gebhart/patrepeval huggingface dataset:
Comparison of two surface preparations used in the homoepitaxial growth of silicon films by plasma enhanced chemical vapor deposition (2003)

The effect of surface preparation on the growth of epitaxial Si films by plasma enhanced chemical vapor deposition was investigated. The surface preparations considered were an ex situ ozone scrub and an in situ Ar/H2-plasma clean. Both methods were found to be effective at removing carbon contamination from the substrate surface which is critical for epitaxial growth. The thin-film quality was determined by Rutherford backscatter spectrometry, high-resolution x-ray diffraction, and transmission electron microscopy. To gain insight into mechanisms controlling the in situ cleaning process, hydrogen was replaced by deuterium in the plasma clean prior to film growth. The film/substrate interface was then analyzed by secondary ion mass spectrometry. Surprisingly, the plasma clean had little influence on the interfacial hydrogen concentration established by the previous hydrofluoric acid dip. It was found that hydrogen remains bound to C and O contaminants at the interface caused by the initial growth surface, and that neither an ex situ process containing an ozone scrub nor an in situ process containing a hydrogen-plasma clean could completely remove them.
Oxidative stress as a pathogenic factor in inflammatory bowel disease — radicals or ridiculous? (2002)

Virtually all inflammatory mediators investigated to date seem to be dysregulated in the inflamed intestinal mucosa of patients with inflammatory bowel disease. However, which of these are actually involved in the initiation and perpetuation of intestinal tissue damage is still not fully understood. Amongst these mediators are the reactive oxygen metabolites, produced in large amounts by the massively infiltrating leucocytes. These reactive oxygen metabolites are believed to constitute a major tissue-destructive force and may contribute significantly to the pathogenesis of inflammatory bowel disease. This paper provides a concise overview of reactive oxygen metabolite biochemistry, the types of cell and tissue damage potentially inflicted by them, and the endogenous antioxidants which should prevent these harmful effects. An up-to-date summary of the available human experimental data suggests that reactive oxygen metabolite-mediated injury is important in both the primary and downstream secondary pathophysiological mechanisms underlying intestinal inflammation. Nonetheless, how the individual components of the mucosal antioxidant enzymatic cascade respond to inflammatory conditions is a neglected area of research. This particular aspect of intestinal mucosal oxidative stress therefore merits further study, in order to provide a sound, scientific basis for the design of antioxidant-directed treatment strategies for inflammatory bowel disease patients.
Type IV collagen and laminin‐related antigens in human serum in alcoholic liver disease (1985)

The two major constituents of basement membranes are type IV collagen and laminin. Specific radioimmunoassays are described here for two structural domains of these proteins (7-S collagen and the fragment P1, respectively) that allow the related antigens to be quantified in human serum. The serum 7-S collagen antigen was uniform in size, whereas the laminin P1 antigenicity was heterogeneous. These proteins were measured in sera from sixty-three alcoholics, divided on the basis of liver histology into four groups: normal light microscopy, fatty liver, alcoholic cirrhosis with hepatitis and inactive cirrhosis. The group with cirrhosis and hepatitis had clearly elevated values in both assays, differing significantly from the others. A few pathological results were also seen in the other groups. The increases noted in 7-S collagen concentration were larger than those in laminin P1. During follow-up of a patient with cirrhosis and hepatitis the 7-S collagen level in particular seemed to reflect the course of the disease. The elevated basement membrane protein concentrations in serum may be associated with the formation of real basement membranes in the perisinusoidal space, a process known as capillarization of the sinusoids which is found during the development of liver cirrhosis.
A tapered hollow metallic microneedle array using backside exposure of SU-8 (2004)

