gebhart/patrepeval huggingface dataset:
Lung surfactants : basic science and clinical applications (2000)

Introduction Introduction to Surface Tension and Surfactants Phospholipids: Introduction to Structure and Biophysics Physicochemical Methods for Studying Lung Surfactants Lung Surfactant Materials, Research Complexities, and Interdisciplinary Correlations Discovery of Endogenous Lung Surfactant and Overview of Its Metabolism and Actions Analyses of Surfactant Activity and Its Contribution to Lung Mechanics and Stability Functional Composition and Component Biophysics of Endogenous Lung Surfactant Lung Surfactant Dysfunction Diseases of Lung Surfactant Deficiency or Dysfunction Lung Surfactant Replacement in Animal Models Clinical Surfactant Replacement Therapy for Neonatal RDS Surfactant and Combined-Modality Therapies for Clinical ARDS and Acute Lung Injury Exogenous Lung Surfactants: Current and Future Glossary of Common Terms and Abbreviations References
Experimental allergic encephalomyelitis: A misleading model of multiple sclerosis (2005)

Despite many years of intensive research, multiple sclerosis (MS) defies understanding and treatment remains suboptimal. The prevailing hypothesis is that MS is immune mediated and that experimental allergic encephalomyelitis (EAE) is a suitable model to elucidate pathogenesis and devise therapy. This review examines critically the validity that EAE is an adequate and useful animal model of MS and finds credible evidence lacking. EAE represents more a model of acute central nervous system inflammation than the counterpart of MS. We propose to reconsider the utilization of EAE, especially when this model is used to define therapy. This will also force us to examine MS without the restraints imposed by EAE, as to what it is, rather than what it looks like.
The Clinical Marker hCG (1987)

List of Figures Lists of Tables List of Trade Names Preface Introduction Technology of hcg Pregnancy Tests Immonochemistry of hCG Reference Standards for hCG Clinical Applications of hCG Tests: Pregnancy Clinical Applications of hCG Tests: Tumors Low-Level hCG Results Tissue Localization of hCG Subunits of hCG Future Perspectives Bibliography Index About the Author
Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation‐induced senescence in Arabidopsis (2005)

An analysis of changes in global gene expression patterns during developmental leaf senescence in Arabidopsis has identified more than 800 genes that show a reproducible increase in transcript abundance. This extensive change illustrates the dramatic alterations in cell metabolism that underpin the developmental transition from a photosynthetically active leaf to a senescing organ which functions as a source of mobilizable nutrients. Comparison of changes in gene expression patterns during natural leaf senescence with those identified, when senescence is artificially induced in leaves induced to senesce by darkness or during sucrose starvation-induced senescence in cell suspension cultures, has shown not only similarities but also considerable differences. The data suggest that alternative pathways for essential metabolic processes such as nitrogen mobilization are used in different senescent systems. Gene expression patterns in the senescent cell suspension cultures are more similar to those for dark-induced senescence and this may be a consequence of sugar starvation in both tissues. Gene expression analysis in senescing leaves of plant lines defective in signalling pathways involving salicylic acid (SA), jasmonic acid (JA) and ethylene has shown that these three pathways are all required for expression of many genes during developmental senescence. The JA/ethylene pathways also appear to operate in regulating gene expression in dark-induced and cell suspension senescence whereas the SA pathway is not involved. The importance of the SA pathway in the senescence process is illustrated by the discovery that developmental leaf senescence, but not dark-induced senescence, is delayed in plants defective in the SA pathway.
Performance of electrokinetic supercharging for high‐sensitivity detection of DNA fragments in chip gel electrophoresis (2004)

Chip gel electrophoresis was explored for high-sensitivity detection of DNA by combining electrokinetic injection with transient isotachophoresis preconcentration (here named electrokinetic supercharging (EKS)). Low concentrations (0.2 mg/L) of DNA sample could be detected without fluorescence labeling using a conventional UV detector (at 260 nm). On a single-channel microchip, identification of PCR product was performed by exploiting both external and internal calibration methods. The deviation between the two calibration methods was about 3.6%, and the identified DNA fragment size matched with the predicted size of the template DNA. On the cross microchip the EKS preconcentration has also been achieved when changing the injection reservoir differing from the one used previously. The procedure was computer-simulated and the influence of the voltage applied to two-side reservoirs on sample preconcentration and dilution was also discussed.
Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem (2010)

