gebhart/patrepeval huggingface dataset:
Carbohydrate antigens in human cancer. (1985)

Studies with naturally occurring and hybridoma-derived monoclonal antibodies have shown that surface and secreted antigens which distinguish human tumour cells from their normal counterparts are predominantly carbohydrate structures. Many of these belong to a family which includes the major blood-group antigens. In fact, the blood-group genes and the related secretor gene account for the individual and tissue-specific patterns of expression of several carbohydrate antigens as normal or as tumour-associated antigens. The biochemical basis of the tumour-associated changes requires investigation. In particular, it will be important to determine whether they are the result of aberrant expression of the glycosyltransferase genes. Their contribution to the disordered growth regulation in tumour cells will also be important to assess, particularly as the blood group family of oligosaccharides are among major antigenic components of the receptor for epidermal growth factor. Monoclonal antibodies to carbohydrate structures have opened new avenues of research into the biochemistry of tumour cells.
GD3 ganglioside is prevalent in fully differentiated neurons from rat retina (1990)

Adult mammalian retinas contain unusually high amounts of GD3, a ganglioside of the lactosylceramide series. In this respect, they differ from adult avian retina and other regions of the adult avian and mammalian brain, where GD3 is a minor ganglioside and gangliosides of the gangliotetraosylceramide series (GM1, GD1a, GD1b, GT1b) are the predominant ones. We compare here the ganglioside patterns of rat, human, horse, and guinea pig retinas, which are known to differ in the degree of vascularization and astrocytic cell content. All these retinas showed a prevalence of pathway "b" gangliosides over pathway "a" gangliosides but showed no correlation between GD3 content and the degree of vascularization and astrocytic cell content. Immunostaining of rat retina sections showed the presence of GD3 in the inner and outer plexiform layers and also in the ganglion cell and inner nuclear layers. About 60% of the cells dissociated from rat retina showed immuno-colocalization of GD3 and the neuronal marker class III beta tubulin isotype or cholera toxin binding. All morphologically identifiable glial Muller cells coexpress GD3 and gangliotetraosylgangliosides. GD3 was a minor ganglioside among these axonally transported by ganglion cells in rats and guinea pigs, suggesting that it is either not synthesized by ganglion cells or, if so, it is restricted to the cell soma and/or dendritic tree. Our results demonstrate that, unlike neurons from avian retina and other regions of avian and mammalian brain, neurons from mammalian retina not only contain gangliosides of the gangliotetraosylceramide series but also keep a prevalence of gangliosides of the lactosylceramide series (GD3) when they are fully differentiated.
Resistance to Ralstonia solanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes (2002)

The identification of two Arabidopsis thaliana genes involved in determining recessive resistance to several strains of the causal agent of bacterial wilt, Ralstonia solanacearum, is reported. Dominant (RRS1-S) and recessive (RRS1-R) alleles from susceptible and resistant accessions encode highly similar predicted proteins differing in length and which present a novel structure combining domains found in plant Toll-IL-1 receptor-nucleotide binding site-leucin-rich repeat resistance proteins and a WRKY motif characteristic of some plant transcriptional factors. Although genetically defined as a recessive allele, RRS1-R behaves as a dominant resistance gene in transgenic plants. Sequence analysis of the RRS1 genes present in two homozygous intragenic recombinant lines indicates that several domains of RRS1-R are essential for its resistance function. Additionally, RRS1-R-mediated resistance is partially salicylic acid- and NDR1-dependent, suggesting the existence of similar signaling pathways to those controlled by resistance genes in specific resistance.
Rotation thromboelastometry (ROTEM®) stability and reproducibility over time☆ (2009)

ROTEM yields stable results over 120 min with a minimal variability on the same ROTEM device. However, small but significant differences between ROTEM devices were observed. Analysis should be performed on the same ROTEM device if small differences are of importance for treatment.
Semiconductor Clusters, Nanocrystals, and Quantum Dots (1996)

