gebhart/patrepeval huggingface dataset:
Preferential inhibition of 72- and 92-kDa gelatinases by tissue inhibitor of metalloproteinases-2 (1991)

Transformed human fibroblasts secrete two structurally and functionally related inhibitors of matrix metalloproteinases, tissue inhibitor of metalloproteinases (TIMP) 1 and 2. In assays measuring the relative inhibitory capability of TIMP-1 and TIMP-2 against autoactivated 72-kDa gelatinase, which consists of two major active peptides and several inactive fragments, TIMP-2 was more effective than TIMP-1. The isolated 42.5-kDa active fragment that formed as a result of the autoactivation of 72-kDa gelatinase showed the greatest preference for TIMP-2; at half-maximal inhibition, TIMP-2 was greater than 10-fold more effective than TIMP-1. TIMP-2 was also greater than 2-fold more effective than TIMP-1 at inhibiting 72-kDa gelatinase-TIMP-2 complexes activated with 4-aminophenylmercuric acetate, and greater than 7-fold more effective than TIMP-1 at inhibiting 92-kDa gelatinase activated with 4-aminophenylmercuric acetate. Furthermore, these active gelatinases preferentially bound 125I-TIMP-2 when incubated with equal amounts of radiolabeled TIMP-1 and TIMP-2. The ratios of 125I-TIMP-2/125I-TIMP-1 binding to 92-kDa gelatinase, autoactivated 72-kDa gelatinase, and 42.5-kDa fragment were 4.4, 10, and 33, respectively. On the other hand, interstitial collagenase was inhibited by TIMP-1 greater than 2-fold more effectively than TIMP-2 in assays measuring cleavage of loose collagen fibrils.
Extreme scaling enabled by 5 tracks cells: Holistic design-device co-optimization for FinFETs and lateral nanowires (2016)

By optimizing design rules, layout, devices and parasitics, we show how 5 Tracks standard cells with one fin can be enabled. This reduces area by 16% without pitch scaling and provides 34% energy gain from 6T cells. The loss in speed of 15% can be recovered by different front-end solutions. Air gap spacers are the most efficient booster and provide an extra 16% gain in energy. Lateral Nanowires can compete in speed with FinFETs with an extra energy gain of 12% if tight vertical pitch of 10 nm between wires can be achieved.
The first epidermal growth factor domain of human coagulation factor VII is essential for binding with tissue factor (1992)

The intrinsic pathway of coagulation is initiated when zymogen factor VII binds to its cell surface receptor tissue factor to form a catalytic binary complex. Both the activation of factor VIIa and the expression of serine protease activity of factor VIIa are dependent on factor VII binding to tissue factor lipoprotein. To better understand the molecular basis of these rate-limiting events, the interaction of zymogen factor VII and tissue factor was investigated using as probes both a murine monoclonal antibody and a monospecific rabbit antiserum to human factor VII. To measure factor VIIa functional activity, a two-stage chromogenic assay was used; an assay which measures the factor Xa generated by the activation of factor VII to factor VIIa. Purified immunoglobulin from murine monoclonal antibody 231-7, which was shown to be reactive with amino acid residues 51-88 of the first epidermal growth factor-like (EGF) domain of human factor VII, inhibited the activation of factor VII to factor VIIa in a dose-dependent manner. The mechanism of this inhibition was demonstrated using a novel solid-phase ELISA which quantitatively measured the binding of purified factor VII zymogen to tissue factor adsorbed onto microtiter wells. Thus, the binding of factor VII zymogen to immobilized tissue factor was inhibited by antibody 231-7, again in a dose-dependent manner. Similar results were obtained using a monospecific rabbit antiserum to human factor VII which also reacted with the beta-galactosidase fusion proteins containing amino acid residues 51-88 (exon 4) of human factor VII. We conclude therefore that the exon 4-encoded amino acids of the first EGF domain of human factor VII constitute an essential domain participating in the binding of factor VII to tissue factor.
Response of an extraordinary magnetoresistance read head to a magnetic bit (2003)