• An association genetics approach was used to examine individual genes and alleles at the loci responsible for complex traits controlling lignocellulosic biosynthesis in black cottonwood (Populus trichocarpa). Recent interest in poplars as a source of renewable energy, combined with the vast genomic resources available, has enabled further examination of their genetic diversity. • Forty candidate genes were resequenced in a panel of 15 unrelated individuals to identify single nucleotide polymorphisms (SNPs). Eight hundred and seventy-six SNPs were successfully genotyped in a clonally replicated population (448 clones). The association population (average of 2.4 ramets per clone) was phenotyped using pyrolysis molecular beam mass spectrometry. Both single-marker and haplotype-based association tests were implemented to identify associations for composite traits representing lignin content, syringyl : guaiacyl ratio and C6 sugars. • Twenty-seven highly significant, unique, single-marker associations (false discovery rate Q < 0.10) were identified across 40 candidate genes in three composite traits. Twenty-three significant haplotypes within 11 genes were discovered in two composite traits. • Given the rapid decay of within-gene linkage disequilibrium and the high coverage of amplicons across each gene, it is likely that the numerous polymorphisms identified are in close proximity to the causative SNPs and the haplotype associations reflect information present in the associations between markers.
Heat‐Shock Proteins (2003)

Heat-shock proteins (HSPs), or stress proteins, are highly conserved and present in all organisms and in all cells of all organisms. Selected HSPs, also known as chaperones, play crucial roles in folding/unfolding of proteins, assembly of multiprotein complexes, transport/sorting of proteins into correct subcellular compartments, cell-cycle control and signaling, and protection of cells against stress/apoptosis. More recently, HSPs have been implicated in antigen presentation with the role of chaperoning and transferring antigenic peptides to the class I and class II molecules of the major histocompatibility complexes. In addition, extracellular HSPs can stimulate professional antigen-presenting cells of the immune system, such as macrophages and dendritic cells. HSPs constitute a large family of proteins that are often classified based on their molecular weight: hsp10, hsp40, hsp60, hsp70, hsp90, etc. This unit contains a table that lists common HSPs and summarizes their characteristics including (a) name, (b) subcellular localization, (c) known function, (d) chromosome assignment, (e) brief comments, and (f) references.
Placenta growth factor (PlGF) induces vascular endothelial growth factor (VEGF) secretion from mononuclear cells and is co-expressed with VEGF in synovial fluid (2000)

The aims of this study were (i) to determine whether PlGF, VEGF and PlGF/VEGF heterodimers are detected in synovial fluid (SF) and plasma samples from patients with a range of arthropathies; (ii) to describe whether any correlation exists between SF PlGF, VEGF and PlGF/VEGF heterodimer levels and the total and differential SF leucocyte counts; and (iii) to investigate the regulation of peripheral blood mononuclear cell (PBMC) VEGF secretion by stimuli relevant to inflammatory joints. PlGF, VEGF and PlGF/VEGF heterodimer levels were measured in the SF and plasma of patients with a range of arthropathies and normal controls by ELISA. Western blotting for PlGF was performed on SF from three patients with rheumatoid arthritis (RA) and primary inflammatory arthropathies. VEGF was quantified in cell culture supernatants after stimulation with lipopolysaccharide (LPS), PlGF or cobalt ions of PBMC isolated from RA patients and controls. PlGF and VEGF were detected in all SF samples. PlGF/VEGF heterodimers were detected in 10.2% of SF samples, most frequently in RA samples. Western blotting confirmed the presence of PlGF in RA SF. PlGF was detected in 52% of RA and 31% of control plasma samples, and VEGF was detected in 38% of RA and 38% of control plasma samples. PlGF/VEGF heterodimers were detected in 21% of RA samples and none of the control samples. In primary inflammatory arthropathy patients, SF PlGF and VEGF levels correlated significantly with the SF total leucocyte count and the neutrophil count. PlGF was the most potent inducer of PBMC VEGF production in both RA and control subjects. This is the first report of the detection of PlGF and PlGF/VEGF heterodimers in the SF of patients with inflammatory arthropathies, and we have shown for the first time that PlGF up-regulates PBMC VEGF production. PlGF may therefore play a key role in the production of VEGF in the inflammatory joint.
Characterization of primary human keratinocytes transformed by human papillomavirus type 18 (1988)

