gebhart/patrepeval huggingface dataset:
The Influence of Extracellular Matrix on Gene Expression: Is Structure The Message? (1987)

The study of the regulation of gene expression in cultured cells, particularly in epithelial cells, has been both hampered and facilitated by the loss of function that accompanies culture on traditional plastic substrata. Initially, investigations of differentiated function were thwarted by the inadequacy of tissue culture methods developed to support growth of mesenchymal cells. However, with the recognition that the unit of function in higher organisms is larger than the cell itself, and that gene expression is dependent upon cell interactions with hormones, substrata and other cells, came the understanding that the epithelial cell phenotype is profoundly influenced by the extracellular environment. In the last decade research on epithelial cells has centred on culture conditions that recreate the appropriate environment for function with very promising and important results. The investigations into the modulation of phenotype in culture produced not only a better model, but also contributed to a better understanding of the regulation of normal function. Using cultured mammary gland epithelial cells as a primary model of these interactions, our studies of gene expression are based on three premises. (1) That the extracellular matrix (ECM) on which the cells sit is an extension of the cells and an active participant in the regulation of cellular function; i.e. the ECM is an 'informational' entity in the sense that it receives, imparts and integrates structural and functional signals. (2) That ECM-induced functional differentiation in the mammary gland is mediated through changes in cell shape, i.e. that the structure is in large part 'the message' required to maintain differentiated gene expression. (3) That the unit of function includes the cell plus its extracellular matrix; in a larger context, the unit is the organ itself. These tenets and the data presented below are consistent with a model of 'Dynamic Reciprocity', where the ECM is postulated to exert an influence on gene expression via transmembrane proteins and cytoskeletal components. In turn, cytoskeletal association with polyribosomes affects mRNA stability and rates of protein synthesis, while its interaction with the nuclear matrix could affect mRNA processing and, possibly, rates of transcription.
On the inheritance of abdominal aortic aneurysm. (1991)

To determine the mode of inheritance of abdominal aortic aneurysm, data on first-degree relatives of 91 probands were collected. Results of segregation analysis performed on these data are reported. Many models, including nongenetic and genetic models, were compared using likelihood methods. The nongenetic model was rejected; statistically significant evidence in favor of a genetic model was found. Among the many genetic models compared, the most parsimonious genetic model was that susceptibility to abdominal aortic aneurysm is determined by a recessive gene at an autosomal diallelic major locus. A multifactorial component in addition to the major locus does not increase the likelihood of the data significantly.
ASBMR 29th Annual Meeting (2007)

Protein kinase D, also known as PKCp, is a serinelthreonine protein kinase that responds to phorbol esters and diacylglycerol. Using MC3T3-EI cells, we demonstrated that PKD is activated during DMSO-induced osteoblast differentiation. We further demonstrated that prolonged activation of protein kinase C pathways alone, i.e. in the absence of osteogenic inducers such as BMP-2 and/or DMSO, is sufficient to induce bone formation in preosteoblast cells in vitro. In this study, we examined the functional roles of PKD in osteoblastogenesis. Phorbol 12-myristate 13-acetate (PMA) activates most PKCs including PKD. Treatment of MC cells with PMA enhances osteoblast differentiation as indicated by increased ALP activity and bone nodules formation. Treatment with Gd6976, a specific inhibitor for PKD, at 0.02 and 0.2 pM resulted in a significant dose-dependent decrease in alkaline phosphatase (ALP) activity during osteoblast differentiation of MC cells mediated by DMSO, BMP2 or PMA. Bone nodule formation was attenuated simultaneously. Semi-quantitative RT-PCR analyses demonstrated that GO6976 treatment resulted in reduced Runx2, Osterix and ALP transcript expression in MC cells. However, a general PKC inhibitor GU6983 that does not inhibit PKD showed little effect on osteoblast differentiation, suggesting that PKD is crucial in the process. To confirm the functional roles of PKD, we overexpressed wild-type (PKD-WT), constitutively active (PKD-CA) and dominant negative (PKD-DN) PKD in MC cells and examine the effect of PKD modulation on osteoblast differentiation. In the absence of osteogenic inducers, MC cells transfected with PKD-CA resulted in enhanced bone nodules formation as compared to the PKD-DN transfectants. These findings are in good concordance to our previous observations that PKD activation alone is sufficient for inducing osteoblast differentiation. Using both pharmacological and PKD overexpression studies, our findings suggested that PKD plays essential roles in osteoblast differentiation and that osteoblast differentiation can be modulated via the activation of PKD.
The modulated lapped transform, its time-varying forms, and its applications to audio coding standards (1997)