Current research into semiconductor clusters is focused on the properties of quantum dots—fragments of semiconductor consisting of hundreds to many thousands of atoms—with the bulk bonding geometry and with surface states eliminated by enclosure in a material that has a larger band gap. Quantum dots exhibit strongly size-dependent optical and electrical properties. The ability to join the dots into complex assemblies creates many opportunities for scientific discovery.
Reliability Characteristics of TANOS (TaN/AlO/SiN/Oxide/Si)NAND Flash Memory with Rounded Corner (RC) Structure (2008)

Charge trap flash (CTF) memory is one of the most promising technologies for the next generation NAND technology. Among various CTF memories, excellent manufacturability of TaN-Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> -Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> -SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -Si (TANOS) structure has been successfully developed by achieving 32Gb MLC NAND flash using 40nm technology node (Y. Park et al., 2006). 3 dimensional NAND cells such as hemispherical corner (HC) (D. Kwak et al., 2007) and FinFET TANOS (S. Lee et al., 2006) devices with suppressed short-channel effects and improved data retention characteristic were also proposed as cell structures for the next generation beyond 40nm technology node. However, understanding of other device characteristics such as disturb characteristics of the structures is still insufficient. In this paper, various device characteristics of rounded corner (RC) TANOS including disturb and data retention characteristics are investigated and compared with the conventional planar TANOS. Finally, the rendering of RC TANOS for improving disturb characteristics was proposed.
Surface Plasmon-Mediated Photothermal Chemistry (2014)

Surface plasmon resonance (SPR)-induced photothermal heating has garnered a substantial amount of research interest across various disciplines. The first applications of SPR-induced light-to-heat energy conversion were in biological systems to photothermally ablate cancer cells in vivo. More recently, this spatially localized and highly tunable heating technique has been extensively used for a variety of chemical reactions and other associated applications. This feature article highlights the recent developments in surface plasmon-mediated photothermal chemistry. We review the current theoretical and experimental work toward estimating the photothermal heating-induced surface temperatures of plasmonic nanostructures. From a mechanistic perspective, we show how this local heating can activate reactant molecules and boost numerous types of chemical reactions. We also discuss the physical changes occurring in a surrounding solvent, such as water, during the photothermal process. Finally, we extend the scope of SPR-induced photothermal chemical reactions by manipulating the plasmonic nanostructure to facilitate nanomaterial fabrication, paving the way for a wide range of applications based on SPR-mediated photothermal chemistry. This perspective establishes a framework for the current applications, potential uses, and remaining challenges associated with harnessing SPR-induced photothermal heating.
Comparative analysis of common CFTR polymorphisms poly-T, TG-repeats and M470V in a healthy Chinese population (2008)

The polymorphisms of poly-T, TG-repeats, and M470V distribution were similar to those in other East Asians, but they had marked differences in frequency from those single haplotype polymorphisms or linkage haplotypes in Caucasians. Thus, they may be able to explain the low incidence of CF and CF-like diseases in Asians.
Rational Design of a Block Copolymer with a High Interaction Parameter (2014)

A series of poly(4-tert-butylstyrene-block-2-vinylpyridine) [P(tBuSt-b-2VP)] block copolymers (BCPs) with varying volume fractions, molecular weights, and narrow dispersities were synthesized from the commercially available monomers by sequential living anionic polymerization. The copolymers were thoroughly characterized by 1H NMR spectroscopy, size exclusion chromatography, thermal gravimetric analysis, and differential scanning calorimetry (DSC). To examine the effect of the tert-butyl group on the effective interaction parameter (χeff) relative to poly(styrene-block-2-vinylpyridine) [(P(S-b-2VP)], the self-assembly of symmetric copolymers was studied by small-angle X-ray scattering (SAXS) and transmission electron microscopy. Order-to-disorder transitions (ODTs) were identified by both DSC and SAXS on five copolymers, to define the equation χeff(T) = (67.9 ± 1.3)/T – (0.0502 ± 0.0029), which shows a higher enthalpic contribution to χeff than P(S-b-2VP) and approximately 1.5 times larger χeff. This enables a minimum full pitch of 9.6 nm for the symmetric copolymers. Asymmetric copolymers were also examined for bulk self-assembly by SAXS and TEM, exploring both P2VP and PtBuSt cylindrical phases with diameters as small as 6 nm. Feasibility of thin film assembly by thermal annealing was demonstrated for a P2VP cylinder forming BCPs to yield parallel cylinders that were seeded with Pt ions and etched to yield Pt nanowires with diameters as small as 5.8 nm.
Analysis and Comparison of Partial Sequences of Clones from a Taste-bud-enriched cDNA Library (1997)