It has been proposed earlier that the extraordinary magnetoresistance (EMR) observed at room temperature in nonmagnetic semiconducting materials containing metallic inhomogeneities can be used in suitably constructed read heads for magnetic storage devices. Here, we show that such read heads are much simpler in design, and allow for higher sensitivity than is observed using magnetic layered structures that employ the phenomenon of giant magnetoresistance. We calculate, with no adjustable material parameters, the room-temperature response of an EMR read-head design, using finite element analysis, as a function of the position of the magnetic bit relative to the read head. The scaling property of the EMR bodes well for increasing the storage density to 1 Tbit/in.2 in the near future.
Suppression of oxidation-enhanced boron diffusion in silicon by carbon implantation and characterization of MOSFETs with carbon-implanted channels (1997)

In NMOS transistors with boron-doped channels, Oxdation-Enhanced Diffusion (OED) is a key contributor to boron profile broadening. Starting with the arguments presented in several recent reports on the role of carbon in silicon as a sink for self-interstitials, we have explored the feasibility of using carbon in the Metal Oxide Silicon Field Effect Transistor (MOSFET) active region to retard boron diffusion during gate oxidation. A highly effective suppression of OED of boron was observed providing more than an order of magnitude reduction in boron diffusivity. MOSFETs with carbon- and boron-implanted channels have been fabricated to evaluate the impact of carbon on the electrical properties of Si. Boron diffusion, activation, and critical electrical parameters including subthreshold swing, threshold voltage, off-state leakage current, and channel mobility have been evaluated as a function of the carbon dose. While our results show that carbon can effectively suppress boron diffusion daring gate oxidation, carbon can also lead to poor boron activation and degradation in MOSFET performance when carbon dose levels above a threshold of /spl sim/10/sup 14/ cm/sup -2/ are utilized. Our results, however, indicate considerable improvement in boron activation with increases in the thermal budget. We show that if carbon implantation damage is annealed out prior to boron implantation, not only is boron activation improved, but carbon continues to serve as a sink for self-interstitials, thereby effectively suppressing OED.
Compound Core–Shell Polymer Nanofibers by Co‐Electrospinning (2003)

Co‐electrospinning of core–shell polymer nanofibers (see Figure) is introduced. This process can be used for manufacturing of coaxial nanofibers made of pairs of different materials. Non‐spinnable materials can be forced into 1D arrangements by co‐electrospinning using a spinnable shell polymer. The method results in a novel two‐stage approach for fabrication of nanotubes instead of the previously used three‐stage process.
Electrophoretically Homogeneous Anti-DNP Antibodies with Restricted Isoelectric Points Elicited in Mice by Immunization with the Antigen Papain-S-DNPL (1970)

The primary immunization of outbred mice with the antigen Pap-S-DNPL results in the generation of low titers of anti-DNP antibody which in about one-third of the responding animals is as homogeneous as a myeloma protein by the combined criteria of (a) isoelectric focusing in gels and (b) gel electrophoresis of the antibody light chains. The electrophoretically homogeneous antibodies show a marked restriction of isoelectric points near pH 5.0. Such marked selectivity of the antihapten antibodies appears to result from the chemical and structural homogeneity of the Pap-S-DNPL antigen.
Solvent effects in thermal (2 + 2) cycloaddition reactions. Intramolecular capture of 1,4-dipolar intermediates vs. (2 + 2) cycloaddition in reactions of 3-(1-pyrrolidinyl)thiophenes with electron-deficient acetylenes (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolvent effects in thermal (2 + 2) cycloaddition reactions. Intramolecular capture of 1,4-dipolar intermediates vs. (2 + 2) cycloaddition in reactions of 3-(1-pyrrolidinyl)thiophenes with electron-deficient acetylenesDavid N. Reinhoudt, Jan Geevers, Willem P. Trompenaars, Sybolt Harkema, and Gerrit J. Van HummelCite this: J. Org. Chem. 1981, 46, 2, 424–434Publication Date (Print):January 1, 1981Publication History Published online1 May 2002Published inissue 1 January 1981https://pubs.acs.org/doi/10.1021/jo00315a038https://doi.org/10.1021/jo00315a038research-articleACS PublicationsRequest reuse permissionsArticle Views561Altmetric-Citations40LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Rational design of point mutation-selective antisense DNA targeted to codon 12 of Ha-rasmRNA in human cells (1995)

