gebhart/patrepeval huggingface dataset:
Preoperative Three-dimensional CT Predicts Intraoperative Findings in Hip Arthroscopy (2012)

Our data suggest CT has moderate value in predicting mechanically based labral tear patterns, although better parameters for assessment of pincer lesions are needed. Diagnostic assessment of patients with suspected FAI may be improved with use of 3D CT.
Lack of detectable somatic hypermutation in the V region of the Ig H chain gene of a human chronic B lymphocytic leukemia. (1988)

Monoclonal human B cell tumors are a model system for the study of somatic hypermutation of the Ig genes of humans. It was previously shown that a number of B cell lymphomas exhibited striking V region point mutation, hypothesized to result from the somatic hypermutation mechanism. In this study we have extended the analysis to chronic lymphocytic leukemia. We have cloned and sequenced the productive Vh representing five different cells from a monoclonal chronic lymphocytic leukemia. All five Vh sequences were identical. Therefore, the Vh region in this leukemia was not the subject of detectable somatic mutation. These data suggest that chronic lymphocytic leukemia might lack the mechanism for somatic hypermutation and represent a stage of normal B lymphocyte differentiation in which the somatic hypermutation mechanism is not active.
Expression of Basal and Luminal Epithelium-Specific Keratins in Normal, Benign, and Malignant Breast Tissue1 (1988)

Journal Article Expression of Basal and Luminal Epithelium-Specific Keratins in Normal, Benign, and Malignant Breast Tissue1 Get access Shahnaz Hashmi Dairkee, Shahnaz Hashmi Dairkee Search for other works by this author on: Oxford Academic PubMed Google Scholar Lynn Puett, Lynn Puett Search for other works by this author on: Oxford Academic PubMed Google Scholar Adeline J. Hackett Adeline J. Hackett 2Peralta Cancer Research Institute3023 Summit St., Oakland, CA 94609 Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 80, Issue 9, 6 July 1988, Pages 691–695, https://doi.org/10.1093/jnci/80.9.691 Published: 06 July 1988 Article history Received: 01 February 1988 Revision received: 04 April 1988 Accepted: 12 April 1988 Published: 06 July 1988
Reducing Mortality from Colorectal Cancer by Screening for Fecal Occult Blood (1993)

Annual fecal occult-blood testing with rehydration of the samples decreased the 13-year cumulative mortality from colorectal cancer by 33 percent.
The co-receptor function of CD4. (1991)

CD4 is a critical component of the T cell receptor complex that recognizes peptides bound to MHC class II molecules. This can be observed at all stages of T cell development, activation, and function. CD4 has been termed a co-receptor to indicate that its most important activity is to bind the same peptide: self class II MHC complex as the T cell receptor and to transduce positive activating signals in conjunction with the T cell receptor. This behavior has been shown by several independent experimental systems: direct cross-linking of the T cell receptor to CD4, the inhibition of T cell activation by anti-CD4, the transfection of CD4 into CD4- T cells, and by the phenomenon of epitope interference, as described in this review. All of these approaches suggest that the participation of CD4 as a co-receptor in antigen: self class II MHC recognition potentiates activation by 100-fold. Given the complex nature of the ligand recognized by the T cell receptor, the co-receptor function of CD4 virtually eliminates the possibility of CD4 T cells recognizing peptides presented by class I MHC molecules, in keeping with many in vivo observations.
Infection of HTLV-III/LAV in HTLV-I-Carrying Cells MT-2 and MT-4 and Application in a Plaque Assay (1985)

The human T-cell lines MT-2 and MT-4 carry the human T-cell leukemia virus type I (HTLV-I). When MT-2 and MT-4 were infected with HTLV-III, the probable etiologic agent of the acquired immune deficiency syndrome (AIDS), rapid cytopathogenic effects and cytotoxicity were observed that made it possible to titrate the biologically active virus in a plaque-forming assay. The cytopathogenic effects were preceded by the rapid induction and increase of HTLV-III antigens as revealed by immunofluorescence and immunoprecipitation. Activities of HTLV-III were neutralized by the human antibodies against the virus when immunofluorescence and plaque assays were used. Essentially the same results were obtained with the lymphadenopathy-associated virus (LAV1).
Electro-optic multimode waveguide modulator or switch (1979)