Differential patterns of cellular development and function are determined, at least in part, by the specific gene expression of particular cells. Thus, determination of differential patterns of gene expression between tissues is likely to help elucidate molecular details of tissue-specific processes. Our hypothesis was that cells of the circumvallate papilla involved in taste perception would express genes that are not expressed in the surrounding epithelium and that determination of the nature of these genes could be helpful in our understanding of the molecular details of taste. Using partial sequencing of clones derived from rat circumvallate papillae, we have begun to characterize genes that could be important in taste. We prepared a cDNA library of whole circumvallate papillae and, by means of a novel subtraction procedure, enriched taste-specific clones. Characterization of the libraries showed that subtraction resulted in good enrichment of taste-specific clones. Here we report the partial sequencing and analysis of 410 cDNA clones from the taste-bud-enriched cDNA library. Approximately 25% of the genes were identified on the basis of their high homology to known transcripts. These included the developmentally important molecules Pax-1, esp1, Notch 1, and Notch 3 that may play roles in the continuous turnover of taste receptor cells. A further 20% of the genes had no significant homology to known DNA sequences and were identified as taste-specific by Southern blot analysis.
Camel Heavy Chain Antibodies Against Prostate-Specific Membrane Antigen (2012)

Prostate-specific membrane antigen (PSMA), a type II integral membrane glycoprotein, is highly overexpressed in all forms of prostate cancer tissues. It has also been demonstrated in a wide range of neovasculature of non-prostatic solid tumors, including bladder, pancreas, lung, kidney, colorectal, and gastric cancers. Given the unique expression of PSMA, it is considered an alluring target for antibody-based imaging and therapy of cancer. In the present study, the production and characterization of camel heavy chain antibodies (HCAbs) specific for the external domain of the PSMA are reported. Due to the absence of the CH1 domain, HCAbs are smaller than their counterparts in conventional antibodies. In this study, camel antibodies were generated through immunization of Camelus dromedarius with a synthetic 28 amino acid peptide corresponding to the external surface domain of antigen and PSMA-expressing cell lines. Different binding properties to protein A and protein G affinity columns were deployed to separate three subclasses of camel IgG. The affinity purified HCAbs bound selectively to the synthetic peptide in enzyme linked immunosorbent assay (ELISA) and reacted specifically with PSMA-expressing cell line through immunocytochemistry study. Currently, we are attempting to develop recombinant variable domain of these heavy chain antibodies (VHH or nanobody) for tumor imaging and cancer therapy.
Clenbuterol, a beta agonist, induces growth in innervated and denervated rat soleus muscle via apparently different mechanisms (1987)

Dietary administration of the anabolic agent, clenbuterol, has already been shown to inhibit or reverse denervation-induced atrophy in rat soleus muscles. We now show that the ameliorative effects of clenbuterol in denervated rat muscles are due principally to a large increase in protein synthesis. This results from both an increase in protein synthetic capacity and a normalised translational efficiency. The responses of innervated and denervated muscles are therefore fundamentally different, the changes in denervated muscles being reminiscent of the classical pleiotypic response of cells to growth factors.
Cachexia and the acute‐phase protein response in inflammation are regulated by interleukin‐6 (1993)

