gebhart/patrepeval huggingface dataset:
IL-12 p40 Homodimer-Dependent Macrophage Chemotaxis and Respiratory Viral Inflammation Are Mediated through IL-12 Receptor β1 (2003)

Leukocyte recruitment to the airway lumen is a central feature of inflammatory conditions such as asthma and respiratory viral infection. Characterization of mediators that regulate leukocyte recruitment in these conditions revealed increased IL-12 p40 homodimer (p80) levels were associated with enhanced airway macrophage accumulation. To examine this association, we used in vivo and in vitro assays to demonstrate p80, but not IL-12 or p40, provided a macrophage chemoattractant signal. Macrophages from genetically deficient mice indicated p80-dependent chemotaxis was independent of IL-12 and required IL-12Rbeta1 (Rbeta1) expression. Furthermore, analysis of murine cell lines and primary culture macrophages revealed Rbeta1 expression, with an intact cytoplasmic tail, was necessary and sufficient to mediate p80-dependent chemotaxis. To examine the role for Rbeta1 in mediating macrophage accumulation in vivo, we contrasted Sendai virus-driven airway inflammation in wild-type and Rbeta1-deficient mice. Despite similar viral burden and production of the macrophage chemoattractant p80, the Rbeta1-deficient mice displayed a selective decrease in airway macrophage accumulation and resistance to viral-dependent mortality. Thus, Rbeta1 mediates p80-dependent macrophage chemotaxis and inhibition of the p80-Rbeta1 interaction may provide a novel anti-inflammatory strategy to manipulate the inflammation associated with asthma and respiratory viral infection.
Acrolein: Sources, metabolism, and biomolecular interactions relevant to human health and disease (2008)

Acrolein (2-propenal) is ubiquitously present in (cooked) foods and in the environment. It is formed from carbohydrates, vegetable oils and animal fats, amino acids during heating of foods, and by combustion of petroleum fuels and biodiesel. Chemical reactions responsible for release of acrolein include heat-induced dehydration of glycerol, retro-aldol cleavage of dehydrated carbohydrates, lipid peroxidation of polyunsaturated fatty acids, and Strecker degradation of methionine and threonine. Smoking of tobacco products equals or exceeds the total human exposure to acrolein from all other sources. The main endogenous sources of acrolein are myeloperoxidase-mediated degradation of threonine and amine oxidase-mediated degradation of spermine and spermidine, which may constitute a significant source of acrolein in situations of oxidative stress and inflammation. Acrolein is metabolized by conjugation with glutathione and excreted in the urine as mercapturic acid metabolites. Acrolein forms Michael adducts with ascorbic acid in vitro, but the biological relevance of this reaction is not clear. The biological effects of acrolein are a consequence of its reactivity towards biological nucleophiles such as guanine in DNA and cysteine, lysine, histidine, and arginine residues in critical regions of nuclear factors, proteases, and other proteins. Acrolein adduction disrupts the function of these biomacromolecules which may result in mutations, altered gene transcription, and modulation of apoptosis.
Classification of Imbalanced Data by Using the SMOTE Algorithm and Locally Linear Embedding (2006)

The classification of imbalanced data is a common practice in the context of medical imaging intelligence. The synthetic minority oversampling technique (SMOTE) is a powerful approach to tackling the operational problem. This paper presents a novel approach to improving the conventional SMOTE algorithm by incorporating the locally linear embedding algorithm (LLE). The LLE algorithm is first applied to map the high-dimensional data into a low-dimensional space, where the input data is more separable, and thus can be oversampled by SMOTE. Then the synthetic data points generated by SMOTE are mapped back to the original input space as well through the LLE. Experimental results demonstrate that the underlying approach attains a performance superior to that of the traditional SMOTE
Partial migration to seasonally‐unstable habitat facilitates biological invasions in a predator‐dominated system (2015)

