gebhart/patrepeval huggingface dataset:
Selective inhibition of integrin function by antibodies specific for ligand-occupied receptor conformers. (1990)

We have hypothesized that ligand-induced binding sites (LIBS), i.e. sites expressed on cell surface receptors only after ligand binding causes the receptor to change shape, mediate subsequent biological events. To test this hypothesis, we have raised monoclonal antibodies that preferentially react with an integrin (platelet glycoprotein (GP) IIb-IIIa) after it bind Arg-Gly-Asp-containing ligands. The 13 anti-LIBS antibodies obtained define at least three distinct GPIIb-IIIa epitopes; one of these epitopes is also expressed following occupancy of another integrin, the vitronectin receptor. Certain of these LIBSs appear to mediate functions, since the antibodies that define them inhibit GPIIb-IIIa-mediated fibrin clot contraction or platelet adhesion to collagen. Nevertheless, none of the anti-LIBS antibodies inhibit binding of the primary ligand, fibrinogen. These data indicate that LIBS may mediate distinct consequences of receptor occupancy.
Near-field optical imaging of plasmon modes in gold nanorods (2005)

We have investigated optical properties of single gold nanorods by using an apertured-type scanning near-field optical microscope. Near-field transmission spectrum of single gold nanorod shows several longitudinal surface plasmon resonances. Transmission images observed at these resonance wavelengths show oscillating pattern along the long axis of the nanorod. The number of oscillation increases with decrement of observing wavelength. These spatial characteristics were well reproduced by calculated local density-of-states maps and were attributed to spatial characteristics of plasmon modes inside the nanorods. Dispersion relation for plasmons in gold nanorods was obtained by plotting the resonance frequencies of the plasmon modes versus the wave vectors obtained from the transmission images.
SMART 6: recent updates and new developments (2008)

Simple modular architecture research tool (SMART) is an online tool (http://smart.embl.de/) for the identification and annotation of protein domains. It provides a user-friendly platform for the exploration and comparative study of domain architectures in both proteins and genes. The current release of SMART contains manually curated models for 784 protein domains. Recent developments were focused on further data integration and improving user friendliness. The underlying protein database based on completely sequenced genomes was greatly expanded and now includes 630 species, compared to 191 in the previous release. As an initial step towards integrating information on biological pathways into SMART, our domain annotations were extended with data on metabolic pathways and links to several pathways resources. The interaction network view was completely redesigned and is now available for more than 2 million proteins. In addition to the standard web access to the database, users can now query SMART using distributed annotation system (DAS) or through a simple object access protocol (SOAP) based web service.
Continuous-Flow pI-Based Sorting of Proteins and Peptides in a Microfluidic Chip Using Diffusion Potential (2006)

Efficient sample preparation tools are the key to measuring molecular signals in a complex biological system. A novel continuous-flow isoelectric point (pI)-based sorting technique has been developed for proteins and peptides in a microfluidic chip format. It can sort biomolecules at a relatively high flow rate of up to 10 microL/min and does not require carrier ampholytes, which can create molecular backgrounds for subsequent analysis. Furthermore, the electrophoretic field required to run the pI-based sorting is generated by the diffusion of buffer ions in situ, at the liquid junction between two laminar flows within the microfluidic channel. Utilizing the diffusion potential in combination with a pH difference between the buffers, we demonstrated a separation of binary mixtures of pI markers and proteins without applying any external field. The sorting resolution and its efficiency are sufficiently high for sample preparation and could be further improved by optimizing buffers or with an additional transverse electric field. Once fully developed, it can potentially be a pI-based sample fractionation tool for proteomic analysis of complex biomolecule samples.
Machine Learning for Encrypted Malware Traffic Classification (2017)

