gebhart/patrepeval huggingface dataset:
Her-2/neu Overexpression and Amplification in Uterine Papillary Serous Carcinoma (2004)

Positive IHC overexpression of Her-2/neu was seen in 18% of UPSCs but was rarely correlated with Her-2/neu gene amplification. Overexpression of Her-2/neu was associated with a worse overall prognosis. The use of trastuzumab (Herceptin; Genentech, South San Francisco, CA) in women with UPSC should be further evaluated in a clinical trial setting.
Multichannel Simultaneous Measurements of Single-Molecule Translocation in α-Hemolysin Nanopore Array (2009)

We present a microarray system that enables simultaneous monitoring of multiple ionic currents through transmembrane alpha-hemolysin nanopores arrayed at bilayer lipid membranes. We applied the self-assembling ability of lipid molecules interfaced between an aqueous solution and organic solvent to induce bilayer membrane formation at a microfluidic device; the device consists of a hydrophobic polymer film that serves to suspend the lipid-containing solvent at micrometer-sized apertures as well as to separate the aqueous solution into two chambers. In this study, we confirmed that expeditious and reproducible bilayer formation is realized by control of the composition of the solvent, a mixture of n-decane and 1-hexanol, which permits simultaneous incorporation of the alpha-hemolysin nanopores to the membrane array. Monitoring the eight wells on the array at once, we obtained a maximum of four relevant, synchronous signals of translocating ionic current through the nanopores. The system was also able to detect translocation events of nucleic acid molecules through the pore via the profile of a blocked current, promising its potential for high-throughput applications.
OPTIMAL CASE-CONTROL MATCHING IN PRACTICE (1995)

We illustrate modern matching techniques and discuss practical issues in defining the closeness of matching for retrospective case-control designs (in which the pool of subjects already exists when the study commences). We empirically compare matching on a balancing score, analogous to the propensity score for treated/control matching, with matching on a weighted distance measure. Although both methods in principle produce balance between cases and controls in the marginal distributions of the matching covariates, the weighted distance measure provides better balance in practice because the balancing score can be poorly estimated. We emphasize the use of optimal matching based on efficient network algorithms. An illustration is based on the design of a case-control study of hepatitis B virus infection as a possible confounder and/or effect modifier of radiation-related primary liver cancer in atomic bomb survivors.
Ultrahigh-risk Group Within the High-risk Neuroblastoma Category (2013)

Children with high-risk neuroblastoma (NBL) constitute a heterogenous group, but little attention has been paid to further subdivision of the high-risk group. Although the current therapies including multiple high-dose consolidations have neared their efficacy and tolerability limits, alternative therapies are needed. We wanted to define an ultrahigh-risk group among high-risk NBL patients, to be potential candidates for novel therapies given up-front. Children with high-risk NBL (n=59) treated at a single institution during 1987 to 2010 were evaluated for upfront prognostic factors at diagnosis and response to induction therapy. The overall outcome was not different during 1987 to 1994 versus 1995 to 2010. Therapy consisted of induction chemotherapy, surgery, and high dose-consolidation (single, tandem, or triple) with autologous stem cell rescue, followed by local irradiation and cis-retinoic acid. MYCN amplification and bone metastases were powerful upfront prognostic factors, and a combination of these determined an ultrahigh-risk group with a 5-year event-free survival of 0.125±0.083. The combination of MYCN amplification and bone metastases overruled the intensity of the therapy given and remained the only significant predictor (P<0.019) in a multiple step-wise forward Cox regression analysis. We conclude that high-risk NBL patients can be categorized into prognostic subgroups based on MYCN status and bone metastases. MYCN amplification and bone metastases combined determined an ultrahigh-risk group of patients being suitable candidates for novel alternative therapies.
PowerForms: Declarative Client-Side Form Field Validation (2000)

