gebhart/patrepeval huggingface dataset:
Natural Peptides as Building Blocks for the Synthesis of Large Protein-like Molecules with Hydrazone and Oxime Linkages (1996)

Methods are known for the production of synthetic protein-like molecules of nonlinear architecture with molecular masses in the 10-20 kDa range. To synthesize such compounds of higher molecular mass and complexity, chemoselective ligation of natural (as opposed to synthetic) peptide building blocks was studied. In preliminary experiments with model peptides, conditions for the formation of peptide oximes were investigated, and their stability at alkaline pH was examined, to resolve a literature controversy. It was found that low pH (down to 2.1) was suitable for polyoxime formation and that the oxime bond was stable for up to 65 h at pH 8 and for more than 2 h at pH 9. Then, using natural peptides, it was found to be possible to synthesize, and characterize by mass spectrometry, nine-component species with molecular masses > 48 kDa. This is about twice the size of homogeneous artificial proteins previously described. Such complex molecules of defined structure are beginning to find applications as vaccine candidates, as radioimmunodiagnostic agents, and as nonviral gene therapy delivery vehicles.
Dengue Virus Structural Differences That Correlate with Pathogenesis (1999)

The understanding of dengue virus pathogenesis has been hampered by the lack of in vitro and in vivo models of disease. The study of viral factors involved in the production of severe dengue, dengue hemorrhagic fever (DHF), versus the more common dengue fever (DF), have been limited to indirect clinical and epidemiologic associations. In an effort to identify viral determinants of DHF, we have developed a method for comparing dengue type 2 genomes (reverse transcriptase PCR in six fragments) directly from patient plasma. Samples for comparison were selected from two previously described dengue type 2 genotypes which had been shown to be the cause of DF or DHF. When full genome sequences of 11 dengue viruses were analyzed, several structural differences were seen consistently between those associated with DF only and those with the potential to cause DHF: a total of six encoded amino acid charge differences were seen in the prM, E, NS4b, and NS5 genes, while sequence differences observed within the 5' nontranslated region (NTR) and 3' NTR were predicted to change RNA secondary structures. We hypothesize that the primary determinants of DHF reside in (i) amino acid 390 of the E protein, which purportedly alters virion binding to host cells; (ii) in the downstream loop (nucleotides 68 to 80) of the 5' NTR, which may be involved in translation initiation; and (iii) in the upstream 300 nucleotides of the 3' NTR, which may regulate viral replication via the formation of replicative intermediates. The significance of four amino acid differences in the nonstructural proteins NS4b and NS5, a presumed transport protein and the viral RNA polymerase, respectively, remains unknown. This new approach to the study of dengue virus genome differences should better reflect the true composition of viral RNA populations in the natural host and permit their association with pathogenesis.
The Development of Murine Plasmacytoid Dendritic Cell Precursors Is Differentially Regulated by FLT3-ligand and Granulocyte/Macrophage Colony-Stimulating Factor (2002)

Plasmacytoid predendritic cells or type 1 interferon (IFN)-producing cells (IPCs) have recently been identified in mice. Although culture systems giving rise to different murine dendritic cell subsets have been established, the developmental regulation of murine plasmacytoid IPCs and the culture conditions leading to their generation remain unknown. Here we show that large numbers of over 40% pure CD11c(+)CD11b(-)B220(+)Gr-1(+) IPCs can be generated from mouse bone marrow cultures with FLT3-ligand. By contrast GM-CSF or TNF-alpha, which promote the generation of CD11c(+)CD11b(+)B220(-) myeloid DCs, block completely the development of IPCs. IPCs generated display similar features to human IPCs, such as the plasmacytoid morphology, the ability to produce large amounts of IFN-alpha in responses to herpes simplex virus, and the capacity to respond to ligands for Toll-like receptor 9 (TLR-9; CpG ODN 1668), but not to ligands for TLR-4 (lipopolysaccharide [LPS]). Unlike human IPCs which produce little IL-12p70, mouse IPCs produce IL-12p70 in response to CpG ODN 1668 and herpes simplex virus. This study demonstrates that the development of murine CD11c(+)CD11b(-)B220(+)Gr-1(+) IPCs and CD11c(+)CD11b(+)B220(-) myeloid DCs is differentially regulated by FLT3-ligand and granulocyte/macrophage colony-stimulating factor. Human IPCs and mouse IPCs display different ability to produce IL-12p70. Large numbers of mouse IPCs can now be obtained from total bone marrow culture.
Plasma carboxypeptidases as regulators of the plasminogen system. (1995)