Antisense oligodeoxynucleotides targeted to Ha-ras mRNA have been designed to discriminate between the codon 12-mutated oncogene and the normal proto-oncogene. An in vitro assay using two different sources of RNase H (rabbit reticulocyte lysates and nuclear extract from HeLa cells) was used to characterize oligonucleotide binding to normal and mutated Ha-ras mRNA. Short oligonucleotides (12- or 13mers) centered on the mutation had a very high discriminatory efficiency. Longer oligonucleotides (16mers) did not discriminate efficiently between the mutated and the normal mRNA. We have tested the efficacy of dodecanucleotides to induce RNase H cleavage of the full-length mRNA, moving the target sequence from the loop to the stem region which is formed in the vicinity of mutated codon 12. The most selective oligonucleotides were centered on the mutation which is located near the junction between the loop and stem regions even though they were less efficient at inducing RNase H cleavage than those targeted to the loop region. The 12mer antisense oligonucleotide with the highest discriminatory power was selected for cell culture studies. This oligonucleotide inhibited the proliferation of a human cell line which had been transformed with the mutated Ha-ras gene (HBL100ras1) but had no effect on the parental cell line which was transfected with the vector DNA (HBL 100neo) and expressed only the normal Ha-ras gene. Growth inhibition of HBL100ras1 cells was associated with specific ablation of targeted Ha-ras mRNA as shown by RT-PCR. These results show that 'in vitro' evaluation using an RNase H assay allowed us to select an antisense oligonucleotide which elicited a selectivity towards point-mutated Ha-ras mRNA when added at 10 microM concentration to the culture medium of cells expressing wild type and mutated Ha-ras mRNA.
Generalization of the cross-entropy error function to improve the error backpropagation algorithm (2002)

This paper generalizes the cross-entropy error function to improve the EBP (error back propagation) algorithm of multilayer perceptrons. The generalized error function reduces the probability that output nodes are near the wrong extreme value as well as the correct extreme value of sigmoid function. As a result, we can accelerate the learning speed of the EBP algorithm with improved generalization performance. The effectiveness of the proposed method is demonstrated in a handwritten digit recognition task.
Cross-linking and Conformational Change in T-cell Receptors: Role in Activation and in Repertoire Selection (1989)

TCRs undergo a series of interactions with ligands during development. We have characterized the interaction of a TCR with its ligand and the attendant co-receptor and co-ligand structures. This characterization has led to the model in which the TCR not only binds to class II MHC, but also binds to CD4 co-receptors and co-ligands such as Mls. We have shown that both cross-linking and conformational change in the TCR are required for optimal T-cell activation. Finally, we have used the observation that a particular self-peptide found abundantly associated with class II MHC in the periphery is essentially lacking from thymic cortical epithelium to argue that positive selection for self-MHC recognition may occur by a novel process in the thymic cortex. A TCR recognizing class II MHC with low affinity could either be multiply cross-linked in the absence of conformational change, which here would be driven by a unique peptide, or could be conformationally changed without cross-linking due to the rarity of the individual high-affinity peptide on thymic cortical epithelial cells. Either proposal leads to a partial signal one delivered via the TCR, which we refer to as signal one-half. This signal one-half would induce the cell to repress its other co-receptor molecule and to undergo maturation events such as up-regulation in TCR expression. Such cells are then rigorously screened for activating interactions with autologous structures, such as Mls. The threshold for clonal deletion is set very low to avoid autoreactivity. By this combination of signaling events, a mature TCR repertoire is generated that has the functional characteristics observed in immune systems.
Capillary electrophoresis system for hemoglobin A1c determinations evaluated. (1997)