Although partial migration, a phenomenon in which some individuals in a population conduct seasonal migrations while others remain resident, is common among animals, its importance in facilitating biological invasions has not been demonstrated. To illustrate how partial migration might facilitate invasions in spatially complex habitats, we developed an individual‐based model of common carp Cyprinus carpio in systems of lakes and winterkill‐prone marshes in the Upper Mississippi River Basin (UMRB). Our model predicted that common carp are unable to become invasive in lakes of the UMRB unless they conduct partial migrations into winterkill‐prone marshes in which recruitment rates are high in the absence of native predators that forage on carp eggs and larvae. Despite low dispersal rates of juveniles and higher mortality rates of migrants, partial migration was adaptive across a wide range of migration rates and winterkill frequencies. Partial migration rates as low as 10% and winterkill occurrence as infrequent as once in 20 years were sufficient to cause invasiveness because of carp's reproductive potential and longevity. Consistent with the results of our model, empirical data showed that lake connectivity to winterkill‐prone marshes was an important driver of carp abundance within the study region. Our results demonstrate that biological invasions may be driven by a small, migratory contingent of a population that exploits more beneficial reproductive habitats.
Electric‐Field‐Directed Growth of Gold Nanorods in Aqueous Surfactant Solutions (2004)

Abstract The factors affecting the nucleation and growth of gold nanorods, (Jana et al., Adv. Mater. 2001 , 13 , 1389) have been investigated. It is shown that the size and aspect ratio can be controlled through the use of different sized seed particles. The length of the rods can be tuned from 25–170 nm, while the width remains almost constant at 22–25 nm. The formation of rods requires the presence of the cationic surfactant cetyltrimethylammonium bromide (CTAB). Lower temperature favors rod formation, although this reduces CTAB solubility. The addition of chloride ions or the use of dodecyltrimethylammonium bromide (DTAB) leads to shorter‐aspect rods. Au III and Au I are shown to be quantitatively bound to the CTAB micelles. We propose an electrochemical mechanism for rod formation, whereby the flux of Au I bound to cationic micelles to the seed surface is maximized at points of highest curvature, where the electrical double layer gradient is highest. Initial numerical solutions to the electric potential and field around an ellipsoid in a 1:1 electrolyte are provided, which indicate that the field at the particle tip scales linearly with the aspect ratio. Mean free passage times for ions are found to be shortest at the tips. The results provide a general explanation for the formation of non‐equilibrium crystal habits and a mechanism for controlling crystal growth.
Sequence of the Cloned Gene for the Constant Region of Murine γ2b Immunoglobulin Heavy Chain (1979)

The complete nucleotide sequence of the gamma 2b constant region gene cloned from BALB/c liver DNA is reported. The sequence of approximately 1870 base pairs includes the 5' flanking, 3' untranslated, and 3' flanking regions and three introns. The C gamma 2b coding region is divided by these introns into four segments corresponding to the homology domains and hinge region of the protein. The introns separating the hinge from the CH2 domain and the CH2 from the CH3 domain are small (106 and 119 base pairs). A larger intervening sequence of 314 base pairs separates the CH1 and hinge regions. The stretch of DNA comprising this large intron plus the hinge shows a strong homology with the other CH domains.
Polarization rotation Bragg grating using Si wire waveguide with non-vertical sidewall (2014)

We report polarization independent Bragg grating wavelength filter using polarization rotation. A non-vertical waveguide sidewall and antisymmetric grating structure can be used to generate the polarization rotation of the fundamental modes. The diffraction efficiencies and peaks becomes the same for two orthogonal input polarizations. The concept was verified by simulation and experiment.
High‐dose cyclophosphamide inhibition of humoral immune response to murine monoclonal antibody 3F8 in neuroblastoma patients: Broad implications for immunotherapy (2006)

HD-Cy reliably blocks humoral responses to a murine antibody. This capacity to prevent host rejection of foreign or not fully humanized proteins raises the possibility of a broad role for HD-Cy in immunotherapeutic strategies.
The herpes simplex virus type 1 regulatory protein ICP0 enhances virus replication during acute infection and reactivation from latency (1993)