The application of machine learning for the detection of malicious network traffic has been well researched over the past several decades; it is particularly appealing when the traffic is encrypted because traditional pattern-matching approaches cannot be used. Unfortunately, the promise of machine learning has been slow to materialize in the network security domain. In this paper, we highlight two primary reasons why this is the case: inaccurate ground truth and a highly non-stationary data distribution. To demonstrate and understand the effect that these pitfalls have on popular machine learning algorithms, we design and carry out experiments that show how six common algorithms perform when confronted with real network data. With our experimental results, we identify the situations in which certain classes of algorithms underperform on the task of encrypted malware traffic classification. We offer concrete recommendations for practitioners given the real-world constraints outlined. From an algorithmic perspective, we find that the random forest ensemble method outperformed competing methods. More importantly, feature engineering was decisive; we found that iterating on the initial feature set, and including features suggested by domain experts, had a much greater impact on the performance of the classification system. For example, linear regression using the more expressive feature set easily outperformed the random forest method using a standard network traffic representation on all criteria considered. Our analysis is based on millions of TLS encrypted sessions collected over 12 months from a commercial malware sandbox and two geographically distinct, large enterprise networks.
Gastrointestinal symptoms in diabetic patients: lack of association with neuropathy. (1989)

Symptoms suggesting gastrointestinal motor dysfunction were determined in 114 diabetic subjects (type 1 and type 2) to see if they were most significantly related to diabetic neuropathy or to psychiatric illness. Presence of neuropathy was established using peripheral nerve conduction studies and objective tests of autonomic function. Affective and anxiety disorders were determined with a structured interview and standard diagnostic criteria. Symptoms were reported by the subsets of subjects with and without neuropathy, ranging in prevalence from 8% to 35%. Log-linear analysis indicated that each group of symptoms (upper gastrointestinal symptoms, altered bowel habits, and abdominal discomforts) was more significantly associated with psychiatric illness (p less than 0.01 for each) than with peripheral neuropathy (p greater than 0.2 for each). In this study, where anxiety and depression were prevalent, no symptom group was significantly associated with autonomic neuropathy once the effects of psychiatric illness on the analysis were taken into account (p greater than 0.2 for each). These findings suggest that gastrointestinal symptoms occurring in diabetic patients are poorly related to neuropathic complications and may often represent gastrointestinal syndromes commonly associated with psychiatric illness.
The Genomic Region of rbcLS in Synechococcus sp. PCC 7942 Contains Genes Involved in the Ability to Grow under Low CO2 Concentration and in Chlorophyll Biosynthesis (1995)

Several genes involved in the ability of Synechococcus sp. PCC 7942 to grow under different CO2 concentrations were mapped in the genomic region of rbcLS (the operon encoding the large and small subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase). Insertion of a cartridge encoding kanamycin resistance within open reading frame (ORF) 78, designated ccmJ, located 7 kb upstream of rbcLS, resulted in a kanamycin-resistant, high-CO2-requiring mutant, M3, which does not contain normal carboxysomes. ccmJ shows significant homology to csoS1 encoding a carboxysomal shell polypeptide in Thiobacillus neopolitanus. Analysis of the polypeptide pattern of a carboxysome-enriched fraction indicated several differences between the wild type and the mutant. The amount of the ribulose-1,5-bisphosphate carboxylase/oxygenase subunits was considerably smaller in the carboxysomal fraction of the mutant when compared to the wild type. On the basis of the sequence analyses, ORF286 and ORF466, located downstream of ccmJ, were identified as chlL and chlN, respectively, which are involved in chlorophyll biosynthesis in the dark.
Human cytomegalovirus clinical isolates carry at least 19 genes not found in laboratory strains (1996)