Hb A1c is the analyte of choice for monitoring metabolic control in patients with diabetes mellitus. Here we present a new analytical technique for measuring Hb A1c, capillary electrophoresis. The Hb A1c determination is not influenced by the labile Hb A1c fraction or by carbamylated or acetylated hemoglobin derivatives. Also, hemoglobin variants (Hb F, Hb S, and Hb C) do not interfere. This new application of capillary electrophoresis seems to be a valuable analytical tool for measuring Hb A1c in the clinical laboratory.
Protein stability curves (1987)

Abstract The stability curve of a protein is defined as the plot of the free energy of unfolding as a function of temperature. For most proteins the change in heat capacity on denaturation, or unfolding, is large but approximately constant. When unfolding is s two‐state process, most of the salient features of the stability curves of proteins can be derived from this fact. A number of relations are obtained, including the special features of low‐temperature denaturation, the properties of the maximum in stability, and the interrelationships of the characteristic temperatures of the protein. The paper closes with a formula that permits one to calculate small changes in stabilization free energy from changes in the melting temperature of the protein.
Expression of the protooncogene bcl-2 in the prostate and its association with emergence of androgen-independent prostate cancer. (1992)

The significance of apoptosis in relation to the development and progression of prostate cancer remains largely undefined. bcl-2 is an oncogene that functions by overriding apoptosis. bcl-2 expression was localized to the basal epithelial cells in the normal human prostate with the use of immunohistochemistry. Androgen-dependent and androgen-independent prostate carcinomas were evaluated immunohistochemically for bcl-2 expression. bcl-2 was undetectable in 13 of 19 cases of androgen-dependent cancers. In contrast, androgen-independent cancers displayed diffuse, high levels of bcl-2 staining (P < 0.01). In rats, steady-state levels of bcl-2 mRNA, assessed by S1 assays, reached maximum levels 10 days following castration. Addition of exogenous testosterone with, or without, flutamide demonstrated that the increased bcl-2 mRNA resulted from androgen ablation. Our findings indicate that bcl-2 expression is augmented following androgen ablation and is correlated with the progression of prostate cancer from androgen dependence to androgen independence.
Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences (1999)

Peptides that mediate dimerization of attached zinc finger DNA-binding domains have been evolved in vitro starting from random sequences. We first used phage display to select dimerization elements from libraries of random 15-residue polypeptides that were fused to the N terminus of the zinc finger domains. We then reoptimized these peptides by sequentially randomizing five-residue blocks (proceeding across the peptide in three steps) and selecting variant peptides that further stabilized the protein-DNA complex. Biochemical experiments confirmed that the selected peptides promote dimerization of the zinc fingers on an appropriate DNA target site. These results demonstrate that dimerization units can be obtained readily from random polypeptide libraries of moderate complexity. Our success reemphasizes the utility of searching random peptide libraries in protein design projects, and the sequences presented here may be useful when designing novel transcription factors.
Single-Step Coating of Mesoporous Silica on Cetyltrimethyl Ammonium Bromide-Capped Nanoparticles (2007)

A generalized, single-step synthesis procedure to coat individual cetyltrimethyl ammonium bromide- (CTAB) capped nanoparticles with a thin layer of mesoporous silica is outlined. This coating method was demonstrated on CTAB-capped Au nanorods and CTAB-transferred CdSe/ZnS quantum dots with silica coatings approximately 15 nm thick containing pores approximately 4 nm in diameter. This porous silica coating can serve as a platform for further surface modification to facilitate the rapid translation of nanoparticles to a wide range of end applications.
New Thermally Remendable Highly Cross-Linked Polymeric Materials (2003)

Two new remendable highly cross-linked polymers, 2ME4F and 2MEP4F, were prepared without solvent. Solid-state NMR (nuclear magnetic resonance) was used to study the thermal reversibility of Diels−Alder (DA) cross-linking, and it was found that DA connections and disconnections of both polymers are thermally reversible. Differential scanning calorimeter and dynamical mechanical analysis were applied to study thermal and mechanical properties of these materials, and it is found that the glass transition temperature (Tg) of 2ME4F is about 30−40 °C and that of 2MEP4F is about 80 °C. A qualitative study of the healing efficiency of 2MEP4F showed that cracks can be healed effectively with a simple thermal healing procedure. This process can be repeated to heal cracks multiple times.
Label-free DNA detection on the surface of an optical fiber tip (2006)

