gebhart/patrepeval huggingface dataset:
Chronic Social Stress and Susceptibility to Concentrated Ambient Fine Particles in Rats (2010)

CAPs effects on respiratory measures differed significantly, and substantively, by stress group. Higher CAPs exposures were associated with a rapid, shallow breathing pattern only under chronic stress. Blood measures provided evidence of inflammatory responses. Results support epidemiologic findings that chronic stress may alter respiratory response to air pollution and may help elucidate pathways for differential susceptibility.
Neuropeptide Y receptor binding sites in rat brain: differential autoradiographic localizations with 125I-peptide YY and 125I- neuropeptide Y imply receptor heterogeneity (1989)

Neuropeptide Y (NPY) receptor binding sites have been localized in the rat brain by in vitro autoradiography using picomolar concentrations of both 125I-NPY and 125I-peptide YY (PYY) and new evidence provided for differentially localized receptor subtypes. Equilibrium binding studies using membranes indicate that rat brain contains a small population of high-affinity binding sites and a large population of moderate-affinity binding sites. 125I-PYY (10 pM) is selective for high-affinity binding sites (KD = 23 pM), whereas 10 pM 125I-NPY labels both high- and moderate-affinity sites (KD = 54 pM and 920 pM). The peptide specificity and affinity of these ligands in autoradiographic experiments match those seen in homogenates. Binding sites for 125I-PYY are most concentrated in the lateral septum, stratum oriens, and radiatum of the hippocampus, amygdala, piriform cortex, entorhinal cortex, several thalamic nuclei, including the reuniens and lateral posterior nuclei, and substantia nigra, pars compacta, and pars lateralis. In the brain stem, 125I-PYY sites are densest in a variety of nuclei on the floor of the fourth ventricle, including the pontine central grey, the supragenual nucleus, and the area postrema. 125I-NPY binding sites are found in similar areas, but relative levels of NPY binding and PYY binding differ regionally, suggesting differences in sites labeled by the two ligands. These receptor localizations resemble the distribution of endogenous NPY in some areas, but others, such as the hypothalamus, contain NPY immunoreactivity but few binding sites.
[Optimization of the shape of implantable electrocardiostimulators]. (1987)

The deficiencies of current electrocardiostimulation equipment are being discussed on the basis of analysis of cases with the device implantation. The authors propose changing the shape of the electrocardiostimulator so, that the frame of the device were surrounded by soft tissue.
The random subspace method for constructing decision forests (1998)

Much of previous attention on decision trees focuses on the splitting criteria and optimization of tree sizes. The dilemma between overfitting and achieving maximum accuracy is seldom resolved. A method to construct a decision tree based classifier is proposed that maintains highest accuracy on training data and improves on generalization accuracy as it grows in complexity. The classifier consists of multiple trees constructed systematically by pseudorandomly selecting subsets of components of the feature vector, that is, trees constructed in randomly chosen subspaces. The subspace method is compared to single-tree classifiers and other forest construction methods by experiments on publicly available datasets, where the method's superiority is demonstrated. We also discuss independence between trees in a forest and relate that to the combined classification accuracy.
A Reference Architecture And Score Representation For Popular Music Human-Computer Music Performance Systems (2011)

Popular music (characterized by improvised instrumental parts, beat and measure-level organization, and steady tempo) poses challenges for human-computer music performance (HCMP). Pieces of music are typically rearrangeable on-the-fly and involve a high degree of variation from ensemble to ensemble, and even between rehearsal and performance. Computer systems aiming to participate in such ensembles must therefore cope with a dynamic high-level structure in addition to the more traditional problems of beat-tracking, score-following, and machine improvisation. There are many approaches to integrating the components required to implement dynamic human-computer music performance systems. This paper presents a reference architecture designed to allow the typical sub-components (e.g. beat-tracking, tempo prediction, improvisation) to be integrated in a consistent way, allowing them to be combined and/or compared systematically. In addition, the paper presents a dynamic score representation particularly suited to the demands of popular music performance by computer.
Watching Proteins in the Wild: Fluorescence Methods to Study Protein Dynamics in Living Cells (2000)

