gebhart/patrepeval huggingface dataset:
Damage evaluation and analysis of composite pressure vessels using fiber Bragg gratings to determine structural health (2005)

With the augmented use of high performance composite materials in critical structures, it has become increasingly important for 'smart' systems to monitor these materials and provide rapid evaluation. Using fiber Bragg gratings embedded into the weave structure of carbon fiber epoxy composites allow the capability to monitor these composites during manufacture, cure, general aging, and damage. Fiber optic sensors allow greater insight into damage progression and can be used to verify analytical models. This paper emphasizes the results of recent work in which multiple arrays of Bragg gratings were wound into composite vessels and monitored while the part was damaged. Based on the response of these sensors, algorithms were developed to identify the location of damage impacts. Results were verified against eddy current and ultrasonic NDE methods.
A computational theory of spike-timing dependent plasticity: achieving robust neural responses via conditional entropy minimization. (2005)

Experimental studies have observed synaptic potentiation when a presynaptic neuron fires shortly before a postsynaptic neuron, and synaptic depression when the presynaptic neuron fires shortly after. The dependence of synaptic modulation on the precise timing of the two action potentials is known as spike-timing dependent plasticity or STDP. We derive STDP from a simple computational principle: synapses adapt so as to minimize the postsynaptic neuron's variability to a given presynaptic input, causing the neuron's output to become more reliable in the face of noise. Using an entropy-minimization objective function and the biophysically realistic spike-response model of Gerstner (2001), we simulate neurophysiological experiments and obtain the characteristic STDP curve along with other phenomena including the reduction in synaptic plasticity as synaptic efficacy increases. We compare our account to other efforts to derive STDP from computational principles, and argue that our account provides the most comprehensive coverage of the phenomena. Thus, reliability of neural response in the face of noise may be a key goal of unsupervised cortical adaptation
Exonization of AluYa5 in the human ACE gene requires mutations in both 3' and 5' splice sites and is facilitated by a conserved splicing enhancer (2005)

Ancient Alu elements have been shown to be included in mature transcripts by point mutations that improve their 5' or 3' splice sites. We have examined requirements for exonization of a younger, disease-associated AluYa5 in intron 16 of the human ACE gene. A single G>C transversion in position -3 of the new Alu exon was insufficient for Alu exonization and a significant inclusion in mRNA was only observed when improving several potential splice donor sites in the presence of 3' CAG. Since complete Alu exonization was not achieved by optimizing traditional splicing signals, including the branch site, we tested whether auxiliary elements in AluYa5 were required for constitutive inclusion. Exonization was promoted by a SELEX-predicted heptamer in Alu consensus sequence 222-228 and point mutations in highly conserved nucleotides of this heptamer decreased Alu inclusion. In addition, we show that Alu exonization was facilitated by a subset of serine/arginine-rich (SR) proteins through activation of the optimized 3' splice site. Finally, the haplotype- and allele-specific ACE minigenes generated similar splicing patterns in both ACE-expressing and non-expressing cells, suggesting that previously reported allelic association with plasma ACE activity and cardiovascular disease is not attributable to differential splicing of introns 16 and 17.
EGF, TGF-a, and EGF-R in Human Colorectal Adenocarcinoma (1998)

The over-expression of epidermal growth factor receptor (EGF-R), EGF and transforming growth factor alpha (TGFalpha) could be a mechanism for colorectal tumor cells to escape normal growth controls. Our aims were: (i) to evaluate EGF, TGFalpha, and EGF-R concentrations in neoplastic tissue and surrounding mucosa from 40 patients with colorectal adenocarcinoma, and (ii) to assess the expression of these growth factors and their receptor in relation to the tumor site. EGF, TGFalpha, and EGF-R were detected in either colorectal neoplastic tissue or surrounding mucosa. Significantly increased levels of EGF and EGF-R were present in neoplastic samples compared to surrounding mucosa. Furthermore, a significant increase in TGFalpha and in EGF levels was observed in the left-sided surrounding mucosa and left-sided neoplastic tissue, respectively. EGF-R stimulation by its ligands may play an important role in colorectal neoplastic tissue. Moreover, the higher content of growth factors in the left-side than the right-side colon suggests different growth properties in the proximal and distal colon.
The human DINB1 gene encodes the DNA polymerase Polθ (2000)