Nucleotide sequence comparisons were performed on a highly heterogeneous region of three human cytomegalovirus strains, Toledo, Towne, and AD169. The low-passage, virulent Toledo genome contained a DNA segment of approximately 13 kbp that was not found in the Towne genome and a segment of approximately 15 kbp that was not found in the AD169 genome. The Towne strain contained approximately 4.7 kbp of DNA that was absent from the AD169 genome, and only about half of this segment was present, arranged in an inverted orientation, in the Toledo genome. These additional sequences were located at the unique long (UL)/b' (IRL) boundary within the L component of the viral genome. A region representing nucleotides 175082 to 178221 of the AD169 genome was conserved in all three strains; however, substantial reduction in the size of the adjacent b' sequence was found. The additional DNA segment within the Toledo genome contained 19 open reading frames not present in the AD169 genome. The additional DNA segment within the Towne genome contained four new open reading frames, only one of which shared homology with the Toledo genome. This comparison was extended to five additional clinical isolates, and the additional Toledo sequence was conserved in all. These findings reveal a dramatic level of genome sequence complexity that may explain the differences that these strains exhibit in virulence and tissue tropism. Although the additional sequences have not altered the predicted size of the viral genome (230 to 235 kbp), a total of 22 new open reading frames (denoted UL133 to UL154), many of which have sequence characteristics of glycoproteins, are now defined as cytomegalovirus specific. Our work suggests that wild-type virus carries more than 220 genes, some of which are lost by large-scale deletion and rearrangement of the UL/b' region during laboratory passage.
Effects of Chondroitinase ABC on Intradiscal Pressure in Sheep (2001)

Chondroitinase ABC can induce the reduction of intradiscal pressure in the lumbar spine.
Sequence-specific interaction of Tat protein and Tat peptides with the transactivation-responsive sequence element of human immunodeficiency virus type 1 in vitro. (1990)

Bacterially expressed Tat protein of human immunodeficiency virus type 1 binds selectively to short RNA transcripts containing the viral transactivation-responsive element (TAR). Sequences sufficient for Tat interaction map to the distal portion of the TAR stem-loop. We show that critical sequences for Tat binding are located in the single-stranded "bulge," but no requirement for specific "loop" sequences could be demonstrated. TAR RNA competed for complex formation, and TAR mutants exhibited up to 10-fold reduced affinity for Tat. Synthetic peptides containing the basic region of Tat bound selectively to TAR RNA and exhibited the same sequence requirements and similar relative affinities for mutant TAR RNA as the intact protein. These results suggest that Tat contains a small RNA-binding domain capable of recognizing TAR and implicate functional relevance for direct Tat-TAR interaction in transactivation.
Characterizing ECM Production by Cells Encapsulated in Hydrogels (2009)

Hydrogels composed of hydrophilic polymers such as polyethylene glycol and alginate have been used as scaffolds for various tissue engineering applications. This chapter describes procedures for encapsulation of cells in hydrogels and subsequently characterizing the extracellular matrix (ECM) production by those cells using biochemical assays, gene expression analysis, and histology. In particular, the biochemical assays described here are used to quantify collagen, glycosaminoglycan (GAG), and DNA content in each scaffold. The methods for analyzing the level of gene expression of specific ECM molecules such as collagen I, collagen II, and aggrecan are also described. Finally, included are protocols for histological methods used to analyze overall matrix production and GAG synthesis via hematoxylin and eosin staining and Safranin-O, respectively. These methods can be modified so that other scaffolds apart from hydrogels can be used.
Radiation dose enhancement in tumors with iodine (1983)

The loading of tissue with iodine can result in the enhancement of the radiation dose absorbed from low-energy x-ray or gamma ray sources. We have explored the potential of this phenomenon for radiation therapy. We have demonstrated the effect of iodine concentration and radiation quality on this dose enhancement in lymphocytes, we have calculated the effect of such enhancement on depth dose distributions in the brain, we have estimated the iodine content in two human brain tumors during computerized tomography (CT) scans, we have studied the dispersion of the iodine contrast media after direct injection into rabbit tumors, and we have demonstrated that the combination of x-ray and contrast media injection is far more effective than either agent alone in causing the regression of mouse tumors. These results suggest that there may be a therapeutic advantage from loading tumors with iodine and treating them with low-energy photons.
Cardiac Tissue Engineering in an In Vivo Vascularized Chamber (2007)

