gebhart/patrepeval huggingface dataset:
Complete amino acid sequence of a human monocyte chemoattractant, a putative mediator of cellular immune reactions. (1989)

In a study of the structural basis for leukocyte specificity of chemoattractants, we determined the complete amino acid sequence of human glioma-derived monocyte chemotactic factor (GDCF-2), a peptide that attracts human monocytes but not neutrophils. The choice of a tumor cell product for analysis was dictated by its relative abundance and an amino acid composition indistinguishable from that of lymphocyte-derived chemotactic factor (LDCF), the agonist thought to account for monocyte accumulation in cellular immune reactions. By a combination of Edman degradation and mass spectrometry, it was established that GDCF-2 comprises 76 amino acid residues, commencing at the N terminus with pyroglutamic acid. The peptide contains four half-cystines, at positions 11, 12, 36, and 52, which create a pair of loops, clustered at the disulfide bridges. The relative positions of the half-cystines are almost identical to those of monocyte-derived neutrophil chemotactic factor (MDNCF), a peptide of similar mass but with only 24% sequence identity to GDCF. Thus, GDCF and MDNCF have a similar gross secondary structure because of the loops formed by the clustered disulfides, and their different leukocyte specificities are most likely determined by the large differences in primary sequence.
Oscillation Damping Control Using Multiple High Voltage DC Transmission Lines: Controllability Exploration (2018)

This paper explores the controllability of power system oscillation modes by multiple high voltage DC (HVDC) transmission lines. The controllability exploration is performed in a reduced model of the Western Electricity Coordination Council (WECC) system, with added HVDC lines according to previously proposed lines. The exploration shows that various oscillation modes, across several system areas, can be simultaneously controlled by coordinating three or more HVDC lines. The degree of damping in each oscillation mode can be selected by designing a multi-input multi-output control system on the HVDC lines.
Multichannel wavelength division multiplexing with photonic crystals (2001)

A multichannel wavelength-division-multiplexing system consisting of a two-dimensional photonic crystal is proposed. The system consists of two parts, a waveguiding element, realized by defects in a photonic crystal, and frequency-selective elements, realized by photonic crystal microcavities. Simulations, performed with a two-dimensional finite-difference time-domain technique with a perfectly matched layer absorbing boundary condition, showed the ability to filter an incident pulse into six spectral channels with a FWHM of 2 nm.
Treating lung inflammation with agonists of the adenosine A2Areceptor: promises, problems and potential solutions (2008)

Adenosine A(2A) receptor agonists may be important regulators of inflammation. Such conclusions have come from studies demonstrating that, (i) adenosine A(2A) agonists exhibit anti-inflammatory properties in vitro and in vivo, (ii) selective A(2A) antagonists enhance inflammation in vivo and, (iii) knock outs of this receptor aggravate inflammation in a wide variety of in vivo models. Inflammation is a hallmark of asthma and COPD and adenosine has long been suggested to be involved in disease pathology. Two recent publications, however, suggested that an inhaled adenosine A(2A) receptor agonist (GW328267X) did not affect either the early and late asthmatic response or symptoms associated with allergic rhinitis suggesting that the rationale for treating inflammation with an adenosine A(2A) receptor agonist may be incorrect. A barrier to fully investigating the role of adenosine A(2A) receptor agonists as anti-inflammatory agents in the lung is the side effect profile due to systemic exposure, even with inhalation. Unless strategies can be evolved to limit the systemic exposure of inhaled adenosine A(2A) receptor agonists, the promise of treating lung inflammation with such agents may never be fully explored. Using strategies similar to that devised to improve the therapeutic index of inhaled corticosteroids, UK371,104 was identified as a selective agonist of the adenosine A(2A) receptor that has a lung focus of pharmacological activity following delivery to the lung in a pre clinical in vivo model of lung function. Lung-focussed agents such as UK371,104 may be suitable for assessing the anti-inflammatory potential of inhaled adenosine A(2A) receptor agonists.
Electrons in Finite-Sized Water Cavities: Hydration Dynamics Observed in Real Time (2004)

