gebhart/patrepeval huggingface dataset:
Orientation of epitopes influences the immunogenicity of synthetic peptide dimmers (1988)

The immunogenicity of synthetic peptide dimers based on epitope sequences derived from the mycobacterial 65-kDa antigen and the foot and mouth disease virus (FMDV) VP1 protein was examined in inbred mice. The analysis was directed towards the potential helper role of a T cell stimulatory mycobacterial epitope (65-85) with respect to poorly immunogenic sites either from the same molecule (422-436) or from VP1 (141-160). The 65-85 repeat homodimer induced an antibody response in CBA/ca but not in C57BL/6 mice, both nonresponders to the 65-85 monomer, and amplified the antibody response in BALB/c, monomer-responder mice. Analysis of the immunogenicity of hybrid dimers in BALB/c mice showed that the orientation of peptides within the dimer is critical for the extent of the produced antibody response. Only the 422-436/65-85 but not the 65-85/422-436 induced antibodies binding to the 422-436 sequence which was nonimmunogenic when injected either as a monomer or dimer. Despite the striking difference in immunogenicity, both tested hybrid dimers reacted equally in the solid-phase immunoassay with antisera raised to 65-85-dimer or 422-436/65-85 peptides or with a monoclonal antibody to the 422-436 epitope. The described differences in antibody responsiveness also cannot be attributed merely to the extent of T cell stimulation since the proliferative responses were uniformly expressed for all relevant combinations of peptides. Antisera to 65-85 dimer and 422-436/65-85 hybrid also reacted with the native 65-kDa protein. Furthermore, the production of FMDV-neutralizing antibodies in response to the 141-160 (VP1-derived)/65-85 hybrid peptide in 141-160 nonresponder B10.D2 mice also confirmed the helper activity of the 65-85 epitope. Thus, combining heterologous peptides with the N-terminal of the mycobacterial 65-85 sequence may be generally applicable for the potentiation of peptide vaccines.
Intratumoral distribution of tritiated-FDG in breast carcinoma: correlation between Glut-1 expression and FDG uptake. (1996)

Our results demonstrate significant positive correlation between the expression of the facilitative glucose transporter Glut-1 and FDG accumulation in viable cancer cells in the syngeneic rat breast cancer. They suggest that the regulation of FDG uptake may be mediated by Glut-1 and the heterogeneous expression of Glut-1 and tracer uptake may reflect localized variations in the metabolic conditions.
Binding of laminin to oral and endocarditis strains of viridans streptococci (1987)

Attachment of bacteria to the host tissue is regarded as a crucial step in the development of many types of infections. Recent studies by us and others have shown that matrix proteins which serve as adhesion proteins for eucaryotic cells may also be recognized by some bacteria. In the present communication, we report that several strains of viridans streptococci are able to bind to laminin. Most strains isolated from blood and heart valves of patients with endocarditis expressed laminin receptors, whereas only a few of the strains isolated from the oral cavity recognized this protein. This observation indicates that laminin binding might be an important factor in the pathogenesis of viridans endocarditis. Laminin binding to two strains (Streptococcus mitis UAB594 and UAB597) isolated from patients with endocarditis was characterized further. The bacterial cells expressed a limited number of laminin receptors (4 X 10(2) to 1 X 10(3) per cell) which bound the protein in a high-affinity interaction (Kd, 40 to 80 nM). This receptor of S. mitis UAB594 was heat labile and could be solubilized from bacteria by brief digestion with trypsin. Solubilized receptors which competed with cell-bound receptors for 125I-laminin could be adsorbed on laminin-Sepharose but not on Sepharose substituted with fibrinogen or fibronectin. Comparison of laminin receptors from S. mitis with those previously described for Streptococcus pyogenes suggest that different sites in the laminin molecule are recognized by the two bacteria and hence that the corresponding receptor molecules are not identical.
Monocyte subsets differentially employ CCR2, CCR5, and CX3CR1 to accumulate within atherosclerotic plaques (2007)

