gebhart/patrepeval huggingface dataset:
The nature of the carbohydrate-peptide linkage region in glycoproteins from the cellulosomes of Clostridium thermocellum and Bacteroides cellulosolvens. (1993)

The cellulase complexes of two cellulolytic bacteria, Clostridium thermocellum and Bacteroides cellulosolvens, were subjected to extensive Pronase digestion. Glycopeptide fractions were isolated by gel permeation and fast protein liquid chromatography and analyzed by monosaccharide analysis, amino acid analysis, methylation analysis, and 1H NMR spectroscopy. Alkaline borohydride-induced deglycosylation/amino acid conversion and periodate oxidation studies on the glycopeptide fraction of the C. thermocellum cellulosome demonstrated that the earlier established collection of carbohydrate moieties with 3-O-Me-D-GlcpNAc-alpha (1-->2)-[D-Galp-alpha (1-->3)]-D-Galf-alpha (1-->2)-D-Gal (where 3-O-Me-D-GlcpNAc is 3-O-methyl-N-acetylglucopyranosamine, Galp is galactopyranose, and Galf is galactofuranose) as the major component, is O-linked to threonine via galactopyranose. Using the same approach for the glycopeptide fraction of the cellulase complex of B. cellulosolvens, it was found that the reported collection of carbohydrate moieties with D-Galf-alpha (1-->3)-D-GlcpNAc-alpha (1-->2)-D-Galf-alpha (1-->2)-[D-Galf-beta (1-->3)]-D-Gal as the major component, is O-linked mainly to threonine and partly to serine via galactopyranose. In both species, the hydroxyamino-acid-bound galactopyranose residue has probably an alpha-configuration. The carbohydrate chains appear as clusters located in highly Thr/Pro-rich peptide regions of the glycoproteins. The results are consistent with the notion that the glycosylation sites are localized in linker sequences which connect the various binding domains of the noncatalytic S1 subunit of the cellulosome.
Magnetic Resonance Imaging Relaxation Times and Gadolinium-DTPA Relaxivity Values in Human Cerebrospinal Fluid (1998)

This work demonstrates that a single measurement of relaxation times after contrast-enhanced magnetic resonance imaging could be used to determine the Gd-DTPA concentration in CSF. It may thus be feasible, using this technique, to measure intersubject and intraregional variability in the quantity of Gd-DTPA transferred across the blood-brain barrier after intravenous injection of contrast agent.
Detecting patterns and OLAP operations in the GOLD model (1999)

The aim of our GOLD model ([7], [9]) is to provide an Object Oriented (OO) Multidimensional data model supported by an OO formal specification language that allows us to automatically generate prototypes from the specification at the conceptual level, and therefore, to animate and check system properties. Within the context of OO modeling and automatic prototyping, the basis of the mapping from modeling to programming is focused on the identification of (cardinality and behavioral) patterns in the design phase and their relationships with the data model, process model and interface design.
Role of C-Reactive Protein in Cardiovascular Disease (2003)

CRP appears to be a valuable tool for predicting future vascular events in patients striving for primary or secondary prevention of cardiovascular disease. While several pharmacologic and nonpharmacologic interventions have been shown to lower CRP levels, the impact on clinical outcomes requires further study.
Nanoengineered Films via Surface‐Confined Continuous Assembly of Polymers (2011)

A highly generalizable, surface-confined, continuous polymer assembly process, amenable to various substrates, reaction conditions and macromolecules, enables the synthesis of a range of nanoscale supported and freestanding cross-linked polymer films. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Acquisition of the rfb-gnd Cluster in Evolution of Escherichia coli O55 and O157 (2000)