The advent of GFP imaging has led to a revolution in the study of live cell protein dynamics. Ease of access to fluorescently tagged proteins has led to their widespread application and demonstrated the power of studying protein dynamics in living cells. This has spurred development of next generation approaches enabling not only the visualization of protein movements, but correlation of a protein's dynamics with its changing structural state or ligand binding. Such methods make use of fluorescence resonance energy transfer and dyes that report changes in their environment, and take advantage of new chemistries for site-specific protein labeling.
Selective Inhibition of ADAM Metalloproteases as a Novel Approach for Modulating ErbB Pathways in Cancer (2007)

Inhibition of ErbB ligand shedding offers a potentially novel and well-tolerated therapeutic strategy for the treatment of human cancers and is currently being evaluated in the clinic.
An Externally Powered, Multichannel, Implantable Stimulator for Versatile Control of Paralyzed Muscle (1987)

Through the use of semicustom integrated circuit technology, an implantable muscle stimulator has been developed. The unit is small, lightweight, has low power consumption, and is intended for permanent usage. The stimulator circuitry is externally controlled and powered by a single encoded radio frequency carrier. Up to eight independently controlled stimulus output channels are provided, with output channel selection, stimulus pulse width, and stimulus pulse frequency under external control. A constant current biphasic stimulus pulse is used, in which the stimulus current amplitude can be preset by a single resistor value. The stimulator circuitry has been implemented in thick film hybrid form, and has undergone laboratory evaluation for 48 months.
Searching networks with unrestricted edge costs (2001)

Best-first and depth-first heuristic search algorithms often assume underlying search graphs with only nonnegative edge costs and attempt to optimize simple objective functions. Applicability of these algorithms to graphs with both positive and negative edge costs is not completely studied. In the paper, two new problems are identified: one in computational geometry and the other in the layout design of very large scale integrated (VLSI) circuits. The former problem relates to a weight-balanced bipartitioning of a given set of points in a plane. The goal of the second problem is to find an area-balanced staircase path in a VLSI floorplan. Formulations of these problems lead to an interesting directed acyclic search graph with positive, zero and negative edge costs and an objective function of general nature. These problems are NP-hard. To solve such general problems optimally, search schemes are proposed. Experimental results reveal the efficacy and versatility of the proposed schemes, the depth-first scheme being the better choice. It is shown that the classical number-partitioning problem can also be formulated in this framework.
Radiosensitization of Normal Tissue by Chloroquine (1977)

Severe radiation reaction with chest wall necrosis occurred following 5,000 rads of 60Co irradiation. The patient was arthritic and on chloroquine therapy. This delayed reaction was due to chloroquine radiosensitization. Rats treated with combined chloroquine and chest wall irradiation were compared to rats receiving irradiation alone. The acute radiation reaction was greater in the drug treated animals.
Induction of Androgen Receptor Expression by Phosphatidylinositol 3-Kinase/Akt Downstream Substrate, FOXO3a, and Their Roles in Apoptosis of LNCaP Prostate Cancer Cells (2005)

The phosphatidylinositol 3-kinase (PI3K)/Akt pathway plays important roles for prostate cancer cell survival, and the androgen receptor (AR) plays essential roles for prostate cancer cell proliferation. How these two signals cooperate to control cell growth and death, however, remains unclear and debated. Here we provide the first linkage by the identification of Forkhead transcription factor FOXO3a, the PI3K/Akt downstream substrate, as a positive regulator for the induction of AR gene expression. Both Western blot and real time PCR assays demonstrate that FOXO3a can induce AR expression at the protein and mRNA levels, and gel shift and chromatin immunoprecipitation assays further demonstrate that FOXO3a can induce 5' AR promoter activity via binding to the consensus DNA-binding sequence in the AR 5' promoter -1290 to -1297 (5'-TTGTTTCA-3'). Under normal growth conditions, blocking PI3K/Akt signals by LY294002 causes LNCaP cell arrest in G1 phase rather than apoptosis. However, further blocking of AR functions by AR small interfering RNA leads to dramatic LNCaP cell death, suggesting that AR may play important protective roles when the PI3K/Akt signal pathway is blocked by LY294002. Together, our data provide the first model to explain how PI3K/Akt and AR can cooperate to control LNCaP cell growth and death under normal conditions.
Production and characterization of monoclonal antibodies against the O-5 antigen of Salmonella typhimurium lipopolysaccharide (1996)