Carboxy-terminal lysine residues on the surface of cells and fibrin bind plasminogen and control its activation. Since plasma contains basic carboxypeptidases, which remove carboxy-terminal lysines from protein substrates, we investigated if these enzymes are involved in the regulation of plasminogen binding sites. Plasma reduced plasminogen binding to cells, and this effect could be ascribed to the activity of the plasma carboxypeptidases. Purified carboxypeptidase N, which is constitutively active, and plasma carboxypeptidase B, which circulates as a zymogen, were both capable of significantly reducing plasminogen binding to cells. Dose titration experiments verified that plasma concentrations of either carboxypeptidase were sufficient to maximally affect plasminogen binding to cells. Furthermore, plasma carboxypeptidase B, but not carboxypeptidase N, reduced the rate of whole blood clot lysis induced by tissue-type plasminogen activator. These findings establish that plasma carboxypeptidases can modulate plasminogen binding to cells and control the rate of fibrinolysis. These functions delineate a novel role for the plasma carboxypeptidases in the regulation of the plasminogen system.
InGaN Solar Cells: Present State of the Art and Important Challenges (2012)

Solar cells are a promising renewable and carbon-free electric energy resource to address the fossil-fuel shortage and global warming. Energy conversion efficiencies over 40% have been recently achieved using conventional III–V semiconductor compounds as photovoltaic materials. The revision of InN bandgap to a much narrower value has extended the fundamental bandgap of the group III-nitride alloy system over a wider spectral region (from 0.64 eV for InN to 3.4 eV for GaN or 6.2 eV for AlN), raising the possibility of a variety of new applications. The tunable bandgap, predicted high radiation resistance, and strong absorption coefficient of the In <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_x$</tex></formula> Ga <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_{ 1-x}$</tex></formula> N material system are promising for high-efficiency photovoltaic systems. During the past few years, the interest in In <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_x$</tex></formula> Ga <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_{ 1-x}$</tex> </formula> N solar cells has been remarkable. The development of high-performance solar cells using In <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_x$</tex></formula> Ga <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_{1-x}$</tex></formula> N materials is one of the most important goals when compared with the existing solar cells using Si and other III–V materials. Significant efforts and progress have been made toward this goal, while great opportunities and grand challenges coexist. In this paper, we present a review on the present state of the art of In <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_x$</tex> </formula> Ga <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_{1-x}$</tex></formula> N-based solar cells. The most important challenges toward the high-efficiency In <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX"> $_x$</tex></formula> Ga <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$_{ 1-x}$</tex></formula> N-based solar cells are discussed in the context of the recent results.
Phase-Only Complex-Valued Spatial Filter* (1971)

A new type of phase-only filter is described for wave-front construction, in which both the amplitude and phase information necessary to construct an arbitrary image over a limited field are encoded. It is shown that this phase-only filter can duplicate the performance of an ideal complex-valued spatial filter (a filter that controls both amplitude and phase transmittance). This phase-only filter controls the amplitude transmittance by the use of a modulated high-frequency phase carrier that diffracts a controlled amount of light into the image. This type of filter is particularly useful in the implementation of computational wave-front construction, because the maximum spatial frequency that must be plotted is associated with the image and not the carrier. The performance of the filter is examined both numerically and experimentally.
Detection of TSH Receptor RNA in Cultured Fibroblasts from Patients with Graves' Ophthalmopathy and Pretibial Dermopathy (1993)

Fibroblasts are target cells for the autoimmune process in Graves' ophthalmopathy and pretibial dermopathy. Because the autoantigen involved in the hyperthyroidism of Graves' disease is the TSH receptor, we sought to determine whether RNA encoding this receptor might be present in retroocular and pretibial fibroblasts. RNA was reverse transcribed and the resulting cDNA was amplified by the polymerase chain reaction using primers spanning a region of the extracellular domain of the human TSH receptor. The predicted amplified product, verified by direct sequencing, was detected when RNA was derived from fibroblasts, but not from the nonfibroblast cells studied. The demonstration in fibroblasts of RNA encoding this important autoantigen in Graves' disease suggests that the TSH receptor might play a role in the pathogenesis of the connective tissue manifestations of this disease.
Preparation and applications of magnetostrictive thin films (1994)

Amorphous magnetostrictive films of the binary compound SmxFe1−x as well as of the ternary compound (TbyDy1−y)xFe1−x were prepared by rf or dc magnetron sputtering using either a multitarget arrangement with pure element targets or cast composite-type targets. The magnetostrictive properties of (Tb0.3Dy0.7)0.4Fe0.6 and Sm0.4Fe0.6 films were investigated in relation to their preparation conditions. Depending upon these conditions (especially upon the deposition rate, the bias voltage, and the Ar sputtering pressure) amorphous films with a giant magnetostriction of about 250 ppm (−220 ppm) at 0.1 T and 400 ppm (−300 ppm) at 0.5 T for the TbDyFe (SmFe) and an in-plane magnetic easy axis could be prepared. In view of applications in microsystem technologies (e.g., pumps, valves, positioning elements) these films have been tested in a simple cantilever arrangement and the predicted deflection of a magnetostrictive actuated membrane has been calculated.
Diversity of G Proteins in Signal Transduction (1991)

