gebhart/patrepeval huggingface dataset:
Mechanically Corner-Coupled Square Microresonator Array for Reduced Series Motional Resistance (2006)

Substantial reductions in vibrating micromechanical resonator series motional resistance R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> have been attained by mechanically coupling and exciting a parallel array of corner-coupled polysilicon square plate resonators. Using this technique with seven resonators, an effective R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> of 480 Omega has been attained at 70 MHz, which is more than 5.9X smaller than the 2.82 kOmega exhibited by a stand-alone transverse-mode corner-supported square resonator, and all this achieved while still maintaining an effective Q>9000. This method for R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> -reduction is superior to methods based on brute force scaling of electrode-to-resonator gaps or dc-bias increases, because it allows a reduction in R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> without sacrificing linearity, and thereby breaks the R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> versus dynamic range tradeoff often seen when scaling. This paper also compares two types of anchoring schemes for transverse-mode square micromechanical resonators and models the effect of support beam parameters on resonance frequency
Bovine viral diarrhea virus NS3 serine proteinase: polyprotein cleavage sites, cofactor requirements, and molecular model of an enzyme essential for pestivirus replication (1997)

Members of the Flaviviridae encode a serine proteinase termed NS3 that is responsible for processing at several sites in the viral polyproteins. In this report, we show that the NS3 proteinase of the pestivirus bovine viral diarrhea virus (BVDV) (NADL strain) is required for processing at nonstructural (NS) protein sites 3/4A, 4A/4B, 4B/5A, and 5A/5B but not for cleavage at the junction between NS2 and NS3. Cleavage sites of the proteinase were determined by amino-terminal sequence analysis of the NS4A, NS4B, NS5A, and NS5B proteins. A conserved leucine residue is found at the P1 position of all four cleavage sites, followed by either serine (3/4A, 4B/5A, and 5A/5B sites) or alanine (4A/4B site) at the P1' position. Consistent with this cleavage site preference, a structural model of the pestivirus NS3 proteinase predicts a highly hydrophobic P1 specificity pocket. trans-Processing experiments implicate the 64-residue NS4A protein as an NS3 proteinase cofactor required for cleavage at the 4B/5A and 5A/5B sites. Finally, using a full-length functional BVDV cDNA clone, we demonstrate that a catalytically active NS3 serine proteinase is essential for pestivirus replication.
Molecular Cloning of the Interleukin-1β Converting Enzyme (1992)

Interleukin-1 beta (IL-1 beta) mediates a wide range of immune and inflammatory responses. The active cytokine is generated by proteolytic cleavage of an inactive precursor. A complementary DNA encoding a protease that carries out this cleavage has been cloned. Recombinant expression in COS-7 cells enabled the cells to process precursor IL-1 beta to the mature form. Sequence analysis indicated that the enzyme itself may undergo proteolytic processing. The gene encoding the protease was mapped to chromosomal band 11q23, a site frequently involved in rearrangement in human cancers.
Comparison between exhaled and sputum oxidative stress biomarkers in chronic airway inflammation (2004)

The aim of the present study was to compare aldehyde levels resulting from lipid peroxidation in exhaled breath condensate (EBC) and induced sputum (IS) supernatant of subjects with asthma and chronic obstructive pulmonary disease (COPD). Aldehydes (malondialdehyde (MDA), acrolein, n-hexanal (C6), n-heptanal (C7), n-nonanal (C9), 4-hydroxynonenal (HNE) and 4-hydroxyhexenal (HHE)) in both biological fluids were measured by liquid chromatography-tandem mass spectrometry. MDA concentrations in sputum were 132.5 nM (82.5-268.8) and 23.7 nM (9-53.7) in EBC. Similarly, C6, C7 and C9 concentrations in IS were 1.5-4.7-fold higher than in EBC. Acrolein levels were 131.1 nM (55.6-264.6) in IS and 45.3 nM (14.4-127.1) in EBC. The concentrations of HNE and HHE in IS were not significantly different from the levels in EBC. Aldehyde levels in EBC did not show any correlation with aldehyde levels in IS or with differential sputum cellular count. In COPD, MDA in EBC, but not its IS counterpart, was negatively correlated with the severity of disease. In conclusion, the data presented here show that aldehydes can be detected in both exhaled breath condensate and supernatant of induced sputum, but that their relative concentrations are different and not correlated with each other. Therefore, with regard to lipid peroxidation products, exhaled breath condensate and induced sputum must be considered as independent techniques.
Human gene transfer: characterization of human tumor-infiltrating lymphocytes as vehicles for retroviral-mediated gene transfer in man. (1990)

