gebhart/patrepeval huggingface dataset:
Full Operating Range Robust Hybrid Control of a Coal-Fired Boiler/Turbine Unit (2008)

Multi-input-multi-output robust controllers recently designed for the megawatt output/throttle pressure control in a coal-fired power plant boiler/turbine unit have demonstrated performance robustness noticeably superior to that of the currently employed nonlinear PID-based controller. These controllers, however, have been designed only for the range of 150–185MW around the 185MW nominal operating point, exhibiting a significant loss of performance in the lower range of 120–150MW. Through system identification, the reason for this performance loss is demonstrated in the current work to be a pronounced dependence of the boiler/turbine unit steady state gains on the operating point. This problem is addressed via a hybrid control law consisting of two robust controllers and a robust switch between them activated by the set point change. The controllers are designed to cover the corresponding half-ranges of the full operating range. This permits attainment of the desired overall performance as well as reduction of modeling uncertainty induced by the operating point change to approximately 25% of that associated with the previous designs. Robust switching is accomplished through a novel hybrid mode of behavior—robustly controlled discrete transition. The latter mode is produced through realizing that the off-line transfer speedup suggested by Zaccarian and Teel (2005, “The L2(l2) bumpless Transfer Problem for Linear Parts: Its Definition and Solution,” Automatica, 41, pp. 1273–1280) can be taken to the limit and incorporating the result into a robust bumpless transfer technique recently developed by the authors. As demonstrated by simulation results, the proposed strategy provides an adequate solution to the problem of robust boiler/turbine unit performance over the full operating range. This fact combined with numerical algorithm tractability, relative ease of its design, its insensitivity to implementation nonidealities, and accompanying identification methodology for nominal model generation makes it a viable candidate for industrial acceptance.
The 5-methylcytosine content of DNA from human tumors (1983)

The overall 5-methylcytosine (m5C) content of DNA from normal tissues varies considerably in a tissue-specific manner. By high-performance liquid chromatography, we have examined the (m5C) contents of enzymatic digests of DNA from 103 human tumors including benign, primary malignant and secondary malignant neoplasms. The diversity and large number of these tumor samples allowed us to compare the range of DNA methylation levels from neoplastic tissues to that of normal tissues from humans. Most of the metastatic neoplasms had significantly lower genomic (m5C) contents than did most of the benign neoplasms or normal tissues. The percentage of primary malignancies with hypomethylated DNA was intermediate between those of metastases and benign neoplasms. These findings might reflect an involvement of extensive demethylation of DNA in tumor progression. Such demethylation could be a source of the continually generated cellular diversity associated with cancer.
Evidence of ζ Protein Kinase C Involvement in Polymorphonuclear Neutrophil Integrin-dependent Adhesion and Chemotaxis (1998)

Classical chemoattractants and chemokines trigger integrin-dependent adhesion of blood leukocytes to vascular endothelium and also direct subsequent extravasation and migration into tissues. In studies of human polymorphonuclear neutrophil responses to formyl peptides and to interleukin 8, we show evidence of involvement of the atypical zeta protein kinase C in the signaling pathway leading to chemoattractant-triggered actin assembly, integrin-dependent adhesion, and chemotaxis. Selective inhibitors of classical and novel protein kinase C isozymes do not prevent chemoattractant-induced neutrophil adhesion and chemotaxis. In contrast, chelerythrine chloride and synthetic myristoylated peptides with sequences based on the endogenous zeta protein kinase C pseudosubstrate region block agonist-induced adhesion to fibrinogen, chemotaxis and F-actin accumulation. Biochemical analysis shows that chemoattractants trigger rapid translocation of zeta protein kinase C to the plasma membrane accompanied by rapid but transient increase of the kinase activity. Moreover, pretreatment with C3 transferase, a specific inhibitor of Rho small GTPases, blocks zeta but not alpha protein kinase C plasma membrane translocation. Synthetic peptides from zeta protein kinase C also inhibit phorbol ester-induced integrin-dependent adhesion but not NADPH-oxidase activation, and C3 transferase pretreatment blocks phorbol ester-triggered translocation of zeta but not alpha protein kinase C. These data suggest the involvement of zeta protein kinase C in chemoattractant-induced leukocyte integrin-dependent adhesion and chemotaxis. Moreover, they highlight a potential link between atypical protein kinase C isozymes and Rho signaling pathways leading to integrin-activation.
Cloning of Pinus sylvestris SCARECROW gene and its expression pattern in the pine root system, mycorrhiza and NPA‐treated short roots (2007)