Monocytes participate critically in atherosclerosis. There are 2 major subsets expressing different chemokine receptor patterns: CCR2(+)CX3CR1(+)Ly-6C(hi) and CCR2(-)CX3CR1(++)Ly-6C(lo) monocytes. Both C-C motif chemokine receptor 2 (CCR2) and C-X(3)-C motif chemokine receptor 1 (CX3CR1) are linked to progression of atherosclerotic plaques. Here, we analyzed mouse monocyte subsets in apoE-deficient mice and traced their differentiation and chemokine receptor usage as they accumulated within atherosclerotic plaques. Blood monocyte counts were elevated in apoE(-/-) mice and skewed toward an increased frequency of CCR2(+)Ly-6C(hi) monocytes in apoE(-/-) mice fed a high-fat diet. CCR2(+)Ly-6C(hi) monocytes efficiently accumulated in plaques, whereas CCR2(-)Ly-6C(lo) monocytes entered less frequently but were more prone to developing into plaque cells expressing the dendritic cell-associated marker CD11c, indicating that phagocyte heterogeneity in plaques is linked to distinct types of entering monocytes. CCR2(-) monocytes did not rely on CX3CR1 to enter plaques. Instead, they were partially dependent upon CCR5, which they selectively upregulated in apoE(-/-) mice. By comparison, CCR2(+)Ly-6C(hi) monocytes unexpectedly required CX3CR1 in addition to CCR2 and CCR5 to accumulate within plaques. In many other inflammatory settings, these monocytes utilize CCR2, but not CX3CR1, for trafficking. Thus, antagonizing CX3CR1 may be effective therapeutically in ameliorating CCR2(+) monocyte recruitment to plaques without impairing their CCR2-dependent responses to inflammation overall.
Biochemical Techniques for the Characterization of G-Quadruplex Structures: EMSA, DMS Footprinting, and DNA Polymerase Stop Assay (2009)

The proximal promoter region of many human growth-related genes contains a polypurine/polypyrimidine tract that serves as multiple binding sites for Sp1 or other transcription factors. These tracts often contain a guanine-rich sequence consisting of four runs of three or more contiguous guanines separated by one or more bases, corresponding to a general motif known for the formation of an intramolecular G-quadruplex. Recent results provide strong evidence that specific G-quadruplex structures form naturally within these polypurine/polypyrimidine tracts in many human promoter regions, raising the possibility that the transcriptional control of these genes can be modulated by G-quadruplex-interactive agents. In this chapter, we describe three general biochemical methodologies, electrophoretic mobility shift assay (EMSA), dimethylsulfate (DMS) footprinting, and the DNA polymerase stop assay, which can be useful for initial characterization of G-quadruplex structures formed by G-rich sequences.
Software for Signaling Networks, Electronic and Cellular (2002)

Cellular signaling networks have many similarities with electronic circuits. Therefore, the tools used to test and analyze electronic circuits can be adapted to analyze cellular signaling processes. Lok describes some of these signaling network analysis tools, their underlying principles, and their limitations.
Hypoxic pulmonary vasoconstriction after combined burn and inhalation injury* (2006)

Department of Surgery, University of California, Davis, Shriners Hospitals for Children Northern California, Davis, CA
Anxieties of Ending (1997)

This chapter discusses not merely the psychological violence that characterises the anatomical investigations of tragic drama but a larger violence implicit in the narrative design of tragedy, with its ferocious concentration upon mortal ends and its need to mimic the arrest of death in its most sudden and brutal forms. The self-conscious metadrama of an episode such as Hieronimo's suicide allows an unusually sharp glimpse of the ambivalence attaching to such designs. The end is what the tragic dramatist most wishes to bring about, but it is also what he most dreads; it is both the end of his writing, and the very thing it wishes to defer. The narrative anxiety generated by that peculiarly tense contradiction is the subject of this chapter. This anxiety is perhaps only a subspecies of the generalised human nervousness about the aesthetics of closure that Frank Kermode has examined in The Sense of an Ending.
ElSe: Ellipse Selection for Robust Pupil Detection in Real-World Environments (2015)