Tumor-infiltrating lymphocytes (TILs) are cells generated from tumor suspensions cultured in interleukin 2 that can mediate cancer regression when adoptively transferred into mice or humans. Since TILs proliferate rapidly in vitro, recirculate, and preferentially localize at the tumor site in vivo, they provide an attractive model for delivery of exogenous genetic material into man. To determine whether efficient gene transfer into TILs is feasible, we transduced human TILs with the bacterial gene for neomycin-resistance (NeoR) using the retroviral vector N2. The transduced TIL populations were stable and polyclonal with respect to the intact NeoR gene integration and expressed high levels of neomycin phosphotransferase activity. The NeoR gene insertion did not alter the in vitro growth pattern and interleukin 2 dependence of the transduced TILs. Analyses of T-cell receptor gene rearrangement for beta- and gamma-chain genes revealed the oligoclonal nature of the TIL populations with no major change in the DNA rearrangement patterns or the levels of mRNA expression of the beta and gamma chains following transduction and selection of TILs in the neomycin analog G418. Human TILs expressed mRNA for tumor necrosis factors (alpha and beta) and interleukin 2 receptor P55 but not for interleukin 1 beta, granulocyte/macrophage colony-stimulating factor, interleukin 6, and interferon gamma when grown with high-dose interleukin 2 without subsequent activation with mitogen or specific antigen. This pattern of cytokine-mRNA expression was not significantly altered following the transduction of TILs. The NeoR gene-transduced TILs could thus be used to follow the trafficking and survival of TILs in vivo, and clinical protocols using these transduced TILs in cancer patients have begun. The studies demonstrate the feasibility of TILs as suitable cellular vehicles for the introduction of therapeutic genes into patients receiving autologous TILs.
Fast two-layer two-photon imaging of neuronal cell populations using an electrically tunable lens (2011)

Functional two-photon Ca(2+)-imaging is a versatile tool to study the dynamics of neuronal populations in brain slices and living animals. However, population imaging is typically restricted to a single two-dimensional image plane. By introducing an electrically tunable lens into the excitation path of a two-photon microscope we were able to realize fast axial focus shifts within 15 ms. The maximum axial scan range was 0.7 mm employing a 40x NA0.8 water immersion objective, plenty for typically required ranges of 0.2-0.3 mm. By combining the axial scanning method with 2D acousto-optic frame scanning and random-access scanning, we measured neuronal population activity of about 40 neurons across two imaging planes separated by 40 μm and achieved scan rates up to 20-30 Hz. The method presented is easily applicable and allows upgrading of existing two-photon microscopes for fast 3D scanning.
The Aryl Hydrocarbon Receptor: Multitasking in the Immune System (2014)

The aryl hydrocarbon receptor (AhR), for many years almost exclusively studied by the pharmacology/toxicology field for its role in mediating the toxicity of xenobiotics such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), has more recently attracted the attention of immunologists. The evolutionary conservation of this transcription factor and its widespread expression in the immune system point to important physiological functions that are slowly being unraveled. In particular, the emphasis is now shifting from the role of AhR in the xenobiotic pathway toward its mode of action in response to physiological ligands. In this article, we review the current understanding of the molecular interactions and functions of AhR in the immune system in steady state and in the presence of infection and inflammation, with a focus on barrier organs such as the skin, the gut, and the lung.
cDNA cloning and regional distribution of a novel member of the opioid receptor family (1994)

We have cloned a cDNA for a novel member of the opioid receptor family, designated as ROR-C, from the rat cerebrum cDNA library using the probe derived from the delta-opioid receptor subtype cDNA. The deduced amino acid sequence of ROR-C shows high homology with those of ROR-A (rat delta-opioid receptor subtype), ROR-B (rat mu-subtype) and ROR-D (rat kappa-subtype). RNA blot hybridization and in situ hybridization analysis revealed that ROR-C mRNA is expressed in discrete regions of the rat central nervous system.
Intracellular Transport of Acid α-Glucosidase in Human Fibroblasts: Evidencefor Involvement of Phosphomannosyl Receptor-Independent System1 (1988)