ICP0 is a potent activator of herpes simplex virus type 1 gene expression in transient assays and in productive infection. A role for ICP0 in reactivation from latency in vivo has also been suggested on the basis of the observation that viruses with mutations in both copies of the diploid gene for ICP0 reactivate less efficiently than wild-type virus. Because the ICP0 gene is contained entirely within the coding sequences for the latency-associated transcripts (LATs), ICP0 mutants also contain mutations in LAT coding sequences. This overlap raises the question of whether mutations in ICP0 or the LATs, which have also been implicated in reactivation, are responsible for the reduced reactivation frequencies characteristic of ICP0 mutants. Two approaches were taken to examine more definitively the role of ICP0 in the establishment and reactivation of latency. First, a series of ICP0 nonsense, insertion, and deletion mutant viruses that exhibit graded levels of ICP0-specific transactivating activity were tested for parameters of the establishment and reactivation of latency in a mouse ocular model. Although these mutants are ICP0 LAT double mutants, all nonsense mutants induced the synthesis of near-wild-type levels of the 2-kb LAT, demonstrating that the nonsense linker did not disrupt the synthesis of this LAT species. All mutants replicated less efficiently than the wild-type virus in mouse eyes and ganglia during the acute phase of infection. The replication efficiencies of the mutants at these sites corresponded well with the ICP0 transactivating activities of individual mutant peptides in transient expression assays. All mutants exhibited reduced reactivation frequencies relative to those of wild-type virus, and reactivation frequencies, like replication efficiencies in eyes and ganglia, correlated well with the level of ICP0 transactivating activity exhibited by individual mutant peptides. The amount of DNA of the different mutants varied in latently infected ganglia, as demonstrated by polymerase chain reaction analysis. No correlation was evident between reactivation frequencies and the levels of viral DNA in latently infected ganglia. Thus, replication and reactivation efficiencies of ICP0 mutant viruses correlated well with the transactivating efficiency of the corresponding mutant peptides. In a second approach to examining the role of ICP0 in latency, a single copy of the wild-type gene for ICP0 was inserted into the genome of an ICP0- LAT- double mutant, 7134, which exhibits a marked impairment in its ability to replicate in the mouse eye and reactivate from latency.(ABSTRACT TRUNCATED AT 400 WORDS)
Declining brain activity in cognitively normal apolipoprotein E ɛ4 heterozygotes: A foundation for using positron emission tomography to efficiently test treatments to prevent Alzheimer's disease (2001)

Cross-sectional positron emission tomography (PET) studies find that cognitively normal carriers of the apolipoprotein E (APOE) epsilon4 allele, a common Alzheimer's susceptibility gene, have abnormally low measurements of the cerebral metabolic rate for glucose (CMRgl) in the same regions as patients with Alzheimer's dementia. In this article, we characterize longitudinal CMRgl declines in cognitively normal epsilon4 heterozygotes, estimate the power of PET to test the efficacy of treatments to attenuate these declines in 2 years, and consider how this paradigm could be used to efficiently test the potential of candidate therapies for the prevention of Alzheimer's disease. We studied 10 cognitively normal epsilon4 heterozygotes and 15 epsilon4 noncarriers 50-63 years of age with a reported family history of Alzheimer's dementia before and after an interval of approximately 2 years. The epsilon4 heterozygotes had significant CMRgl declines in the vicinity of temporal, posterior cingulate, and prefrontal cortex, basal forebrain, parahippocampal gyrus, and thalamus, and these declines were significantly greater than those in the epsilon4 noncarriers. In testing candidate primary prevention therapies, we estimate that between 50 and 115 cognitively normal epsilon4 heterozygotes are needed per active and placebo treatment group to detect a 25% attenuation in these CMRgl declines with 80% power and P = 0.005 in 2 years. Assuming these CMRgl declines are related to the predisposition to Alzheimer's dementia, this study provides a paradigm for testing the potential of treatments to prevent the disorder without having to study thousands of research subjects or wait many years to determine whether or when treated individuals develop symptoms.
DNA Extraction from Formalin-fixed, Paraffin-embedded Tissues (1997)

