gebhart/patrepeval huggingface dataset:
Pimavanserin, a 5-HT2A inverse agonist, reverses psychosis-like behaviors in a rodent model of Parkinson's disease (2011)

Parkinson's disease psychosis (PDP) is a condition for which a safe, tolerated, and effective therapy is lacking. Treatment with typical or atypical antipsychotics may be contraindicated in patients with PDP because of the potential for aggravating motor symptoms. This study used a novel animal model with features of both Parkinson's disease (PD) and psychosis to examine a potential mechanism for reversing PDP. Animals with bilateral 6-hydroxydopamine lesions of the substantia nigra displayed motoric impairments characteristic of humans with PD. In addition, they displayed augmented head twitches, augmented amphetamine-induced locomotor activity, and disrupted prepulse inhibition compared with sham controls, behavioral indices frequently used to assess antipsychotic activity in animal models. Pimavanserin, a selective 5-HT2A antagonist/inverse agonist, reversed the psychotic-like behavioral deficits, suggesting that nigrostriatal (6-hydroxydopamine) lesions induced alterations in 5-HT2A-mediated signaling. The selective 5-HT2A inverse agonist M100907, but not the selective 5-HT2C inverse agonist SB 252084 paralleled the effects of pimavanserin. Of note, the reversal of psychotic-like behaviors produced by 5-HT2A inverse agonists occurred without disrupting motor behaviors in lesioned subjects, suggesting that 5HT2A antagonism/inverse agonism may be beneficial in the treatment of PDP.
An Antisense Oligonucleotide to the Notch Ligand Jagged Enhances Fibroblast Growth Factor-induced Angiogenesis in Vitro (1996)

Angiogenesis, or the formation of new blood vessels, plays a central role in a number of physiologic and pathologic conditions, including wound healing, diabetic retinopathy, and solid tumor growth, and endothelial cells can be induced to mimic this process in vitro. Using a modification of the differential display method (Zimrin, A. B., Villeponteau, B., and Maciag, T. (1995) Biochem. Biophys. Res. Commun. 213, 630-638), we isolated the human homolog of the Jagged ligand for the Notch receptor from human endothelial cells exposed to fibrin and demonstrate that the Jagged transcript, but not the Notch 1 or Notch 2 transcripts, are up-regulated by fibrin. Interestingly, the addition of an antisense Jagged oligomer to bovine microvascular endothelial cells grown on a collagen gel resulted in a marked increase in invasion and tube formation in the underlying gel in response to fibroblast growth factor. In contrast, no effect was observed on vascular endothelial growth factor-induced angiogenesis under identical conditions. These data suggest that Jagged-Notch signaling is able to regulate fibroblast growth factor-induced endothelial cell migration in vitro, an early event during angiogenesis in vivo.
Adhesion of human basophils, eosinophils, and neutrophils to interleukin 1-activated human vascular endothelial cells: contributions of endothelial cell adhesion molecules. (1991)

Cytokines such as interleukin 1 (IL-1) promote adhesiveness in human umbilical vein endothelial cells for leukocytes including basophils, eosinophils, and neutrophils, and induce expression of adherence molecules including ICAM-1 (intercellular adhesion molecule-1), ELAM-1 (endothelial-leukocyte adhesion molecule-1), and VCAM-1 (vascular cell adhesion molecule-1). In the present study, blocking monoclonal antibodies (mAb) recognizing ICAM-1, ELAM-1, and VCAM-1 have been used to compare their roles in IL-1-induced adhesion of human basophils, eosinophils, and neutrophils. IL-1 treatment of endothelial cell monolayers for 4 hours induced a four- to eight-fold increase in adhesion for each cell type. Treatment of endothelial cells with either anti-ICAM-1 or anti-ELAM-1 mAb inhibited IL-1-induced adherence of each cell type. In contrast, treatment with anti-VCAM-1 mAb inhibited basophil and eosinophil (but not neutrophil) adhesion, and was especially effective in blocking eosinophil adhesion. The effects of these mAb were at least additive. Indirect immunofluorescence and flow cytometry demonstrated expression of VLA-4 alpha (very late activation antigen-4 alpha, a counter-receptor for VCAM-1) on eosinophils and basophils but not on neutrophils. These data document distinct roles for ICAM-1, ELAM-1, and VCAM-1 during basophil, eosinophil, and neutrophil adhesion in vitro, and suggest a novel mechanism for the recruitment of eosinophils and basophils to sites of inflammation in vivo.
CD4+CXCR4highCD69+ T Cells Accumulate in Lung Adenocarcinoma (2006)