Intracellular transport of two lysosomal enzymes, acid alpha-glucosidase and beta-hexosaminidase, was analyzed in human fibroblasts. The precursors of beta-hexosaminidase in normal fibroblasts were released from the membrane fraction by treatment with mannose 6-phosphate, but the precursor of alpha-glucosidase was not. Percoll density gradient centrifugation revealed a normal amount of acid alpha-glucosidase activity in heavy lysosomes in I-cell disease fibroblasts despite impaired maturation and defective phosphorylation, and beta-hexosaminidase activity was markedly reduced in lysosomes. It was concluded that the membrane-bound precursor of acid alpha-glucosidase is transported to lysosomes by a phosphomannosyl receptor-independent system although the enzyme lacks the recognition marker for the phosphomannosyl receptor and processing of an intermediate form to mature forms does not occur in this disease.
Long‐chain acyl‐CoA oxidases of Arabidopsis (1999)

Full-length cDNAs coding for two distinct acyl-CoA oxidases were isolated by screening an Arabidopsis cDNA library. The genes for the two acyl-CoA oxidases have been termed AtACX1 and AtACX2. AtACX1 encodes a peptide of 664 amino acids possessing a molecular mass of 74.3 kDa. AtACX2 encodes a peptide of 691 amino acids in length with a molecular mass of 77.5 kDa. Peroxisomal targeting signals were identified in the primary sequences. AtACX1 has a putative PTS1, whereas AtACX2 has a characteristic PTS2. Expression of AtACX1 and AtACX2 in Escherichia coli gave active enzymes for enzymatic and biochemical analysis. AtACX1 was active with both medium-and long-chain saturated fatty acyl-CoAs and showed maximal activity with C14-CoA. Activity with mono-unsaturated acyl-CoAs was slightly higher than with the corresponding saturated acyl-CoA. AtACX2 was active with long-chain acyl-CoAs and showed maximal activity with C18-CoA. AtACX2 activity with mono-unsaturated acyl-CoAs was approximately twice as high as with the corresponding saturated acyl-CoA. Both enzymes have an apparent Km of approximately 5 microM with the preferred substrate. Northern analysis was conducted to determine the expression patterns of AtACX1 and AtACX2 during germination and in various tissues of a mature plant. The two genes showed generally similar expression profiles and steady-state mRNA levels in seedlings and mature tissues, but subtle differences were observed. Enzymatic analyses of plant extracts revealed that AtACX1 and AtACX2 are members of a family that includes acyl-CoA oxidases specific for shorter-chain acyl-CoAs. Through expression of antisense constructs of the individual genes, we were able to decrease long-chain oxidase activity only in antisense AtACX1 plants. Seedlings with long-chain oxidase activity reduced down to 30% of wild-type levels germinated and established normally; however, reduced root growth appeared to be a general feature of antisense AtACX1 plants.
Electronic forms: benefits drawbacks of a World Wide Web-based approach to data entry. (1997)

It has long been realized that, compared to paper-based records, electronic record systems provide many advantages in the healthcare environment, including increased availability, improved legibility, long-term accessibility, (potentially) greater completeness, data encoding, and automated decision support and analysis. In spite of these recognized benefits, collection of patient data at the point of service generally does not occur, in large part because each such effort usually requires application-specific software and hardware, and, most significantly, provider time. Given the presence of WWW browsers now available on nearly every desktop, the support and access concerns for data entry applications can be substantially lessened. Despite these advantages, there are also downsides to the use of the WWW for data entry, including user interface issues and security. At CPMC, we are currently using web-based forms to gather patient charge data from physical and occupational therapists. Benefits of this approach have included a 98.2% user compliance rate for at least weekly data entry, and the reduction of charge posting from an average of 24.3 days to 2.3 days following the date of service. Drawbacks to WWW-based applications have included increased security exposure and persistent human tendencies to enter data in batches rather than at the time of service. A final conclusion was that, in the absence of a strong central mandate, providers must perceive a clear benefit in order to be willing to learn and use a new technology.
Evidence for a p53‐independent pathway for upregulation of SDI1/CIP1/WAF1/P21 RNA in human cells (1994)