Three murine monoclonal antibodies (MAbs) were produced by fusion of P3X63-Ag8.653 myeloma cells and splenocytes of a mouse immunized with heat-attenuated (20 min, 80 degrees C) Salmonella typhimurium cells. MAbs 5A5 and 5B2 were of the immunoglobulin M (IgM) class, while MAb 4A8 was IgG2a. All possessed the kappa light chains. The MAbs were specific to the lipopolysaccharide (LPS) O-5 antigen of Salmonella B serogroup, as determined by electrophoresis followed by immunoblotting. All MAbs recognized the same epitope, as determined by an additive enzyme-linked immunosorbent assay (ELISA), although IgM MAbs exhibited higher avidity than the IgG MAb. ELISA analyses revealed that all three MAbs reacted with S. typhimurium (LPS O:1, 4, 5, and 12) while failing to recognize S. typhimurium var. copenhagen (LPS O:1, 4, and 12). The MAbs reacted equally with live and heat-attenuated Salmonella B serovars containing LPS O-5 antigen. The ability of the MAbs to detect live bacterial cells was further confirmed by transmission electron microscopy. Treatment of bacteria with cholic acid and extremely low pH did not affect antibody binding to S. typhimurium. However, when S. typhimurium cells were exposed to alkaline conditions prior to reaction with all three MAbs, no binding was observed. The use of MAbs to discriminate between S. typhimurium and S. typhimurium var. copenhagen in meat samples was investigated.
The inactivation of human plasma alpha 1-proteinase inhibitor by proteinases from Staphylococcus aureus. (1986)

The interaction of three proteinases (seryl, cysteinyl, and metallo-) from Staphylococcus aureus with human plasma alpha 1-proteinase inhibitor has been investigated. As expected, none of the enzymes was inactivated by this protein, each, instead causing the conversion of the native inhibitor into an inactive form of decreased molecular weight. Amino-terminal sequence analysis indicated that inhibitor inactivation had occurred by peptide bond cleavage near the reactive center of this protein. When the inhibitor was modified by this treatment, it became resistant to both pH and temperature denaturation and, in contrast to the intact denatured protein, did not undergo further proteolytic degradation. This process of inactivation of alpha 1-proteinase inhibitor by pathogenic proteinases could result in a deregulation of its target enzyme, neutrophil elastase, and, therefore, may be important in the consumption of some plasma proteins by this enzyme during septicemia.
Comparative study of DNA-based immunization vectors: effect of secretion signals on the antibody responses in mice (1997)

The presence of a signal sequence preceding the gene encoding a target antigen in a DNA vaccine should facilitate secretion of the in vivo translated antigen. The immune responses elicited upon injection with such a vector could differ from those induced by the same vector lacking a signal sequence. In the present study, the humoral responses elicited in mice immunized with two plasmids, either containing or lacking the human tissue plasminogen activator signal sequence, were compared. Both plasmids encode the chimeric antigen ZZN4, containing a malaria antigen Pf332-derived sequence (N4) linked to a bacterial fusion partner (ZZ). In vitro transfection of COS cells with each plasmid and treatment of the transfectants with brefeldin A confirmed that secretion of ZZN4 via the endoplasmic reticulum and Golgi pathway only occurred in cells transfected with the signal peptide-encoding plasmid. Repeated intramuscular injections of mice with either of the plasmids elicited comparable antibody responses to ZZN4 with regard to kinetics, specific IgG levels and persistence. These results indicate that in vivo transfection of muscle cells by either of these two plasmids generated comparable levels of antigen available for B-cell recognition and for uptake by antigen-presenting cells, despite the differential intracellular targeting of the encoded antigen. The relevance of these findings for the design of DNA vaccine vectors is discussed.
Recent Advances in Axial-Flux Permanent-Magnet Machine Technology (2012)

This paper reviews the progress that has been made in the analysis and design of axial-flux permanent-magnet machines over the past decade, with particular attention to aspects such as electromagnetic and thermal modeling, materials, manufacturing, pulsating torque, and extended speed range. Comparisons with other machine types and applications are also reviewed.
miR-33a Modulates ABCA1 Expression, Cholesterol Accumulation, and Insulin Secretion in Pancreatic Islets (2012)