Fast and robust pupil detection is an essential prerequisite for video-based eye-tracking in real-world settings. Several algorithms for image-based pupil detection have been proposed, their applicability is mostly limited to laboratory conditions. In realworld scenarios, automated pupil detection has to face various challenges, such as illumination changes, reflections (on glasses), make-up, non-centered eye recording, and physiological eye characteristics. We propose ElSe, a novel algorithm based on ellipse evaluation of a filtered edge image. We aim at a robust, resource-saving approach that can be integrated in embedded architectures e.g. driving. The proposed algorithm was evaluated against four state-of-the-art methods on over 93,000 hand-labeled images from which 55,000 are new images contributed by this work. On average, the proposed method achieved a 14.53% improvement on the detection rate relative to the best state-of-the-art performer. download:ftp://emmapupildata@messor.informatik.unituebingen. de (password:eyedata).
Antagonism of Sphingosine 1-Phosphate Receptor-2 Enhances Migration of Neural Progenitor Cells Toward an Area of Brain Infarction (2008)

Our findings suggest that S1P is a chemoattractant for NPCs released from an infarcted area and regulation of S1P(2)R function further enhances the migration of NPCs toward a brain infarction.
Broadening the Bandwidth in Terminal Antennas by Tuning the Coupling between the Element and its Ground (2005)

The intensive research on terminal antennas in recent years examined new ideas that resulted in the formulation of guidelines on how specific antenna parameters could be accomplished. Among the more challenging variables in obtaining parameters, two gained our particular attention: a broad bandwidth and a radiation pattern that does not produce SAR values exceeding the permissible level. Broadening the bandwidth at the lowest resonance in multiresonant antennas featuring the highest possible scale of miniaturization was the most difficult task. Owing to the possible highest scale of miniaturization, various modifications of PIFAs have attracted much attention. We present an equivalent circuit model for a dual-band antenna. The model reflects the importance of a strong mutual coupling in miniaturized PIFAs. Providing very broad bandwidths with highly miniaturized antenna was possible when parts of the PIFA element were inserted into the slits in the small ground plate. The measured efficiency values are high and meet the expectations of modern wireless device designers.
Memory, but not naive, peripheral blood B lymphocytes differentiate into Ig-secreting cells after CD40 ligation and costimulation with IL-4 and the differentiation factors IL-2, IL-10, and IL-3 (1997)

The ligation of CD40 on B lymphocytes by CD40 ligand, transiently expressed on activated Th cells, provides a key activation signal required for the germinal center B cell response. In vitro, human B cell activation has been investigated extensively by coculturing tonsillar B cells with CD32-transfected fibroblasts coated with anti-CD40 Abs, in the presence of cytokines (the CD40 system). When tonsillar IgD+ B cells are cultured in the CD40 system with IL-4, cells proliferate and switch to IgG, but they display a block of differentiation illustrated by the persistence of IgD expression on cycling B cells. In this study, we analyzed the responses of peripheral blood B lymphocyte fractions, which may contain fewer in vivo activated cells than those from tonsils. While the differentiation block was confirmed with peripheral naive B cells cultured in the CD40 system with IL-4, it was also observed with the combination of IL-2, IL-10, and IL-3 alone or together with IL-4 (persistence of >90% IgD+ cells, including 24-60% IgD+, IgG+ cells, and <6% IgD+, IgA+ cells after 8 days). IgD+, IgG-, and IgA- (naive) B cells secreted 70-fold less Ig than IgG+, IgA+ (memory) B cells in response to anti-CD40 plus IL-2, IL-10, and IL-3. IgG-, IgA- B cells, or IgD-, IgM+, which should include IgM+ memory cells, strongly secreted IgM, but no IgG. In conclusion, only memory B cells secreted Ig; like memory T cells, their activation requirements to differentiate into effector cells seem less stringent than those of the naive cells.
Cysteine auxotrophy of human leukemic lymphoblasts is associated with decreased amounts of intracellular cystathionase protein (1981)

A series of human lymphoblastoid cell lines derived from nonleukemic donors are known to be cysteine prototrophs (cys+), while several lymphoblastoid lines derived from leukemic donors are cysteine auxotrophs (cys-). We have tested representative cell lines of each type for their content of cystathionase enzyme activity by a specific catalytic assay and their total cystathionase protein content by immunoprecipitation of in vivo labeled protein. There was a close correlation between the cellular content of the enzyme as determined in the two assays. Specifically, those cys+ lines having readily measureable enzyme by catalytic assay were found to contain significantly higher levels of immunoprecipitable Mr 43 000 cystathionase subunit than those cys- lines tested which were depleted in active enzyme. Thus, the absolute cysteine requirement of the leukemic, cys- cell lines tested is likely due to an intracellular reduction of cystathionase protein.
Computer vision and artificial intelligence in mammography. (1994)