The rfb region specifies the structure of lipopolysaccharide side chains that comprise the diverse gram-negative bacterial somatic (O) antigens. The rfb locus is adjacent to gnd, which is a polymorphic gene encoding 6-phosphogluconate dehydrogenase. To determine if rfb and gnd cotransfer, we sequenced gnd in five O55 and 13 O157 strains of Escherichia coli. E. coli O157:H7 has a gnd allele (allele A) that is only 82% identical to the gnd allele (allele D) of closely related E. coli O55:H7. In contrast, gnd alleles of E. coli O55 in distant lineages are >99.9% identical to gnd allele D. Though gnd alleles B and C in E. coli O157 that are distantly related to E. coli O157:H7 are more similar to allele A than to allele D, there are nucleotide differences at 4 to 6% of their sites. Alleles B and C can be found in E. coli O157 in different lineages, but we have found allele A only in E. coli O157 belonging to the DEC5 lineage. DNA 3' to the O55 gnd allele in diverse E. coli lineages has sequences homologous to tnpA of the Salmonella enterica serovar Typhimurium IS200 element, E. coli Rhs elements (including an H-rpt gene), and portions of the O111 and O157 rfb regions. We conclude that rfb and gnd cotransferred into E. coli O55 and O157 in widely separated lineages and that recombination was responsible for recent antigenic shifts in the emergence of pathogenic E. coli O55 and O157.
On the Optimality of One-Unit Cycle Scheduling of Multi-Cluster Tools with Single-Blade Robots (2007)

In semiconductor manufacturing, finding an efficient way for scheduling a multi-cluster tool is crucial for productivity improvement and cost reduction. In this paper, we analyze optimal scheduling of multi-cluster tools under a general configuration with non-zero constant transfer robot traveling time. A resource-based method is developed to analyze optimal scheduling of single-cluster tools. Optimality conditions for obtaining minimum one-unit cycle time for multi-cluster tools are established. Under these conditions, it is shown that the optimal one-unit cycle can be achieved by first optimally scheduling each single-cluster tool separately and then combining the schedules to form the optimal schedule for the multi-cluster tool. A polynomial-time algorithm is presented to find the optimal one-unit cycle time and its corresponding schedules for a multi-cluster tool.
Molecular and functional analysis of a lymphocyte chemoattractant factor: association of biologic function with CD4 expression. (1994)

Lymphocyte chemoattractant factor (LCF) is a lymphocyte cell product that stimulates a migratory response in CD4+ lymphocytes, monocytes, and eosinophils. In concert with its chemoattractant activity, LCF induces human T-lymphocyte expression of interleukin 2 receptor. Here we describe the molecular cloning of cDNA encoding human LCF. It is a novel interleukin with no significant homology to any previously described cytokine families. There is an absolute requirement for both autoaggregation of LCF monomers and for membrane-expressed CD4 molecules for LCF-induced migration in lymphocytes.
Adaptive simulated annealing (ASA): Lessons learned (2000)

Adaptive simulated annealing (ASA) is a global optimization algorithm based on an associated proof that the parameter space can be sampled much more efficiently than by using other previous simulated annealing algorithms. The author's ASA code has been publicly available for over two years. During this time the author has volunteered to help people via e-mail, and the feedback obtained has been used to further develop the code. Some lessons learned, in particular some which are relevant to other simulated annealing algorithms, are described.
A conserved sequence in the T-cell receptor beta-chain promoter region. (1988)

The antigen-specific receptors of T and B lymphocytes are distinct, though structurally related, molecules. During development, lymphoid cells assemble functional variable (V) region genes for each receptor chain from separate multimember gene families by somatic DNA rearrangements of individual germ-line segments. Transcription may play a role in regulating the tissue and stage specificity of these rearrangements by controlling the accessibility of germ-line loci to the recombinational machinery. Immunoglobulin V-region genes are transcribed from tissue-specific promoters that have been well characterized. We report here the characterization of 14 T-cell receptor beta-chain V-region gene promoters. Sequence analysis indicates that these promoters do not contain the conserved octamer that is located upstream of all immunoglobulin genes. However, a unique decanucleotide sequence, not present in immunoglobulin genes, is conserved in the promoter region of murine and human V beta genes. We identify this sequence as a potential regulatory element, based on its position, conservation, and sequence homology to sites known to bind transcription-activating factors. The possibility that the distinct structures of immunoglobulin and T-cell receptor gene promoters may contribute to the tissue-specific rearrangement and expression of receptor gene families is discussed.
Evaluation of Multiple-Valued Packet Multiplexing Scheme for Network-on-Chip Architecture (2006)