This paper presents a label-free method for direct detection of deoxyribonucleic acid (DNA) sequences using layer-by-layer electrostatic self-assembly (L-b-L ESA) technique. The sensor features sequence specificity, cost efficiency, speed, and ease of use.
Comparison of tocilizumab monotherapy versus methotrexate monotherapy in patients with moderate to severe rheumatoid arthritis: the AMBITION study (2009)

Tocilizumab monotherapy is better than methotrexate monotherapy, with rapid improvement in RA signs and symptoms, and a favourable benefit-risk, in patients for whom treatment with methotrexate or biological agents has not previously failed.
On triazoles XVIII. . an unexpected rearrangement observed during the reaction of 5‐amino‐1,2,4‐triazoles with N‐heterocyclic β‐oxo‐esters (1989)

Abstract In the course of the synthesis of pyrido[4,3‐ d ]‐1,2,4‐triazolo[1,5‐a]pyrimidine derivatives 3c representing a novel ring system an unexpected rearrangement of the intermediate enamines to yield 5 was observed. A mechanism of the formation of 5 was suggested. The isomeric pyrido[4,3‐ e ]‐1,2,4‐triazolo[1,5‐ a ]pyrimidine derivatives 4c containing also a new ring system were obtained, too. The structure of products obtained was proved with the help of their uv, cmr and X‐ray spectra.
Aspects of Fetal Learning and Memory (2009)

Ninety-three pregnant women were recruited to assess fetal learning and memory, based on habituation to repeated vibroacoustic stimulation of fetuses of 30-38 weeks gestational age (GA). Each habituation test was repeated 10 min later to estimate the fetal short-term memory. For Groups 30-36, both measurements were replicated in a second session at 38 weeks GA for the assessment of fetal long-term memory. Within the time frame considered, fetal learning appeared GA independent. Furthermore, fetuses were observed to have a short-term (10-min) memory from at least 30 weeks GA onward, which also appeared independent of fetal age. In addition, results indicated that 34-week-old fetuses are able to store information and retrieve it 4 weeks later.
Conditional differentiation of heartand smooth muscle-derived cells transformed by a temperature-sensitive mutant of SV40 T antigen (1996)

To create muscle cell lines that conditionally differentiate in vitro we introduced a temperature-sensitive SV40 T antigen by retroviral infection into rat aortic smooth muscle cells (SMCs) and neonatal heart-derived cells. After G418 selection cell lines isolated were characterized at permissive (33 degrees C) and non-permissive (39 degrees C) temperatures. [3H]Thymidine uptake showed tht progression through the cell cycle is greatly reduced at 39 degrees C. Cytoskeletal proteins, such as actins and vimentin did not change significantly after temperature shift, while the number of desmin-positive SMCs significantly increased when cells were switched to 39 degrees C. Heart-derived muscle cells showed sarcomeric myosin heavy chain reactivity only when grown at 39 degrees C. After thrombin stimulation intracellular calcium in both cell types increased severalfold in 39 degrees C-cells but not in 33 degrees C-cells. Whole cell patch-clamp recordings of SMCs and heart-derived cells revealed a strong increase in nicardipine-sensitive Ca2+ current when cells were switched to 39 degrees C. Nicardipine-insensitive Ca2+ current also increased in both cell types at the non-permissive temperature. Na+ current in SMCs was large at 33 degrees C and small or not detectable at 39 degrees C and absent in heart-derived cells. Using a cDNA probe specific for the alpha 1 subunit of the dihydropyridine-sensitive Ca2+ channel we demonstrate a temperature-sensitive expression of the dihydropyridine receptor mRNA in smooth muscle-derived cells but not in heart-derived H10 cells. Our results suggest that upon downregulation of SV40 T antigen these cells become quiescent and exhibit a more differentiated phenotype. These cell lines may provide a useful tool to investigate ion channel- and receptor signal transduction, as well as cell cycle control in smooth and possibly cardiac muscle cell differentiation.