Details of an investigation of a new type of electro-optic multimode waveguide modulator or switch are reported. The device makes use of the concept of imaging in a multimode waveguide. Simultaneous switching of a few low-order modes is obtained electro-optically by nonuniform modulation of the refractive-index profile of the active waveguide section. Small fabrication tolerances can be compensated for by electrical means and the device can be realized in various sizes and configurations for easy and efficient coupling to lasers, fibers, and other components. Modulation, switching, and power division have been demonstrated in waveguide devices of various widths and lengths fabricated on Ti-diffused LiNbO3. Coupling losses as low as 0.5 dB have been observed and extinction ratios of 13–20 dB with 20–80 V drive have been obtained.
Comparative characterization and autoradiographic distribution of neuropeptide Y receptor subtypes in the rat brain (1993)

Some evidence has suggested the existence and differential distribution of neuropeptide Y (NPY) receptor subtypes in the mammalian brain (Dumont et al., 1990; Aicher et al., 1991). We now report on the extensive characterization and visualization of at least two classes of NPY receptor sites using a highly selective Y1 analog, [Leu31,Pro34]-NPY or [Pro34]-NPY, and a relatively specific Y2 competitor, NPY13-36. Autoradiographic studies using 125I-peptide YY (125I-PYY) clearly reveal that the Y1 receptor subtype is most abundant in various cortical areas, the dentate gyrus of the hippocampal formation, the claustrum, and the reuniens nucleus of the thalamus. In most other regions, 125I-PYY binding is potently inhibited by increasing concentrations of either NPY2-36 or NPY13-36, suggesting a Y2-like profile. Furthermore, binding assays using homogenates from discrete brain regions clearly demonstrate that various NPY fragments and analogs compete for 125I-PYY labeling with profiles indicative of heterogeneity of NPY receptor subtypes, even in the presence of a selective Y1 blocker. Thus, it is likely that, in addition to the Y1 receptor, which is particularly concentrated in cortical areas, the rat brain is enriched with a receptor class (Y2) that can exist under high- or low-affinity states or with additional receptor subtypes that are recognized by 125I-PYY. These findings cannot be explained by the existence of the very recently reported Y3 receptor subtype, since PYY does not possess significant affinity to this site (Grundemar et al., 1991). Further experiments are currently in progress to determine the nature and functional significance of each of these NPY/PYY receptor sites.
Major Structural Differences between Pokeweed Antiviral Protein and Ricin A‐Chain do not Account for their Differing Ribosome Specificity (1996)

Pokeweed antiviral protein (PAP) and the A-chain of ricin (RTA) are two members of a family of ribosome-inactivating proteins (RIPS) that are characterised by their ability to catalytically depurinate eukaryotic ribosomes, a modification that makes the ribosomes incapable of protein synthesis. In contrast to RTA, PAP can also inactivate prokaryotic ribosomes. In order to investigate the reason for this differing ribosome specificity, a series of PAP/RTA hybrid proteins was prepared to test for their ability to depurinate prokaryotic and eukaryotic ribosomes. Information from the X-ray structures of RTA and PAP was used to design gross polypeptide switches and specific peptide insertions. Initial gross polypeptide swaps created hybrids that had altered ribosome inactivation properties. Preliminary results suggest that the carboxy-terminus of the RIPs (PAP 219-262) does not contribute to ribosome recognition, whereas polypeptide swaps in the amino-terminal half of the proteins did affect ribosome inactivation. Structural examination identified three loop regions that were different in both structure and composition within the amino-terminal region. Directed substitution of RTA sequences into PAP at these sites, however, had little effect on the ribosome inactivation characteristics of the mutant PAPs, suggesting that the loops were not crucial for prokaryotic ribosome recognition. On the basis of these results we have identified regions of RIP primary sequence that may be important in ribosome recognition. The implications of this work are discussed.
Optimal Wasteload Allocation Procedure for Achieving Dissolved Oxygen Water Quality Objectives. I: Sensitivity Analysis (2004)