All uses of HTML forms may benefit from validation of the specified&lt;br /&gt;input field values. Simple validation matches individual values against specified formats, while more advanced validation may involve interdependencies of form fields.&lt;br /&gt;There is currently no standard for specifying or implementing such validation. Today, CGI programmers often use Perl libraries for simple server-side validation or program customized JavaScript solutions for client-side validation.&lt;br /&gt;We present PowerForms, which is an add-on to HTML forms that&lt;br /&gt;allows a purely declarative specification of input formats and sophisticated interdependencies of form fields. While our work may be seen as inspiration for a future extension of HTML, it is also available for CGI programmers today through a preprocessor that translates a PowerForms&lt;br /&gt;document into a combination of standard HTML and JavaScript that works on all combinations of platforms and browsers.&lt;br /&gt;The definitions of PowerForms formats are syntactically disjoint from the form itself, which allows a modular development where the form is perhaps automatically generated by other tools and the formats and interdependencies are added separately.&lt;br /&gt;PowerForms has a clean semantics defined through a fixed-point process that resolves the interdependencies between all field values. Text fields are equipped with status icons (by default traffic lights) that continuously reflect the validity of the text that has been entered so far, thus providing immediate feed-back for the user. For other GUI components the available options are dynamically filtered to present only the allowed values. PowerForms are integrated into the &lt;bigwig&gt; system for generating interactive Web services, but is also freely available in an Open Source distribution as a stand-alone package.
Recognition of Stress-Induced MHC Molecules by Intestinal Epithelial γδ T Cells (1998)

T cells with variable region Vdelta1 gammadelta T cell receptors (TCRs) are distributed throughout the human intestinal epithelium and may function as sentinels that respond to self antigens. The expression of a major histocompatibility complex (MHC) class I-related molecule, MICA, matches this localization. MICA and the closely related MICB were recognized by intestinal epithelial T cells expressing diverse Vdelta1 gammadelta TCRs. These interactions involved the alpha1alpha2 domains of MICA and MICB but were independent of antigen processing. With intestinal epithelial cell lines, the expression and recognition of MICA and MICB could be stress-induced. Thus, these molecules may broadly regulate protective responses by the Vdelta1 gammadelta T cells in the epithelium of the intestinal tract.
A new look at the biogenesis of glycogen (1995)

The discovery of glycogenin as a self-glucosylating protein that primes glycogen synthesis has significantly increased our understanding of the structure and metabolism of this storage polysaccharide. The amount of glycogenin will influence how much glycogen the cell can store. Therefore, the production of active glycogenin primer in the cell has the potential to be the overall rate-limiting process in glycogen formation, capable of overriding the better understood hormonally controlled mechanisms of protein phosphorylation/dephosphorylation that regulate the activities of glycogen synthase and phosphorylase. There are indications that a similar covalent modification control is also being exerted on glycogenin. Glycogenin has the ability to glucosylate molecules other than itself and to hydrolyze UDPglucose. These are independent of self-glucosylation, so that glycogenin, even when it has completed its priming role and become part of the glycogen molecule, retains its catalytic potential. Another new component of glycogen metabolism has been discovered that may have even greater influence on total glycogen stores than does glycogenin. This is proglycogen, a low molecular mass (approximately 400 kDa) form of glycogen that serves as a stable intermediate on the pathways to and from depot glycogen (macroglycogen, mass 10(7) Da, in muscle). It is suggested that glycogen oscillates, according to glucose supply and energy demand, between the macroglycogen and proglycogen, but not usually the glycogenin, forms. The proportion of proglycogen to macroglycogen varies widely between liver, skeletal muscle, and heart, from 3 to 15% to 50% by weight, respectively. On a molar basis, proglycogen is greatly in excess over macroglycogen in muscle and heart, meaning that if the proglycogen in these tissues could be converted into macroglycogen, they could store much more total glycogen. Discovering the factors that regulate the balance between glycogenin, proglycogen, and macroglycogen may have important implications for the understanding and management of noninsulin-dependent diabetes and for exercise physiology.
Comparison of Live, Attenuated H1N1 and H3N2 Cold-Adapted and Avian-Human Influenza A Reassortant Viruses and Inactivated Virus Vaccine in Adults (1988)

