gebhart/patrepeval huggingface dataset:
Quantitative Study of the Resolving Power of Arrays of Carbon Black−Polymer Composites in Various Vapor-Sensing Tasks (1998)

A statistical metric, based on the magnitude and standard deviations along linear projections of clustered array response data, was utilized to facilitate an evaluation of the performance of detector arrays in various vapor classification tasks. This approach allowed quantification of the ability of a 14-element array of carbon black-insulating polymer composite chemiresistors to distinguish between members of a set of 19 solvent vapors, some of which vary widely in chemical properties (e.g., methanol and benzene) and others of which are very similar (e.g., n-pentane and n-heptane). The data also facilitated evaluation of questions such as the optimal number of detectors required for a specific task, whether improved performance is obtained by increasing the number of detectors in a detector array, and how to assess statistically the diversity of a collection of detectors in order to understand more fully which properties are underrepresented in a particular set of array elements. In addition, the resolving power of arrays of carbon black-polymer composites was compared to the resolving power of specific collections of bulk conducting organic polymer or tin oxide detector arrays in a common set of vapor classification tasks.
Aberrant integrin expression in the endometrium of women with endometriosis. (1994)

Integrins are ubiquitous cell adhesion molecules that undergo dynamic alterations during the normal menstrual cycle in the human endometrium. The alpha v beta 3 vitronectin receptor integrin is expressed in endometrium at the time of implantation, but its presence is delayed in endometrium that is assessed to be out of phase using classical histological features. To investigate the expression of this integrin in women with endometriosis, we assessed the presence of the beta 3-subunit throughout the menstrual cycle in 268 "in-phase" endometrial biopsies, using immunohistochemistry. The beta 3-subunit was expressed on endometrial epithelium after days 19-20 of the menstrual cycle. In 241 women whose biopsies were obtained after day 19, a lack of beta 3 expression was found to be closely related to the diagnosis of endometriosis (by Wilcoxon test, P = 0.02). This defect in integrin expression was associated with nulliparity, inversely related to the stage of disease, and occurred despite the presence of in-phase histological features. In a prospective double blind assessment of this integrin, we found endometrial beta 3 analysis to have a high specificity and positive predictive value as a nonsurgical diagnostic test for minimal and mild endometriosis. In conclusion, aberrant integrin expression in the native endometrium is associated with the finding of endometriosis and may identify some women with decreased cycle fecundity due to defects in uterine receptivity.
Matrix Metalloproteinase Inhibitors and Cancer—Trials and Tribulations (2002)

For at least 30 years, matrix metalloproteinases (MMPs) have been heralded as promising targets for cancer therapy on the basis of their massive up-regulation in malignant tissues and their unique ability to degrade all components of the extracellular matrix. Preclinical studies testing the efficacy of MMP suppression in tumor models were so compelling that synthetic metalloproteinase inhibitors (MPIs) were rapidly developed and routed into human clinical trials. The results of these trials have been disappointing. Here we review the studies that brought MPIs into clinical testing and discuss the design and outcome of the trials in light of new information about the cellular source, substrates, and mode of action of MMPs at different stages of tumor progression. The important lessons learned from the MPI experience may be of great value for future studies of MPIs and for cancer drug development in general.
Dimeric Versions of Two Short N-cadherin Binding Motifs (HAVDI and INPISG) Function as N-cadherin Agonists (2002)

N-cadherin is a member of the classical cadherin family of homophilic binding molecules. Peptide competition studies have identified the HAVDI and INPISGQ sequences as functional binding motifs in extracellular domain 1 (ECD1) of N-cadherin. Whereas monomeric versions of these motifs function as specific N-cadherin antagonists, we now show that cyclic peptides containing a tandem repeat of the individual motifs function as N-cadherin agonists. In this context, when presented to neurons as soluble molecules, the dimeric versions of the motifs stimulate neurite outgrowth in a similar manner to native N-cadherin. The response to the dimeric agonist peptides was inhibited by monomeric versions of the same motif and also by recombinant N-cadherin ECD1 protein. The responses were also inhibited by antibodies to a fibroblast growth factor receptor (FGFR) binding motif in ECD4 of N-cadherin and by a specific FGFR antagonist (PD17304). These data suggest that the peptides function by binding to and clustering N-cadherin in neurons and thereby activating an N-cadherin/FGFR signaling cascade. The novel agonists will be invaluable for dissecting out those cadherin functions that rely on signaling as opposed to adhesion and clearly have the potential to be developed as therapeutic agents for the promotion of cell survival and axonal regeneration.
Molecular Regulation Mechanisms and Interactions Between Reactive Oxygen Species and Mitophagy (2018)