The SCARECROW (SCR) gene is central to root radial patterning. Its expression has not been investigated in conifers with morphologically different root types. Additional interest in SCR functions in the Pinus sylvestris root system comes from the effect of ectomycorrhiza formation on the short root apical structure. Here, the P. sylvestris SCR gene (PsySCR) was cloned and its expression investigated by northern blot and in situ hybridization of primary, lateral and short roots and mycorrhiza. Short root dichotomization was induced by auxin transport inhibitor (N-1-naphthylphthalamic acid (NPA)). PsySCR has conserved GRAS family protein motifs at the C-terminus and a variable N-terminus. PsySCR expression occurred in young root tissue and mycorrhiza. In root sections the PsySCR signal runs through the tip in initials for stele and root cap column and becomes upwards-restricted to endodermis in all root types. The PsySCR expression pattern suggests for the first time a regulatory role for SCR in maintaining the endodermal characteristics and radial patterning of roots with open meristem organization. The specific PsySCR localization is also an excellent marker for investigation of the dichotomization process in short roots.
Physiological Role of Peroxisome Proliferator-Activated Receptors Type Alpha on Dopamine Systems (2013)

The discovery that N-acylethanolamines, such as oleoylethanolamide (OEA) and palmitoylethanolamide (PEA), acting as endogenous ligands of alpha-type peroxisome proliferator-activated receptors (PPARα), block nicotine-induced excitation of dopamine neurons revealed their role as important endogenous negative modulators of nicotinic receptors containing β2 subunits (denoted β2*-nAChRs) on dopamine neurons, which are key to the brain reward system. Using mass-spectrometry data analysis from rodent brain slices containing the midbrain, we characterized the effects induced by modulation of PPARα on PEA and OEA levels. PEA and OEA constitutive levels in the midbrain are higher than endocannabinoids (e.g. anandamide, 2-arachidonoylglycerol), and depend upon excessive input drive and the metabolic state of the cells. Accordingly, OEA and PEA synthesis is affected when adding low concentrations of fatty acids (endogenous PPARα ligands), most likely through activation of PPARα. Indeed, PPARα activation increases PEA and OEA levels, which may further sustain PPARα activity. Given this, it is likely that these molecules dynamically affect dopamine function and excitability, as well as their dependent behaviour. Consequently, N-acylethanolamines may confer less vulnerability towards disruption of dynamic balance of dopamine-acetylcholine systems through PPARα activation. Finally, using pharmacological and/or nutritional strategies which target PPARα might represent a promising therapeutic approach to prevent disorders often related to neuro-inflammation, stress and abnormal β2*-nAChR function.
Identification and evaluation of the security requirements in medical applications (2003)

The author summarizes the security aspects of today's medical information systems and evaluates the software security requirements necessary for the computerized systems of tomorrow. She then discusses how these concerns are addressed by today's technology. Particular emphasis is placed on the security gaps in today's technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Fast connected component labeling algorithm using a divide and conquer technique. (2000)

We investigate a method to speed up the O(n) labeling algorithm of Rosenfeld and Pfaltz for segmenting binary images, which is unduly complex for large images. That algorithm searches line-by-line, top to bottom, to assign a blob label to each current pixel that is connected to a blob. A large number K of labels arises of which many are equivalent, so the equivalence must be resolved. This requires a KxK matrix to represent the connectivity and O(K) operations for resolution, which is very large for large images. Our approach partitions the binary image into NxN rectangles and perform local equivalence resolution on each while keeping track of the global equivalence with list pointers to equivalence lists. Such divide and conquer technique greatly increases the run time speed.
Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure (1988)