Primary human epithelial cells were cotransfected with pHPV-18 and pSV2neo, and cell strains were generated by selecting in G418. One cell strain (FE-A), which exhibits an extended life span, is currently in its 30th passage. In comparison, control cultures can only be maintained up to the seventh passage. Southern blot analysis revealed the presence of at least one intact, integrated viral genome in these cells. FE-A cells showed altered growth properties, characterized by a change in morphology, and clonal density. Differentiation markers analyzed by Western blotting (immunoblotting), such as cytokeratins and involucrin, indicated that the cells resembled a partially differentiated epithelial population. Increased expression of the 40-kilodalton cytokeratin was observed in FE-A cells, similar to that observed in simian virus 40-immortalized human keratinocytes (M. Steinberg and V. Defendi, J. Cell Physiol. 123:117-125, 1985). FE-A cells were also found to be defective in their response to terminal differentiation stimuli. Calcium and 12-O-tetradecanoyl-phorbol-13-acetate treatment induced normal epithelial cells to differentiate, whereas the human papillomavirus 18 (HPV-18)-containing keratinocytes were resistant to these signals, indicating their partially transformed nature. These cells were not able to induce tumors in nude mice over a period of up to 8 months. A second cell strain, FE-H18L, also generated by transfecting HPV-18, also exhibited an extended life span and similar alterations in morphology. Viral RNA transcribed from the early region of HPV-18 was detected in both cell strains by Northern (RNA) blot analysis. These cell strains should provide a useful model for determining the role of HPV in carcinogenesis.
Performance Evaluation of Mathematical Formula Identification (2012)

This paper presents a performance evaluation system for mathematical formula identification. First, a ground-truth dataset is constructed to facilitate the performance comparison of different mathematical formula identification algorithms. Statistics analysis of the dataset shows the diversities of the dataset to reflect the real-world documents. Second, a performance evaluation metric for mathematical formula identification is proposed, including the error type definitions and the scenario-adjustable scoring. The proposed metric enables in-depth analysis of mathematical formula identification systems in different scenarios. Finally, based on the proposed evaluation metric, a tool is developed to automatically evaluate mathematical formula identification results. It is worth noting that the ground-truth dataset and the evaluation tool are freely available for academic purpose.
Cerebellomedullary Cistern Delivery for AAV-Based Gene Therapy: A Technical Note for Nonhuman Primates (2016)

Accessing cerebrospinal fluid (CSF) from the craniocervical junction through the posterior atlanto-occipital membrane via cerebellomedullary injection (also known as cisternal puncture or cisterna magna injection) has become a standard procedure in preclinical studies. Such delivery provides broader coverage to the central and peripheral nervous system unlike local parenchymal delivery alone. As a clinical application, this approach offers a more reliable method for neurological gene replacement delivery in infants, where skull-mounted devices are not indicated. Here we describe a consistent, precise, and safe method for CSF injection with minimal equipment and technical skills.
Dynamic evolution of bitter taste receptor genes in vertebrates (2009)

These results further support the hypotheses that T2R gene repertoires are closely related to the dietary habits of different species and that birth-and-death evolution is associated with adaptations to dietary changes.
Effects of Long-Term Administration of 9-cis-Retinyl Acetate on Visual Function in Mice (2009)

Deteriorating photoreceptor function documented in mice at 10 and 14 versus 4 months of age was improved significantly by long-term, monthly administration of 9-cis-R-Ac. These findings suggest a potential therapeutic approach to prevent age-related retinal dysfunction.
A Magnetic Switch for Spin-Catalyzed Interconversion of Nuclear Spin Isomers (2010)

The interconversion of ortho-hydrogen (oH(2)) and para-hydrogen (pH(2)), the two nuclear spin isomers of dihydrogen, requires a paramagnetic spin catalyst such as a nitroxide. We report the design and demonstration of spin catalysis of the interconversion of oH(2) and pH(2) incarcerated in an endofullerene based on a reversible nitroxide/hydroxylamine system. The system is an example of a reversible magnetic spin catalysis switch that can increase the rate of interconversion of the nuclear spin isomers of H(2) by a factor of approximately 10(4).
Synthesis of RNA from cellulose-bound complementary DNA. (1977)