The chemokine receptor CXCR4 is involved in the growth and metastasis of tumor cells. However, the expression of its ligand, the chemokine CXCL12, in tumors and its role in regulating the accumulation of immune cells within the tumors is not clear. Using ELISA and immunohistochemistry we found that CXCL12 is expressed in the majority of nonsmall cell lung cancer tissue sections obtained from stage IA to IIB nonsmall cell lung cancer patients undergoing operation. Histopathologic examination of these sections indicated that high CXCL12 expression correlated with increased tumor inflammation. In addition, disease recurrence rates in a subgroup of adenocarcinoma patients showed a tendency to correlate with high CXCL12 expression in the tumor. Isolation of adenocarcinoma-infiltrating immune cells demonstrated an increase in the percentage of CD4+CD69+CXCR4+ T cells as compared with normal lung tissue. About 30% of these cells expressed the regulatory T cell markers CD25high and FoxP3. The percentage of CD8 T cells within the tumor did not change, however; the percentage of NK and NK T cells was significantly reduced. In correlation with CXCR4 expression, CD4 T cells showed increased migration in response to CXCL12 compared with CD8 T cells and NK cells. Overall, these observations suggest that CXCL12 expression may influence tumor progression by shaping the immune cell population infiltrating lung adenocarcinoma tumors.
Ion formation mechanisms in UV-MALDI (2006)

Matrix Assisted Laser Desorption/Ionization (MALDI) is a very widely used analytical method, but has been developed in a highly empirical manner. Deeper understanding of ionization mechanisms could help to design better methods and improve interpretation of mass spectra. This review summarizes current mechanistic thinking, with emphasis on the most common MALDI variant using ultraviolet laser excitation. A two-step framework is gaining acceptance as a useful model for many MALDI experiments. The steps are primary ionization during or shortly after the laser pulse, followed by secondary reactions in the expanding plume of desorbed material. Primary ionization in UV-MALDI remains somewhat controversial, the two main approaches are the cluster and pooling/photoionization models. Secondary events are less contentious, ion-molecule reaction thermodynamics and kinetics are often invoked, but details differ. To the extent that local thermal equilibrium is approached in the plume, the mass spectra may be straightforwardly interpreted in terms of charge transfer thermodynamics.
Genotype by Environment Interaction and Genetic Correlations Among Parities for Somatic Cell Count and Milk Yield (1990)

Lactation measures of somatic cell concentration and total SCC production were developed. Data were separated into three parity groups. Within parity, five data sets were created: four subsets by herd-year average SCC, and one with all records. Records on lactation SCC, total SCC production, and 305-d milk were analyzed by a sire model separately in each subset within parity. Variance components estimates were by REML. For SCC and total SCC production, heritability estimates averaged .12 and were lowest in the highest level of herd-year average SCC. Estimates of genetic correlation between SCC and total SCC production were over .95; between SCC and 305-d milk were around .25 in first and -.15 in later parities; between total SCC and 305-d milk were around .50 in first and .15 in later parities. Product-moment correlations between sire effects in different levels of herd-year average SCC were obtained. Ratios of product-moment correlations to their expected value were above .80 for all traits in all parities. High ratios indicated little genotype by environment interaction. A sire by herd interaction was fitted in the model and accounted for less than 2% of total phenotypic variance for SCC and total SCC production, and 4% for 305-d milk. Estimates of genetic correlation of first with later parities were .71 to .86 for all traits. Between second and third parity genetic correlation estimates were around unity for all traits. Records from all parities should be used for sire evaluation.
Pseudomonas aeruginosa outer-membrane protein F epitopes are highly immunogenic in mice when expressed on a plant virus (1999)