Finding novel leads from which to design drug molecules has traditionally been a matter of screening and serendipity. We present a method for finding a wide assortment of chemical structures that are complementary to the shape of a macromoleculer receptor site whose X-ray crystallographic structure is known. Each of a set of small molecules from the Cambridge Crystallographic Database (Allen; et al. J. Chem. Doc. 1973, 13, 119) is individually docked to the receptor in a number of geometrically permissible orientations with use of the docking algorithm developed by Kuntz et al. (J. Mol. Biol. 1982, 161, 269). The orientations are evaluated for goodness-of-fit, and the best are kept for further examination using the molecular mechanics program AMBER (Weiner; Kollman J. Comput. Chem. 1981, 106, 765). The shape-search algorithm finds known ligands as well as novel molecules that fit the binding site being studied. The highest scoring orientations of known ligands resemble binding modes generated by interactive modeling or determined crystallographically. We describe the application of this procedure to the binding sites of papain and carbonic anhydrase. While the compounds recovered from the Cambridge Crystallographic Database are not, themselves, likely to be inhibitors or substrates of these enzymes, we expect that the structures from such searches will be useful in the design of active compounds.
Bacteremia and fungemia in hematological and oncological children with neutropenic fever: two-year study in a medical center. (1998)

A retrospective study of bacteremia in children with neutropenic fever admitted to a medical center in Taiwan from Jan. 1994 to Dec. 1995 was performed. There were in total 273 episodes of neutropenic fever during this period, but only 79 pathogens were isolated from blood specimens in 70 episodes. Klebsiella pneumoniae (27.8%), E. coli (10.1%), Staphylococcus aureus (10.1%) and Pseudomonas aeruginosa (7.6%) were the most common pathogens. All the isolates of S. aureus were methicillin sensitive. About half of K. pneumoniae (10/22) was multiple-drug resistant. There were seven infection-related mortality cases, three due to multiple-drug resistant K. pneumoniae, one due to S. aureus, one alpha-hemolytic streptococcus and two fungemia (Cryptococcus neoformans and Fusarium sp.). Vancomycin is not necessary in initial empiric therapy of neutropenic fever, while cefazolin or oxacillin may be included in cases with central venous access device. Antibiotics to cover intestinal flora, especially K. pneumoniae, are paramount in our hospital.
Controlling cell-cell interactions in hepatic tissue engineering using microfabrication (1997)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Whitaker College of Health Sciences and Technology, 1997.
A re-examination of the pathway for ornithine biosynthesis in a thermophilic and two mesophilic Bacillus species (1992)

Summary: The expression of Bacillus stearothermophilus genes complementing arginine auxotrophs of Escherichia coli was studied. The activity responsible for the formation of ornithine in B. stearothermophilus was identified as a repressible ornithine acetyltransferase (genetic symbol argJ) encoded by the same DNA fragment as the argC, orgA and argB genes. Bacillus subtilis and Bacillus licheniformis displayed the same pattern of enzyme activities as B. stearothermophilus. In contrast to previous reports, these organisms consequently use the cyclic pathway of ornithine biosynthesis. B. stearothermophilus also possesses a broad specificity aminoacylase which exhibits low affinity towards N 2-acetyl-l-ornithine.
The Human Glucokinase Gene β-Cell-Type Promoter: An Essential Role of Insulin Promoter Factor 1/PDX-1 in Its Activation in HIT-T15 Cells (1996)

The glycolytic enzyme glucokinase plays a primary role in the glucose-responsive secretion of insulin, and defects of this enzyme can cause NIDDM. As a step toward understanding the molecular basis of glucokinase (GK) gene regulation, we assessed the structure and regulation of the human GK gene beta-cell-type promoter. The results of reporter gene analyses using HIT-T15 cells revealed that the gene promoter was comprised of multiple cis-acting elements, including two primarily important cis-motifs: a palindrome structure, hPal-1, and the insulin gene cis-motif A element-like hUPE3. While both elements were bound specifically by nuclear proteins, it was the homeodomain-containing transcription factor insulin promoter factor 1 (IPF1)/STF-1/PDX-1 that bound to the hUPE3 site: IPF1, when expressed in CHO-K1 cells, became bound to the hUPE3 site and activated transcription. An anti-IPF1 antiserum used in gel-mobility shift analysis supershifted the DNA protein complex formed with the hUPE3 probe and nuclear extracts from HIT-T15 cells, thus supporting the involvement of IPF1 in GK gene activation in HIT-T15 cells. In contrast to the insulin gene, however, neither the synergistic effect of the Pan1 expression on the IPF1-induced promoter activation nor the glucose responsiveness of the activity was observed for the GK gene promoter. These results revealed some conservative but unique features for the transcriptional regulation of the beta-cell-specific genes in humans. Being implicated in insulin and GK gene regulations as a common transcription factor, IPF1/STF-1/PDX-1 is likely to play an essential role in maintaining normal beta-cell functions.
Structural studies on sulfated oligosaccharides derived from the carbohydrate‐protein linkage region of chondroitin sulfate proteoglycans of whale cartilage (1991)