We directly observed the hydration dynamics of an excess electron in the finite-sized water clusters of (H2O)n- with n = 15, 20, 25, 30, and 35. We initiated the solvent motion by exciting the hydrated electron in the cluster. By resolving the binding energy of the excess electron in real time with femtosecond resolution, we captured the ultrafast dynamics of the electron in the presolvated ("wet") and hydrated states and obtained, as a function of cluster size, the subsequent relaxation times. The solvation time (300 femtoseconds) after the internal conversion [140 femtoseconds for (H2O)35-] was similar to that of bulk water, indicating the dominant role of the local water structure in the dynamics of hydration. In contrast, the relaxation in other nuclear coordinates was on a much longer time scale (2 to 10 picoseconds) and depended critically on cluster size.
Diffusion of DNA in Nanoslits (2008)

We observed the free diffusion of individual 10 kbp, (1/2)λ (24.2 kbp), and λ (48.5 kbp) double-stranded deoxyribonucleic acid (DNA) molecules in fused-silica nanoslits with depths from 541 to 24 nm using epifluorescence video microscopy. Diffusivity, D, scaled with nanoslit depth, h, according to D ∝ hα, where α was 0.47 ± 0.05, 0.51 ± 0.06, and 0.47 ± 0.05 for 10 kbp, (1/2)λ, and λ DNA, respectively, in disagreement with the value of two-thirds predicted by blob theory. We observed no change in scaling behavior for h less than the persistence length of DNA, as predicted by reflecting rod theory. The scaling of D with DNA length, N, followed D ∝ N−1, indicating hydrodynamic screening in accordance with Rouse dynamics. Our results establish these scaling exponents for smaller h and greater DNA confinement than previous studies.
Oral l-Arginine Stimulates GLP-1 Secretion to Improve Glucose Tolerance in Male Mice (2013)

Pharmacological and surgical interventions that increase glucagon-like peptide 1 (GLP-1) action are effective to improve glucose homeostasis in type 2 diabetes mellitus. In light of this, nutritional strategies to enhance postprandial GLP-1 secretion, particularly in the context of diet-induced obesity, may provide an alternative therapeutic approach. Importantly, recent evidence suggests the amino acid L-arginine, a well-known insulin secretagogue, can also stimulate release of GLP-1 from isolated rat intestine. Here we tested the hypothesis that oral L-arginine acts as a GLP-1 secretagogue in vivo, to augment postprandial insulin secretion and improve glucose tolerance. To test this, we administered L-arginine or vehicle by oral gavage, immediately prior to an oral glucose tolerance test in lean and diet-induced obese mice. In both lean and obese mice oral L-arginine increased plasma GLP-1 and insulin and substantially improved glucose clearance. To directly assess the contribution of GLP-1 receptor (GLP-1R)-signaling to these improvements, L-arginine was given to Glp1r knockout mice and their wild-type littermates. In this experiment oral l-arginine significantly augmented insulin secretion and improved glucose clearance in WT mice, but not in Glp1r knockout littermates. Taken together these findings identify L-arginine as a GLP-1 secretagogue in vivo and demonstrate that improvement of glucose tolerance by oral L-arginine depends on GLP-1R-signaling. These findings raise the intriguing possibility that L-arginine-based nutritional and/or pharmaceutical therapies may benefit glucose tolerance by improving the postprandial GLP-1 response in obese individuals.
Online handwriting recognition-a survey (2003)

The state of the art of online handwriting recognition is surveyed based on an extensive review of the literature. Shape recognition algorithms, preprocessing and postprocessing techniques, experimental systems, and commercial products are examined. It is found that online recognizers, except for bar-code readers and other specialized equipment, are not applicable to machine-printed characters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cassette Vectors for Conversion of Fab Fragments into Full-length Human IgG 1 Monoclonal Antibodies by Expression in Stably Transformed Insect Cells (2003)