The generation of reactive oxygen species (ROS) in response to oxidative stress has important effects on cell development, normal function, and survival. It may cause oxidative damage to intracellular macromolecular substances and mitochondria through several signaling pathways. However, the damaged mitochondria promote further ROS generation, creating a vicious cycle that can cause cellular injury. In addition, excessive ROS produced by damaged mitochondria can trigger mitophagy, a process that can scavenge impaired mitochondria and reduce ROS level to maintain stable mitochondrial function in cells. Therefore, mitophagy heaps maintain cellular homeostasis under oxidative stress. In this article, we review recent advances in cellular damage caused by excessive ROS, the mechanism of mitophagy, and the close relationship between ROS and mitophagy. This review provides a new perspective on therapeutic strategies for related diseases.
Hyperphosphorylated Truncated Protein Tau Induces Caspase-3 Independent Apoptosis-Like Pathway in the Alzheimer's Disease Cellular Model (2011)

Neurofibrillary degeneration and neuronal loss represent key pathological hallmarks of Alzheimer's disease (AD). It has been demonstrated that the decrease of total neuronal numbers correlates with the presence of neurofibrillary degeneration in AD brain. In order to unravel the mechanism leading to the cell death in AD, we developed a stably transfected human neuroblastoma cellular model with doxycycline-regulatable expression of AD truncated tau protein (AT tau, 151-391 4R). Cells expressing the longest tau isoform (Tau 40) were used as a control. We found that more than 80% of the total amount of AT tau and Tau 40 were phosphorylated. Strikingly, both AT tau and Tau 40 reduced the metabolic activity of the cells in a time-dependent manner (p < 0.0001) suggesting that tau overexpression slows down cell proliferation. However, AT tau showed significantly higher toxicity than Tau 40 (p < 0.0001), which indicates that truncation leads to a toxic gain of function. The analysis of the type of the cell death revealed the characteristic features of apoptosis such as cell shrinkage, nuclear, and DNA fragmentation. However, we did not find either the activation of executive caspase (caspase-3) or the caspase cleavage products (PARP and fodrin). These results show that posttranslationally modified truncated tau protein induces caspase-3-independent apoptosis-like programmed cell death, a phenomenon we term tauoptosis.
Tuning MPC using H ∞ loop shaping (2000)

In this paper tuning procedures are outlined for the infinite horizon model predictive control (MPC). The infinite horizon formulation takes advantage of recent extensions to the theory of MPC, which allows the use of infinite horizons in the presence of hard constraints. The Model Predictive Control structure which will be considered here is a constrained regulator in series with a stable observer. The solution makes use of H∞ loopshaping and results on the normalized left coprime factorization (NLCF) optimal control problem for discrete time systems.
Methods of endotoxin removal from biological preparations: a review. (2007)

Efficient and cost-effective removal of endotoxins from pharmaceutical and biotechnology preparations is challenging. Despite development of novel methods, such as the two-phase aqueous micellar systems, in recent years, more research is needed in this field.
A phase I trial of taxol given by a 6-hour intravenous infusion. (1991)

Taxol is a unique mitotic inhibitor that has entered phase II investigation. Phase I studies demonstrated hypersensitivity reactions that were related to the cremophor vehicle and to the rate of drug infusion. As a result, the time span of intravenous (IV) infusion of taxol was routinely prolonged to 6 hours or beyond, and premedication with diphenhydramine, dexamethasone, and cimetidine was initiated. Early studies showed antitumor activity, especially against malignant melanoma and ovarian carcinoma. This phase I trial was performed giving taxol, as a 6-hour IV infusion every 21 days, without premedication. The purpose was to study the necessity of premedication and its impact on toxicity and pharmacokinetics. Thirty-one patients received 64 assessable courses of taxol. One patient had a hypersensitivity reaction, which was easily controlled using routine measures. Myelosuppression was dose-limiting, but sporadic, with two fatalities due to sepsis. Nonhematologic toxicity was of grade 1 and 2 except for one patient with grade 3 mucositis and two patients with grade 3 neuropathy. The neuropathy consisted of reversible painful paresthesias, requiring discontinuation of drug in two patients. Four partial responses were seen (three in patients with non-small-cell lung cancer, one in a patient with adenocarcinoma of unknown primary). Pharmacokinetic values were consistent with those previously reported. The occurrence of myelosuppression or neurotoxicity appeared to be associated with the area under the concentration x time curve (AUC) of taxol. The recommended phase II starting dose on this schedule is 225 mg/m2. Taxol merits broad investigation at the phase II level.
All ApoB-Containing Lipoproteins Induce Monocyte Chemotaxis and Adhesion When Minimally Modified (1999)