From the carbohydrate-protein linkage region of whale cartilage proteoglycans, which bear predominantly chondroitin 4-sulfate, one nonsulfated, two monosulfated and one disulfated hexasaccharide alditols were isolated after exhaustive digestions with Actinase E and chondroitinase ABC, and subsequent beta-elimination. Their structures were analyzed by chondroitinase ACII digestion in conjunction with HPLC and by 500-MHz 1H-NMR spectroscopy. The nonsulfated compound (A) had the following conventional structure: delta GlcA(beta 1-3)-GalNAc(beta 1-4)GlcA(beta 1-3)Gal(beta 1-4)Xylol, where GlcA, delta GlcA and GalNAc are glucuronic acid; 4,5-unsaturated glucuronic acid and 2-deoxy-2-N-acetylamino-D-galactose, respectively. The other compounds were sulfated derivatives of compound A. Two monosulfated compounds (B and C) had an ester sulfate on C4 or C6 of the GalNAc residue, respectively and the disulfated compound (D) had two ester sulfate groups, namely, one on C4 of the GalNAc and the other on C4 of the Gal residue substituted by GlcA. The molar ratio of A/B/C/D was 0.21:0.16:0.36:0.27. The compound containing Gal-4-O-sulfate was previously isolated by us in the form of a sulfated glycoserine [delta GlcA(beta 1-3)GalNAc(4-O- sulfate)(beta 1-4)GlcA(beta 1-3)Gal(4-O-sulfate)(beta 1-3)-Gal(beta 1- 4)Xyl beta 1-O-Ser] from the carbohydrate-protein linkage region of rat chondrosarcoma chondroitin-4-sulfate proteoglycans [Sugahara K., Yamashina, I., DeWaard, P., Van Halbeek, H. & Vliegenthart, J.F.G. (1988) J. Biol. Chem. 263, 10,168-10,174]. The discovery of this structure in the carbohydrate-protein linkage region of chondroitin 4-sulfate proteoglycans from nontumorous cartilage indicates that it is not a tumor-associated product but rather a physiological biosynthetic product since it represents a significant proportion. The biological significance of this structure is discussed in relation to glycosaminoglycan biosynthesis.
Type I interferons act directly on CD8 T cells to allow clonal expansion and memory formation in response to viral infection (2005)

T cell expansion and memory formation are generally more effective when elicited by live organisms than by inactivated vaccines. Elucidation of the underlying mechanisms is important for vaccination and therapeutic strategies. We show that the massive expansion of antigen-specific CD8 T cells that occurs in response to viral infection is critically dependent on the direct action of type I interferons (IFN-Is) on CD8 T cells. By examining the response to infection with lymphocytic choriomeningitis virus using IFN-I receptor-deficient (IFN-IR(0)) and -sufficient CD8 T cells adoptively transferred into normal IFN-IR wild-type hosts, we show that the lack of direct CD8 T cell contact with IFN-I causes >99% reduction in their capacity to expand and generate memory cells. The diminished expansion of IFN-IR(0) CD8 T cells was not caused by a defect in proliferation but by poor survival during the antigen-driven proliferation phase. Thus, IFN-IR signaling in CD8 T cells is critical for the generation of effector and memory cells in response to viral infection.
Adult Height in Patients with Congenital Adrenal Hyperplasia: A Systematic Review and Metaanalysis (2010)

Evidence derived from observational studies suggests that the final height of CAH patients treated with glucocorticoids is lower than the population norm and is lower than expected given parental height.
Tetanus and Botulinum Neurotoxins Are Zinc Proteases Specific for Components of the Neuroexocytosis Apparatusa (1994)