The heterotrimeric guanine nucleotide-binding proteins (G proteins) act as switches that regulate information processing circuits connecting cell surface receptors to a variety of effectors. The G proteins are present in all eukaryotic cells, and they control metabolic, humoral, neural, and developmental functions. More than a hundred different kinds of receptors and many different effectors have been described. The G proteins that coordinate receptor-effector activity are derived from a large gene family. At present, the family is known to contain at least sixteen different genes that encode the alpha subunit of the heterotrimer, four that encode beta subunits, and multiple genes encoding gamma subunits. Specific transient interactions between these components generate the pathways that modulate cellular responses to complex chemical signals.
One melanocortin 4 and two melanocortin 5 receptors from zebrafish show remarkable conservation in structure and pharmacology (2002)

We report the cloning, genome mapping, functional expression, pharmacology and anatomical distribution of three melanocortin (MC) receptors from zebrafish (z). Phylogenetic analysis showed with high bootstrap support that these genes represent one MC4 receptor and two MC5 receptors. Chromosomal mapping showed conserved synteny between regions containing zMC4 and human (h) MC4 receptors, whereas the two zMC5 receptor genes map on chromosome segments in which the zebrafish has several genes with two orthologues of a single mammalian gene. It is likely that the two copies of zMC5 receptors arose through a separate duplication in the teleost lineage. The zMC4, zMC5a, and zMC5b receptors share 70-71% overall amino acid identity with the respective human orthologues and over 90% in three TM regions believed to be most important for ligand binding. All three zebrafish receptors also show pharmacological properties remarkably similar to their human orthologues, with similar affinities and the same potency order, when expressed and characterized in radioligand binding assay for the natural MSH) peptides alpha-, beta-, and gamma-MSH. Stimulation of transfected mammalian cells with alpha-MSH caused a dose-dependent increase in intracellular cAMP levels for all three zebrafish receptors. All three genes were expressed in the brain, eye, ovaries and gastrointestinal tract, whereas the zMC5b receptor was also found in the heart, as determined by RT-PCR. Our studies, which represent the first characterization of MC receptors in a nonamniote species, indicate that the MC receptor subtypes arose very early in vertebrate evolution. Important pharmacological and functional properties, as well as gene structure and syntenic relationships have been highly conserved over a period of more than 400 million years implying that these receptors participate in vital physiological functions.
Chemistry in superacids. 8. Superacid-catalyzed carbonylation of methane, methyl halides, methyl alcohol, and dimethyl ether to methyl acetate and acetic acid (1990)

Superacid-catalyzed (BF, BF3-H2O, HF-BF3, and CF3SO3H) carbonylation of methane and its substituted derivatives (particularly, methyl alcohol and dimethyl ether) gave acetic acid and methyl acetate. HF-BF3 was found to be the most effective catalyst, giving nearly complete conversion of methyl alcohol or dimethyl ether. CF3SO3H led to lower yields and also to the formation of methyl trifluoromethanesulfonate. Possible reaction pathways and mechanisms are discussed on the basis of experimental results. Contrasted with Rh-catalyzed carbonylation of methyl alcohol, the superacid-catalyzed reaction does not necessitate expensive catalyst and conditions necessary with sensitive organometallic catalyst systems.
Carbamoyl-Substituted N-Heterocyclic Carbene Complexes of Palladium(II):  Application to Sonogashira Cross-Coupling Reactions (2002)

[reaction: see text]. The first examples of N-carbamoyl-substituted heterocyclic carbene Pd(II) complexes are described. These thermal and hydrolytically stable complexes are readily prepared from carbamoyl imidazolium salts and efficiently promote Sonogashira cross-coupling reactions under mild conditions. Cesium carbonate is also shown to be an effective base for the coupling of aryl bromides.
Chemistry meets proteomics: The use of chemical tagging reactions for MS‐based proteomics (2006)

As proteomics matures from a purely descriptive to a function-oriented discipline of the life sciences, there is strong demand for novel methodologies that increase the depth of information that can be obtained from proteomic studies. MS has long played a central role for protein identification and characterization, often in combination with dedicated chemical modification reactions. Today, chemistry is helping to advance the field of proteomics in numerous ways. In this review, we focus on those methodologies that have a significant impact for the large-scale study of proteins and peptides. This includes approaches that allow the introduction of affinity tags for the enrichment of subclasses of peptides or proteins and strategies for in vitro stable isotope labeling for quantification purposes, among others. Particular attention is given to the study of PTMs where recent advancements have been promising, but many interesting targets are not yet being addressed.
The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium (2002)