The revolution in digital computer technology that has made possible new and sophisticated imaging techniques may next influence the interpretation of radiologic images. In mammography, computer vision and artificial intelligence techniques have been used successfully to detect or to characterize abnormalities on digital images. Radiologists supplied with this information often perform better at mammographic detection or characterization tasks in observer studies than do unaided radiologists. This technology therefore could decrease errors in mammographic interpretation that continue to plague human observers.
In Vitro Engagement of CD3 and CD28 Corrects T Cell Defects in Chronic Lymphocytic Leukemia (2005)

Chronic lymphocytic leukemia (CLL) is characterized by the accumulation of leukemic B cells concomitant with immunological abnormalities and depressed immune responses. The T cell abnormalities found in CLL patients are thought to increase the risk of infection and hamper immune recognition and elimination of leukemic cells. We evaluated whether providing signals through CD3 and CD28 would correct some of these T cell defects. PBMC were incubated with anti-CD3 and anti-CD28 mAbs conjugated to superparamagnetic beads for 12-14 days. This resulted in a 1400-fold increase in T cell numbers. Activated T cells expressed high levels of CD25, CD54, CD137, and CD154, and produced IFN-gamma, TNF-alpha, and GM-CSF. The mean T cell composition of cultures increased from approximately 6% to >90% and leukemic B cells decreased from a mean of approximately 85% to 0.1% or less. Leukemic B cells up-regulated expression of CD54, CD80, CD86, and CD95. Receptor up-regulation required direct cell contact with the activated T cells and could be blocked with anti-CD154 mAb, suggesting that the CD40-CD40L pathway helped mediate these effects. Poor T cell responses to allostimulation were corrected by the activation and expansion process. The skewing in the TCR repertoire returned to normal, or near normal following the culture process in eight of nine patients with abnormal TCR repertoires. Activated T cells had potent in vitro antileukemic effects in contrast to nonactivated T cells. Based upon these findings, a clinical trial has been initiated to test the potential therapeutic effects of T cells activated using this approach in patients with CLL.
What Mechanisms Underlie Diastolic Dysfunction in Heart Failure? (2004)

Abnormalities of diastolic function are common to virtually all forms of cardiac failure. However, their underlying mechanisms, precise role in the generation and phenotypic expression of heart failure, and value as specific therapeutic targets remain poorly understood. A growing proportion of heart failure patients, particularly among the elderly, have apparently preserved systolic function, and this is fueling interest for better understanding and treating diastolic abnormalities. Much of the attention in clinical and experimental studies has focused on relaxation and filling abnormalities of the heart, whereas chamber stiffness has been less well studied, particularly in humans. Nonetheless, new insights from basic and clinical research are helping define the regulators of diastolic dysfunction and illuminate novel targets for treatment. This review puts these developments into perspective with the major aim of highlighting current knowledge gaps and controversies.
Field peas: Chemical composition and energy and amino acid availabilities for poultry (1997)