A method is presented to compute sensitivities of in-stream dissolved oxygen (DO) with respect to perturbations in the load vector and the reaction coefficients that make up the eutrophication cycle. It is shown that the direct sensitivity method, i.e., the repetitive solution of the direct problem, produces the desired information, however at a large computational cost. The utilization of the adjoint sensitivity method proves to be a much more efficient way to compute these sensitivities as large subsets of the sensitivity information domain can be easily extracted with just a few runs. It is found that for the given problem setup, in-stream DO is most sensitive to ammonia, effluent DO, algae, and carbonaceous biochemical oxygen demand (CBOD) loads. Additionally, the computed sensitivities vary considerably in their general trend over the simulation time. Sensitivities also are computed with respect to the reaction coefficients (26 total) that govern the interdependency of all constituents. Sediment oxygen demand proves to be the coefficient with the highest influence that is three orders of magnitude higher than the next set of coefficients comprised of reaeration, CBOD degradation, nitrification, and denitrification. All other coefficients have a negligible influence on DO concentrations. Computations are carried out using a two-dimensional model formulation applied to a long rectangular channel with varying width and slope and periodic but unsteady flow conditions.
Assembly and Analysis of Conical Models for the HIV-1 Core (1999)

The genome of the human immunodeficiency virus (HIV) is packaged within an unusual conical core particle located at the center of the infectious virion. The core is composed of a complex of the NC (nucleocapsid) protein and genomic RNA, surrounded by a shell of the CA (capsid) protein. A method was developed for assembling cones in vitro using pure recombinant HIV-1 CA-NC fusion proteins and RNA templates. These synthetic cores are capped at both ends and appear similar in size and morphology to authentic viral cores. It is proposed that both viral and synthetic cores are organized on conical hexagonal lattices, which by Euler's theorem requires quantization of their cone angles. Electron microscopic analyses revealed that the cone angles of synthetic cores were indeed quantized into the five allowed angles. The viral core and most synthetic cones exhibited cone angles of approximately 19 degrees (the narrowest of the allowed angles). These observations suggest that the core of HIV is organized on the principles of a fullerene cone, in analogy to structures recently observed for elemental carbon.
Use of a Mouse Model to Examine Anti-Helicobacter pylori Agents (1991)

A mouse model of Helicobacter infection of the gastric mucosa was evaluated for in vivo screening of new anti-Helicobacter pylori therapies. The aim of the study was to test antimicrobial agents with known anti-H. pylori effects in humans to validate that similar results were obtained in the mouse model. Specific pathogen-free mice were colonized with H. felis, a cat stomach isolate that has been shown to induce chronic gastritis in gnotobiotic mice. In H. felis-inoculated mice 4 weeks after treatment, only 25% were cleared with erythromycin, 47% with metronidazole, 0% with tetracycline, 70% with amoxycillin, and 25% with bismuth subcitrate. In contrast, triple therapy with metronidazole, amoxycillin, and bismuth subcitrate resulted in 80% eradication, whereas triple therapy with metronidazole, tetracycline, and bismuth subcitrate eradicated the Helicobacter from all the animals. We believe the similarities of these treatments to those reported in the literature for humans warrant the use of this model for the early screening of possible anti-H. pylori therapies, especially as in vitro testing has been found to be so non-predictive of therapeutic success.
Proteoglycans are required for maintenance of Wnt-11 expression in the ureter tips (1996)

Development of the metanephric kidney requires the concerted interaction of two tissues, the epithelium of the ureteric duct and the metanephric mesenchyme. Signals from the ureter induce the metanephric mesenchyme to condense and proliferate around the ureter tip, reciprocal signals from the mesenchyme induce the ureter tip to grow and to branch. Wnt genes encode secreted glycoproteins, which are candidate mediators of these signaling events. We have identified three Wnt genes with specific, non-overlapping expression patterns in the metanephric kidney, Wnt-4, Wnt-7b and Wnt-11. Wnt-4 is expressed in the condensing mesenchyme and the comma- and S-shaped bodies. Wnt-7b is expressed in the collecting duct epithelium from 13.5 days post coitum onward. Wnt-1l is first expressed in the nephric duct adjacent to the metanephric blastema prior to the outgrowth of the ureteric bud. Wnt-l1 expression in Danforth's short-tail mice suggests that signaling from the mesenchyme may regulate Wnt-ll activation. During metanephric development, Wnt-11 expression is confined to the tips of the branching ureter. Maintenance of this expression is independent of Wnt-4 signaling and mature mesenchymal elements in the kidney. Moreover, Wnt-ll expression is maintained in recombinants between ureter and lung mesenchyme suggesting that branching morphogenesis and maintenance of Wnt-ll expression are independent of metanephric mesenchyme-specific factors. Interference with proteoglycan synthesis leads to loss of Wnt-ll expression in the ureter tip. We suggest that Wnt-11 acts as an autocrine factor within the ureter epithelium and that its expression is regulated at least in part by proteoglycans.
eek and erk, new members of the eph subclass of receptor protein-tyrosine kinases. (1991)