This paper presents a novel fabrication process for a tapered hollow metallic microneedle array using backside exposure of SU-8, and analytic solutions of critical buckling of a tapered hollow microneedle. An SU-8 mesa was formed on a Pyrex glass substrate and another SU-8 layer, which was spun on top of the SU-8 mesa, was exposed through the backside of the glass substrate. An array of SU-8 tapered pillar structures, with angles in the range of 3.1°–5°, was formed on top of the SU-8 mesa. Conformal electrodeposition of metal was carried out followed by a mechanical polishing using a planarizing polymeric layer. All organic layers were then removed to create a metallic hollow microneedle array with a fluidic reservoir on the backside. Both 200 µm and 400 µm tall, 10 by 10 arrays of metallic microneedles with inner diameters of the tip in the range of 33.6–101 µm and wall thickness of 10–20 µm were fabricated. Analytic solutions of the critical buckling of arbitrary-angled truncated cone-shaped columns are also presented. It was found that a single 400 µm tall hollow cylindrical microneedle made of electroplated nickel with a wall thickness of 20 µm, a tapered angle of 3.08° and a tip inner diameter of 33.6 µm has a critical buckling force of 1.8 N. This analytic solution can be used for square or rectangular cross-sectioned column structures with proper modifications.
Recent advances in understanding of preeclampsia. (2005)

Despite intensive research, preeclampsia still accounts for significant morbidity and mortality for the mother and the neonate, especially in developing countries. Recent studies have suggested that excess secretion of a naturally occurring anti-angiogenic molecule of placental origin referred to as soluble fms-like tyrosine kinase-1 (sFlt-1, also referred to as sVEGFR-1) may contribute to the pathogenesis of preeclampsia. sFlt-1 acts by antagonizing two pro-angiogenic molecules - vascular endothelial growth factor (VEGF) and placental growth factor (PlGF). Abnormalities in the angiogenic balance have been proposed as having a major role in the molecular cascade leading to proteinuria, hypertension, and endothelial dysfunction. Further evidence supports the hypothesis that angiogenic balance is crucial to differentiation and invasion of cytotrophoblasts. The abnormal placentation and the accompanying hypoxia may, in turn, result in more sFlt-1 production, thus leading to a vicious cycle of sFlt-1 production, eventually causing preeclampsia. These recent discoveries may facilitate the development of novel strategies for the diagnosis and therapy of preeclampsia.
DNA probes on beads arrayed in a capillary, 'Bead-array', exhibited high hybridization performance (2002)

A DNA analysis platform called 'Bead-array' is presented and its features when used in hybridization detection are shown. In 'Bead-array', beads of 100- micro m diameter are lined in a determined order in a capillary. Each bead is conjugated with DNA probes, and can be identified by its order in the capillary. This probe array is easily produced by just arraying beads conjugated with probes into the capillary in a fixed order. The hybridization is also easily completed by introducing samples (1-300 micro l) into the capillary with reciprocal flow. For hybridization detection, as little as 1 amol of fluorescent-labeled oligo DNA was detected. The hybridization reaction was completed in 1 min irrespective of the amount of target DNA. When the number of target molecules was smaller than that of probe molecules on the bead, 10 fmol, almost all targets were captured on the bead. 'Bead-array' enables reliable and reproducible measurement of the target quantity. This rapid and sensitive platform seems very promising for various genetic testing tasks.
Active immunotherapy with allogeneic tumor cell vaccines: present status. (1998)

This review will concentrate on allogeneic vaccines for melanoma The important principles of melanoma vaccine effectiveness are discussed in detail, followed by a review of the progress of several clinical trials investigating allogeneic vaccines. No therapeutic cancer vaccine has yet been approved for general use by the US Food and Drug Administration. However, much progress has been made in the field of vaccine immunotherapy, especially for the treatment of melanoma. Active immunotherapy with tumor vaccines is progressing rapidly as an emerging option for cancer therapy.
Variability in Heparin Sensitivity of APTT Reagents (1986)

Activated partial thromboplastin time (APTT) is the most widely used coagulation test for monitoring heparin therapy. This study quantitates the differences in heparin sensitivity of seven commercially available APTT reagents, using plasma samples obtained from 20 subjects. The reagents studied were Actin, Actin FS, Automated APTT, Cephotest, Coagachek KAPTT, Platelin plus activator, and Activated Thrombofax. The relationship between plasma heparin and APTT was established for all reagents in each subject. For each reagent studied there was a marked intersubject variability in heparin sensitivity. There was also a marked difference in heparin sensitivity among the different reagents. The average plasma heparin activities required to double baseline APTT values ranged from 0.19 +/- 0.04 (mean +/- SD) unit/mL for the most sensitive reagents (Platelin and Actin FS) to 0.43 +/- 0.12 unit/mL for the least sensitive reagent (Actin). It is concluded that reagent variability may significantly contribute to overdosage and under dosage of heparin in the individual patient. These results stress that a standard APTT reagent be developed.
Industrial-Scale Production of Inactivated Poliovirus Vaccine Prepared by Culture of Vero Cells on Microcarrier (1984)