The human DINB1 gene shares a high degree of homology with the Escherichia coli dinB gene. Here, we purify the hDINB1-encoded protein and show that it is a DNA polymerase. Because hDinB1 is the eighth eukaryotic DNA polymerase to be described, we have named it DNA polymerase (Pol) theta. hPoltheta is unable to bypass a cis-syn thymine-thymine dimer, nor does it bypass a (6-4) photoproduct or an abasic site. We also examine the fidelity of hPoltheta on nondamaged DNA templates by steady-state kinetic analyses and find that hPoltheta misincorporates deoxynucleotides with a frequency of about 10(-3) to 10(-4). We discuss the relationship between the fidelity of hPoltheta and its inability to bypass DNA damage.
Expression of EGF receptor mRNA in rat nigrostriatal system (1994)

In situ hybridization with a cRNA probe was used to determine the cellular expression of mRNA for the epidermal growth factor receptor (EGF-R) within the rat dopaminergic nigrostriatal system. Hybridization for EGF-R mRNA was distributed throughout the ventral mesencephalon within cells of the substantia nigra pars compacta and ventral tegmental area (VTA). Unilateral lesion of the nigrostriatal pathway with the neurotoxin 6-hydroxydopamine resulted in substantial elimination of EGF-R cRNA hybridization in the ipsilateral substantia nigra and VTA. EGF-R mRNA was also demonstrated within a population of striatal somata, with highest levels of expression detected neonatally. These results indicate that a subpopulation of ventral midbrain dopaminergic neurons, as well as striatal perikarya, express the EGF-R and, thus, may be directly responsive to endogenous EGF, transforming growth factor-alpha, or another EGF-R ligand in vivo.
Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy (2014)

Antigen-specific immunotherapy combats autoimmunity or allergy by reinstating immunological tolerance to target antigens without compromising immune function. Optimization of dosing strategy is critical for effective modulation of pathogenic CD4(+) T-cell activity. Here we report that dose escalation is imperative for safe, subcutaneous delivery of the high self-antigen doses required for effective tolerance induction and elicits anergic, interleukin (IL)-10-secreting regulatory CD4(+) T cells. Analysis of the CD4(+) T-cell transcriptome, at consecutive stages of escalating dose immunotherapy, reveals progressive suppression of transcripts positively regulating inflammatory effector function and repression of cell cycle pathways. We identify transcription factors, c-Maf and NFIL3, and negative co-stimulatory molecules, LAG-3, TIGIT, PD-1 and TIM-3, which characterize this regulatory CD4(+) T-cell population and whose expression correlates with the immunoregulatory cytokine IL-10. These results provide a rationale for dose escalation in T-cell-directed immunotherapy and reveal novel immunological and transcriptional signatures as surrogate markers of successful immunotherapy.
Isolation and characterization of a novel type of growth factor derived from serum‐free conditioned medium of chicken embryo fibroblasts (1992)

A strong mitogenic activity for fibroblastic cells has been found in serum-free medium of growth-arrested primary cultures of chicken embryo fibroblasts (CEF). This serum-free conditioned medium promoted growth of NIH/3T3 cells and primary as well as secondary cultures of CEF. The mitogenic activity was as potent as 5% serum. Half-maximum stimulation was obtained with 20% of the initial concentration of the conditioned medium. The activity eluted at high M(r) (1-2 x 10(5)) from a gel-filtration column under nondenaturing conditions and was trypsin insensitive and thiol insensitive. Treatment with acid or urea converted the mitogen to a low-molecular-mass form, which showed a delayed induction of DNA synthesis. Purification of this factor (10000-fold) to apparent homogeneity was achieved by preparative isoelectric focusing, gel filtration, reverse-phase HPLC and nonreducing SDS/PAGE. The factor, termed CEF-derived growth factor (CDGF) was a 32-kDa, disulfide-linked heterodimer of a 15-kDa and a 17-kDa subunit as judged by SDS/PAGE, with a pI of approximately 7 in 8 M urea. It exhibited partial stability towards heat treatment and was trypsin sensitive. CDGF was active only in its dimeric form and half-maximum stimulation of NIH/3T3 cells was obtained at approximately 10 pM. The mitogenic activity was not suppressible by an antibody neutralizing the activity of transforming growth factor beta 1, 2 and 3 (TGF-beta). The physico-chemical properties suggest that CDGF is not identical with one of the common growth factors like fibroblast growth factor, platelet-derived growth factor, epidermal growth factor, insulin-like growth factor, or TGF-beta but rather represents a novel type of growth factor.
Phase II and pharmacologic study of docetaxel as initial chemotherapy for metastatic breast cancer. (1996)