Several DNA extraction methods have been used for formalin-fixed, paraffin-embedded tissues, with variable results being reported regarding the suitability of DNA obtained from such sources to serve as template in polymerase chain reaction (PCR)-based genetic analyses. We present a method routinely used for archival material in our laboratory that reliably yields DNA of sufficient quality for PCR studies. This method is based on extended proteinase K digestion (250 micrograms/ml in an EDTA-free calcium-containing buffer supplemented with mussel glycogen) followed by phenol-chloroform extraction. Agarose gel electrophoresis of both digestion buffer aliquots and PCR amplification of the beta-globin gene tested the suitability of the retrieved DNA for PCR amplification.
Tumor-associated and microbial proteases compromise host IgG effector functions by a single cleavage proximal to the hinge (2009)

The successful elimination of pathogenic cells and microorganisms by the humoral immune system relies on effective interactions between host immunoglobulins and Fc gamma receptors on effector cells, in addition to the complement system. Essential Ig motifs that direct those interactions reside within the conserved IgG lower hinge/CH2 interface. We noted that a group of tumor-related and microbial proteases cleaved human IgG1s in that region, and the "nick" of just one of the heavy chains profoundly inhibited IgG1 effector functions. We focused on IgG1 monoclonal antibodies (mAbs) since IgG1 is the most abundant human subclass and demonstrates robust Fc-mediated effector functions. The loss of Fc-mediated cell killing activities was correlated with diminished binding to the Fc gamma family of receptors, but a similar decrease in affinity was not observed toward the FcRn receptor that maintains IgG in circulation. Endogenous human IgG cleavage products of comparable size to mAbs with the single cleavage were detected by Western blot analysis in synovial fluid from patients with rheumatoid arthritis and in breast carcinoma extracts. Their detection is problematic under physiological conditions, since there is no loss of structure, and antigen-binding capability is unaffected. These findings suggest that within the hostile proteolytic microenvironments associated with many diseases, key effector functions of host IgGs, or therapeutic Abs, may be compromised.
Hydrophilic spacer groups in polymerizable lipids: formation of biomembrane models from bulk polymerized lipids (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrophilic spacer groups in polymerizable lipids: formation of biomembrane models from bulk polymerized lipidsR. Elbert, A. Laschewsky, and H. RingsdorfCite this: J. Am. Chem. Soc. 1985, 107, 14, 4134–4141Publication Date (Print):July 1, 1985Publication History Published online1 May 2002Published inissue 1 July 1985https://pubs.acs.org/doi/10.1021/ja00300a007https://doi.org/10.1021/ja00300a007research-articleACS PublicationsRequest reuse permissionsArticle Views287Altmetric-Citations108LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Neural and Cancer Stem Cells in Tumor Suppressor Mouse Models of Malignant Astrocytoma (2008)

Malignant astrocytomas are highly invasive brain tumors that portend poor prognosis and dismal survival. Mouse models that genetically resemble the human malignancy provide insight into the nature and pathogenesis of these cancers. We previously reported tumor suppressor mouse models based on conditional inactivation of human astrocytoma-relevant genes p53, Nf1, and Pten. These mice develop, with full penetrance, varying grades of astrocytic malignancy that recapitulate the human condition histologically and molecularly. Our studies indicate a central role for neural stem cells and stem-cell-like cancer cells in tumor initiation and progression. These mouse models thus represent powerful tools for investigating various aspects of tumor development that otherwise cannot be explored in humans. Further studies will provide a better understanding of the biology of these tumors and will hopefully pave the way for more effective therapeutic approaches for these devastating diseases.
Role of beta-1 integrins in organ specific adhesion of melanoma cells in vitro. (1993)

These data suggest that alpha 2 beta 1 and alpha 6 beta 1 mediate differential melanoma cell attachment to organ tissue sections in vitro and that differences in integrin expression of these melanoma cells may be involved in differential organ colonization in vivo.
A machine learning based approach for table detection on the web (2002)

