gebhart/patrepeval huggingface dataset:
Dipeptidyl peptidase IV in the human lung and spinocellular lung cancer. (1991)

The isoelectric point and proportions of soluble and membrane bound dipeptidyl peptidase IV (DPP-IV) in human lung and spinocellular lung cancer tissue were tested. It was found that soluble DPP-IV is relatively less frequent in the cancer than in normal lung tissue. We demonstrated multiple molecular forms of DPP-IV in normal and cancer lung tissues, differing probably not only in the degree of sialylation. DPP-IV from lung cancer tissue consists of more basic molecular forms than that from normal lung tissue. These results suggest that the molecular properties of DPP-IV in normal and cancerous lung tissues may be different.
RAFT polymerization of a novel activated ester monomer and conversion to a terpyridine‐containing homopolymer (2007)

Abstract Developing new materials with unique properties for nanotechnology applications, in general, and supramolecular polymers, in particular, lie at the heart of much ongoing research. In line with these efforts, we have been exploring polymers containing terpyridine (terpy) in the side chain. Here we report a new monomer that effectively undergoes reversible addition fragmentation chain transfer polymerization (RAFT) to yield high‐molecular‐weight ( M n ) polymers with narrow polydispersity (PDI). The monomer is an N ‐succinimide activated ester of p ‐vinyl benzoic acid. Under RAFT conditions, poly( N ‐succinimide p ‐vinylbenzoate)s were generated, with M n ranging between 44 and 61 kDa and PDI of 1.03–1.07. One of these homopolymers was reacted with an amine functionalized terpy, creating a new homopolymer containing terpy ligands on every monomer. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 5618–5625, 2007
Manipulating Enzymes Properties with DNA Nanostructures (2019)

Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology-and indeed its initial motivation-is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.
Serum myostatin-immunoreactive protein is increased in 60-92 year old women and men with muscle wasting. (2002)

These findings suggest that serum myostatin may be a biomarker of age-associated sarcopenia. They are consistent with the hypothesis that the human myostatin gene product is a suppressor of skeletal muscle growth in advancing age.
Fabricating three-dimensional nanostructures using two photon lithography in a single exposure step (2006)

Conformable phase masks, transparent photopolymers and two photon effects provide the basis for a simple, parallel lithographic technique that can form complex, but well defined three-dimensional (3D) nanostructures in a single exposure step. This paper describes the method, presents examples of its ability to form 3D nanostructures (including freestanding particles with controlled shapes) and comprehensive modeling of the associated optics. Single step, large area 3D pattern definition, subwavelength resolution and experimental simplicity represent features that make this method potentially useful for applications in photonics, biotechnology and other areas.
Transcutaneous immunization and immunostimulant strategies: capitalizing on the immunocompetence of the skin (2003)

The skin is an attractive target for vaccine delivery. Topical application of adjuvants results in potent immune responses and good safety profiles. Adjuvants can be coadministered in a patch with vaccine antigens (transcutaneous immunization) or similar delivery format, or administered separately with an injection or IS patch (Iomai), leading to enhanced immune responses. These observations have moved into the clinic, highlighting the likelihood that skin delivery of vaccines will play an important future role in vaccine applications.
Letter to the Editor: Does Dicer Expression Affect shRNA Processing? (2009)

Elevated Dicer and Drosha mRNA levels have been documented across a range of tumor types (including ovarian carcinoma) by a number of investigators without any demonstrable correlation with patient survival nor evidence of interference with shRNA processing. A recent publication by Merritt et al. (NEJM 359(25):2641-50, 2008) reporting their findings in patients with ovarian carcinoma reach opposite conclusions. Further study will be needed to resolve this issue.
Monomeric (glycine-proline-hydroxyproline)10 repeat sequence is a partial agonist of the platelet collagen receptor glycoprotein VI (1999)