In 1980, the authors reported preliminary results of large-scale production of inactivated poliovirus vaccine in which virus was produced in Vero cell culture on a microcarrier. For this first stage of development, 150-liter tanks were used. The virus is now produced in 1,000-liter tanks. The main point concerning the quality of Vero cells, namely the absence of tumorigenicity, has been demonstrated, qualifying them for use in the Institut M erieux cell bank. The purity of the cell line has also been determined by checking for the absence of bacteria, fungi, mycoplasmas, and viruses. The search for oncornavirus and for reverse transcriptase activity was carried out, and the results were negative but are not described in this paper. The quality of the purification process was checked by a search for residual cellular DNA in concentrated, purified, and inactivated vaccine. With use of a molecular hybridization procedure, a specific probe was prepared to detect approximately 50 pg of DNA per filter. The preliminary results show that the purification procedure fulfills the World Health Organization's requirements. T1 oligonucleotide mapping has also shown the identity of poliovirus RNA extracted from virus grown on Vero cells and that from primary monkey kidney cells. These data have led to the awarding of a license by the French government to the Institut M erieux for production of this new, reassessed, inactivated poliovirus vaccine.
Response: antiapoptotic function of Toso (Faim3) in death receptor signaling (2012)

We appreciate the interest in our work. In their comment Honjo et al argue that Toso per se would not have antiapoptotic activity on CD95-induced apoptosis,[1][1] as, in contrast to our findings,[2][2] inhibitory activity would only be observed upon on CD95-ligation by the IgM mAb CH11. Our
Impairment of Cardiac Function and Bioenergetics in Adult Transgenic Mice Overexpressing the Bovine Growth Hormone Gene* (2000)

Cardiovascular abnormalities represent the major cause of death in patients with acromegaly. We evaluated cardiac structure, function, and energy status in adult transgenic mice overexpressing bovine GH (bGH) gene. Female transgenic mice expressing bGH gene (n = 11) 8 months old and aged matched controls (n = 11) were used. They were studied with two-dimensional guided M-mode and Doppler echocardiography. The animals (n = 6) for each group were examined with 31P magnetic resonance spectroscopy to determine the cardiac energy status. Transgenic mice had a significantly higher body weight (BW), 53.2+/-2.4 vs. 34.6+/-3.7 g (P < 0.0001) and hypertrophy of left ventricle (LV) compared with normal controls: LV mass/BW 5.6+/-1.6 vs. 2.7+/-0.2 mg/g, P < 0.01. Several indexes of systolic function were depressed in transgenic animals compared with controls mice such as shortening fraction 25+/-3.0% vs. 39.9+/-3.1%; ejection fraction, 57+/-9 vs. 77+/-5; mean velocity of circumferential shortening, 4.5+/-0.8 vs. 7.0+/-1.1 circ/sec, p < 0.01. Creatine phosphate-to-ATP ratio was significantly lower in bGH overexpressing mice (1.3+/-0.08 vs. 2.1+/-0.23 in controls, P < 0.05). Ultrastructural examination of the hearts from transgenic mice revealed substantial changes of mitochondria. This study provides new insight into possible mechanisms behind the deteriorating effects of long exposure to high level of GH on heart function.
Role of neuroinflammation and latent transcription factors in pathogenesis of Parkinson’s disease (2016)