Cachexia and the acute-phase response are common manifestations of inflammation and are presumed to be the product of increased synthesis and release of cytokines, including tumor necrosis factor (TNF), interleukin-1 (IL-1) and interleukin-6 (IL-6). IL-1 receptor blockade has been previously shown to attenuate the weight loss, anorexia and acute-phase protein responses associated with a turpentine abscess. However, IL-1 receptor blockade was also associated with a reduced plasma IL-6 response, suggesting that the benefit achieved by IL-1 receptor blockade may be mediated by reduced systemic IL-6 production. To gain a better understanding of the role of IL-6 in this model of inflammation, C57BL/6 mice were passively immunized with either a monoclonal anti-IL-6 antibody (20F3), an anti-IL-1 type I receptor monoclonal antibody (35F5), a non-immune rat IgG, or a combined therapy of 35F5 and 20F3, before receiving a sterile turpentine abscess. IL-6 or IL-1 receptor blockade equally spared body weight and food intake. Compared to IL-1 receptor blockade, passive immunization against IL-6 further reduced the hepatic acute-phase protein response, as represented by serum amyloid P and complement 3. Combined blockade of IL-6 and IL-1 receptor did not result in a further sparing of body weights or improvement of food intake. These results confirm that IL-1 contributes to host cachexia and the acute-phase response following a turpentine abscess, but also show that these actions are dependent upon an IL-6 response. We conclude that the influence of IL-1 on cachexia and the acute-phase response is mediated, at least in part, through IL-6 and, thus, IL-6 may play a pivotal role in the cachexia and acute-phase response to inflammation.
Fulvestrant (Faslodex®)—How to Make a Good Drug Better (2007)

Fulvestrant (Faslodex); AstraZeneca Pharmaceuticals, Wilmington, DE) is an estrogen receptor (ER) antagonist with a novel mode of action; it binds, blocks, and increases degradation of ER. Fulvestrant (at the approved dose [250 mg/month]) is at least as effective as anastrozole (1 mg/day) in the treatment of postmenopausal women with hormone receptor-positive advanced breast cancer (HR(+) ABC) progressing or recurring on antiestrogen therapy, and is also an active first-line treatment. Although fulvestrant (250 mg/month) is clearly effective, it takes 3-6 months to achieve steady-state plasma levels. Steady-state concentrations are approximately twofold higher than those achieved with a single dose; reaching this earlier, for example, via a loading-dose (LD) regimen (250 mg/month plus 500 mg on day 0 and 250 mg on day 14 of month 1), may allow responses to be achieved more quickly and limit the possibility of early relapse. Fulvestrant high-dose (HD) regimens (500 mg/month) offer the possibility of greater antitumor activity, because (a) ER downregulation is a dose-dependent process (an approximately 70% reduction is observed with a single 250 mg dose of fulvestrant) and (b) evidence correlates greater ER downregulation with superior efficacy. A fulvestrant HD regimen offers the potential of achieving near 100% ER downregulation. There is also potential to increase fulvestrant-ER binding by reducing plasma estrogen levels, for example, with concomitant aromatase inhibitor treatment. Several ongoing trials use LD, HD, and combination regimens; results from these studies are awaited with interest. Meanwhile, fulvestrant (250 mg/month) remains a valuable additional endocrine treatment for postmenopausal women with HR(+) ABC recurring or progressing on antiestrogen therapy.
Lung Cancer Survival Among Chinese Americans, 2000 to 2010 (2016)

Focusing on factors associated with marital status, community socioeconomic status, and characteristics unique to National Cancer Institute-designated cancer centers may help to identify potential strategies for improving the length of survival for Chinese Americans.
A Complex Oscillating Network of Signaling Genes Underlies the Mouse Segmentation Clock (2006)

The segmental pattern of the spine is established early in development, when the vertebral precursors, the somites, are rhythmically produced from the presomitic mesoderm. Microarray studies of the mouse presomitic mesoderm transcriptome reveal that the oscillator associated with this process, the segmentation clock, drives the periodic expression of a large network of cyclic genes involved in cell signaling. Mutually exclusive activation of the notch-fibroblast growth factor and Wnt pathways during each cycle suggests that coordinated regulation of these three pathways underlies the clock oscillator.
Metabolic engineering of medicinal plants: transgenic Atropa belladonna with an improved alkaloid composition. (1992)

The tropane alkaloid scopolamine is a medicinally important anticholinergic drug present in several solanaceous plants. Hyoscyamine 6 beta-hydroxylase (EC 1.14.11.11) catalyzes the oxidative reactions in the biosynthetic pathway leading from hyoscyamine to scopolamine. We introduced the hydroxylase gene from Hyoscyamus niger under the control of the cauliflower mosaic virus 35S promoter into hyoscyamine-rich Atropa belladonna by the use of an Agrobacterium-mediated transformation system. A transgenic plant that constitutively and strongly expressed the transgene was selected, first by screening for kanamycin resistance and then by immunoscreening leaf samples with an antibody specific for the hydroxylase. In the primary transformant and its selfed progeny that inherited the transgene, the alkaloid contents of the leaf and stem were almost exclusively scopolamine. Such metabolically engineered plants should prove useful as breeding materials for obtaining improved medicinal components.
Modelling melanoma in mice (2011)