The modulated lapped transform (MLT) is used in both audio and video data compression schemes. This paper describes its properties and how it can be used to generate a time-varying filterbank. Examples of its implementation in two audio coding standards are presented.
Presymptomatic Genetic Testing for Neurodegenerative Diseases (2004)

Presymptomatic genetic testing for neurodegenerative diseases can help patients make effective treatment decisions, but the medical profession needs to ensure that the increasing use of the tests is done responsibly.
Semiconductor materials and radiation detection (2006)

While Si and Ge have become detection standards for X-ray and gamma-ray spectroscopy in the laboratory, their use for an increasing range of applications is becoming marginalized by one or more of their physical limitations; namely the need for ancillary cooling systems or bulky cryogenics, their modest stopping powers and radiation intolerance. Wide band-gap compounds offer the ability to operate in a range of chemical, thermal and radiation environments while still maintaining sub-keV spectral resolution at X-ray wavelengths. In addition, these materials encompass such a wide range of physical properties that it is technically feasible to engineer materials to specific applications. However, while compound materials are used routinely in the optical and infrared wave bands, their development at hard X- and gamma-ray wavelengths has been plagued by material and fabrication problems. In this paper an overview of suitable materials is presented and the current progress in producing X- and gamma-ray radiation detectors is reviewed.
Origin of Oligodendrocytes within the Human Spinal Cord (1996)

To determine the time and site of origin of the oligodendrocyte lineage in the developing human spinal cord, we have examined tissues from 45 to 83 d postconception (dpc) using sets of probes and antibodies recognizing oligodendrocyte-specific glycolipids, transcripts, and proteins. We found that two clusters of oligodendrocyte precursors appear on or before 45 dpc on each side of the cord ventral ependyma above the floor plate. These precursors express glycolipids recognized by the O4 and Rmab antibodies, platelet-derived growth factor alpha-receptor, myelin basic protein (MBP), and 2', 3'-cyclic nucleotide 3' phosphodiesterase as well as MBP and proteolipid transcripts. Expression of the morphogen sonic hedgehog was detected in the floor plate at 45 dpc and decreased at 58 dpc. During this period, oligodendrocyte precursors emerged in the ventral and lateral region of the forming white matter, a process occurring first in cervical and later in lumbar cord. The majority of O4(+) cells express the proliferating cell nuclear antigen (PCNA), and their pattern of dispersion suggests that these cells progressively populate the lateral and dorsal cord regions. Oligodendrocytes expressing galactocerebroside appeared at 53 dpc and did not express PCNA. Oligodendrocyte precursors were detected in dorsal cord regions at 74 dpc and at 83 dpc when myelination started in the ventral roots. Thus, oligodendrocyte precursors expressing myelin transcripts and proteins emerge in the ventral region of the embryonic cord several weeks before myelination.
Substrate Synthesis and Activity Assay for MurG (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSubstrate Synthesis and Activity Assay for MurGHongbin Men, Peter Park, Min Ge, and Suzanne WalkerView Author Information Department of Chemistry, Princeton University Princeton, New Jersey 08544 Cite this: J. Am. Chem. Soc. 1998, 120, 10, 2484–2485Publication Date (Web):February 28, 1998Publication History Received15 December 1997Published online28 February 1998Published inissue 1 March 1998https://pubs.acs.org/doi/10.1021/ja974221phttps://doi.org/10.1021/ja974221prapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views790Altmetric-Citations79LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Anions,Assays,Hydroxyls,Lipids,Peptides and proteins Get e-Alerts
Sucrose Phosphate Synthase and Acid Invertase as Determinants of Sucrose Concentration in Developing Muskmelon (Cucumis melo L.) Fruits (1989)