Parkinson's disease (PD) the second most common age-associated progressive neurodegenerative disorder is characterized by loss of dopaminergic neurons, cytoplasmic inclusions of aggregated proteins (Lewy bodies), and neuroinflammation. The inflammation of neurons causes release of various inflammatory mediators (IFNs, EGF, IL5, IL6, HGF, LIF and BMP2). The hallmarks of neuroinflammation are the presence of activated microglia and reactive astrocytes in the parenchyma of the CNS and increased production of cytokines, chemokines, prostaglandins, complement cascade proteins, and reactive oxygen and nitrogen species (ROS/RNS) which in some cases can result in disruption of the blood brain barrier and direct participation of the adaptive immune system. Latent transcription factors such as NF-κB, STAT 3, AP1, and SMAD 7, Toll like receptors and FAF 1 are constitutively upregulated in activated microglia. Toll-like receptors when activated promote NF-κB signaling thus promoting a vicious cycle of neuroinflammation. These transcription factors take dopaminergic neurons to apoptotic pathway via p53 and other death domain receptors. Neuroprotective signaling pathways such as mTOR, SOCS, and TGF-β down regulated during development of PD. YY1 signaling, which has protective effect against α-Synuclein toxicity, is significantly decreased in PD patients. In summary we can say that transcription factors promoting inflammation such as NF-κB, STAT 3, AP 1, and Toll-like receptors are constitutively upregulated in PD, while neuroprotective pathways such as mTOR, TGF-β, and YY1 are substantially downregulated in microglia of PD patients.
Lineage-restricted expression of homeobox-containing genes in human hematopoietic cell lines. (1989)

We investigated the role of homeobox-containing genes in human hematopoiesis because homeobox genes (i) control cell fate in the Drosophila embryo, (ii) are expressed in specific patterns in human embryos, and (iii) appear to function as transcription factors that control cell phenotype in other mammalian organs. Using four homeobox probes from the HOX2 locus and a previously undescribed homeobox cDNA (PL1), we screened mRNAs from 18 human leukemic cell lines representing erythroid, myeloid, and T- and B-cell lineages. Complex patterns of lineage-restricted expression are observed: some are restricted to a single lineage, while others are expressed in multiple lineages. No single homeobox gene is expressed in all types of hematopoietic cells, but each cell type exhibits homeobox gene expression. HOX2.2 and -2.3 homeobox-containing cDNAs were cloned from an erythroleukemia cell (HEL) cDNA library, while the homeobox cDNA PL1 was isolated from a monocytic cell (U-937) library. Differentiation of HEL and K-562 cells with various inducers results in modulation of specific homeobox transcripts. In addition, HOX2.2 is expressed in normal bone marrow cells. We have demonstrated (i) lineage-restricted expression of five homeobox genes in erythroid and monocytic cell lines; (ii) expression of additional homeobox genes in other cell lineages (HL-60 and lymphoid cells); (iii) expression of one homeobox gene in normal marrow cells; and (iv) modulation of expression during differentiation. These data suggest that these genes play a role in human hematopoietic development and lineage commitment.
Gene‐dosage dependent overexpression at the 13q amplicon identifies DIS3 as candidate oncogene in colorectal cancer progression (2014)

Colorectal cancer (CRC) development is in most cases marked by the accumulation of genomic alterations including gain of the entire q-arm of chromosome 13. This aberration occurs in 40%-60% of all CRC and is associated with progression from adenoma to carcinoma. To date, little is known about the effect of the 13q amplicon on the expression of the therein located genes and their functional relevance. We therefore aimed to identify candidate genes at the 13q amplicon that contribute to colorectal adenoma to carcinoma progression in a gene dosage-dependent manner. Integrative analysis of whole genome expression and DNA copy number signatures resulted in the identification of 36 genes on 13q of which significant overexpression in carcinomas compared with adenomas was linked to a copy number gain. Five genes showing high levels of overexpression in carcinomas versus adenomas were further tested by quantitative reverse transcription-PCR in two independent sample sets of colorectal tumors (n = 40 and n = 47). DIS3 and LRCH1 revealed significant overexpression in carcinomas compared with adenomas in a 13q gain dependent manner. Silencing of DIS3 affected important tumorigenic characteristics such as viability, migration, and invasion. In conclusion, significant overexpression of DIS3 and LRCH1 associated with adenoma to carcinoma progression is linked to the CRC specific gain of 13q. The functional relevance of this copy number aberration was corroborated for DIS3, thereby identifying this gene as novel candidate oncogene contributing to the 13q-driven adenoma to carcinoma progression.
Molecular and functional characterization of the Salmonella invasion gene invA: homology of InvA to members of a new protein family (1992)