The complete genome of the green-sulfur eubacterium Chlorobium tepidum TLS was determined to be a single circular chromosome of 2,154,946 bp. This represents the first genome sequence from the phylum Chlorobia, whose members perform anoxygenic photosynthesis by the reductive tricarboxylic acid cycle. Genome comparisons have identified genes in C. tepidum that are highly conserved among photosynthetic species. Many of these have no assigned function and may play novel roles in photosynthesis or photobiology. Phylogenomic analysis reveals likely duplications of genes involved in biosynthetic pathways for photosynthesis and the metabolism of sulfur and nitrogen as well as strong similarities between metabolic processes in C. tepidum and many Archaeal species.
Efficient evaluation of XQuery over streaming data (2005)

With the growing popularity of XML and emer-gence of streaming data model, processing queries over streaming XML has become an important topic. This paper presents a new framework and a set of techniques for processing XQuery over streaming data. As compared to the existing work on supporting XPath/XQuery over data streams, we make the following three contributions: 1. We propose a series of optimizations which transform XQuery queries so that they can be cor-rectly executed with a single pass on the dataset. 2. We present a methodology for determining when an XQuery query, possibly after the trans-formations we introduce, can be correctly exe-cuted with only a single pass on the dataset. 3. We describe a code generation approach which can handle XQuery queries with user-dened ag-gregates, including recursive functions. We ag-gressively use static analysis and generate exe-cutable code, i.e., do not require a query plan to be interpreted at runtime. We have evaluated our implementation using sev-eral XMark benchmarks and three other XQuery queries driven by real applications. Our ex-perimental results show that as compared to Qizx/Open, Saxon, and Galax, our system: 1) is at least 25 % faster on XMark queries with small datasets, 2) is signicantly faster on XMark queries with larger datasets, 3) at least one or-der of magnitude faster on the queries driven by real applications, as unlike other systems, we can
Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes (2005)

Exonic splicing enhancers (ESEs) are pre-mRNA cis-acting elements required for splice-site recognition. We previously developed a web-based program called ESEfinder that scores any sequence for the presence of ESE motifs recognized by the human SR proteins SF2/ASF, SRp40, SRp55 and SC35 (http://rulai.cshl.edu/tools/ESE/). Using ESEfinder, we have undertaken a large-scale analysis of ESE motif distribution in human protein-coding genes. Significantly higher frequencies of ESE motifs were observed in constitutive internal protein-coding exons, compared with both their flanking intronic regions and with pseudo exons. Statistical analysis of ESE motif frequency distributions revealed a complex relationship between splice-site strength and increased or decreased frequencies of particular SR protein motifs. Comparison of constitutively and alternatively spliced exons demonstrated slightly weaker splice-site scores, as well as significantly fewer ESE motifs, in the alternatively spliced group. Our results underline the importance of ESE-mediated SR protein function in the process of exon definition, in the context of both constitutive splicing and regulated alternative splicing.
Protection of side-branches in coronary lesions with a new stent design (1998)

Side-branches often complicate stenting of coronary lesions. We investigated a new stent, characterized by four wider cells in its center, which can be expanded up to 3.5 mm and which are meant to be placed over the ostium of a major side-branch. Forty-seven consecutive patients with lesions involving 48 side-branches received one side-branch stent each. Stent deployment was successful in all patients. Twenty-five side-branches needed additional treatment. Nineteen side-branches received a PTCA, and 6 additional side-branches were stented. Postinterventional CK-(creatine kinase) elevation was observed in 3 patients (6%). One additional patient was sent for CABG on the day of the procedure due to loss of a stent intended to be placed into the side-branch. The investigated stent proved to be a safe and effective tool to treat this complex subgroup of stenoses in the presence of favorably preserved flow in the side-branches, with a low incidence of periprocedural complications.
Automotive FM Diversity Systems, Part I: Propagation Channel Modeling and Multipath Review (2007)

&lt;div class="htmlview paragraph"&gt;This paper represents Part I of a three part series on automotive FM diversity systems. Part I focuses on a review of multipath fading. Part II (2007-01-1732) deals with analog diversity systems which have been developed to combat the effects of this fading in an FM broadcast and Part III (2007-01-1734) discusses new digital implementations of FM diversity systems that have been implemented in DSP algorithms.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper reviews propagation channel modeling and multipath. Three cases are studied: Additive white Gaussian noise channel, the Rician channel and the Rayleigh channel. It is further noted that the Rician and Rayleigh channels can be either flat or frequency selective based on the values of the time delays in the reflected signal paths. When the delays are relatively short the channel acts like a wide filter and the fading acts on all spectral components of the signal equally. When the time delays are long the channel acts like a narrow band filter resulting in frequency selective fading.&lt;/div&gt;