Changes in cellular cholesterol affect insulin secretion, and β-cell-specific deletion or loss-of-function mutations in the cholesterol efflux transporter ATP-binding cassette transporter A1 (ABCA1) result in impaired glucose tolerance and β-cell dysfunction. Upregulation of ABCA1 expression may therefore be beneficial for the maintenance of normal islet function in diabetes. Studies suggest that microRNA-33a (miR-33a) expression inversely correlates with ABCA1 expression in hepatocytes and macrophages. We examined whether miR-33a regulates ABCA1 expression in pancreatic islets, thereby affecting cholesterol accumulation and insulin secretion. Adenoviral miR-33a overexpression in human or mouse islets reduced ABCA1 expression, decreased glucose-stimulated insulin secretion, and increased cholesterol levels. The miR-33a-induced reduction in insulin secretion was rescued by cholesterol depletion by methyl-β-cyclodextrin or mevastatin. Inhibition of miR-33a expression in apolipoprotein E knockout islets and ABCA1 overexpression in β-cell-specific ABCA1 knockout islets rescued normal insulin secretion and reduced islet cholesterol. These findings confirm the critical role of β-cell ABCA1 in islet cholesterol homeostasis and β-cell function and highlight modulation of β-cell miR-33a expression as a means to influence insulin secretion.
CpG DNA is a potent enhancer of systemic and mucosal immune responses against hepatitis B surface antigen with intranasal administration to mice. (1998)

Mucosal immunity is difficult to induce with subunit vaccines unless such vaccines are administered with a mucosal adjuvant such as cholera toxin (CT); however, CT is toxic in humans. Synthetic oligodeoxynucleotides containing immunostimulatory CpG motifs (CpG) are potent adjuvants for the induction of Th1-like systemic immune responses against parenterally delivered proteins. Here, we show in mice that intranasal delivery of hepatitis B surface Ag, which alone has no effect, elicits good immune responses when given with CpG oligodeoxynucleotides and/or CT. Overall, CpG is superior to CT for the induction of humoral and cell-mediated systemic immunity as well as mucosal immune responses (IgA) at local (lung) and distant (feces) sites. Furthermore, CpG and CT act synergistically, giving stronger responses than those observed with 10 times more of either adjuvant alone. Ab isotypes were predominantly IgG1 (Th2-like) with CT, mixed IgG1/IgG2a (Th0) with CpG, and predominantly IgG2a (Th1-like) with CpG and CT together.
ABAM: on-demand associativity-based multicast routing for ad hoc mobile networks (2002)

Multicast has emerged as a very desirable feature in communication networks. With multicast, data can be distributed to multiple recipients in an efficient and economical manner. We present a performance evaluation of a novel multicast routing strategy for a mobile ad hoc network environment, which is characterized by a highly-dynamic topology with constrained bandwidth and limited power. The associativity-based ad hoc multicast (ABAM) protocol establishes multicast session on demand and utilizes an association stability concept, which is introduced in the ABR protocol for mobile ad hoc unicast routing. The performance of ABAM is simulated and compared with a flooding-based multicast routing protocol. The results show impressive throughput and very low communication overhead.
Design of VLSI implementation-oriented LDPC codes (2003)

Recently, low-density parity-check (LDPC) codes have attracted much attention because of their excellent error-correcting performance and highly parallelizable decoding scheme. However, the effective VLSI implementation of an LDPC decoder remains a big challenge and is a crucial issue in determining how well we can exploit the benefits of the LDPC codes in real applications. In this paper, following the joint code and decoder design philosophy, we propose a semi-random design scheme to construct the LDPC codes that not only exhibit very good error-correcting performance but also effectively fit to partially parallel VLSI decoder implementations. The corresponding partially parallel decoder has a very regular structure and simple control mechanism. Our computer simulations show that such LDPC codes achieve very good performance comparable to their counterparts constructed in a fully random scheme, which however have little chance of fitting to partially parallel decoder implementations.
Functional Analysis of the Staphylococcus aureus Collagen Adhesin B Domain (1999)