SDI1 is an inhibitor of DNA synthesis that we isolated by expression screening cDNAs prepared from senescent, terminally nondividing human cells. Other groups then cloned this gene as a cyclin-dependent kinase (cdk)-interacting protein (CIP1, p21) that inhibits cdks; the gene was also isolated by screening for genes transactivated by p53 (WAF1). p53 levels are low in senescent and quiescent contact-inhibited or serum-deprived normal human cells, which we have found express high levels of SDI1 mRNA. This indicates that alternate pathways for upregulation of message level of this gene may exist. We therefore proceeded with the study presented here, treating human cells with a variety of growth-arrest-inducing agents, including some that damaged DNA, and found that RNA levels of SDI1 were increased in all cases that resulted in growth inhibition. More important, with the exception of gamma-radiation, most of these agents were able to elevate SDI1 message levels in cells lacking wild-type p53. At least two distinct kinetic profiles for RNA induction were observed, one that implicated p53 transactivation and occurred early enough to cause arrest, and another that clearly was p53 independent and suggested a role for the SDI1 gene product in the maintenance rather than in the cause of inhibition of DNA synthesis.
Functional studies with anti-CD3 heavy chain isotype switch-variant monoclonal antibodies. Accessory cell-independent induction of interleukin 2 responsiveness in T cells by epsilon-anti-CD3. (1987)

A series of heavy chain isotype switch-variant anti-CD3 monoclonal antibodies (mAb) was used to study the proliferation requirements of purified T cells. None of the variant antibodies was able by itself to induce proliferation. In the presence of exogenous interleukin 2 (IL-2) strong mitogenesis was observed upon stimulation with epsilon-anti-CD3, whereas gamma 1, gamma 2b, gamma 2a, and alpha-anti-CD3 failed to induce T cell proliferation. All variant antibodies induced vigorous proliferation in combination with phorbol myristate acetate. Purified T cells, cultured in the presence of epsilon-anti-CD3, in the absence of IL-2, did not express detectable amounts of TAC-antigen (CD25). The binding of the variant antibodies to the CD3 antigen was evaluated in cross-blocking experiments. It was demonstrated that the epsilon-anti-CD3 antibody, in comparison with the other variant mAb, has a relatively low avidity for the CD3 antigen. In modulation experiments, the IgE variant antibody was unable to induce a substantial loss of CD3 antigen. T cell triggering was investigated at the level of Ca2+ mobilization by means of the dye Indo-1. In contrast to the gamma 1, gamma 2b, gamma 2a, and alpha mAb, which induced a rapid and high rise in the free intracellular calcium level, epsilon-anti-CD3 caused a slow and low rise. These studies indicate that the epsilon-anti-CD3 antibody has a low avidity for the CD3 antigen, compared with the other variant mAb, possibly as a result of monovalent binding. Apparently, the avidity and/or valency of CD3 antigen binding not only has a major influence on CD3 modulation and anti-CD3-induced Ca2+ mobilization, but also sets T cell requirements for IL-2 responsiveness.
Chondrogenesis in Outgrowths of Muscle Tissue Onto Modified Bone Matrix in Tissue Culture (1977)

Optimal clinical workflow leads to faster treatment&lt;br/&gt;times and a potential to cater to a larger number of patients. A&lt;br/&gt;key part of this is preventing collisions between moving medical&lt;br/&gt;systems and patient. For interventional environments, highspeed&lt;br/&gt;rotational angiography (RA) scans are prone to potential&lt;br/&gt;collisions between the C-arm X-ray system and the patient. To&lt;br/&gt;ensure safety, a low speed safety-run is executed before the&lt;br/&gt;actual high-speed scan. However, several iterations of the safetyrun&lt;br/&gt;are often required before a scan is collision-free leading to&lt;br/&gt;a suboptimal clinical work-flow. This work proposes a RGB-D&lt;br/&gt;camera based collision prediction system which detects collisions&lt;br/&gt;before the actual RA scan. Additionally, a motion planner is&lt;br/&gt;designed to provide appropriate patient repositioning such that&lt;br/&gt;the collision is avoided. The system is introduced as a first proofof-&lt;br/&gt;concept to eliminate the safety-run and improve clinical safety&lt;br/&gt;and workflow.
Actinobacillus actinomycetemcomitans in Human Periodontal Disease: Prevalence in Patient Groups and Distribution of Biotypes and Serotypes Within Families (1983)

