, which allow great flexibility and diversity in the interpolant, making it potentially useful in approximation theory. Estimtes and exact values for the fractal dimensions of G and the graph of f are obtained.
Subdiffraction resolution in far-field fluorescence microscopy (1999)

We overcame the resolution limit of scanning far-field fluorescence microscopy by disabling the fluorescence from the outer part of the focal spot. Whereas a near-UV pulse generates a diffraction-limited distribution of excited molecules, a spatially offset pulse quenches the excited molecules from the outer part of the focus through stimulated emission. This results in a subdiffraction-sized effective point-spread function. For a 1.4 aperture and a 388-nm excitation wavelength spatial resolution is increased from 150 +/- 8 nm to 106 +/- 8 nm with a single offset beam. Superior lateral resolution is demonstrated by separation of adjacent Pyridine 2 nanocrystals that are otherwise indiscernible.
Modeling “psychosis” in vitro by inducing disordered neuronal network activity in cortical brain slices (2009)

An in vitro model of psychosis is proposed based on the two different approaches to cause aberrant network activity in layer V pyramidal cells of prefrontal brain slices: (1) psychedelic hallucinogens such as lysergic acid diethylamide and (2) minimal GABA(A) receptor antagonism, modeling the GABA interneuron deficit in schizophrenia. A test of this model would be to determine if drugs that normalize aberrant networks in brain slices have efficacy in the treatment of schizophrenia. Selective agonists of glutamate mGlu2/3 metabotropic receptors, which are highly effective in suppressing aberrant network activity in slices, are the most advanced toward reaching that clinical endpoint. In accord with the model, a recent phase II clinical trial shows that an mGlu2/3 receptor agonist is equivalent in efficacy to a standard antipsychotic drug for both negative and positive symptoms in schizophrenic patients, but without the usual side effects. D1/5 dopamine receptor agonists are also effective in normalizing aberrant network activity induced by both hallucinogens and minimal GABA(A) antagonism; clinical efficacy remains to be determined. A general model of network regulation is presented, involving astrocytes, GABA interneurons, and glutamatergic pyramidal cells, revealing a wide range of potential sites hitherto not considered as therapeutic targets.