We have identified human and rat DNAs encoding two novel members of the eph subclass of putative receptor protein-tyrosine kinases. Rat cDNA clones encoding eek (eph- and elk-related kinase) were isolated from a brain cDNA library probed with DNA encoding the kinase region of the insulin receptor-related receptor. The predicted eek protein contains all the amino acid residues conserved in the catalytic domains of protein-tyrosine kinases and is most similar to two putative receptor protein-tyrosine kinases of the eph subclass, elk (69%) and eph (57%). Human genomic DNAs encoding part of eek (EEK) as well as another putative protein-tyrosine kinase most similar to elk (90%), ERK (elk-related kinase), were isolated and partially characterized. The novel identity of these two eph-family genes was further supported by Southern blot analyses and localization to human chromosome 1. In Northern blot analysis of rat RNA, DNAs encoding rat eek and human ERK hybridized to transcripts most abundant in brain and lung, respectively. These two new members of the eph subclass of receptor protein-tyrosine kinases, eek and erk, may therefore have tissue-specific functions distinct from those of other eph family members.
Differences in the susceptibility of herpes simplex virus types 1 and 2 to modified heparin compounds suggest serotype differences in viral entry (1996)

Although heparan sulfate (HS) serves as an initial receptor for the binding of both herpes simplex virus type 1 (HSV-1) and HSV-2 to cell surfaces, the two serotypes differ in epidemiology, cell tropism, and ability to compete for viral receptors in vitro. These observations are not necessarily contradictory and can be explained if the two serotypes recognize different structural features of HS. To compare the specific features of HS important for the binding and infection of HSV-1 and HSV-2, we took advantage of structural similarities between heparin and cell surface HS and compared the abilities of chemically modified heparin compounds to inhibit plaque formation. We found that the antiviral activity of heparin for both serotypes was independent of anticoagulant activity. Moreover, specific negatively charged regions of the polysaccharide, including N sulfations and the carboxyl groups, are key structural features for interactions of both HSV-1 and HSV-2 with cell surfaces since N desulfation or carboxyl reduction abolished heparin's antiviral activity. In contrast, 6-O sulfations and 2-,3-O sulfations are important determinants primarily for HSV- 1 infection. The O-desulfated heparins had little or no inhibitory effect on HSV-1 infection but inhibited HSV-2 infection. Using a series of intertypic recombinant mutant viruses, we found that susceptibility to O-desulfated heparins can be transferred to HSV-1 by the gene for glycoprotein C of HSV-2 (gC-2). This supports the notion that the envelope glycoproteins of HSV-1 and HSV-2 interact with different affinities for different structural features of heparin. To determine if the modified heparin compounds inhibited plaque formation by competing with cell surface HS for viral attachment, binding studies were also performed. As anticipated, most compounds inhibited binding and plaque formation in parallel. However, several compounds inhibited the binding of HSV-1 to cells during the initial attachment period at 4 degrees C; this inhibitory effect was reversed when the cells and inoculum were shifted to 37 degrees C. This temperature-dependent differential response to modified heparin compounds was evident primarily when glycoprotein C of HSV-1 (gC-1) was present in the virion envelope. Minimal temperature-dependent differences were seen for HSV-1 with gC-1 deleted and for HSV-2. These results suggest differences in the interactions of HSV-1 and HSV-2 with cell surface HS that may influence cell tropism.
Use of recombinant adenovirus to transfer the herpes simplex virus thymidine kinase (HSVtk) gene to thoracic neoplasms: an effective in vitro drug sensitization system. (1994)