We have previously reported that a triple-helical, collagen-related peptide (CRP; also known as CRP-XL) containing a glycine-proline-hydroxyproline (GPP*) repeat motif and cross-linked through cysteine residues at its N-terminus and C-terminus is a powerful stimulus of platelet aggregation and secretion through the surface receptor glycoprotein VI (GPVI). The activation of platelets is associated with tyrosine phosphorylation of the tyrosine kinase Syk and phospholipase C gamma2 (PLCgamma2). We now report that the non-cross-linked backbone of CRP, monomeric CRP (mCRP), stimulates the tyrosine phosphorylation of Syk and PLCgamma2 in platelets and induces the weak secretion of [3H]5-hydroxytryptamine ([3H]5-HT) and aggregation. The action of mCRP does not seem to be due to spontaneous cross-linking, because alkylation of the cysteine residues leads to an increase in activity. The tripeptide backbone of CRP, GPP*10 (in which P* represents hydroxyproline) also stimulates platelet shape change and the weak tyrosine phosphorylation of Syk and PLCgamma2, but is unable to induce aggregation or secretion. The monomeric peptides partly inhibit the release of [3H]5-HT by CRP, suggesting that they are partial agonists of the collagen receptor GPVI. These results demonstrate that GPP* present as a repeat motif is sufficient to activate the platelet collagen receptor GPVI but that the cross-linking of monomers brings about an increase in activity.
Pyrosequencing as a tool for better understanding of human microbiomes (2012)

Next-generation sequencing technologies have revolutionized the analysis of microbial communities in diverse environments, including the human body. This article reviews several aspects of one of these technologies, the pyrosequencing technique, including its principles, applications, and significant contribution to the study of the human microbiome, with especial emphasis on the oral microbiome. The results brought about by pyrosequencing studies have significantly contributed to refining and augmenting the knowledge of the community membership and structure in and on the human body in healthy and diseased conditions. Because most oral infectious diseases are currently regarded as biofilm-related polymicrobial infections, high-throughput sequencing technologies have the potential to disclose specific patterns related to health or disease. Further advances in technology hold the perspective to have important implications in terms of accurate diagnosis and more effective preventive and therapeutic measures for common oral diseases.
Novel Histone Demethylase LSD1 Inhibitors Selectively Target Cancer Cells with Pluripotent Stem Cell Properties (2011)

Histone modification determines epigenetic patterns of gene expression with methylation of histone H3 at lysine 4 (H3K4) often associated with active promoters. LSD1/KDM1 is a histone demethylase that suppresses gene expression by converting dimethylated H3K4 to mono- and unmethylated H3K4. LSD1 is essential for metazoan development, but its pathophysiologic functions in cancer remain mainly uncharacterized. In this study, we developed specific bioactive small inhibitors of LSD1 that enhance H3K4 methylation and derepress epigenetically suppressed genes in vivo. Strikingly, these compounds inhibited the proliferation of pluripotent cancer cells including teratocarcinoma, embryonic carcinoma, and seminoma or embryonic stem cells that express the stem cell markers Oct4 and Sox2 while displaying minimum growth-inhibitory effects on non-pluripotent cancer or normal somatic cells. RNA interference-mediated knockdown of LSD1 expression phenocopied these effects, confirming the specificity of small molecules and further establishing the high degree of sensitivity and selectivity of pluripotent cancer cells to LSD1 ablation. In support of these results, we found that LSD1 protein level is highly elevated in pluripotent cancer cells and in human testicular seminoma tissues that express Oct4. Using these novel chemical inhibitors as probes, our findings establish LSD1 and histone H3K4 methylation as essential cancer-selective epigenetic targets in cancer cells that have pluripotent stem cell properties.
Mobile reception of DVB-T services by means of AL-FEC protection (2009)