Fruits of orange-fleshed and green-fleshed muskmelon (Cucumis melo L.) were harvested at different times throughout development to evaluate changes in metabolism which lead to sucrose accumulation, and to determine the basis of differences in fruit sucrose accumulation among genotypes. Concentrations of sucrose, raffinose saccharides, hexoses and starch, as well as activities of the sucrose metabolizing enzymes sucrose phosphate synthase (SPS) (EC 2.4.1.14), sucrose synthase (EC 2.4.1.13), and acid and neutral invertases (EC 3.2.1.26) were measured. Sucrose synthase and neutral invertase activities were relatively low (1.7 +/- 0.3 micromole per hour per gram fresh weight and 2.2 +/- 0.2, respectively) and changed little throughout fruit development. Acid invertase activity decreased during fruit development, (from as high as 40 micromoles per hour per gram fresh weight) in unripe fruit, to undetectable activity in mature, ripened fruits, while SPS activity in the fruit increased (from 7 micromoles per hour per gram fresh weight) to as high as 32 micromoles per hour per gram fresh weight. Genotypes which accumulated different amounts of sucrose had similar acid invertase activity but differed in SPS activity. Our results indicate that both acid invertase and SPS are determinants of sucrose accumulation in melon fruit. However, the decline in acid invertase appears to be a normal function of fruit maturation, and is not the primary factor which determines sucrose accumulation. Rather, the capacity for sucrose synthesis, reflected in the activity of SPS, appears to determine sucrose accumulation, which is an important component of fruit quality.
531 nm Green Lasing of InGaN Based Laser Diodes on Semi-Polar {20\bar21} Free-Standing GaN Substrates (2009)

Lasing in pure green region around 520 nm of InGaN based laser diodes (LDs) on semi-polar {201} free-standing GaN substrates was demonstrated under pulsed operation at room temperature. The longest lasing wavelength reached to 531 nm and typical threshold current density was 8.2 kA/cm2 for 520 nm LDs. Utilization of a novel {201} plane enabled a fabrication of homogeneous InGaN quantum wells (QWs) even at high In composition, which is exhibited with narrower spectral widths of spontaneous emission from LDs than those on other planes. The high quality InGaN QWs on the {201} plane advanced the realization of the green LDs.
Transmission line theory of collective plasma excitations in periodic two-dimensional electron systems: Finite plasmonic crystals and Tamm states (2012)

We present a comprehensive theory of the one-dimensional plasmonic crystal formed in the grating-gated two-dimensional electron gas (2DEG) in semiconductor heterostructures. To describe collective plasma excitations in the 2DEG, we develop a generalized transmission line theoretical formalism consistent with the plasma hydrodynamic model. We then apply this formalism to analyze the plasmonic spectra of 2DEG systems with steplike periodic changes of electron density, gate screening, or both. We show that in a periodically modulated 2DEG, a plasmonic crystal is formed, and we derive closed-form analytical expressions describing its energy band spectrum for both infinite and finite size crystals. Our results demonstrate a nonmonotonic dependence of the plasmonic band gap width on the electron density modulation. At so-called transparency points, where the plasmon propagates through the periodic 2DEG in a resonant manner, the plasmonic band gaps vanish. In semi-infinite plasmonic crystals, we demonstrate the formation of plasmonic Tamm states and analytically derive their energy dispersion and spatial localization. Finally, we present detailed numerical analysis of the plasmonic band structure of a finite four-period plasmonic crystal terminated either by an ohmic contact or by an infinite barrier on each side. We trace the evolution of the plasmonic band spectrum, including the Tamm states, with changing electron density modulation and analyze the boundary conditions necessary for formation of the Tamm states. We also analyze interaction between the Tamm states formed at the opposite edges of the short length plasmonic crystal. The validity of our theoretical approach was confirmed in experimental studies of plasmonic crystals in short, modulated plasmonic cavities [Dyer et al., Phys. Rev. Lett. 109, 126803 (2012)], which demonstrated excellent quantitative agreement between theory and experiment.
Role of Triptolide as an Adjunct Chemotherapy for Ovarian Cancer (2007)