Table is a commonly used presentation scheme, especially for describing relational information. However, table understanding remains an open problem. In this paper, we consider the problem of table detection in web documents. Its potential applications include web mining, knowledge management, and web content summarization and delivery to narrow-bandwidth devices. We describe a machine learning based approach to classify each given table entity as either genuine or non-genuine. Various features reflecting the layout as well as content characteristics of tables are studied.In order to facilitate the training and evaluation of our table classifier, we designed a novel web document table ground truthing protocol and used it to build a large table ground truth database. The database consists of 1,393 HTML files collected from hundreds of different web sites and contains 11,477 leaf TABLE elements, out of which 1,740 are genuine tables. Experiments were conducted using the cross validation method and an F-measure of 95.89% was achieved.
Characterization of the WW Domain of Human Yes-associated Protein and Its Polyproline-containing Ligands (1997)

We had previously identified the WW domain as a novel globular domain that is composed of 38-40 semiconserved amino acids and is involved in mediating protein-protein interaction. The WW domain is shared by proteins of diverse functions including structural, regulatory, and signaling proteins in yeast, nematode, and mammals. Functionally it is similar to the Src homology 3 domain in that it binds polyproline ligands. By screening a 16-day mouse embryo expression library, we identified two putative ligands of the WW domain of Yes kinase-associated protein which we named WW domain-binding proteins 1 and 2. These proteins interacted with the WW domain via a short proline-rich motif with the consensus sequence of four consecutive prolines followed by a tyrosine. Herein, we report the cDNA cloning and characterization of the human orthologs of WW domain-binding proteins 1 and 2. The products encoded by these cDNA clones represent novel proteins with no known function. Furthermore, these proteins show no homology to each other except for a proline-rich motif. By fluorescence in situ hybridization on human metaphase chromosomes, we mapped the human genes for WW domain-binding proteins 1 and 2 to chromosomes 2p12 and 17q25, respectively. In addition, using site-directed mutagenesis, we determined which residues in the WW domain of Yes kinase-associated protein are critical for binding. Finally, by synthesizing peptides in which the various positions of the four consecutive proline-tyrosine motif and the five surrounding residues were replaced by all possible amino acid residues, we further elucidated the binding requirements of this motif.
Comparison of three methods for the measurement of printed antenna efficiency (1988)

Three methods for the measurement of antenna efficiency are evaluated: (1) the Wheeler cap method, (2) the radiometric method, and (3) the directivity/gain method. Each of these methods was used to measure the efficiency of four different printed antennas (three microstrip patches with various feeds, and an eight-element series-fed microstrip array). These methods and the experimental results which were obtained are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Stable expression of biogenic amine transporters reveals differences in inhibitor sensitivity, kinetics, and ion dependence. (1994)

We have constructed stable cell lines expressing transporters for dopamine (DA), norepinephrine (NE), and serotonin (5-HT) by transfection with cloned cDNAs. The parental LLC-PK1 cell does not express any of these neurotransmitter transporters. Therefore, monoamine transport activities in each of these cell lines are due to the transfected DNA only, allowing comparison in the same background. Drug inhibition profiles for each cell line are distinct and as expected for each transporter. LLC-NET and LLC-DAT cells transported both NE and DA and both cell types exhibited a lower KM for DA transport than for NE transport. Analysis of Vmax data for LLC-NET cells suggests that substrate is bound to the NE transporter during the rate-limiting step(s) in transport. The cocaine analog 2-beta-carbomethoxy-3 beta-(4-[125I]iodophenyl)tropane binds to each cell type, and is displaced by transport substrate in each case. Binding and transport measurements on parallel cell cultures allowed estimation of turnover numbers for norepinephrine, dopamine, and serotonin transporters. All three transporters require external Na+ and Cl-. The Na+ concentration dependence suggests that a single Na+ ion is involved in transport catalyzed by norepinephrine and serotonin transporters while more than one Na+ ion participate in transport mediated by the dopamine transporter.