Actinobacillus actinomycetemcomitans is a Gram-negative oral bacterium which has been implicated in the etiology of localized juvenile periodontitis. In this study, 403 subjects from four study groups were examined for A actinomycetemcomitans in subgingival dental plaque. Samples pooled from at least six periodontal sites were included from each subject. A actinomycetemcomitans was detected in 28 of 29 localized juvenile periodontitis patients but in only 15% of the other subjects including 28 of 134 adult periodontitis patients, 24 of 142 periodontally healthy subjects and 5 of 98 insulin dependent juvenile diabetics with varying degrees of gingivitis. A actinomycetemcomitans isolates from members of five families with localized juvenile periodontitis patients were biotyped on the basis of variable fermentation of dextrin, maltose, mannitol and xylose and serotyped by indirect immunofluorescence using serotype specific rabbit antisera. Individuals within a family all harbored A actinomycetemcomitans of the same biotype and serotype. However, even in families with individuals heavily infected with A actinomycetemcomitans, some family members did not appear to be infected with the organism. The apparent poor transmissibility of A actinomycetemcomitans between individuals may, in part, explain the overall low prevalence of localized juvenile periodontitis and the familial pattern of the disease. The high prevalence of A actinomycetemcomitans in the subgingival plaque of localized juvenile periodontitis patients, compared to the much lower prevalence in other patient groups, supports the hypothesis that A actinomycetemcomitans is an etiologic agent in this periodontal disease.(ABSTRACT TRUNCATED AT 250 WORDS)
Rising Supply Price (1987)

Rising supply price' is a name that partial equilibrium theorists give to their encounters with general equilibrium reasoning. Such encounters must have occurred ever since economics began but for us the story begins in 1912 with Pigou, who asserted that:These conclusions led him to argue that taxes should be placed on decreasing returns industries and bounties on increasing returns industries. Assuming, what Clapham (1922) seriously doubted, that actual industries can be sorted into such boxes, this is a policy recommendation that appears remarkably specific in content and general in application.
Two Novel Types of O-Glycans on the Mugwort Pollen Allergen Art v 1 and Their Role in Antibody Binding (2005)

Art v 1, the major allergen of mugwort (Artemisia vulgaris) pollen contains galactose and arabinose. As the sera of some allergic patients react with natural but not with recombinant Art v 1 produced in bacteria, the glycosylation of Art v 1 may play a role in IgE binding and human allergic reactions. Chemical and enzymatic degradation, mass spectrometry, and 800 MHz (1)H and (13)C nuclear magnetic resonance spectroscopy indicated the proline-rich domain to be glycosylated in two ways. We found a large hydroxyproline-linked arabinogalactan composed of a short beta1,6-galactan core, which is substituted by a variable number (5-28) of alpha-arabinofuranose residues, which form branched side chains with 5-, 2,5-, 3,5-, and 2,3,5-substituted arabinoses. Thus, the design of the Art v 1 polysaccharide differs from that of the well known type II arabinogalactans, and we suggest it be named type III arabinogalactan. The other type of glycosylation was formed by single (but adjacent) beta-arabinofuranoses linked to hydroxyproline. In contrast to the arabinosylation of Ser-Hyp(4) motifs in other hydroxyproline-rich glycoproteins, such as extensins or solanaceous lectins, no oligo-arabinosides were found in Art v 1. Art v 1 and parts thereof produced by alkaline degradation, chemical deglycosylation, proteolytic degradation, and/or digestion with alpha-arabinofuranosidase were used in enzyme-linked immunosorbent assay and immunoblot experiments with rabbit serum and with the sera of patients. Although we could not observe antibody binding by the polysaccharide, the single hydroxyproline-linked beta-arabinose residues appeared to react with the antibodies. Mono-beta-arabinosylated hydroxyproline residues thus constitute a new, potentially cross-reactive, carbohydrate determinant in plant proteins.
Synthesis of a ZSM-5/NaA hybrid zeolite membrane using kaolin as a modification layer (2018)

A kaolin modification layer, which makes the surface of the support smooth and covers the defects on the support, not only attracts Si/Al active materials to the surface of the ceramic tube, but also dissolves under alkaline conditions to assist the growth of zeolite membranes.