This paper proposes and investigates the use of Application Layer Forward Error Correction (AL-FEC) based on Raptor codes for digital television DVB-T (Digital Video Broadcasting - Terrestrial) services. By means of AL-FEC it is possible to increase the robustness of traditional DVB-T transmissions for the provision of mobile TV. The AL-FEC protection is introduced in a backwards compatible way with the legacy DVB-T standard and does not alter the originally transmitted multimedia data. In order to evaluate the performance of AL-FEC in mobile channel environments, we employ laboratory measurements along with dynamic shadowing simulations. The paper presents direct comparisons with the link layer protection mechanism of DVB-H - referred to as MPE-FEC (Multi Protocol Encapsulation - Forward Error Correction) - and illustrates the link margin gains that can be achieved in mobile DVB-T reception by means of AL-FEC.
Four-Stranded Nucleic Acid Structures 25 Years Later: From Guanosine Gels to Telomer DNA (1990)

The subject of four-stranded nucleic acid structures is reviewed. Studies on gels formed by guanosine and its analogues have provided appropriate models for the structures of poly(I) and poly(G). The stabilizing influence of certain cations, in particular K+, on Guo-5'-P gels and poly(I) is discussed in the light of recent data on selective K+ stabilization of telomeric DNA structures. The topological possibilities these dG containing sequences could adopt are discussed. In particular the role of the glycosidic linkage (anti/syn), the polarity of the strands and the orientation of the G-tetrad stacks is highlighted.
Measurement of a monoclonal-antibody-defined antigen (90K) in the sera of patients with ovarian cancer. (1988)

Serum levels of CA125 and 90K, a new tumor-associated antigen, were measured in 73 ovarian cancer patients and 70 patients with benign gynecological conditions. Abnormally high serum CA 125 and 90K levels were found in 49% and 78% of these patients, respectively. When a combination of the two markers was used, the sensitivity increased to 86%. The percentage of 90K positivity did not significantly correlate with stage of disease or with histological type. A statistically significant correlation was found between 90K positivity rate and grade of tumor differentiation. Elevated serum CA 125 and 90K levels were present in 32% and 29% of patients with benign ovarian tumors, respectively. Only 1 case out of 26 with endometriosis had high 90K levels, compared to 7 patients with abnormal CA 125 levels. Serial measurements of 90K concentrations were found to be correlated with the clinical behaviour of the disease during chemotherapy. Moreover, rising levels of 90K preceded the clinical detection of recurrence with a median lead-time of 3 months. In 2 of these cases the serial changes in 90K values were better correlated with the course of disease than changes in CA 125 levels. Our data suggest that 90K combined with CA 125 may be applied for the detection and monitoring of ovarian cancer.
Analysis of Smad nucleocytoplasmic shuttling in living cells (2004)

Transforming growth factor beta (TGF-beta) signalling leads to phosphorylation and activation of receptor-regulated Smad2 and Smad3, which form complexes with Smad4 and accumulate in the nucleus. The Smads, however, do not seem to reside statically in the cytoplasm in the absence of signalling or in the nucleus upon TGF-beta stimulation, but have been suggested to shuttle continuously between these cellular compartments in both the absence and presence of TGF-beta. Here we investigate this nucleocytoplasmic shuttling in detail in living cells using fusions of Smad2 and Smad4 with enhanced GFP. We first establish that the GFPSmad fusions behave like wild-type Smads in a variety of cellular assays. We go on to demonstrate directly, using photobleaching experiments, that Smad2 and Smad4 shuttle between the cytoplasm and nucleus in both TGF-beta-induced cells and in uninduced cells. In uninduced cells, GFPSmad2 is less mobile in the cytoplasm than is GFPSmad4, suggesting that it may be tethered there. In addition, we show that both GFPSmad2 and GFPSmad4 undergo a substantial decrease in mobility in the nucleus upon TGF-beta stimulation, suggesting that active complexes of Smads are tethered in the nucleus, whereas unactivated Smads are more freely diffusible. We propose that regulated cytoplasmic and nuclear retention may play a role in determining the distribution of Smads between the cytoplasm and the nucleus in both uninduced cells and upon TGF-beta induction.
Synthesis and Fungicidal Activity of 2-Imino-3-(4-arylthiazol-2-yl)-thiazolidin-4-ones and Their 5-Arylidene Derivatives (2000)