A synthetic peptide (peptide 10) representing a surface-exposed, linear B cell epitope from outer-membrane (OM) protein F of Pseudomonas aeruginosa was shown previously to afford protection in mice from P. aeruginosa infection. This peptide was expressed in tandem with the protein F peptide 18 on each of the two coat proteins of cowpea mosaic virus (CPMV). The chimaeric virus particles (CVPs) expressing the peptides on the S (small) coat protein (CPMV-PAE4) and L (large) coat protein (CPMV-PAE5) were used to immunize mice. Following subcutaneous immunization in Freund's and QuilA adjuvants, CPMV-PAE4 induced antibodies predominantly against peptide 18, whereas CPMV-PAE5 produced antibodies exclusively against peptide 10, indicating that the site of peptide expression on CPMV influences its immune recognition. The anti-peptide antibodies elicited by CPMV-PAE5 were predominantly of the IgG2a isotype, indicating a highly polarized TH1-type response. The peptide-specific IgG2a strongly recognized the whole F protein, but more importantly, recognized protein F in all seven Fisher-Devlin immunotypes of P. aeruginosa. Furthermore, the peptide-specific IgG2a in CVP/QS-21 adjuvant-immunized mice was shown to bind complement and to augment phagocytosis of P. aeruginosa by human neutrophils in vitro. The ability of CPMV-PAE5 to induce P. aeruginosa-specific opsonic IgG2a gives it potential for further development as a protective vaccine against P. aeruginosa.
Thrombotic Tendencies and Correlation With Clinical Status in Patients Infected With HIV (1995)

Previous publications have described thrombotic events with unclear causes in individuals infected with the human immunodeficiency virus (HIV). We stratified the cases of 52 individuals infected with HIV by degree of immunosuppression and the presence of complicating illnesses. Plasma from these individuals was screened for abnormalities that might predispose to thromboses. We found statistically significant differences between patients with CD4 counts < 200/mm3 and those whose CD4 counts were > 400/mm3 in the following: d-dimers, functional protein C, antigenic protein C, total protein S antigen, free protein S antigen, C4b-binding protein (C4b-BP), and von Willebrand antigen (vWD). Free protein S correlated inversely with C4b-BP; vWD directly with total protein S; and protein C inversely with d-dimers. D-dimers were significantly elevated only in immunosuppressed patients with complicating neoplastic/inflammatory disease. We propose that low-grade disseminated intravascular coagulopathy in severely immunosuppressed individuals with HIV and infectious, inflammatory, or neoplastic complications is responsible for depressed protein C, which, together with elevations in total protein S and vWD (markers of endothelial injury), indicates a thrombotic predisposition.
Clinical Application of Microwave Coagulation Therapy for Hepatocellular Carcinoma (2010)

Objective: To explore the clinical effect of treating hepatocellular carcinoma (HCC) with microwave coagulation therapy (MCT) and analyze the relevant complications. Methods: A total of 154 patients with 279 nodules (average, 1.5 nodules) of HCC underwent MCT (188 procedures). The average maximum diameter of the nodule was 2.6±1.5 (0.8-5.0) cm. Thirty-one of the patients were recurrent HCC after hepatectomy. All patients were treated with MCT by using a percutaneous or open intraoperative approach. Follow-up examinations were performed with US, contrast enhanced US, contrast enhanced CT and tumor mark after MCT. Results: The contrast enhanced CT was performed 1 month after MCT. The complete ablation rate was 95.3% for 279 HCC nodules. These patients were followed up for 3-39 months. The local tumor recurrence rate was 9.4%. The first, second, and third year survival rates were 89.3%, 75.5% and 55.7%, respectively. The first, second, and third year survival rates in patients of recurrent HCC were 79.4%, 60.8% and 47.3%, respectively. The serious complication rate in patients with MCT was 2.1% (4/188). No one died from the relevant complications of MCT in this study. Conclusion: The method of treating HCC with MCT is safe and effective, having an important clinical significance.
Optical characterization of pseudomorphic InxGa1−xAs–GaAs single-quantum-well heterostructures (1986)