Radioactively labeled RNAs were synthesized from cellulose-bound cDNA templates using Escherichia coli RNA polymerase. Hybridization of this RNA to excess unlabeled cDNA approached 100%, indicating the complementarity of product and template. The average length of the RNA product, as determined by formamide gels, was approximately 40% of the template length. Hybridization of unlabeled globin RNA produced by this technique to labeled globin cDNA indicated the population of RNA sequences represented at least 80% of the template sequences. Approximately 30% of the RNA product by mass contains poly(A) tails as determined by binding to oligo(dT)-cellulose. The template can be reused for several cycles of synthesis with little loss of synthetic capability and therefore, can amplify the amount of mRNA initially used to produce the template.
Identification of the Primase Active Site of the Herpes Simplex Virus Type 1 Helicase-Primase (1995)

Herpes simplex virus type 1 (HSV-1) encodes a heterotrimeric helicase-primase composed of the products of the three DNA replication-specific genes UL5, UL8, and UL52 (Crute, J. J., and Lehman, I. R. (1991) J. Biol. Chem. 266, 4484-4488). The UL5 and UL52 products constitute a heterodimeric subassembly of the holoenzyme that contains both helicase and primase activities (Calder, J. M., and Stow, N. D. (1990) Nucleic Acids Res. 18, 3573-3578; Dodson, M. S., and Lehman, I. R. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 1105-1109). The role of the UL52 product in the active HSV-1 helicase-primase was examined. A sequence located between residues 610 and 636 on the UL52 protein was found to be conserved among the UL52 homologues of eight herpesviruses. The carboxyl-terminal portion of this conserved sequence consisted of two Asp residues separated by a variable hydrophobic amino acid residue and is analogous to the divalent metal-binding site of DNA polymerases and several DNA primases. This motif has been designated the herpesvirus primase DXD motif. To study the role of the HSV-1 primase DXD motif in primase action, three site-directed changes were introduced into the UL52 gene. The helicase activity of the recombinant holoenzymes was unaffected by any of the introduced changes. Changing either of the two Asp residues that constitute the divalent metal-binding site (Asp628 or Asp630) to Ala dramatically reduced the primase activity of the HSV-1 helicase-primase holoenzyme in vitro, whereas alteration of the nearby conserved residue Asn624 to Gly had minimal effect. Therefore, in the three-subunit HSV-1 helicase-primase, the UL52 product provides at least a part of the primase catalytic site.
A high-extraction-efficiency nanopatterned organic light-emitting diode (2003)

To improve light extraction from organic light-emitting diodes (OLEDs), we introduced a photonic crystal pattern into the glass substrate of an OLED. The periodic modulation converts the guided waves in the high-refractive-index indium-tin-oxide/organic layers into external leaky waves. We used the finite-difference time-domain method to optimize the structural parameters of the photonic crystal pattern and to analyze the microcavity effect by the metallic cathode of the OLED. With the use of an optimized photonic crystal pattern, an increase of over 80% in the extraction efficiency of the OLED is expected theoretically. An increase in the extraction efficiency of over 50% was achieved experimentally, without detriment to the crucial electrical properties of the OLED.
Repressor titration: a novel system for selection and stable maintenance of recombinant plasmids (1998)

The propagation of recombinant plasmids in bacterial hosts, particularly in Escherichia coli, is essential for the amplification and manipulation of cloned DNA and the production of recombinant proteins. The isolation of bacterial transformants and subsequent stable plasmid maintenance have traditionally been accomplished using plasmid-borne selectable marker genes. Here we describe a novel system that employs plasmid-mediated repressor titration to activate a chromosomal selectable marker, removing the requirement for a plasmid-borne marker gene. A modified E.coli host strain containing a conditionally essential chromosomal gene (kan) under the control of the lac operator/promoter, lac O/P, has been constructed. In the absence of an inducer (allolactose or IPTG) this strain, DH1 lackan , cannot grow on kanamycin-containing media due to the repression of kan expression by LacI protein binding to lac O/P. Transformation with a high copy-number plasmid containing the lac operator, lac O, effectively induces kan expression by titrating LacI from the operator. This strain thus allows the selection of plasmids without antibiotic resistance genes (they need only contain lac O and an origin of replication) which have clear advantages for use as gene therapy vectors. Regulation in the same way of an essential, endogenous bacterial gene will allow the production of recombinant therapeutics devoid of residual antibiotic contamination.
Synthesis and evaluation of the antidepressant activity of the enantiomers of bupropion (1993)