The infectivity, immunogenicity, and efficacy of live, attenuated influenza A/Texas/1/85 (H1N1) and A/Bethesda/1/85 (H3N2) avian-human (ah) and cold-adapted (ca) reassortant vaccines were compared in 252 seronegative adult volunteers. The immunogenicity and efficacy of the H1N1 reassortant vaccine were also compared with those of the trivalent inactivated virus vaccine. Each reassortant vaccine was satisfactorily attenuated. The 50% human infectious dose was 10(4.9) for ca H1N1, 10(5.4) for ah H1N1, 10(6.4) for ca H3N2, and 10(6.5) TCID50 for ah H3N2 reassortant virus. Within a subtype, the immunogenicities of ah and ca vaccines were comparable. Five to seven weeks after vaccination, volunteers were challenged with homologous wild-type influenza A virus. The magnitude of shedding of virus after challenge was greater than 100-fold less in H1N1 vaccinees and greater than 10-fold less in H3N2 vaccinees compared with unimmunized controls. The vaccines were equally efficacious, as indicated by an 86%-100% reduction in illness. Thus, the ah A/Mallard/New York/6750/78 and the ca A/Ann Arbor/6/60 reassortant viruses are comparable.
Axonal inclusions in spinocerebellar ataxia type 3 (2010)

Protein aggregation is a major pathological hallmark of many neurodegenerative disorders including polyglutamine diseases. Aggregation of the mutated form of the disease protein ataxin-3 into neuronal nuclear inclusions is well described in the polyglutamine disorder spinocerebellar ataxia type 3 (SCA3 or Machado-Joseph disease), although these inclusions are not thought to be directly pathogenic. Neuropil aggregates have not yet been described in SCA3. We performed a systematic immunohistochemical study of serial thick sections through brains of seven clinically diagnosed and genetically confirmed SCA3 patients. Using antibodies against ataxin-3, p62, ubiquitin, the polyglutamine marker 1C2 as well as TDP-43, we analyzed neuronal localization, composition and distribution of aggregates within SCA3 brains. The analysis revealed widespread axonal aggregates in fiber tracts known to undergo neurodegeneration in SCA3. Similar to neuronal nuclear inclusions, the axonal aggregates were ubiquitinated and immunopositive for the proteasome and autophagy associated shuttle protein p62, indicating involvement of neuronal protein quality control mechanisms. Rare TDP-43 positive axonal inclusions were also observed. Based on the correlation between affected fiber tracts and degenerating neuronal nuclei, we hypothesize that these novel axonal inclusions may be detrimental to axonal transport mechanisms and thereby contribute to degeneration of nerve cells in SCA3.
Influence of short circuits on data of contact and via open circuits determined by a novel weave test structure (2002)

The influence that short circuits have on contact hole open circuits and via hole open circuits in regular string test structures will be investigated. To detect open circuits as well as short circuits in adjacent conducting layers of backend process steps, a novel weave test structure (WTS) is presented. Numerous contact strings or via strings are arranged inside boundary pads like a woven piece of cloth. Thus, short circuits between different strings are also electrically detectable.
Engineering of Efficient Panchromatic Sensitizers for Nanocrystalline TiO2-Based Solar Cells (2001)

A new series of panchromatic ruthenium(II) sensitizers derived from carboxylated terpyridyl complexes of tris-thiocyanato Ru(II) have been developed. Black dye containing different degrees of protonation [(C(2)H(5))(3)NH][Ru(H(3)tcterpy)(NCS)(3)] 1, [(C(4)H(9))(4)N](2)[Ru(H(2)tcterpy)(NCS)(3)] 2, [(C(4)H(9))(4)N](3)[Ru(Htcterpy)(NCS)(3)] 3, and [(C(4)H(9))(4)N](4)[Ru(tcterpy)(NCS)(3)] 4 (tcterpy = 4,4',4' '-tricarboxy-2,2':6',2' '-terpyridine) have been synthesized and fully characterized by UV-vis, emission, IR, Raman, NMR, cyclic voltammetry, and X-ray diffraction studies. The crystal structure of complex 2 confirms the presence of a Ru(II)N6 central core derived from the terpyridine ligand and three N-bonded thiocyanates. Intermolecular H-bonding between carboxylates on neighboring terpyridines gives rise to 2-D H-bonded arrays. The absorption and emission maxima of the black dye show a bathochromic shift with decreasing pH and exhibit pH-dependent excited-state lifetimes. The red-shift of the emission maxima is due to better pi-acceptor properties of the acid form that lowers the energy of the CT excited state. The low-energy metal-to-ligand charge-transfer absorption band showed marked solvatochromism due to the presence of thiocyanate ligands. The Ru(II)/(III) oxidation potential of the black dye and the ligand-based reduction potential shifted cathodically with decreasing number of protons and showed more reversible character. The adsorption of complex 3 from methoxyacetonitrile solution onto transparent TiO(2) films was interpreted by a Langmuir isotherm yielding an adsorption equilibrium constant, K(ads), of (1.0 +/- 0.3) x 10(5) M(-1). The amount of dye adsorbed at monolayer saturation was (n(alpha) = 6.9 +/- 0.3) x 10(-)(8) mol/mg of TiO(2), which is around 30% less than that of the cis-di(thiocyanato)bis(2,2'-bipyridyl-4,4'-dicarboxylate)ruthenium(II) complex. The black dye, when anchored to nanocrystalline TiO(2) films achieves very efficient sensitization over the whole visible range extending into the near-IR region up to 920 nm, yielding over 80% incident photon-to-current efficiencies (IPCE). Solar cells containing the black dye were subjected to analysis by a photovoltaic calibration laboratory (NREL, U.S.A.) to determine their solar-to-electric conversion efficiency under standard AM 1.5 sunlight. A short circuit photocurrent density obtained was 20.5 mA/cm(2), and the open circuit voltage was 0.72 V corresponding to an overall conversion efficiency of 10.4%.
37 kiloDalton oncofetal antigen protein and immature laminin receptor protein are identical, universal T-cell inducing immunogens on primary rodent and human cancers. (2000)