Phage display technology allows for the production and rapid selection of antigen-specific, Fab antibody fragments. For purposes of immune therapy, though, complete antibodies that retain the Fc domain are often required. In this regard, we designed cassette vectors for converting human Fab fragments selected from combinatorial phage display libraries into full-length IgG(1) monoclonal antibodies (MAbs). Two expression vectors, pIEI-Light and pIEI-Heavy, were engineered to contain respective light- and heavy-chain human signal sequences downstream of the baculovirus immediate early gene promoter, IEI. Vector pIEI-Heavy also contains the coding region for each of the human IgG(1) constant domains. To generate complete antibody genes, the cassette vectors possess convenient restriction enzyme sites for rapid in-frame cloning of coding regions for full-length light chains in pIEI-Light and for the heavy-chain variable domains in pIEI-Heavy of Fab fragments. Using these constructs and a method that allows for stable transformation of insect cells, complete light- and heavy-chain genes can be inserted into the insect cell genome and subsequently expressed under the control of the baculovirus IEI promoter. This cassette vector system was used to generate stably transformed insect cells that continuously secreted functional full-length, IgG(1) MAbs. The expressed antibodies exhibited light and heavy chains of the appropriate molecular sizes and retained the ability to bind antigen. We conclude that our cassette vectors could serve as valuable tools for generating human IgG(1) antibodies.
Elevating the Vitamin E Content of Plants Through Metabolic Engineering (1998)

alpha-Tocopherol (vitamin E) is a lipid-soluble antioxidant synthesized only by photosynthetic organisms. alpha-Tocopherol is an essential component of mammalian diets, and intakes in excess of the U.S. recommended daily allowance are correlated with decreased incidence of a number of degenerative human diseases. Plant oils, the main dietary source of tocopherols, typically contain alpha-tocopherol as a minor component and high levels of its biosynthetic precursor, gamma-tocopherol. A genomics-based approach was used to clone the final enzyme in alpha-tocopherol synthesis, gamma-tocopherol methyltransferase. Overexpression of gamma-tocopherol methyltransferase in Arabidopsis seeds shifted oil compositions in favor of alpha-tocopherol. Similar increases in agricultural oil crops would increase vitamin E levels in the average U.S. diet.
Effects of Cadmium on the Energy Metabolism of Isolated Hepatocytes: Its Relationship with the Nonviability of Isolated Hepatocytes Caused by Cadmium (1990)

The effects of cadmium on the energy metabolism of mitochondria were studied with isolated hepatocytes and rat liver mitochondria. It was found that cadmium inhibited the respiration of both isolated hepatocytes and mitochondria and decreased the ATP content of isolated hepatocytes. This inhibition of energy metabolism of mitochondria was highly related to the nonviability of isolated hepatocytes caused by cadmium. The site of electron transport of the mitochondrial respiratory chain blocked by cadmium was located between cytochrome b and flavoproteins. The uncoupling effects of mitochondrial oxidative phosphorylation caused by cadmium may have resulted from changes in the fluidity and permeability of the mitochondrial membrane. (c) 1990 Academic Press. Inc.
A complete, multi-level conformational clustering of antibody complementarity-determining regions (2014)

Classification of antibody complementarity-determining region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure relations. Most of the previous work performed conformational clustering on a reduced set of structures or after application of various structure pre-filtering criteria. In this study, it was judged that a clustering of every available CDR conformation would produce a complete and redundant repertoire, increase the number of sequence examples and allow better decisions on structure validity in the future. In order to cope with the potential increase in data noise, a first-level statistical clustering was performed using structure superposition Root-Mean-Square Deviation (RMSD) as a distance-criterion, coupled with second-and third-level clustering that employed Ramachandran regions for a deeper qualitative classification. The classification of a total of 12,712 CDR conformations is thus presented, along with rich annotation and cluster descriptions, and the results are compared to previous major studies. The present repertoire has procured an improved image of our current CDR Knowledge-Base, with a novel nesting of conformational sensitivity and specificity that can serve as a systematic framework for improved prediction from sequence as well as a number of future studies that would aid in knowledge-based antibody engineering such as humanisation.
Loss of constitutive activity of the growth hormone secretagogue receptor in familial short stature (2006)