This paper presents an evaluation of multiple-valued packet multiplexing scheme for a Network-on-Chip (NoC) architecture. In the NoC architecture, data is transferred from one Processing Element (PE) to another PE through the routers in the form of a packet. A router, suitable for both the binary and the multiple-valued packets, is constructed using the Multiple Valued Source-Coupled Logic circuits. A packet is composed of flag, destination PE address and data fields. In the NoC architecture, packets are generated by microprogram control. In the proposed scheme, two binary packets are multiplexed if the destination PE addresses are the same. Based on address matching, packets are transferred from a source PE to a destination PE autonomously. As a result, the total number of packets can be reduced. The router is designed using 0.18ìm CMOS design rule. HSPICE simulation results show that the delay of the router is significantly small for high speed packet transfer. Reduction of microprogram control storage is remarkable in the proposed scheme, because the data transfer can be done autonomously. The advantage is evaluated by simple analysis, and comparison with a conventional pipelined bus architecture is done.
The Expression of microRNA and microRNA Clusters in the Aging Heart (2012)

The data revealed age-related changes in the expression of pri-miRNA transcript, Argonaut proteins and both miR and miR* strands. The major changes occurred later in life, from middle to old age. It is likely that the expression of miR and miR* is regulated by both pri-miRNA transcription as well as Ago1 and Ago2 proteins during adult aging.
PTEN loss in circulating tumour cells correlates with PTEN loss in fresh tumour tissue from castration-resistant prostate cancer patients (2015)

Our results illustrate the potential use of CTCs as a non-invasive, real-time liquid biopsy to determine PTEN gene status. The prognostic and predictive value of PTEN in CTCs warrants investigation in CRPC clinical trials of PI3K/AKT-targeted therapies.
The Primitive Protozoon Trichomonas vaginalisContains Two Methionine γ-Lyase Genes That Encode Members of the γ-Family of Pyridoxal 5′-Phosphate-dependent Enzymes (1998)

Methionine gamma-lyase, the enzyme that catalyzes the breakdown of methionine by an alpha,gamma-elimination reaction and is a member of the gamma-family of pyridoxal 5'-phosphate-dependent enzymes, is present in high activity in the primitive protozoan parasite Trichomonas vaginalis but is absent from mammals. Two genes, mgl1 and mgl2, encoding methionine gamma-lyase, have now been isolated from T. vaginalis. They are both single copy, encode predicted proteins (MGL1 and MGL2) of 43 kDa, have 69% sequence identity with each other, and show a high degree of sequence identity to methionine gamma-lyase from Pseudomonas putida (44%) and other related pyridoxal 5'-phosphate-dependent enzymes such as human cystathionine gamma-lyase (42%) and Escherichia coli cystathionine beta-lyase (30%). mgl1 and mgl2 have been expressed in E. coli as a fusion with a six-histidine tag and the recombinant proteins (rMGL1 and rMGL2) purified by metal-chelate affinity chromatography. rMGL1 and rMGL2 were found to have high activity toward methionine (10.4 and 0.67 mumol/min/mg of protein, respectively), homocysteine (370 and 128 mumol/min/mg of protein), cysteine (6.02 and 1.06 mumol/min/mg of protein), and O-acetylserine (3.74 and 1.51 mumol/min/mg of protein), but to be inactive toward cystathionine. Site-directed mutagenesis of an active site cysteine (C113G for MGL1 and C116G for MGL2) reduced the activity of the recombinant enzymes toward both methionine and homocysteine by approximately 80% (rMGL1) and 90% (rMGL2). In contrast, the activity of mutated rMGL2 toward cysteine and O-acetylserine was increased (to 214 and 142%, respectively), whereas that of mutated rMGL1 was reduced to 39 and 49%, respectively. These findings demonstrate the importance of this cysteine residue in the alpha,beta-elimination and alpha, gamma-elimination reactions catalyzed by trichomonad methionine gamma-lyase.
Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine (2010)