Based upon positive immunologic comparisons, protein and cDNA sequencing, and in vitro and in vivo immunogenicity studies we propose that carcinomas, sarcomas and lymphomas/leukemias of rodents and humans share 37 kDa Onco-Fetal Antigen [OFA] as a T and B-lymphocyte stimulating, universal tumor specific transplantation antigen [UTSTA]. In the past four years, biochemical studies from several laboratories studying laminin receptor protein and immunological studies of OFA from our laboratories independently converged. OFA protein and immature or precursor Laminin Receptor Protein [iLRP] are > 99% identical proteins based on amino acid and cDNA sequencing and immunobiology studies summarized here. Acquired expression of 37 kDa OFA/iLRP enables malignant tumor cells to penetrate laminin tissue and vessel barriers. 37 kDa OFA/iLRP activates precursor thymic anti-OFA/iLRP specific cytotoxic T cell which kill emerging pretumor cells. Our reported findings also demonstrate that OFA/iLRP can function to induce specific immunoregulatory CD8 T-suppressor cells secreting IL-10 which impair effector T-cell killing of emerging tumor cells non-specifically and thereby facilitate tumor progression. Potential applications of OFA/iLRP detection in early cancer formation, for monitoring patient T cell subclass responses to OFA/iLRP as a predictor of tumor progression, and the use of OFA/iLRP peptides for specific anti-tumor immunotherapy are presented.
In vitro Fibroblast and Dermis Fibroblast Activation by Laser Irradiation at Low Energy (1984)

The effects of laser irradiations have been estimated both from the clinical point of view (rate of reduction of the ulcerated area) and in ultrastructural terms. The modification produced by laser in human fibroblasts in culture have also been investigated. Under our clinical and experimental conditions, laser stimulates the secretion of fibroblasts, both in vivo and in vitro, for reasons that are still the object of research. After irradiation the formation of periodic collagen fibrils is not observed, so that complete ' restitutio ad integrum' of the dermal matrix does not occur.
Activation and coupling of pyrrole-1-carboxylic acid in the formation of pyrrole N-carbonyl compounds: pyrrole-1-carboxylic acid anhydride (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTActivation and coupling of pyrrole-1-carboxylic acid in the formation of pyrrole N-carbonyl compounds: pyrrole-1-carboxylic acid anhydrideDale L. Boger and Mona PatelCite this: J. Org. Chem. 1987, 52, 11, 2319–2323Publication Date (Print):May 1, 1987Publication History Published online1 May 2002Published inissue 1 May 1987https://pubs.acs.org/doi/10.1021/jo00387a046https://doi.org/10.1021/jo00387a046research-articleACS PublicationsRequest reuse permissionsArticle Views1449Altmetric-Citations27LEARN 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
Immunization with Envelope Subunit Vaccine Products Elicits Neutralizing Antibodies against Laboratory-Adapted but Not Primary Isolates of Human Immunodeficiency Virus Type 1 (1996)