The growth hormone (GH) secretagogue receptor (GHSR) was cloned as the target of a family of synthetic molecules endowed with GH release properties. As shown recently through in vitro means, this receptor displays a constitutive activity whose clinical relevance is unknown. Although pharmacological studies have demonstrated that its endogenous ligand--ghrelin--stimulates, through the GHSR, GH secretion and appetite, the physiological importance of the GHSR-dependent pathways remains an open question that gives rise to much controversy. We report the identification of a GHSR missense mutation that segregates with short stature within 2 unrelated families. This mutation, which results in decreased cell-surface expression of the receptor, selectively impairs the constitutive activity of the GHSR, while preserving its ability to respond to ghrelin. This first description, to our knowledge, of a functionally significant GHSR mutation, which unveils the critical importance of the GHSR-associated constitutive activity, discloses an unusual pathogenic mechanism of growth failure in humans.
Epithelial Mesenchymal Transition in Drug Resistance and Metastasis of Lung Cancer (2012)

Among all types of cancer, incidence of lung cancer remains the highest with regard to cancer-related mortality. Problems contributing to recurrence of the disease include metastasis and drug resistance. Mounting evidence has demonstrated involvement of epithelial mesenchymal transition (EMT) in cancer progression. EMT is a critical mechanism ensuring tissue remodeling during morphogenesis of multicellular organisms. Therefore, understanding of the biology of this process for identification of potential EMT-targeted therapeutic strategies for the benefit cancer patients is necessary. This review describes recent evidence of EMT involvement in drug resistance and metastasis of cancers, with an emphasis on lung cancer.
Detection of slide transition for topic indexing (2003)

This paper presents an automatic and novel approach in detecting the transitions of slides for video sequences of technical lectures. Our approach adopts a foreground vs background segmentation algorithm to separate a presenter from the projected electronic slides. Once a background template is generated, text captions are detected and analyzed. The segmented caption regions as well as background templates together provide salient visual cues to decide whether a slide is flipped and replaced. The partitioning of videos according to slide changes not only structure the content of video according to topics, but also facilitate the synchronization of video, audio and electronic slides for effective indexing, browsing and retrieval.
Identification of Inhibitors for UDP-Galactopyranose Mutase (2004)

The flavoenzyme uridine 5'-diphosphate (UDP)-galactopyranose mutase (UGM) plays a key role in the cell wall biosynthesis of many pathogens, including Mycobacterium tuberculosis. Using a synthetic fluorescent ligand, we screened 16 000 compounds in a fluorescence polarization assay. Effective inhibitors of UGM were identified.
Intramammary lymph node metastases are an independent predictor of poor outcome in patients with breast carcinoma (2004)

The current retrospective analysis demonstrated that the presence of intraMLN metastases is an independent predictor of poor outcome in patients with breast carcinoma. Identification of an intraMLN on preoperative imaging should prompt further histopathologic assessment. Identification of malignant intraMLNs by lymphatic mapping may help to identify high-risk patients for whom further evaluation of the axillary lymph nodes is warranted despite otherwise clinically negative findings in the axilla.
Novel 5-Substituted Pyrrolo[2,3-d]pyrimidines as Dual Inhibitors of Glycinamide Ribonucleotide Formyltransferase and 5-Aminoimidazole-4-carboxamide Ribonucleotide Formyltransferase and as Potential Antitumor Agents (2015)

A new series of 5-substituted thiopheneyl pyrrolo[2,3-d]pyrimidines 6-11 with varying chain lengths (n = 1-6) were designed and synthesized as hybrids of the clinically used anticancer drug pemetrexed (PMX) and our 6-substituted thiopheneyl pyrrolo[2,3-d]pyrimidines 2c and 2d with folate receptor (FR) α and proton-coupled folate transporter (PCFT) uptake specificity over the reduced folate carrier (RFC) and inhibition of de novo purine nucleotide biosynthesis at glycinamide ribonucleotide formyltransferase (GARFTase). Compounds 6-11 inhibited KB human tumor cells in the order 9 = 10 > 8 > 7 > 6 = 11. Compounds 8-10 were variously transported by FRα, PCFT, and RFC and, unlike PMX, inhibited de novo purine nucleotide rather than thymidylate biosynthesis. The antiproliferative effects of 8 and 9 appeared to be due to their dual inhibitions of both GARFTase and 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase. Our studies identify a unique structure-activity relationship for transport and dual target inhibition.
Hierarchical digital modulation classification using cumulants (2000)