DNA cytosine-5 methylation is a well-studied epigenetic pathway implicated in gene expression control and disease pathogenesis. Different technologies have been developed to examine the distribution of 5-methylcytosine (5mC) in specific sequences of the genome. Recently, substantial amounts of 5-hydroxymethylcytosine (5hmC), most likely derived from enzymatic oxidation of 5mC by TET1, have been detected in certain mammalian tissues. Here, we have examined the ability of several commonly used DNA methylation profiling methods to distinguish between 5mC and 5hmC. We show that techniques based on sodium bisulfite treatment of DNA are incapable of distinguishing between the two modified bases. In contrast, techniques based on immunoprecipitation with anti-5mC antibody (methylated DNA immunoprecipitation, MeDIP) or those based on proteins that bind to methylated CpG sequences (e.g. methylated-CpG island recovery assay, MIRA) do not detect 5hmC and are specific for 5mC unless both modified bases occur in the same DNA fragment. We also report that several methyl-CpG binding proteins including MBD1, MBD2 and MBD4 do not bind to sequences containing 5hmC. Selective mapping of 5hmC will require the development of unique tools for the detection of this modified base.
Stably transmitted triple-promoter retroviral vectors and their use in transformation of primary mammalian cells. (1988)

Retroviral vectors were constructed which coexpressed three inserted genes from independent transcriptional promoters in singly infected cells. Several such triple-promoter vectors were constructed with various combinations of oncogenes and selectable drug resistance genes. All expressed three mRNAs of the expected size in infected cells. One vector expressing the v-Ha-ras, v-myc, and neo genes was characterized in detail. This retrovirus did not undergo rearrangement during the process of infection, as judged by Southern analysis, and infection of primary rat embryo fibroblasts demonstrated that ras-myc-cotransformed cells could be selected in G418. This demonstration that retroviral vectors can be used to express three cistrons independently increases their value as gene transfer vehicles, particularly for studies involving oncogene cooperation in primary cells.
Antisense Oligonucleotides as a Powerful Molecular Strategy for Gene Therapy in Cardiovascular Diseases (2004)

Antisense oligonucleotides (ODN) technology is one of the most promising therapeutic strategies to prevent the progress of diseases through inhibiting the specific gene expression. They are well established to serve as molecular tools for several biologic applications, from the study of single gene function up to complex target validations. From the theoretical simple action, sequence-specific inhibition of mRNA functions after complex formation and presumably enzymatic degradation of the target mRNA, they obviously carry a high therapeutic potential to treat human diseases. In addition to the potential for the treatment, antisense ODN may be applicable for investigations of the mechanism and stereochemistry of biochemical reactions, mapping of nucleic acid protein interactions, and diagnostic applications. However, the design of antisense ODN, is very difficult because many factors affecting their activity and stability must be considered. Especially, the modifications of ODN are very critical and many researchers are trying to establish ODN which have resistance to nucleolytic degradation, high affinity to complementary nucleic acid, high selectivity in binding with complementary nucleic acid, the ability to activate ribonuclease H that selectively degrades the RNA strand of ODN-RNA complex, cell permeability, and favorable pharmacokinetic and pharmacodynamic attributes. In this review we would like to introduce some modifications of ODN design and examples of our applications of antisense ODN in cardiovascular disease in animal models.
Non-Visual Effects of Light on Melatonin, Alertness and Cognitive Performance: Can Blue-Enriched Light Keep Us Alert? (2011)

Our findings suggest that the sensitivity of the human alerting and cognitive response to polychromatic light at levels as low as 40 lux, is blue-shifted relative to the three-cone visual photopic system. Thus, the selection of commercially available compact fluorescent lights with different colour temperatures significantly impacts on circadian physiology and cognitive performance at home and in the workplace.
Depression and Suicide Among Community Elderly (2003)

Abstract The phenomena of hopelessness, depression and, suicidality among the elderly have been long recognized as a social problem. It is commonly agreed that the rates of depression, sense of hopelessness and, suicidality in that age group are higher among older people. Due to its sensitive nature, the gerontological literature has been paid more theoretical and empirical attention to the understanding of such phenomena at the last two decades. The present study concerned hopelessness, depression and, suicidality among an elderly community population. It aimed at providing a demographic profile of factors contributing to depression and suicidality among old people. At five senior citizen centers at the north of Israel, 316 old people living in the community were randomly selected. Subjects were administered the Beck Depression Inventory (BDI), the Beck Hopelessness Scale (HS), and the Scale for Suicidal Ideation (SSI). The data suggest that four main demographic variables contributed to the explanation of suicidality, depression, and hopelessness among the elderly. Practical implications are discussed.
Inhibition of p38 MAP kinase‐and RICK/NF‐κB‐signaling suppresses inflammatory bowel disease (2004)