Mildly oxidized LDL has many proinflammatory properties, including the stimulation of monocyte chemotaxis and adhesion, that are important in the development of atherosclerosis. Although ApoB-containing lipoproteins other than LDL may enter the artery wall and undergo oxidation, very little is known regarding their proinflammatory potential. LDL, IDL, VLDL, postprandial remnant particles, and chylomicrons were mildly oxidized by fibroblasts overexpressing 15-lipoxygenase (15-LO) and tested for their ability to stimulate monocyte chemotaxis and adhesion to endothelial cells. When conditioned on 15-LO cells, LDL, IDL, but not VLDL increased monocyte chemotaxis and adhesion approximately 4-fold. Chylomicrons and postprandial remnant particles were also bioactive. Although chylomicrons had a high 18:1/18:2 ratio, similar to that of VLDL, and should presumably be less susceptible to oxidation, they contained (in contrast to VLDL) essentially no platelet-activating factor acetylhydrolase (PAF-AH) activity. Because PAF-AH activity of lipoproteins may be reduced in vivo by oxidation or glycation, LDL, IDL, and VLDL were treated in vitro to reduce PAF-AH activity and then conditioned on 15-lipoxygenase cells. All 3 PAF-AH-depleted lipoproteins, including VLDL, exhibited increased stimulation of monocyte chemotaxis and adhesion. In a similar manner, lipoproteins from Japanese subjects with a deficiency of plasma PAF-AH activity were also markedly more bioactive, and stimulated monocyte adhesion nearly 2-fold compared with lipoproteins from Japanese control subjects with normal plasma PAF-AH. For each lipoprotein, bioactivity resided in the lipid fraction and monocyte adhesion could be blocked by PAF-receptor antagonists. These data suggest that the susceptibility of plasma lipoproteins to develop proinflammatory activity is in part related to their 18:1/18:2 ratio and PAF-AH activity, and that bioactive phospholipids similar to PAF are generated during oxidation of each lipoprotein. Moreover, LDL, IDL, postprandial remnant particles, and chylomicrons and PAF-AH-depleted VLDL all give rise to proinflammatory lipids when mildly oxidized.
Expression of Biologically Active Human Thyrotropin (hTSH) in a Baculovirus System: Effect of Insect Cell Glycosylation on hTSH Activity in Vitro and in Vivo (1997)

To obtain large amounts of hTSH and to study the role of the N-linked oligosaccharides for its biological activity, hTSH was produced using recombinant baculovirus containing the human α-subunit and a hTSHβ -minigene, respectively, both under the control of the polyhedrin promoter. Expression in insect cells was 800-1000 ng/ml, 30-fold higher than in our optimized mammalian transient transfection system using Chinese hamster ovary (CHO) cells (20–50 ng/ml). The in vitro activity of insect-cell expressed hTSH (IC-hTSH) was increased 5-fold compared with CHO-hTSH, judged by the ability to induce cAMP production in CHO cells stably transfected with the hTSH receptor (JP09) and the rat thyroid cell line FRTL-5, as well as growth promotion in FRTL-5 cells. Lectin binding and enzymatic desialylation studies suggested that in contrast to CHO-hTSH, IC-hTSH lacked complex-type oligosaccharides terminating with sialic acid but contained predominantly high mannose-type oligosaccharides. The in vitro activity of CHO-hTSH also increased 5- to 6-fold upon treatment of the hTSH-producing cells with the oligosaccharide processing inhibitors swainsonine and castanospermine, which inhibit formation of complex, terminally sialylated oligosaccharides, and upon enzymatic desialylation. In contrast, insect cell-expression or treatment with processing inhibitors did not affect TSH receptor binding. Despite the higher in vitro activity, IC-hTSH had a much lower in vivo activity than CHO-hTSH, due to rapid clearance from the circulation. In summary, this study shows for the first time that relatively high levels of recombinant hTSH with high in vitro bioactivity can be produced in a baculovirus system. Cell-dependent glycosylation is a major factor that determines the final in vivo biopotency of recombinant glycoproteins, a finding that should be of general relevance for all insect cell-produced glycosylated proteins. Although not suitable for clinical use, highly bioactive recombinant hTSH derived from high expression in insect cells should be useful in defining structure-function relations of hormone analogs.
BLOOD CHEMISTRY OF BLACK BEARS FROM PENNSYLVANIA DURING WINTER DORMANCY (1988)