The synthesis of the enantiomers of bupropion, (rac)-2-tert-butylamino-3'-chloropropiophenone 1 (Wellbutrin) is described. The enantiomers were compared with the racemate in both the tetrabenazine-induced sedation model and the inhibition of uptake of biogenic amine assay. No significant differences were found in their potencies to reverse tetrabenazine-induced sedation in mice or in their IC50 values as inhibitors of biogenic amine uptake into nerve endings obtained from mouse brain.
The G Protein-Coupled Receptor GPR30 Mediates the Proliferative Effects Induced by 17β-Estradiol and Hydroxytamoxifen in Endometrial Cancer Cells (2005)

The growth of both normal and transformed epithelial cells of the female reproductive system is stimulated by estrogens, mainly through the activation of estrogen receptor alpha (ERalpha), which is a ligand-regulated transcription factor. The selective ER modulator tamoxifen (TAM) has been widely used as an ER antagonist in breast tumor; however, long-term treatment is associated with an increased risk of endometrial cancer. To provide new insights into the potential mechanisms involved in the agonistic activity exerted by TAM in the uterus, we evaluated the potential of 4-hydroxytamoxifen (OHT), the active metabolite of TAM, to transactivate wild-type ERalpha and its splice variant expressed in Ishikawa and HEC1A endometrial tumor cells, respectively. OHT was able to antagonize only the activation of ERalpha by 17beta-estradiol (E2) in Ishikawa cells, whereas it up-regulated c-fos expression in a rapid manner similar to E2 and independently of ERalpha in both cell lines. This stimulation occurred through the G protein-coupled receptor named GPR30 and required Src-related and epidermal growth factor receptor tyrosine kinase activities, along with the activation of both ERK1/2 and phosphatidylinositol 3-kinase/AKT pathways. Most importantly, OHT, like E2, stimulated the proliferation of Ishikawa as well as HEC1A cells. Transfecting a GPR30 antisense expression vector in both endometrial cancer cell lines, OHT was no longer able to induce growth effects, whereas the proliferative response to E2 was completely abrogated only in HEC1A cells. Furthermore, in the presence of the inhibitors of MAPK and phosphatidylinositol 3-kinase pathways, PD 98059 and wortmannin, respectively, E2 and OHT did not elicit growth stimulation. Our data demonstrate a new mode of action of E2 and OHT in endometrial cancer cells, contributing to a better understanding of the molecular mechanisms involved in their uterine agonistic activity.
Barbourin. A GPIIb-IIIa-specific integrin antagonist from the venom of Sistrurus m. barbouri (1991)

Sixty-two snake venoms were screened to identify those which specifically inhibit the adhesive protein binding function of the glycoprotein (GP) IIb-IIIa complex, the receptor-mediating platelet aggregation. Although 52 of these venoms inhibited GPIIb-IIIa, only one of these, from the southeastern pigmy rattlesnake, Sistrurus m. barbouri, was specific for GPIIb-IIIa versus other integrins. The peptide responsible for this activity, termed barbourin, was sequenced and found to be highly homologous to other peptides of the viper venom GPIIb-IIIa antagonist family but was the first member which did not contain the Arg-Gly-Asp (RGD) amino acid sequence, believed to be required for inhibition of receptor function. Instead, barbourin contains the sequence, Lys-Gly-Asp (KGD). The conservative Lys for Arg substitution appears to be the sole structural feature which imparts integrin specificity to barbourin, since venom peptide analogs with Lys substitutions were also specific for GPIIb-IIIa. Thus, barbourin represents a new structural model useful for designing potent and GPIIb-IIIa-specific compounds that may have therapeutic value as platelet aggregation inhibitors.
Survival Trends in Elderly Patients with Glioblastoma in the United States: a Population-based Study (2016)

This study shows that the survival of elderly patients with glioblastoma has improved since the introduction of the Stupp regimen. However, there are significant differences in survival rates among various cohorts.