In summary, the use of a vascularized tissue-engineering chamber allowed generation of a spontaneously beating 3-dimensional mass of cardiac tissue from neonatal rat cardiomyocytes. Further development of this vascularized model will increase the potential of cardiac tissue engineering to provide suitable replacement tissues for acquired and congenital defects.
Conversion of a β-Ketoacyl Synthase to a Malonyl Decarboxylase by Replacement of the Active-Site Cysteine with Glutamine (1999)

beta-Ketoacyl synthases involved in the biosynthesis of fatty acids and polyketides exhibit extensive sequence similarity and share a common reaction mechanism, in which the carbanion participating in the condensation reaction is generated by decarboxylation of a malonyl or methylmalonyl moiety; normally, the decarboxylation step does not take place readily unless an acyl moiety is positioned on the active-site cysteine residue in readiness for the ensuing condensation reaction. Replacement of the cysteine nucleophile (Cys-161) with glutamine, in the beta-ketoacyl synthase domain of the multifunctional animal fatty acid synthase, completely inhibits the condensation reaction but increases the uncoupled rate of malonyl decarboxylation by more than 2 orders of magnitude. On the other hand, replacement with Ser, Ala, Asn, Gly, and Thr compromises the condensation reaction without having any marked effect on the decarboxylation reaction. The affinity of the beta-ketoacyl synthase for malonyl moieties, in the absence of acetyl moieties, is significantly increased in the Cys161Gln mutant compared to that in the wild type and is similar to that exhibited by the wild-type beta-ketoacyl synthase in the presence of an acetyl primer. These results, together with modeling studies of the Cys --> Gln mutant from the crystal structure of the Escherichia coli beta-ketoacyl synthase II enzyme, suggest that the side chain carbonyl group of the Gln-161 can mimic the carbonyl of the acyl moiety in the acyl-enzyme intermediate so that the mutant adopts a conformation analogous to that of the acyl-enzyme intermediate. Catalysis of the decarboxylation of malonyl-CoA requires the dimeric form of the Cys161Gln fatty acid synthase and involves prior transfer of the malonyl moiety from the CoA ester to the acyl carrier protein domain and subsequent release of the acetyl product by transfer back to a CoA acceptor. These results suggest that the role of the Cys --> Gln beta-ketoacyl synthases found in the loading domains of some modular polyketide synthases likely is to act as malonyl, or methylmalonyl, decarboxylases that provide a source of primer for the chain extension reactions catalyzed by associated modules containing fully competent beta-ketoacyl synthases.
Differential expression of 14 genes in amyotrophic lateral sclerosis spinal cord detected using gridded cDNA arrays (2001)

In order to obtain insight into the aetiology and pathogenesis of amyotrophic lateral sclerosis (ALS), high-density gene discovery arrays (GDA human version 1.2) containing 18 400 non-redundant EST cDNAs pooled from different tissue libraries have been used to monitor gene expression in lumbar spinal cord from ALS cases compared with controls. Quantitative filter analysis revealed differential expression of cDNAs normalized to internal standards. These candidates have been further investigated and their expression in spinal cord characterized in a panel of ALS and control subjects. Significant differential expression was obtained for 14 genes, 13 being elevated (up to six-fold) and one decreased (by 80%) in ALS. Amongst those elevated in ALS were thioredoxin and glial fibrilary acid protein, which have already been shown to be up-regulated in ALS, thus supporting the reliability of this approach. The other differentially regulated transcripts confirmed in the expression studies represent potential candidates in ALS pathogenesis being involved in antioxidant systems, neuroinflammation, the regulation of motor neurone function, lipid metabolism, protease inhibition and protection against apoptosis. The use of the GDA system has greatly facilitated the screening and retrieval of sequence information and has generated useful information on the cascade of molecular events occurring in ALS and potentially may highlight new candidates playing a role in the aetiology and progression of this disease.
The Ultrashort-Radius Radial System (1989)