Strain and quantum-size effects in pseudomorphic InxGa1−xAs–GaAs single-quantum-well heterostructures (SQWHs) are examined using low-temperature photoluminescence techniques. Strain effects in InxGa1−xAs epitaxial layers are first described, then photoluminescence data for a series of MBE-grown pseudomorphic SQWHs are presented and discussed. Each SQWH consists of an unintentionally doped, highly strained (ε∼2%) In0.28Ga0.72As quantum well sandwiched between GaAs confining layers. The structures were grown consecutively under identical conditions, with quantum-well thicknesses ranging from 17 to 430 Å. The thinner quantum-well structures exhibit luminescence characteristics indicative of high-quality material (photoluminescence half width ∼6 meV for Lz ∼17 Å), whereas significant broadening and eventual quenching of the photoluminescence peak is observed as alloy layer thicknesses approach and exceed the critical value. Quantum-well luminescence from the thinner (Lz ≤38 Å) SQWHs is dominated by a single, sharp feature which we attribute to n=1 electron-to-heavy hole confined-carrier transitions. An additional shallow (∼20 meV) feature, perhaps impurity related, is present in the photoluminescence spectra of some of the thicker quantum wells, and peak emission intensities are examined as a function of excitation intensity for the various transitions. Finally, the observed dependence of the transition energies upon quantum-well thickness is compared to predictions from an effective-mass SQWH model which incorporates strain effects. Reasonable agreement is obtained for SQWHs with Lz ≤100 Å, the expected critical layer thickness for these samples. This work represents the first optical study of pseudomorphic single wells, and our results should be useful in the design of strained-layer quantum-well lasers.
Robust Incremental Polygon Triangulation for Fast Surface Rendering (2000)

This paper presents a simple, robust and practical, yet fast algorithm for triangulation of trimmed Bzier surfaces. Points on the surface are input to our algorithm by a sampling scheme. A set of polygons (more generically, a planar straight-line graph, or PSLG) is formed from these samples, which are then triangulated. We also show how to update the triangulation when the samples, and hence the polygons, are updated. The output of the algorithm is a set of triangle strips. The algorithm avoids long and thin triangles. In addition, it also detects if the sampling of the trimming curve forms any non-simple polygons and corrects the triangulation by adding more samples. We report an implementation of the algorithm and its performance on extensive simulation.
Role of tumor–host interactions in interstitial diffusion of macromolecules: Cranial vs. subcutaneous tumors (2001)

The large size of many novel therapeutics impairs their transport through the tumor extracellular matrix and thus limits their therapeutic effectiveness. We propose that extracellular matrix composition, structure, and distribution determine the transport properties in tumors. Furthermore, because the characteristics of the extracellular matrix largely depend on the tumor-host interactions, we postulate that diffusion of macromolecules will vary with tumor type as well as anatomical location. Diffusion coefficients of macromolecules and liposomes in tumors growing in cranial windows (CWs) and dorsal chambers (DCs) were measured by fluorescence recovery after photobleaching. For the same tumor types, diffusion of large molecules was significantly faster in CW than in DC tumors. The greater diffusional hindrance in DC tumors was correlated with higher levels of collagen type I and its organization into fibrils. For molecules with diameters comparable to the interfibrillar space the diffusion was 5- to 10-fold slower in DC than in CW tumors. The slower diffusion in DC tumors was associated with a higher density of host stromal cells that synthesize and organize collagen type I. Our results point to the necessity of developing site-specific drug carriers to improve the delivery of molecular medicine to solid tumors.
The expression of the Athb-8 homeobox gene is restricted to provascular cells in Arabidopsis thaliana (1995)

We have characterized an Arabidopsis homeobox gene coding for a putative DNA binding protein that represents an early marker for vascular development. The full-length cDNA encodes a protein of 833 amino acids that we have designated Athb-8; it contains the conserved DNA binding domain that characterizes the HD-Zip family of transcription factors. RNA analysis showed that the Athb-8 gene is expressed during the vegetative and the reproductive phases of plant growth. A higher steady-state level of the Athb-8 mRNA was found in flowering stem and root. In situ mRNA analysis of Arabidopsis plants demonstrated that Athb-8 expression is restricted to the procambial cells of embryo and developing organs. Moreover, Athb-8-GUS expression was found in single parenchyma cells which are differentiating into tracheary elements in wounded tobacco transgenic plants. Finally, we showed that the auxin, indole-3-acetic acid, which is involved in vascular development and differentiation, modulates the expression of the gene. Taken together, these results suggest that Athb-8 might be a regulator of vascular development in Arabidopsis thaliana.
Band-to-Band Hot Hole Erase Mechanism of p-Channel Junctionless Silicon Nanowire Nonvolatile Memory (2015)