In 44% of the animals tested the combined treatment caused complete regression of ovarian cancer. Combined observations indicate TPL may be an effective adjunct chemotherapy for ovarian cancer.
Expression of a maize cell wall hydroxyproline-rich glycoprotein gene in early leaf and root vascular differentiation. (1990)

The spatial pattern of expression for a maize gene encoding a hydroxyproline-rich glycoprotein (HRGP) was determined by in situ hybridization. During normal development of roots and leaves, the expression of the gene was transient and particularly high in regions initiating vascular elements and associated sclerenchyma. Its expression was also associated with the differentiation of vascular elements in a variety of other tissues. The gene encoded an HRGP that had been extracted from the cell walls of maize suspension culture cells and several other embryonic and post-embryonic tissues. The gene was present in one or two copies in different varieties of maize and in the related monocots teosinte and sorghum. A single gene was cloned from maize using a previously characterized HRGP cDNA clone [Stiefel et al. (1988). Plant Mol. Biol. 11, 483-493]. In addition to the coding sequences for the HRGP and an N-terminal signal sequence, the gene contained a single intron in the nontranslated 3' end.
Profile of immunoglobulin heavy chain variable gene repertoires and highly selective detection of malignant clonotypes in acute lymphoblastic leukemia (1995)

The predominant B cell immunoglobulin heavy chain variable gene (IgH-V) usage and the uniquely rearranged, clonotype-specific variable-diversity-joining region gene (VDJ) sequences were identified in patients with B cell acute lymphoblastic leukemia (B-ALL) using a novel DNA-based gene amplification strategy. The approach allows a thorough and sensitive determination of the number of clonal leukemic IgH rearrangements and their precise V gene usage. This strategy may be applied in the detection of minimal residual disease, in surveillance after induction of disease-free states, and in analyzing the effectiveness of purging autologous bone marrow of malignant clones. An initial primary polymerase chain reaction (PCR), directed by an IgH-J generic primer and a complement of family-specific IgH-V primers, defined the major B cell IgH-V gene usage. Use of an IgH-J generic primer supplanted the use of a constant region primer anchor and thus eliminated the need to target mRNA by the traditional RNA reverse transcription-PCR amplification method. Monoclonality of rearranged VDJ bands was further substantiated by high-resolution denaturant gel electrophoretic analysis. The predominant amplified bands were subcloned and sequenced. By sequencing through VDJ juxtaposed regions, that is, the third complementarity-determining region, clonotype-specific primers were developed and used in a secondary clonotype primer-directed PCR (CPD-PCR) to detect, with extreme sensitivity and specificity, a unique B cell clone. Analysis of the products of the CPD-PCR permitted the detection of a single malignant cell among 1 million polyclonal cells and superseded the constraints of prior studies that have provided a limited evaluation of family variable gene repertoire usage. Leukemic clonal rearrangements were detected in 100% of the eight cases of pediatric and two cases of adult B-ALL studied. Two or more clonal IgH-VDJ amplified sequences were observed in 50% of the B-ALL bone marrows analyzed. In two cases, clonotype-specific oligodeoxynucleotide primers, derived from B-ALL VDJ sequences, directed the secondary CPD-PCR, and disease activity was monitored after chemotherapy and allogeneic bone marrow transplantation.
Molecular Architecture and Electrostatic Properties of a Bacterial Porin (1991)