Twelve pea cultivars (yellow-, green- and brown-seeded) were evaluated for chemical composition and digestibility in poultry. The evaluation involved analyses for protein, amino acids (AAs), fat, starch, dietary fibre, ash, calcium, phosphorus and tannins. True metabolizable energy [nitrogen corrected (TME n ) and uncorrected (TME)] and true AA bioavailability values were also determined with adult cockerels. The cultivars showed a wide range of protein (207.5–264.0 g kg −1 ) and starch (385.3–436.8 g kg −1 ) contents which were not related to the seed coat colours. The concentrations of several AAs varied among the cultivars. With the exception of arginine, the concentrations of all other essential AAs on a protein basis decreased as protein levels increased. Out of 10 essential AAs including cystine, only arginine had a positive correlation (r = 0.79) with protein content. The dietary fibre contents varied between 190.7 and 223.1 g kg −1 and the values were slightly higher in the brown-seeded cultivars. The brown-seeded cultivars contained appreciable quantities of tannins, while the yellow- and green-seeded cultivars were devoid of tannins. The cultivars were almost devoid of fat and calcium but relatively high in phosphorus. Starch and dietary fibre were negatively correlated with protein content (r = −0.78 and −0.46, respectively), and accounted for the greatest difference in protein content. The TME values ranged from 11.6 to 13.3 MJ kg −1 while the TME n values ranged from 11.0 to 12.9 MJ kg −1 . The mean availabilities of AAs ranged from a high of 89.6 to a low of 75.9%, with total sulphur AAs (cystine and methionine) having the lowest value and glutamic acid having the highest value. There was a trend (P ≤ 0.05) towards lower AA bioavailability values in the brown-seeded cultivars. It can be concluded that these cultivars varied in chemical composition, metabolizable energy content and bioavailability of AAs. Key words: Field peas, composition, digestibility, chicken, poultry
Analysis of sequence variation among smeDEF multi drug efflux pump genes and flanking DNA from defined 16S rRNA subgroups of clinical Stenotrophomonas maltophilia isolates (2004)

These data provide further evidence that it is possible to group clinical isolates of the inherently variable species, S. maltophilia, based on genotypic properties. Isolate D457, in which most work concerning smeDEF expression has been performed, does not fall into S. maltophilia subgroup A, which is the most typical.
High-Throughput Selection, Enumeration, Electrokinetic Manipulation, and Molecular Profiling of Low-Abundance Circulating Tumor Cells Using a Microfluidic System (2011)

A circulating tumor cell (CTC) selection microfluidic device was integrated to an electrokinetic enrichment device for preconcentrating CTCs directly from whole blood to allow for the detection of mutations contained within the genomic DNA of the CTCs. Molecular profiling of CTCs can provide important clinical information that cannot be garnered simply by enumerating the selected CTCs. We evaluated our approach using SW620 and HT29 cells (colorectal cancer cell lines) seeded into whole blood as a model system. Because SW620 and HT29 cells overexpress the integral membrane protein EpCAM, they could be immunospecifically selected using a microfluidic device containing anti-EpCAM antibodies immobilized to the walls of a selection bed. The microfluidic device was operated at an optimized flow rate of 2 mm s(-1), which allowed for the ability to process 1 mL of whole blood in <40 min. The selected CTCs were then enzymatically released from the antibody selection surface and hydrodynamically transported through a pair of Pt electrodes for conductivity-based enumeration. The efficiency of CTC selection was found to be 96% ± 4%. Following enumeration, the CTCs were hydrodynamically transported at a flow rate of 1 μL min(-1) to an on-chip electromanipulation unit, where they were electrophoretically withdrawn from the bulk hydrodynamic flow and directed into a receiving reservoir. Using an electric field of 100 V cm(-1), the negatively charged CTCs were enriched into an anodic receiving reservoir to a final volume of 2 μL, providing an enrichment factor of 500. The collected CTCs could then be searched for point mutations using a PCR/LDR/capillary electrophoresis assay. The DNA extracted from the CTCs was subjected to a primary polymerase chain reaction (PCR) with the amplicons used for a ligase detection reaction (LDR) to probe for KRAS oncogenic point mutations. Point mutations in codon 12 of the KRAS gene were successfully detected in the SW620 CTCs for samples containing <10 CTCs in 1 mL of whole blood. However, the HT29 cells did not contain these mutations, consistent with their known genotype.
Hospitalizations Associated With Influenza and Respiratory Syncytial Virus in the United States, 1993–2008 (2012)

Overall US hospitalization rates for influenza and RSV are similar; however, their age-specific burdens differ dramatically. Our estimates are consistent with those from previous studies focusing either on influenza or RSV. Our approach provides robust national comparisons of hospitalizations associated with these 2 viral respiratory pathogens by age group and over time.
Promise of Low-Density Lipoprotein–Lowering Therapy for Primary and Secondary Prevention (2008)

It is not good to settle into a set of opinions. At first putting forth great effort to be sure that you have grasped the basics, then practicing so that they may come to fruition is something that will never stop for your whole lifetime. Do not rely on following the degree of understanding that you have discovered, but simply think. . .