Twenty-four serum chemistries were measured in blood samples collected from 20 adult female black bears (Ursus americanus) and their offspring, including 14 yearlings and 37 cubs, in northeastern Pennsylvania during winter 1984. Four other captive adult females were bled before, during, and after they were subjected to unseasonably warm temperatures during February. Levels of serum urea nitrogen (SUN) and creatinine were lower (P less than 0.05), and iron was higher (P less than 0.05) in male cubs compared to female cubs; serum chemistries were similar (P greater than or equal to 0.05) between sexes for yearlings. Total protein, albumin and creatinine levels increased with age of bears, whereas chloride, alkaline phosphatase, potassium, inorganic phosphorus and SUN/creatinine were higher (P less than 0.05) in cubs than in yearlings and adults. The relatively high serum calcium in cubs was probably related to rapid bone development and dietary intake of calcium during winter dormancy in cubs. Low serum calcium in adults was attributed to lactation and a lack of dietary intake. Urea/creatinine ratios averaged 5.5 and 4.6 for yearling females and males, respectively, 6.3 for adult females, and 29.0 and 22.8 for female and male cubs, respectively. Levels of serum chemistries of black bears apparently are relatively stable during winter denning, when bears are without food or water and do not urinate or defecate for several months. This stability indicates that black bears are resistant to the extremes in extrinsic environmental conditions. Abnormal blood chemistry values may indicate metabolic stresses that are not being controlled by bears.(ABSTRACT TRUNCATED AT 250 WORDS)
Osseous Hodgkin Lymphoma (2010)

Post, Ginell R. MD, PhD*; Escoto, Heather MD†; Kalpatthi, Ramasubramanian MD†; Lazarchick, John MD‡ Author Information
Alien alleles revisited (2005)

A group of 70 professional divers and 47 healthy control subjects who had never dived were examined with magnetic resonance (MR) imaging to determine the prevalence of focal white matter changes in the brain. Spots of high signal intensity in white matter on proton density- and/or T2-weighted spin-echo images were detected in 42% of the control subjects and in 34% of the divers. In the control subjects, the prevalence of more than three changes was related to smoking, use of alcohol, head trauma, age of more than 35 years, and a combination of several cerebrovascular risk factors. This relationship was not present in the divers. The prevalence of changes in divers was inversely related to diving depth, amount of diving, participation in "unsafe diving," and decompression sickness. The reasons for these results could not be ascertained. The results are compared with those of MR imaging studies of white matter changes recently presented by other research groups.
C-C Chemokines in Allergen-Induced Late-Phase Cutaneous Responses in Atopic Subjects: Association of Eotaxin with Early 6-Hour Eosinophils, and of Eotaxin-2 and Monocyte Chemoattractant Protein-4 with the Later 24-Hour Tissue Eosinophilia, and Relationship to Basophils and Other C-C Chemokines (Monocyte Chemoattractant Protein-3 and RANTES) (1999)

The relationship of expression of the C-C chemokines eotaxin, eotaxin 2, RANTES, monocyte chemoattractant protein-3 (MCP-3), and MCP-4 to the kinetics of infiltrating eosinophils, basophils, and other inflammatory cells was examined in allergen-induced, late-phase allergic reactions in the skin of human atopic subjects. EG2+ eosinophils peaked at 6 h and correlated significantly with eotaxin mRNA and protein, whereas declining eosinophils at 24 h correlated significantly with eotaxin-2 and MCP-4 mRNA. In contrast, no significant correlations were observed between BB1+ basophil infiltrates, which peaked at 24 h, and expression of eotaxin, eotaxin-2, RANTES, MCP-3, and MCP-4 or elastase+ neutrophils (6-h peak), CD3+ and CD4+ T cells (24 h), and CD68+ macrophages (72 h). Furthermore, 83% of eosinophils, 40% of basophils, and 1% of CD3+ cells expressed the eotaxin receptor CCR3, while eotaxin protein was expressed by 43% of macrophages, 81% of endothelial cells, and 6% of T cells (6%). These data suggest that 1) eotaxin has a role in the early 6-h recruitment of eosinophils, while eotaxin-2 and MCP-4 appear to be involved in later 24-h infiltration of these CCR3+ cells; 2) different mechanisms may guide the early vs late eosinophilia; and 3) other chemokines and receptors may be involved in basophil accumulation of allergic tissue reactions in human skin.
Transcription from the stromelysin promoter is induced by interleukin-1 and repressed by dexamethasone. (1987)