In this paper, p-channel junctionless (JL) silicon-oxide-nitride-oxide-silicon (SONOS)-type nonvolatile memory (NVM) devices with gate-all-around (GAA) nanowire (NW) structure by using silicon-nanocrystal for the charge-trapping layer are presented. The devices exhibited good erase efficiency and excellent retention behavior and can be used in system-on-panel and 3-D-stacked flash memory applications. In addition, a band-to-band hot hole (BBHH) method for erasing is proposed and compared with the Fowler-Nordheim (FN) tunneling method. Because FN erasing requires a high gate voltage, BBHH erasing, which requires a low voltage, can increase the service life of the memory. Channel hot electron and band-to-band hot electron were used for programming and yielded low programming efficiency for the p-channel JL GAA NW NVM devices because of a lack of electron carriers. The program/erase efficiency is related to the channel type in JL NVM devices.
Impaired B Cell Development and Proliferation in Absence of Phosphoinositide 3-Kinase p85α (1999)

Phosphoinositide 3-kinase (PI3K) activation has been implicated in many cellular responses, including fibroblast growth, transformation, survival, and chemotaxis. Although PI3K is activated by several agents that stimulate T and B cells, the role of PI3K in lymphocyte function is not clear. The mouse gene encoding the PI3K adapter subunit p85alpha and its splice variants p55alpha and p50alpha was disrupted. Most p85alpha-p55alpha-p50alpha-/- mice die within days after birth. Lymphocyte development and function was studied with the use of the RAG2-deficient blastocyst complementation system. Chimeric mice had reduced numbers of peripheral mature B cells and decreased serum immunoglobulin. The B cells that developed had diminished proliferative responses to antibody to immunoglobulin M, antibody to CD40, and lipopolysaccharide stimulation and decreased survival after incubation with interleukin-4. In contrast, T cell development and proliferation was normal. This phenotype is similar to defects observed in mice lacking the tyrosine kinase Btk.
[The estimation of LHRH receptors in the tissue of human leiomyoma, myometrium and endometrium]. (1994)

Uterine leiomyoma is the most common female benign pelvic tumor, affecting 20-25% of women during their reproductive years. There is strong clinical evidence that these tumors are estrogen-dependent for their growth, as also supported by their clear regression after the menopause. Although large clinical trials have not yet been reported, according to the estrogen dependency of uterine fibroids, LHRH agonists have been shown to be effective in the treatment of these conditions because they produce a condition of temporary hypoestrogenism secondary to the specific hypogonadotrophinism. This study was designed to evaluate if specific binding sites for LHRH are present in human uterine leiomyomata, myometrium and endometrial tissue. These tissues were taken from the fresh operative specimens of 14 patients who had undergone total hysterectomy for uterine leiomyomata. The results of this study demonstrate the presence of a LHRH specific binding site in uterine leiomyomata in 26% of cases; this specific binding site is also present both in myometrium and in endometrial tissue in 71% of cases. Moreover our study shows, for the first time, the high specificity of binding between LHRH agonist (goserelin) and natural LHRH receptor. In accordance with our results, a direct effect of LHRH agonists on fibroid tissue can be stressed.
Capacitive RF discharges modelled by particle-in-cell Monte Carlo simulation. II. Comparisons with laboratory measurements of electron energy distribution functions (1993)

For pt.I see ibid., vol.2, no.4, p.261-72 (1993). Bi-Maxwellian electron energy distribution functions (EEDFS) have been measured experimentally in argon RF discharges at 13.56 MHz by Godyak et al. (Plasma Sources Sci. Technol. 1 36 (1992)). The observed EEDFS at low pressures had very-low-energy and high-energy components. We show particle-in-cell Monte-Carlo (PIC-MCC) simulations, which produce the same EEDFS. Excellent agreement is obtained between the effective low and high electron temperatures in simulations and those measured in the laboratory. Our simulations, with the same physical parameters as in the laboratory, obtain the same transition point in the electron heating mode, from stochastically dominated heating at low pressures to ohmically dominated heating at high pressures.