A simple method, based on elementary fourth-order cumulants, is proposed for the classification of digital modulation schemes. These statistics are natural in this setting as they characterize the shape of the distribution of the noisy baseband I and Q samples. It is shown that cumulant-based classification is particularly effective when used in a hierarchical scheme, enabling separation into subclasses at low signal-to-noise ratio with small sample size. Thus, the method can be used as a preliminary classifier if desired. Computational complexity is order N, where N is the number of complex baseband data samples. This method is robust in the presence of carrier phase and frequency offsets and can be implemented recursively. Theoretical arguments are verified via extensive simulations and comparisons with existing approaches.
Polare Cycloadditionen von elektronenreichen Mehrfachbindungssystemen an 1,3,4‐Oxadiazolium‐Salze: Synthese von 3aH‐[1,3,4]Oxadiazolo[3,2‐α]chinolinen (1979)

Abstract Die 1,3,4‐Oxadiazolium‐Salze 6c,g,h,i,j reagieren mit N,N ‐Diethyl‐1‐amin (7) in einer [4⊕ + 2]‐Cycloaddition zu den 3a H [1,3,4]Oxadiazolo[3,2‐a]chinolinen 8 . Eine [2⊕ + 2] Cycloaddition von Acetlylendicarbonsäure‐diethylester an 8i führt zum Tetracyclus 9 . Die alkalische Hydrolyse von 8 ergibt die Chinolone 10 . Eine [3⊕ + 2]‐Cycloaddition‐Cycloaddition‐Cycloreversion wird bei 6e, I und 18 beobachtet (→ 12, 15, 20 + 21). Auch Keten‐diethylacetal (22) reagiert mit 6k in dieser Weise (→ 23) .
Apolipoprotein A-I Structural Modification and the Functionality of Reconstituted High Density Lipoprotein Particles in Cellular Cholesterol Efflux (1996)

The role of HDL and its major protein constituent, apolipoprotein (apo) A-I, in promoting the removal of excess cholesterol from cultured cells has been well established; however, the mechanisms by which this occurs are not completely understood. To address the effects of apoA-I modification on cellular unesterified (free) cholesterol (FC) efflux, three recombinant human apoA-I deletion mutants and plasma apoA-I were combined with 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) and FC to make reconstituted high density lipoprotein (rHDL) discoidal complexes. These particles were characterized structurally and for their efficiency as acceptors of mouse L-cell fibroblast cholesterol. The deletion mutant proteins lacked NH2-terminal (apoA-I (Delta44-126)), central (apoA-I (Delta139-170)), or COOH-terminal (apoA-I (Delta190-243)) domains of apoA-I. The three deletion mutants all displayed lipid-binding abilities and formed discoidal complexes that were similar in major diameter (13.2 +/- 1.5 nm) to those formed by human apoA-I when reconstituted at a 100:5:1 (POPC:FC:protein) mole ratio. Gel filtration profiles indicated unreacted protein in the preparation made with apoA-I (Delta190-243), which is consistent with the COOH terminus portion of apoA-I being an important determinant of lipid binding. Measurements of the percent alpha-helix content of the proteins, as well as the number of protein molecules per rHDL particle, gave an indication of the arrangement of the deletion mutant proteins in the discoidal complexes. The rHDL particles containing the deletion mutants had more molecules of protein present than particles containing intact apoA-I, to the extent that a similar number of helical segments was incorporated into each of the discoidal species. Comparison of the experimentally determined number of helical segments with an estimate of the available space indicated that the deletion mutant proteins are probably more loosely arranged than apoA-I around the edge of the rHDL. The abilities of the complexes to remove radiolabeled FC were compared in experiments using cultured mouse L-cell fibroblasts. All four discoidal complexes displayed similar abilities to remove FC from the plasma membrane of L-cells when compared at an acceptor concentration of 50 microg of phospholipid/ml. Thus, none of the deletions imposed in this study notably altered the ability of the rHDL particles to participate in cellular FC efflux. These results suggest that efficient apoA-I-mediated FC efflux requires the presence of amphipathic alpha-helical segments but is not dependent on specific helical segments.