Tetanus and botulinum neurotoxins bind to nerve cells, penetrate the cytosol, and block neurotransmitter release. Comparison of their amino-acid sequences shows the presence of the highly conserved His-Glu-x-x-His zinc-binding motif of zinc-endopeptidases (HExxH). Atomic absorption measurements of clostridial neurotoxins show the presence of one atom of zinc/toxin molecule bound to the light chain. The toxin-bound zinc ion is essential for the neurotoxins inhibition of neurotransmitter release in Aplysia neurons injected with the toxins. Phosphoramidon, a very specific inhibitor of zinc-endopeptidases, blocks the intracellular activity of the clostridial neurotoxins. Highly purified preparations of the light chain of tetanus and botulinum B and F neurotoxins cleaved specifically VAMP/synaptobrevin, an integral membrane protein of small synaptic vesicles, both in vivo and in vitro. From these studies, it can be concluded that the clostridial neurotoxins responsible for tetanus and botulism block neuroexocytosis via the proteolytic cleavage of specific components of the neuroexocytotic machinery.
Shape Guided Object Segmentation (2006)

We construct a Bayesian model that integrates topdown with bottom-up criteria, capitalizing on their relative merits to obtain figure-ground segmentation that is shape-specific and texture invariant. A hierarchy of bottom-up segments in multiple scales is used to construct a prior on all possible figure-ground segmentations of the image. This prior is used by our top-down part to query and detect object parts in the image using stored shape templates. The detected parts are integrated to produce a global approximation for the object’s shape, which is then used by an inference algorithm to produce the final segmentation. Experiments with a large sample of horse and runner images demonstrate strong figure-ground segmentation despite high object and background variability. The segmentations are robust to changes in appearance since the matching component depends on shape criteria alone. The model may be useful for additional visual tasks requiring labeling, such as the segmentation of multiple scene objects.
Autonomous Robotic Fish as Mobile Sensor Platforms: Challenges and Potential Solutions (2011)

Abstract With advances in actuation and sensing materials and devices, there is a growing interest in developing underwater robots that propel and maneuver themselves as real fish do. Such robots, often known as robotic fish, could provide an engineering tool for understanding fish swimming. Equipped with communication capabilities and sensors, they could also serve as economical, dynamic samplers of aquatic environments. In this paper we discuss some of the major challenges in realizing adaptive, cost-effective, mobile sensor networks that are enabled by resource-constrained robotic fish. Such challenges include maneuvering in the presence of ambient disturbances, localization with adequate precision, sustained operation with minimal human interference, and cooperative control and sensing under communication constraints. We also present potential solutions and promising research directions for addressing these challenges, some of which are inspired by how fish solve similar problems.
Evaluation of Insulin‐Like Growth Factor Binding Protein‐1 as a Diagnostic Tool for Rupture of the Membranes (1998)

The measurement of IGFBP-1 in vaginal fluids is useful for the diagnosis of ruptured fetal membranes.
A New Set of Arabidopsis Expressed Sequence Tags from Developing Seeds. The Metabolic Pathway from Carbohydrates to Seed Oil, (2000)

Large-scale single-pass sequencing of cDNAs from different plants has provided an extensive reservoir for the cloning of genes, the evaluation of tissue-specific gene expression, markers for map-based cloning, and the annotation of genomic sequences. Although as of January 2000 GenBank contained over 220,000 entries of expressed sequence tags (ESTs) from plants, most publicly available plant ESTs are derived from vegetative tissues and relatively few ESTs are specifically derived from developing seeds. However, important morphogenetic processes are exclusively associated with seed and embryo development and the metabolism of seeds is tailored toward the accumulation of economically valuable storage compounds such as oil. Here we describe a new set of ESTs from Arabidopsis, which has been derived from 5- to 13-d-old immature seeds. Close to 28,000 cDNAs have been screened by DNA/DNA hybridization and approximately 10,500 new Arabidopsis ESTs have been generated and analyzed using different bioinformatics tools. Approximately 40% of the ESTs currently have no match in dbEST, suggesting many represent mRNAs derived from genes that are specifically expressed in seeds. Although these data can be mined with many different biological questions in mind, this study emphasizes the import of photosynthate into developing embryos, its conversion into seed oil, and the regulation of this pathway.