Ulcerative colitis and Crohn's disease are the two entities of chronic inflammatory bowel diseases (IBD). One of the main pathogenic mechanisms is probably a dysregulated immune response triggered by products of the enteric bacterial flora. The goal of this study was to evaluate the effects of the p38 mitogen-activated protein kinase (MAPK) inhibitor SB203580 on inflammatory responses using the DSS-induced experimental colitis model in mice reflecting human IBD. We found that SB203580 improved the clinical score, ameliorates the histological alterations, and reduces the mRNA levels of proinflammatory cytokines. In addition to p38 kinase activity, the "classical" and the "alternative" NF-kappaB pathways were also strongly activated during colitis induction. All three pathways were drastically down-regulated by SB203580 treatment. An analysis of the molecular basis of NF-kappaB activation revealed that Rip-like interacting caspase-like apoptosis-regulatory protein kinase (RICK), a key component of a pathway leading to NF-kappaB induction, is also strongly inhibited by SB203580. Since RICK is an effector kinase of NOD2, an intracellular receptor of bacterial peptidoglycan, these results support the notion that NOD signaling could play a pivotal role in the IBD pathogenesis. Thus, RICK could represent a novel target for future therapies in human IBD.
Changing Exchange Bias in Spin Valves with an Electric Current (2007)

We show that a high-density electric current, injected from a point contact into an exchange-biased spin valve, systematically changes the exchange bias. The bias can either increase or decrease depending upon the current direction. This observation is not readily explained by the well-known spin-transfer torque effect in ferromagnetic metal circuits, but could be evidence for the recently predicted current-induced torques in antiferromagnetic metals.
Simultaneous 2D images and 3D geometric model registration for texture mapping utilizing reflectance attribute (2002)

Texture mapping on scanned objects, that is, the method to map current color images on a 3D geometric model measured by a range sensor, is a key technique of photometric modeling for virtual reality. Usually range and color images are obtained from different viewing positions, through two independent range and color sensors. Thus, in order to map those color images on the geometric model, it is necessary to determine relative relations between these two viewpoints. In this paper, we propose a new calibration method for the texture mapping; the method utilizes reflectance images and iterative pose estimation based on a robust Mestimator. Moreover, since a 2D texture image taken from one viewing point is a partial view of an object, several images must be mapped onto the object in order to cover the entire 3D geometric model. In this paper, we propose the new simultaneous registration technique of several images and geometric model based on 2D-3D edge correspondence and the epipolar constraint between images.
Production of Genetically Engineered Biotinylated Interleukin-2 and Its Application in a Rapid Nonradioactive Assay for T-Cell Activation (2003)

The development of reliable assay systems that can measure lymphocyte activation in vitro has been a major goal of immunodiagnostics. Traditionally, tritiated thymidine incorporation has been used to monitor T-cell activation. Other methods include enzyme-linked immunosorbent assay (ELISA), enzyme-linked immunospot assay, and colorimetric assays. We have established a lymphocyte activation assay that utilizes fluorescein isothiocyanate (FITC)-streptavidin bound to recombinant biotinylated human interleukin-2 (IL-2). Utilizing recombinant DNA technology, a unique monobiotinylated human IL-2 has been created and isolated using the Promega PinPoint vector system. ELISA has been used to demonstrate streptavidin binding and recognition by a human IL-2-specific antibody. IL-2 function has been demonstrated using a murine IL-2-dependent T-cell line, CTLL-2, responsive to human IL-2. Recombinant biotinylated human IL-2 conjugated to streptavidin-FITC or streptavidin-horseradish peroxidase has been used to monitor T-cell activation in the presence of antigen as well as mitogen. The sensitivity and convenience of this method make this lymphocyte activation assay an attractive alternative to tritiated thymidine incorporation as a method for monitoring T-cell activation. In addition, the availability of a recombinant biotinylated human IL-2 will permit the production of a uniform product suitable for diagnostic and clinical application.