Phase I studies of volunteers not infected with human immunodeficiency virus type 1 (HIV-1) have shown that immunization with envelope subunit vaccine products elicits antibodies that neutralize laboratory-adapted (prototype) HIV-1 strains in vitro. Prototype strains are adapted to grow in continuous (neoplastic) cell lines and are more susceptible to neutralization than are primary isolates cultured in human peripheral blood mononuclear cells. In this study, 50 sera from nine phase I vaccine trials and 16 from HIV-1-infected persons were evaluated for neutralizing antibody activity against 3 laboratory-adapted and 5 primary HIV-1 isolates. Of 50 sera, 49 neutralized at least 1 of the prototype strains; however, none displayed neutralizing activity against primary isolates of HIV-1. Serum from most HIV-1-infected persons neutralized both laboratory-adapted and primary HIV-1 isolates. These data demonstrate a qualitative, or large quantitative, difference in the neutralizing antibody response induced by envelope subunit vaccination and natural HIV-1 infection.
Flexible graphene woven fabrics for touch sensing (2013)

Graphene woven fabric (GWF) prepared from chemical vapor deposition was used as smart self-sensing element to assemble piezoresistor through directly transferring onto the flexible substrate poly(dimethylsiloxane) (PDMS) with the deposited Ti/Au electrodes. A rational strategy was proposed to fabricate flexible touch sensors easily and effectively with the full usage of the mechanical and electrical properties of GWF, whose resistance is highly sensitive to macro-deformation or micro-defect. Compared to commercial and traditional touch sensing, the GWF-on-PDMS piezoresistor is structurally flexible that is demanded under special conditions and meanwhile makes the piezoresistor to have excellent durability.
PYPAF3, a PYRIN-containing APAF-1-like Protein, Is a Feedback Regulator of Caspase-1-dependent Interleukin-1β Secretion (2005)

PYPAF3 is a member of the PYRIN-containing apoptotic protease-activating factor-1-like proteins (PYPAFs, also called NALPs). Among the members of this family, PYPAF1, PYPAF5, PYPAF7, and NALP1 have been shown to induce caspase-1-dependent interleukin-1beta secretion and NF-kappaB activation in the presence of the adaptor molecule ASC. On the other hand, we recently discovered that PYNOD, another member of this family, is a suppressor of these responses. Here, we show that PYPAF3 is the second member that inhibits caspase-1-dependent interleukin-1beta secretion. In contrast, PYPAF2/NALP2 does not inhibit this response but rather inhibits the NF-kappaB activation that is induced by the combined expression of PYPAF1 and ASC. Both PYPAF2 and PYPAF3 mRNAs are broadly expressed in a variety of tissues; however, neither is expressed in skeletal muscle, and only PYPAF2 mRNA is expressed in heart and brain. They are also expressed in many cell lines of both hematopoietic and non-hematopoietic lineages. Stimulation of monocytic THP-1 cells with lipopolysaccharide or interleukin-1beta induced PYPAF3 mRNA expression. Furthermore, the stable expression of PYPAF3 in THP-1 cells abrogated the ability of the cells to produce interleukin-1beta in response to lipopolysaccharide. These results suggest that PYPAF3 is a feedback regulator of interleukin-1beta secretion. Thus, PYPAF2 and PYPAF3, together with PYNOD, constitute an anti-inflammatory subgroup of PYPAFs.
Bacterial signalling involving eukaryotic‐type protein kinases (1996)

Protein Ser, Thr and Tyr kinases play essential roles in signal transduction in organisms ranging from yeast to mammals, where they regulate a variety of cellular activities. During the last few years, a number of genes that encode eukaryotic-type protein kinases have also been identified in four different bacterial species, suggesting that such enzymes are also widespread in prokaryotes. Although many of them have yet to be fully characterized, several studies indicate that eukaryotic-type protein kinases play important roles in regulating cellular activities of these bacteria, such as cell differentiation, pathogenicity and secondary metabolism. A model based on the possible coupling between two-component systems and eukaryotic-type protein kinases is proposed to explain the function of eukaryotic-type protein kinases in bacterial signalling in the light of studies in bacteria, as well as in plants and yeast. These two groups of eukaryotes possess signal-transduction pathways involving both two-component systems and eukaryotic protein kinases.