Five derivatives of 2-imino-3-(4-arylthiazol-2-yl)-thiazolidin-4-ones and a series of their 5-arylidene derivatives have been synthesized and tested for antifungal activity against seven agricultural fungi. 2-Imino-3-(2,4-dichloro-5-fluorophenylthiazol-2-yl)-4-thiazolidi-none and 2-imino-3-(2,4-dichlorophenylthiazol-2-yl)-4-thiazolidione, both of them new compounds, exhibited higher fungicidal effects than the other compounds prepared.
Morphology and electro-optic properties of polymer-dispersed liquid-crystal films (1997)

An attractive way of making polymer-dispersed liquid-crystal (PDLC) films is through photopolymerization-induced phase separation. The electro-optic properties of these films are determined in large part by the size, shape, and packing of the embedded liquid-crystal drops. We explore the relationships between the conditions of phase separation, morphology, and electro-optic properties. A strikingly strong dependence of electro-optic properties on the fraction of liquid crystal in the film is demonstrated and explained by consideration of the phase separation process. Also, confocal microscopy is shown to be a useful, noninvasive means of obtaining three-dimensional information on PDLC morphology. Not only does it provide very clear images of liquid crystalline drops in the film, but unexpected features were revealed. The drops exhibit a morphology much like a polyhedral foam in the films studied. Polymeric filaments inside the drops were observed as well as a drift in the average size of the drops with proximity to the film substrates. All of these features have important consequences for the electro-optic performance of PDLC films.
CW room temperature operation of a diode cascade InGaAs-AlGaAs quantum well VCSEL (2003)

Vertical cavity surface emitting lasers (VCSELs) are considered as excellent candidates for optical interconnect applications due to low threshold currents, high wallplug efficiency and high-speed modulation capabilities. On the other hand, common VCSEL devices are characterized by the extremely low roundtrip gain in the cavity that requires high mirror reflectivity. Therefore, thermal rollover limits high-power applications of VCSEL structures due to internal heating. To overcome this distinct disadvantage, diode cascade VCSEL structures are proposed to reduce threshold current and heighten output power by increasing the roundtrip gain. However, the devices can only be demonstrated up to 175 K in continuous-wave (CW) operation. We present the first CW, room temperature operation of a diode cascade VCSEL at 988 nm wavelength.
MOLECULAR ANALYSIS OF THE PATHOGENICITY OF STREPTOCOCCUS PNEUMONIAE: The Role of Pneumococcal Proteins (1993)

For many years the virulence of Streptococcus pneumoniae has largely been attributed to its antiphagocytic polysaccharide capsule. Recent evidence, however, indicates that certain pneumococcal proteins play an important part in the pathogenesis of disease, either as mediators of inflammation or by directly attacking host tissues. Pneumococci carrying defined mutations in the genes encoding any one of at least three pneumococcal proteins (the toxin pneumolysin, the major pneumococcal autolysin, and pneumococcal surface protein A) have significantly reduced virulence. Pneumococcal hydrolytic enzymes, such as neuraminidase, hyaluronidase, and IgA1 protease may also contribute to colonization and/or invasion of the host. Several of these proteins (or their detoxified derivatives) are protective immunogens in animal models and therefore warrant consideration for inclusion in human antipneumococcal vaccine formulations.
A 4.4&#x2013;5.4GHz digital fractional-N PLL using &#x0394;&#x03A3; frequency-to-digital converter (2014)