Docetaxel is active for metastatic breast cancer. Neutropenia and fluid retention are dose-limiting. The AUC did not predict toxicity, but caution is warranted when treating patients with liver dysfunction. An understanding of the pathophysiology of the fluid retention may facilitate prevention. Frequent HSR may warrant prophylactic premedication.
pH dynamics and bacterial community composition in the rumen of lactating dairy cows (2010)

The influence of pH dynamics on ruminal bacterial community composition was studied in 8 ruminally cannulated Holstein cows fitted with indwelling electrodes that recorded pH at 10-min intervals over a 54-h period. Cows were fed a silage-based total mixed ration supplemented with monensin. Ruminal samples were collected each day just before feeding and at 3 and 6h after feeding. Solid and liquid phases were separated at collection, and extracted DNA was subjected to PCR amplification followed by automated ribosomal intergenic spacer analysis (ARISA). Although cows displayed widely different pH profiles (mean pH=6.11 to 6.51, diurnal pH range=0.45 to 1.39), correspondence analysis of the ARISA profiles revealed that 6 of the 8 cows showed very similar bacterial community compositions. The 2 cows having substantially different community compositions had intermediate mean pH values (6.30 and 6.33) and intermediate diurnal pH ranges (averaging 0.89 and 0.81 pH units). Fortuitously, these 2 cows alone also displayed milk fat depression, along with markedly higher ruminal populations of 1 bacterial operational taxonomic unit (OTU) and reduced populations of another ARISA amplicon. Cloning and sequencing of the elevated OTU revealed phylogenetic similarity to Megasphaera elsdenii, a species reportedly associated with milk fat depression. The higher populations of both M. elsdenii and OTU246 in these 2 cows were confirmed using quantitative real-time PCR (qPCR) with species-specific primers, and the fraction of total bacterial rDNA copies contributed by these 2 taxa were very highly correlated within individual cows. By contrast, the fraction of total bacterial rDNA copies contributed by Streptococcus bovis and genus Ruminococcus, 2 taxa expected to respond to ruminal pH, did not differ among cows (mean= <0.01 and 10.6%, respectively, of rRNA gene copies, determined by qPCR). The data indicate that cows with widely differing pH profiles can have similar ruminal bacterial community compositions, and that milk fat depression can occur at intermediate ruminal pH. The results support recent reports that milk fat depression is associated with shifts in bacterial community composition in rumine and is specifically related to the relative abundance of Megasphaera elsdenii.
Antiinflammatory and antinociceptive effects of 1,8-cineole a terpenoid oxide present in many plant essential oils (2000)

1,8-Cineole (cineole), a terpenoid oxide present in many plant essential oils displays an inhibitory effect on some types of experimental inflammation in rats, i.e. paw oedema induced by carrageenan and cotton pellet-induced granuloma. Cineole also inhibits in mice, the acetic acid-induced increase in peritoneal capillary permeability and the chemical nociception induced by intraplantar formalin and intraperitoneal acetic acid. Activity was present in these tests, at an oral dose range of 100-400 mg/kg. In the formalin test, the antinociceptive effect of cineole was not reversed by pretreatment of mice with naloxone (1 mg/kg, s.c.), a mu-opioid receptor antagonist, suggesting the involvement of a non-opioid mechanism. Cineole demonstrated a significant inhibitory effect on locomotion and also potentiated the pentobarbital sleeping time in mice, indicating a plausible depressant effect on the central nervous system. The present results, when taken together with the recent reports that describe the inhibitory effects of cineole on the formation of prostaglandins and cytokines by stimulated monocytes in vitro, may provide additional evidence for its potential beneficial use in therapy as an antiinflammatory and analgesic agent.
FADD Is Required for DR4- and DR5-mediated Apoptosis (2000)

TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) is a member of the tumor necrosis factor family that can kill a wide variety of tumor cells but not normal cells. TRAIL-induced apoptosis in humans is mediated by its receptors DR4 (TRAIL-R1) and DR5 (TRAIL-R2). What constitutes the signaling molecules downstream of these receptors, however, remains highly controversial. Using the FADD dominant negative molecule, several groups have reached different conclusions with respect to the role of FADD in TRAIL-induced apoptosis. More recently, using FADD-deficient (-/-) mouse embryonic fibroblasts, Yeh et al. (Yeh, W.-C., Pompa, J. L., McCurrach, M. E., Shu, H.-B., Elia, A. J., Shahinian, A., Ng, M., Wakeham, A., Khoo, W., Mitchell, K., El-Deiry, W. S., Lowe, S. W., Goeddel, D. V., and Mak, T. W. (1998) Science 279, 1954-1958) concluded that DR4 utilizes a FADD-independent apoptotic pathway. The latter experiment, however, involved transient overexpression, which often leads to nonspecific aggregation of death domain-containing receptors. To address this issue in a more physiological setting, we stably transfected mouse DR4/5, human DR4, or human DR5 into FADD(-/-) mouse embryonic fibroblast cells. We showed that FADD(-/-) MEF cells stably transfected with TRAIL receptors are resistant to TRAIL-mediated cell death. In contrast, TRAIL receptors stably transfected into heterozygous FADD(+/-) cells or FADD(-/-) cells reconstituted with a FADD retroviral construct are sensitive to the TRAIL cytotoxic effect. We conclude that FADD is required for DR4- and DR5-mediated apoptosis.
Leveraging Biospecimen Resources for Discovery or Validation of Markers for Early Cancer Detection (2015)

Validation of early detection cancer biomarkers has proven to be disappointing when initial promising claims have often not been reproducible in diagnostic samples or did not extend to prediagnostic samples. The previously reported lack of rigorous internal validity (systematic differences between compared groups) and external validity (lack of generalizability beyond compared groups) may be effectively addressed by utilizing blood specimens and data collected within well-conducted cohort studies. Cohort studies with prediagnostic specimens (eg, blood specimens collected prior to development of clinical symptoms) and clinical data have recently been used to assess the validity of some early detection biomarkers. With this background, the Division of Cancer Control and Population Sciences (DCCPS) and the Division of Cancer Prevention (DCP) of the National Cancer Institute (NCI) held a joint workshop in August 2013. The goal was to advance early detection cancer research by considering how the infrastructure of cohort studies that already exist or are being developed might be leveraged to include appropriate blood specimens, including prediagnostic specimens, ideally collected at periodic intervals, along with clinical data about symptom status and cancer diagnosis. Three overarching recommendations emerged from the discussions: 1) facilitate sharing of existing specimens and data, 2) encourage collaboration among scientists developing biomarkers and those conducting observational cohort studies or managing healthcare systems with cohorts followed over time, and 3) conduct pilot projects that identify and address key logistic and feasibility issues regarding how appropriate specimens and clinical data might be collected at reasonable effort and cost within existing or future cohorts.
Control of breathing during prolonged exercise (1981)