Summary A group of interrelated horizontal drilling and completion technologies, collectively called the ultrashort-radius radial system (URRS), was developed and is being progressively applied in the field. Multiple radiais can be placed at the same level and on multiple levels. Three-dimensional (3D) surveying is supplied. Horizontal completions can be provided, including 100%-fill gravel packing, in-situ electrolytic perforation and cutting, and flexible sand barriers (FSB's). Initial field applications were in unconsolidated formations.
Prevention of thrombosis and rethrombosis and enhancement of the thrombolytic actions of recombinant tissue‐type plasminogen activator in the canine heart by DMP728, a glycoprotein IIb/IIIa antagonist (1994)

1. We studied DMP728, a non-peptide glycoprotein (GP) IIb/IIIa receptor antagonist, for prevention of coronary artery thrombosis or rethrombosis in a chronic canine model subjected to arterial injury. 2. In protocol I, DMP728 (1.0 mg kg-1, i.v., n = 8) or saline (n = 8) was administered and a 150 microA anodal current was applied to the intimal surface of the left circumflex coronary artery (LCX). Dogs were monitored for 6 h and again on each of 5 subsequent days. 3. Ex vivo platelet aggregation was inhibited but returned to baseline 1 day after drug administration. Thrombus weight was reduced (saline, 20.7 +/- 5.0 mg; DMP728 1.7 +/- 0.4 mg; P < 0.05), as was infarct size [saline, 27.5 +/- 4.3; DMP728, 1.6 +/- 0.7 (per cent left ventricle); P < 0.05]. All control animals died by day 3, while all but one of the treated dogs survived the entire protocol (P < 0.05). 4. In protocol II, an LCX thrombus was induced and thrombolytic therapy was initiated 30 min later. DMP728 (1.0 mg kg-1, i.v., n = 8) or saline (n = 8) was administered 5 min after recombinant tissue-type plasminogen activator infusion had begun. The incidence of reocclusion was reduced by DMP728 (saline, 4/8; DMP728, 1/8). One day after thrombolysis, 7/8 DMP728-treated animals were alive compared with 1/8 in the control group (P = 0.01). 5. DMP728 inhibited ex vivo platelet aggregation, prevented primary and secondary occlusive thrombus formation, reduced thrombus weight and infarct size and increased survival in a chronic canine model of coronary artery thrombus formation. DMP728 is an effective anti-platelet intervention when used as the singular adjunctive agent in association with thrombolytic therapy.
The Pattern of Polymorphism on Human Chromosome 21 (2003)

Polymorphism data from 20 partially resequenced copies of human chromosome 21-more than 20,000 polymorphic sites-were analyzed. The allele-frequency distribution shows no deviation from the simplest population genetic model with a constant population size (although we show that our analysis has no power to detect population growth). The average rate of recombination per site is estimated to be roughly one-half of the rate of mutation per site, again in agreement with simple model predictions. However, sliding-window analyses of the amount of polymorphism and the extent of linkage disequilibrium (LD) show significant deviations from standard models. This could be due to the history of selection or demographic change, but it is impossible to draw strong conclusions without much better knowledge of variation in the relationship between genetic and physical distance along the chromosome.
<title>Using the focus monitor test mask to characterize lithographic performance</title> (1995)

The focus monitor technique has been shown to be a unique and promising method of characterizing lithography tools. The focus monitor test mask employs phase shifting to translate focus error into a measurable overlay error, independent of exposure. We have also employed an exposure monitor structure to measure dose, independent of focus. The combination of focus and exposure monitors is highly sensitive to factors which affect critical dimensions. Using this test mask we have systematically analyzed the performance of the photo processing tools on our line. This paper will review the data and discuss process capability improvements using both methodologies.© (1995) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.