A phase interpolator (PI) based fractional divider is used to improve the quantization noise shaping properties of a 1-bit ΔΣ frequency-to-digital converter (FDC). Fabricated in 65nm CMOS process, the prototype calibration-free fractional-N Type-II PLL employs the proposed FDC in place of a high resolution TDC and achieves −102dBc/Hz in-band phase noise and 852fs <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</inf> integrated jitter (1k–40M) while generating 5.054GHz output from 31.25MHz input.
Nickel Compounds Act through Phosphatidylinositol-3-kinase/Akt-Dependent, p70S6k-Independent Pathway to Induce Hypoxia Inducible Factor Transactivation and Cap43 Expression in Mouse Epidermal Cl41 Cells (2004)

Nickel compounds are a somewhat unique class of carcinogens. Previous studies have demonstrated that NiCl(2) exposure leads to marked induction of hypoxia inducible factor 1 (HIF-1) in human osteosarcoma and BALB/c 3T3 cells, a transcription factor that has been considered to play an important role in tumor promotion and progression. However, the signal transduction pathways leading to HIF-1 induction are not well understood. The present study indicated that exposure of mouse epidermal Cl41 cells to either Ni(3)S(2) or NiCl(2) resulted in activation of phosphatidylinositol 3-kinase (PI-3K), Akt, and p70 S6 kinase (p70(S6k)). Inhibition of PI-3K, Akt, and p70(S6k) by overexpression of a dominant-negative mutant of PI-3K (Deltap85) impaired nickel-induced HIF-1 transactivation. Furthermore, an overexpression of the dominant-negative Akt mutant (Akt-T308A/S473A) blocked nickel-induced Akt phosphorylation and HIF-1 transactivation, whereas inhibition of p70(S6k) activation by pretreatment of cells with rapamycin did not show significant inhibitory effects on HIF-1 transactivation induced by nickel compounds. Consistent with HIF-1 transactivation, inhibition of the PI-3K/Akt pathway by either overexpression of Deltap85 or Akt-T308A/S473A caused dramatic inhibition of Cap43 protein expression induced by nickel compounds, whereas pretreatment of cells with rapamycin did not exhibit inhibition of Cap43 induction. These results demonstrated that nickel compounds induce HIF-1 transactivation and Cap43 protein expression through a PI-3K/Akt-dependent and p70(S6k)-independent pathway. This study should help us understand the signal transduction pathways involved in the carcinogenic effects of nickel compounds.
Scalable successive-cancellation hardware decoder for polar codes (2013)

Polar codes, discovered by Arikan, are the first error-correcting codes with an explicit construction to provably achieve channel capacity, asymptotically. However, their error-correction performance at finite lengths tends to be lower than existing capacity-approaching schemes. Using the successive-cancellation algorithm, polar decoders can be designed for very long codes, with low hardware complexity, leveraging the regular structure of such codes. We present an architecture and an implementation of a scalable hardware decoder based on this algorithm. This design is shown to scale to code lengths of up to N = 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20</sup> on an Altera Stratix IV FPGA, limited almost exclusively by the amount of available SRAM.
Deconstruction of a Nutlin: Dissecting the Binding Determinants of a Potent Protein–Protein Interaction Inhibitor (2013)

Protein-protein interaction (PPI) systems represent a rich potential source of targets for drug discovery, but historically have proven to be difficult, particularly in the lead identification stage. Application of the fragment-based approach may help toward success with this target class. To provide an example toward understanding the potential issues associated with such an application, we have deconstructed one of the best established protein-protein inhibitors, the Nutlin series that inhibits the interaction between MDM2 and p53, into fragments, and surveyed the resulting binding properties using heteronuclear single quantum coherence nuclear magnetic resonance (HSQC NMR), surface plasmon resonance (SPR), and X-ray crystallography. We report the relative contributions toward binding affinity for each of the key substituents of the Nutlin molecule and show that this series could hypothetically have been discovered via a fragment approach. We find that the smallest fragment of Nutlin that retains binding accesses two subpockets of MDM2 and has a molecular weight at the high end of the range that normally defines fragments.