Ventilation (VE) climbs steadily throughout prolonged heavy exercise. While this VE "drift" has implications for the adequacy of gas exchange in long-term exercise, its mechanism remains unknown. We examined the behavior of previously proposed mediators of VE drift during one hour of cycle ergometer exercise at constant work rate requiring 2/3 VO2 max in 10 subjects. VE increased 13% from 12 to 61 min of exercise (P less than 0.05). Although body core temperature rose as VE rose, equal elevation of core temperature by passive means failed to increase exercise VE. Rising VE during the hour of exercise occurred despite unchanged arterial pH, PCO2, and lactate and despite unchanged VCO2. Thus, all of the VE increase was calculated to be due to increased dead space ventilation (VD). Tidal volume (VT) was unchanged, while VD/VT rose from 0.16 to 0.24 from 12 to 61 min of work (P less than 0.05). These results show that increased body core temperature does not mediate VE drift, and that changes in previously proposed mediators (arterial pH, arterial lactate, and VCO2) are not necessary for a slow VE rise to occur in prolonged heavy exercise.
Interaction of benzene with TiO2 surfaces: Relevance to contamination of extreme ultraviolet lithography mirror capping layers (2008)

The authors focus on thermal and nonthermal (radiation-induced) surface processes that affect the reflectivity of TiO2-capped multilayer mirrors used in extreme ultraviolet (EUV) lithography. Low energy electron beams mimic excitations initiated by EUV radiation. Where appropriate, comparison is made with electron bombardment in the vapor of methyl methacrylate (C5H8O2). Benzene adsorbs and desorbs reversibly on TiO2, and the steady state coverage Θ is found to be proportional to the logarithm of the benzene pressure p. This behavior is described by the Tempkin adsorption isotherm, which has the form Θ=const+logp. This isotherm is a consequence of a linear dependence of benzene adsorption energy on Θ. In addition, measurements of cross sections σ (cm2) for electron-stimulated dissociation of benzene on clean and C-covered TiO2 in the range of 10–100eV reveal surprisingly large values (e.g., ∼3.5×10−17cm2 at 10eV primary energy). Thus, low energy secondary electrons excited by EUV lithography photons are expected to contribute substantially to carbon accumulation on clean TiO2 cap layers.
Colloid stabilization with grafted polyelectrolytes (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTColloid stabilization with grafted polyelectrolytesPhilip PincusCite this: Macromolecules 1991, 24, 10, 2912–2919Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/ma00010a043https://doi.org/10.1021/ma00010a043research-articleACS PublicationsRequest reuse permissionsArticle Views3246Altmetric-Citations870LEARN 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
Inhibition of Ras-Induced Proliferation and Cellular Transformation by p16 INK4 (1995)

The cyclin-dependent kinase 4 (CDK4) regulates progression through the G1 phase of the cell cycle. The activity of CDK4 is controlled by the opposing effects of the D-type cyclin, an activating subunit, and p16INK4, an inhibitory subunit. Ectopic expression of p16INK4 blocked entry into S phase of the cell cycle induced by oncogenic Ha-Ras, and this block was relieved by coexpression of a catalytically inactive CDK4 mutant. Expression of p16INK4 suppressed cellular transformation of primary rat embryo fibroblasts by oncogenic Ha-Ras and Myc, but not by Ha-Ras and E1a. Together, these observations provide direct evidence that p16INK4 can inhibit cell growth.
Plasmid DNA–Expressed Secreted and Nonsecreted Forms of Herpes Simplex Virus Glycoprotein D2 Induce Different Types of Immune Responses (2000)

Herpes simplex viruses (HSVs) are significant pathogens and major targets of vaccine development. Several attempts have been made to develop prophylactic and therapeutic vaccines for HSV types 1 and 2. Although these vaccines elicit strong humoral responses, the overall impact on pathology has been disappointing. An effective vaccine for HSV must induce both humoral and cellular immune responses. DNA vaccines are ideal candidates for HSV vaccines because they induce both types of immune responses. This study showed that the type of immune response generated by immunization with DNA vaccines is modulated by expression of various forms of an antigen, each with a different cellular localization. Expression of cell-associated forms of HSV-2 glycoprotein D (gD) induces primarily a Th1 response, whereas expression of secreted gD results in a Th2 response. Immunization with plasmids expressing different forms of the antigen may increase the efficacy of a vaccine.