The integral membrane protein porin from Rhodobacter capsulatus consists of three tightly associated 16-stranded beta barrels that give rise to three distinct diffusion channels for small solutes through the outer membrane. The x-ray structure of this porin has revealed details of its shape, the residue distributions within the pore and at the membrane-facing surface, and the location of calcium sites. The electrostatic potential has been calculated and related to function. Moreover, potential calculations were found to predict the Ca2+ sites.
Interaction of Polyelectrolytes and Their Composites with Living Cells (2005)

Since the layer-wise polyelectrolyte deposition offers the opportunity to modify surfaces for biomedical applications, interactions and toxicity between polyelectrolytes and living cells become interesting. The aim of the present work is to determine the different factors such as contact area, charge, and transplantation site that influence the cell reaction to a specific polymer. We found that toxicity is influenced by all these factors and cannot be tested easily in a model.
Tuning Structure and Properties of Graded Triblock Terpolymer-Based Mesoporous and Hybrid Films (2011)

Despite considerable efforts toward fabricating ordered, water-permeable, mesoporous films from block copolymers, fine control over pore dimensions, structural characteristics, and mechanical behavior of graded structures remains a major challenge. To this end, we describe the fabrication and performance characteristics of graded mesoporous and hybrid films derived from the newly synthesized triblock terpolymer, poly(isoprene-b-styrene-b-4-vinylpyridine). A unique morphology, unachievable in diblock copolymer systems, with enhanced mechanical integrity is evidenced. The film structure comprises a thin selective layer containing vertically aligned and nearly monodisperse mesopores at a density of more than 10(14) per m(2) above a graded macroporous layer. Hybridization via homopolymer blending enables tuning of pore size within the range of 16 to 30 nm. Solvent flow and solute separation experiments demonstrate that the terpolymer films have permeabilities comparable to commercial membranes, are stimuli-responsive, and contain pores with a nearly monodisperse diameter. These results suggest that moving to multiblock polymers and their hybrids may open new paths to produce high-performance graded membranes for filtration, separations, nanofluidics, catalysis, and drug delivery.
Mutational analysis of the catalytic and feedback sites of the tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase of Escherichia coli (1988)

The nucleotide sequence of aroH, the structural gene for the tryptophan-sensitive 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase [DAHPS(Trp)], is presented, and the deduced amino acid sequence of AroH is compared with that of the tyrosine-sensitive (AroF) and phenylalanine-sensitive (AroG) DAHPS isoenzymes. The high degree of sequence similarity among the three isoenzymes strongly indicates that they have a common evolutionary origin. In vitro chemical mutagenesis of the cloned aroH gene was used to identify residues and regions of the polypeptide essential for catalytic activity and for tryptophan feedback regulation. Missense mutations leading either to loss of catalytic activity or to feedback resistance were found interspersed throughout the polypeptide, suggesting overlapping catalytic and regulatory sites in DAHPS(Trp). We conclude that the specificity of feedback regulation of the isoenzymes was probably acquired by the duplication and divergent evolution of an ancestral gene, rather than by domain recruitment.
Investigation of spacecraft outgassing by sensitive mass spectrometry (2011)

Rosetta is a solar-powered spacecraft of the European Space Agency on a mission to comet 67P/Churyumov-Gerasimenko. It consists of two main elements: the Rosetta orbiter and the Philea lander. The Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA), one out of ten scientific instruments on board, consists of three sensors: a cometary pressure sensor (COPS), a double focusing mass spectrometer (DFMS) and a reflectron-type time-of-flight mass spectrometer (RT0F). Even prior to launch, fluorine was detected, while chlorine appeared only in space. It is clear that some of the fluorine is due to remnants from brazing, but part of it is certainly due to fluorocarbons contained in structures and tapes. Although contamination control and outgassing restrictions have been considered for a long time during the design and construction of spacecraft, the phenomenon and the associated timescales still seem to be highly underestimated.