Phenotypic and molecular heterogeneity in human melanoma has impaired efforts to explain many of the clinically important features of melanoma. For example, many of the underlying mechanisms that might predict age-of-onset, time to metastasis and other key elements in melanoma progression remain unknown. Furthermore, melanoma staging used to predict outcome and treatment has not yet moved beyond a basic phenotypic classification. While molecularly targeted therapies show great promise for melanoma patients, establishing accurate animal models that recapitulate human cutaneous melanoma progression remains a priority. We examine the relevance of mice as models for human melanoma progression and for key molecular and histopathologic variants of melanoma. These mice may be used as preclinical models to probe the relationships between causative mutations, disease progression and outcome for molecularly targeted therapeutics. We ask how new mouse models, or more detailed histopathologic and molecular analyses of existing mouse models, may be used to advance our understanding of genotype-phenotype correlations in this tumour type. This necessarily involves a consideration of the utility of mice as models for ultraviolet radiation-induced melanoma, and how this might be improved.
Th 17 cells interplay with Foxp3+ Tregs in regulation of inflammation and autoimmunity (2010)

T helper 17 cells (Th17) are a new CD4+ T helper subset that has been implicated in inflammatory and autoimmune diseases. Th17, along with CD4(+)CD25(high) Foxp3(+) regulatory T cells (Tregs) and other new T helper subsets, have expanded the Th1-Th2 paradigm. Although this new eight-subset paradigm significantly improved our understanding on the differentiation and regulation of CD4+ T helper subsets, many questions remain to be answered. Here we will briefly review the following issues: a) Old Th1-Th2 paradigm versus new multi-subset paradigm; b) Structural features of IL-17 family cytokines; c) Th17 cells; d) Effects of IL-17 on various cell types and tissues; e) IL-17 receptor and signaling pathways; f) Th17-mediated inflammations; and g) Protective mechanisms of IL-17 in infections. Lastly, we will examine the interactions of Th17 and Treg in autoimmune diseases and inflammation: Th17 cells interplay with Tregs. Regulation of autoimmunity and inflammation lies in the interplays of the different T helper subsets, therefore, better understanding of these subsets' interactions would greatly improve our approaches in developing therapy to combat inflammatory and autoimmune diseases.
Dairy Herd Management Practices that Impact Nitrogen Utilization Efficiency (2002)

Improving the efficiency of feed N utilization by dairy cattle is the most effective means to reduce nutrient losses from dairy farms. The objectives of this study were to quantify the impact of different management strategies on the efficiency of feed N utilization for dairy farms in the Chesapeake Bay Drainage Basin. A confidential mail survey was completed in December 1998 by 454 dairy farmers in PA, MD, VA, WV, and DE. Nitrogen intake, urinary and fecal N, and efficiency of feed N utilization was estimated from survey data and milk analysis for each herd. Average efficiency of feed N utilization for milk production by lactating dairy cows (N in milk/N in feed x 100) was 28.4% (SD = 3.9). On average, farmers fed 6.6% more N than recommended by the National Research Council, resulting in a 16% increase in urinary N and a 2.7% increase in fecal N. Use of monthly milk yield and component testing, administration of bovine somatotropin (bST), and extending photoperiod with artificial light each increased efficiency of feed N utilization by 4.2 to 6.9%, while use of a complete feed decreased efficiency by 5.6%. Increased frequency of ration balancing and more frequent forage nutrient testing were associated with higher milk production, but not increased N utilization efficiency. Feeding protein closer to recommendations and increasing production per cow both contributed to improving efficiency of feed N utilization.
Tandem dispersion and killing of bacteria from a biofilm (2008)

The combined effects of biofilm dispersion with a 2-aminoimidazole-triazole conjugate and bactericidal activity with a photodynamic inactivation agent suggest a novel combination therapy for treating diverse microbial infections.