The stromelysin gene encodes a potent tissue-degrading proteinase whose activity is important in tissue-remoldeling processes such as wound healing, the inflammatory reaction, rheumatoid arthritis, tumor invasion, and possibly embryonic development. In light of the ability of interleukin-1 to amplify, and ability of glucocorticoids to attenuate the inflammatory response, we tested interleukin-1 and dexamethasone for regulatory effects on stromelysin gene expression. We report that interleukin-1 induces the stromelysin gene, and dexamethasone diminishes the level of induction by interleukin-1, epidermal growth factor, phorbol ester, and cAMP elevation (elicited by cholera toxin). Similar responses are conferred upon a chloramphenicol acetyltransferase coding sequence by a 700-base pair stromelysin 5'-flanking fragment, implying transcription regulation by sequence elements in this region.
A 35-60 GHz single-pole double-throw(SPDT) switching circuit using direct contact MEMS switches and double resonance technique (2004)

In this paper, a single-pole double-throw(SPDT) switching circuit was demonstrated using direct contact MEMS switches and double resonance technique for Q-band and V-band applications. The size of the fabricated SPDT switching circuit is about 1 mm/spl times/2 mm. The direct contact MEMS switches are formed on the CPW transmission lines and actuated with electrostatic force. The fabricated single-pole single-throw(SPST) MEMS switch shows the insertion loss of 0.34 dB and the isolation of 15.5 dB at 50 GHz, respectively. The responses of the fabricated SPDT switching circuit were measured with the frequencies from 0 to 100 GHz. The insertion loss is below 1 dB and isolation is better than 19 dB from 35 GHz to 60 GHz. At the center frequency of 47 GHz, the insertion loss is measured 0.45 dB and isolation is 22 dB. The actuation voltage of the switch is 35V.
Strong, Transparent, Multifunctional, Carbon Nanotube Sheets (2005)

Individual carbon nanotubes are like minute bits of string, and many trillions of these invisible strings must be assembled to make useful macroscopic articles. We demonstrated such assembly at rates above 7 meters per minute by cooperatively rotating carbon nanotubes in vertically oriented nanotube arrays (forests) and made 5-centimeter-wide, meter-long transparent sheets. These self-supporting nanotube sheets are initially formed as a highly anisotropic electronically conducting aerogel that can be densified into strong sheets that are as thin as 50 nanometers. The measured gravimetric strength of orthogonally oriented sheet arrays exceeds that of sheets of high-strength steel. These nanotube sheets have been used in laboratory demonstrations for the microwave bonding of plastics and for making transparent, highly elastomeric electrodes; planar sources of polarized broad-band radiation; conducting appliqués; and flexible organic light-emitting diodes.
Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features (2004)

The underlying causes of learning disability and dysmorphic features in many patients remain unidentified despite extensive investigation. Routine karyotype analysis is not sensitive enough to detect subtle chromosome rearrangements (less than 5 Mb). The presence of subtle DNA copy number changes was investigated by array-CGH in 50 patients with learning disability and dysmorphism, employing a DNA microarray constructed from large insert clones spaced at approximately 1 Mb intervals across the genome. Twelve copy number abnormalities were identified in 12 patients (24% of the total): seven deletions (six apparently de novo and one inherited from a phenotypically normal parent) and five duplications (one de novo and four inherited from phenotypically normal parents). Altered segments ranged in size from those involving a single clone to regions as large as 14 Mb. No recurrent deletion or duplication was identified within this cohort of patients. On the basis of these results, we anticipate that array-CGH will become a routine method of genome-wide screening for imbalanced rearrangements in children with learning disability.