The Staphylococcus aureus collagen adhesin (CNA) occurs in at least four forms that differ in the number (one, two, three, or four) of B domains. The B domains contain 187 amino acids and are located between the domains that anchor CNA to the cell envelope and the ligand-binding A domain. To determine whether a B domain is required for functional expression of CNA, we cloned the 2B cna gene from S. aureus strain Phillips and then eliminated both B domains by overlapping PCR. The absence of a B domain did not affect processing of the collagen adhesin to the cell surface or the ability to bind collagen. Based on our recent demonstration that the capsule can mask CNA on the surface of S. aureus cells (A. F. Gillaspy et al., Infect. Immun. 66:3170-3178, 1998), we also investigated the possibility that multiple B domains can extend the ligand-binding A domain outward from the cell surface and thereby overcome the inhibitory effect of the capsule. Specifically, we cloned the naturally occurring 4B CNA variant from S. aureus UAMS-639 and, by successive elimination of B domains, generated 1, 2, and 3B variants that are isogenic with respect to the 4B clone. After introducing each variant into microencapsulated and heavily encapsulated strains of S. aureus and growing cells under conditions known to affect capsule production (e.g., growth on Columbia agar), we correlated capsule production with exposure of CNA on the cell surface and the ability to bind collagen. Under no circumstance was the masking effect of the capsule reduced by the presence of multiple B domains. These results indicate that the B domains do not extend the ligand-binding A domain outward in a fashion that can overcome the inhibition of collagen binding associated with capsule production.
Wound repair and the potential use of growth factors. (1990)

Failure of wounds to heal increases the physical and financial burden of hospitalization and increases the work load for health care professionals. Although careful attention to nutrition (including adequate replacement of vitamins and trace mineral elements), tissue perfusion and oxygenation, and wound dressing and sanitation promote more rapid and complete healing, some wounds respond only slowly or not at all to these conventional treatment modalities. A group of polypeptide growth factors, including epidermal growth factor, platelet-derived growth factor, transforming growth factor beta, and basic fibroblast growth factor, have been found to promote or hasten healing in animal models. This technology is now moving into the clinical arena where its potential for human healing must be evaluated.
Engineered DNA ligases with improved activities in vitro (2013)

The DNA ligase from bacteriophage T4 is one of the most widely used enzymes in molecular biology. It has evolved to seal single-stranded nicks in double-stranded DNA, but not to join double-stranded fragments with cohesive or blunt ends. Its poor activity in vitro, particularly with blunt-ended substrates, can lead to failed or sub-optimal experimental outcomes. We have fused T4 DNA ligase to seven different DNA-binding proteins, including eukaryotic transcription factors, bacterial DNA repair proteins and archaeal DNA-binding domains. Representatives from each of these classes improved the activity of T4 DNA ligase, by up to 7-fold, in agarose gel-based screens for cohesive- and blunt-ended fragment joining. Overall, the most active variants were p50-ligase (i.e. NF-κB p50 fused to T4 DNA ligase) and ligase-cTF (T4 DNA ligase fused to an artificial, chimeric transcription factor). Ligase-cTF out-performed T4 DNA ligase by ∼160% in blunt end 'vector + insert' cloning assays, and p50-ligase showed an improvement of a similar magnitude when it was used to construct a library for Illumina sequencing. The activity of the Escherichia coli DNA ligase was also enhanced by fusion to p50. Together, these results suggest that our protein design strategy is a generalizable one for engineering improved DNA ligases.
Leptin and the Development of Obesity and Diabetes in Psammomys obesus (1997)

The recently discovered ob gene and its circulating product, leptin, may be critical factors in the control of energy balance. Recent studies in ob/ob mice, which lack circulating leptin, have shown dramatic reductions in food intake and bodyweight after leptin treatment. In addition, studies in both humans with obesity and animal models of obesity have demonstrated hyperleptinemia. Here, we report a longitudinal study examining changes in circulating leptin during the development of obesity and diabetes in Psammomys obesus. Over the 8 weeks of the study, lean animals increased their bodyweight by 154% and leptin levels remained essentially unchanged. In contrast, animals that developed obesity (223% increase in bodyweight), hyperglycemia, and hyperinsulinemia also developed hyperleptinemia between 4 weeks and 8 weeks of age. These results demonstrate that the development of hyperleptinemia is associated with the development of obesity and subsequent metabolic abnormalities.