One of the earliest steps in the pathogenic cycle of the facultative intracellular pathogen Salmonella spp. is the invasion of the cells of the intestinal epithelium. We have previously identified a genetic locus, inv, that allows Salmonella spp. to enter cultured epithelial cells. invA is a member of this locus, and it is the first gene of an operon consisting of at least two additional invasion genes. We have constructed strains carrying nonpolar mutations in invA and examined the individual contribution of this gene to the invasion phenotype of Salmonella typhimurium. Nonpolar S. typhimurium invA mutants were deficient in invasion of cultured epithelial cells although they were fully capable of attaching to the same cells. In addition, unlike wild-type S. typhimurium, invA mutants did not alter the normal architecture of the microvilli of polarized epithelial cells nor did they cause any alterations in the distribution of actin microfilaments of infected cells. The invasion phenotype of invA mutants was readily rescued by wild-type S. typhimurium when cultured epithelial cells were simultaneously infected with both strains. On the contrary, in a similar experiment, the adherent Escherichia coli strain RDEC-1 was not internalized into cultured cells when coinfected with wild-type S. typhimurium. The invA locus was found to be located at about 59 min on the Salmonella chromosome, 7% linked to mutS. The nucleotide sequence of invA showed an open reading frame capable of encoding a polypeptide of 686 amino acids with eight possible membrane-spanning regions and a predicted molecular weight of 75,974. A protein of this size was visualized when invA was expressed in a bacteriophage T7 RNA polymerase-based expression system. The predicted sequence of InvA was found to be homologous to Caulobacter crescentus FlbF, Yersinia LcrD, Shigella flexneri VirH, and E. coli FlhA proteins. These proteins may form part of a family of proteins with a common function, quite possibly the translocation of specific proteins across the bacterial cell membrane.
Optical gain in GaAs/GaAlAs graded-index separate-confinement single-quantum-well heterostructures (1989)

Optical model gain in both the TE and TM polarizations of graded-index separate-confinement single-quantum-well heterostructure lasers measured at various levels of injection current on samples with different quantum-well widths is discussed. Lasers with wide quantum wells (>or=120 AA) have emission and gain spectra which exhibit two peaks, caused by the n=1 and n=2 subband transitions. With ordinary cavity parameters, the saturation gain of the n=1 subband transitions is lower than the cavity loss of the laser, and the lasers always lase at the n=2 transitions. Reducing the quantum-well width increases the saturation gain of the n=1 transitions enough to allow lasing from them, even in cases of higher cavity loss. Further, for a fixed cavity loss, reduction of the quantum-well width decreases the threshold current density for n=1 lasing transitions, while that for n=2 lasing increases. The superlinear increase of the material gain with the decrease of the well width reduces the minimum cavity length for n=1 subband lasing. Narrower quantum wells with higher mirror reflectivity allow shorter cavity lengths while retaining n=1 lasing, resulting in low threshold current.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
c‐Src/Lyn kinases activate Helicobacter pylori CagA through tyrosine phosphorylation of the EPIYA motifs (2002)

The human pathogen Helicobacter pylori colonizes the mucous layer of the stomach. During parasitic infection, freely swimming bacteria adhere to the gastric epithelial cells and trigger intracellular signalling pathways. This process requires the translocation of the effector protein CagA into the host cell through a specialized type IV secretion system encoded in the cag pathogenicity island. Following transfer, CagA is phosphorylated on tyrosine residues by a host cell kinase. Here, we describe how the tyrosine phosphorylation of CagA is restricted to a previously identified repeated sequence called D1. This sequence is located in the C-terminal half of the protein and contains the five-amino-acid motif EPIYA, which is amplified by duplications in a large fraction of clinical isolates. Tyrosine phosphorylation of CagA is essential for the activation process that leads to dramatic changes in the morphology of cells growing in culture. In addition, we observed that two members of the src kinases family, c-Src and Lyn, account for most of the CagA-specific kinase activity in host cell lysates. Thus, CagA translocation followed by tyrosine phosphorylation at the EPIYA motifs promotes a growth factor-like response with intense cytoskeletal rearrangements, cell elongation effects and increased cellular motility.