Transfer of the herpes simplex virus thymidine kinase (HSVtk) gene into tumor cells using retroviral vectors followed by administration of ganciclovir provides a potential strategy for the treatment of malignancy. Because of the limitations of using retroviral vectors for clinical application, the feasibility of using a recombinant adenovirus containing HSVtk was examined. Cell lines derived from human malignant mesotheliomas and non-small cell lung cancers infected with a recombinant adenovirus containing HSVtk showed strong expression of HSVtk protein as determined by immunohistochemical staining. Infection with a recombinant adenovirus containing HSVtk rendered cells sensitive to doses of ganciclovir that were 2-3 logs lower than uninfected cells or those infected with a control virus. A strong "bystander effect" was noted in mesothelioma lines; there was no diminution in the efficacy of ganciclovir treatment until the ratio of infected:uninfected cells fell below 1:10. This study thus demonstrates in vitro efficacy of an adenovirus-transduced HSVtk drug sensitization gene therapy system in thoracic malignancies. Recombinant adenovirus transfer of the HSVtk gene followed by ganciclovir may have promise as an in situ treatment for tumors.
Systolic array implementation of multipliers for finite fields GF(2/sup m/) (1991)

A parallel-in-parallel-out systolic array and a serial-in-serial-out systolic array are proposed for fast multiplication in finite fields GF(2/sup m/) with the standard basis representation. Both of the architectures possess features of regularity, modularity, concurrency, and unidirectional data flow. As a consequence, they have high throughput rates and are well suited to VLSI implementation with fault-tolerant design. As compared to the related multipliers presented by C.S. Yeh et al. (see IEEE Trans. Comput., vol.C-33, p.357-360, Apr. 1984), the proposed parallel implementation makes it easier to incorporate fault-tolerant design, and the proposed serial implementation requires only one control signal instead of two.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antibody Repertoire Development in Fetal and Neonatal Piglets. IX. Three Pathogen-Associated Molecular Patterns Act Synergistically to Allow Germfree Piglets to Respond to Type 2 Thymus-Independent and Thymus-Dependent Antigens (2005)

Newborn piglets maintained germfree (GF) cannot respond to either thymus-dependent (TD) or type 2 thymus-independent Ags (TI-2) unless colonized with bacteria. We show here that pathogen-associated molecular patterns (PAMPs), including muramyl dipeptide (MDP), LPS, and a B-class CpG oligonucleotide (CpG-B), can substitute for gut flora in the induction of neonatal immunoresponsiveness. These PAMPs alone or in combination had little effect on serum IgG and IgA levels, but CpG-B and CpG-B + MDP elevated total IgM levels 3- to 7-fold above that seen in colonized controls after booster immunization. Although only CpG-B could alone stimulate immunoresponsiveness, co-administration of LPS or MDP resulted in a 5-fold increase in the IgG response to both immunogens. Co-administered MDP did not promote secondary IgG responses to either Ag but instead pronounced secondary IgM responses to the epitopes of both immunogens. LPS co-administered with CpG-B may promote class switch recombination or cause differentiation of previously switched cells that become responsive after exposure to CpG-B. Primary and secondary IgG responses equally recognized the epitopes of the TI-2 and TD immunogens, whereas IgM responses favored the TI-2 epitope. Because PAMPs alone can result in Abs to 2,4,6-triitrophenyl and FLU without immunization, it suggests they alone cause differentiation of B cells of the preimmune repertoire. The finding that both bacterial PAMPs and colonization are capable of stimulating Ab responses in both immunized and nonimmunized piglets suggests that PAMPs derived from host flora may play a major role in awakening adaptive immunity in neonates.
Wrapper induction: Efficiency and expressiveness (Extended abstract) (1998)

) Nicholas Kushmerick School of Computer Applications, Dublin City University, Ireland nick@compapp.dcu.ie ABSTRACT Recently, many systems have been built that automatically interact with Internet information resources. However, these resources are usually formatted for use by people; e.g., the relevant content is embedded in HTML pages. Wrappers are often used to extract a resource&amp;apos;s content, but hand-coding wrappers is tedious and error-prone. We advocate wrapper induction, a technique for automatically constructing wrappers. We have identified several wrapper classes that can be learned quickly (most sites require only a handful of examples, consuming a few CPU seconds of processing), yet which are useful for handling numerous Internet resources (70% of surveyed sites can be handled by our techniques). 4.1 Introduction The Internet presents a stunning variety of on-line information resources: telephone directories, retail product catalogs, weather forecasts, and many more. Recen...