gebhart/patrepeval huggingface dataset:
Expression of P30, a protein with adhesive properties, in Schwann cells and neurons of the developing and regenerating peripheral nerve. (1991)

P30 is a heparin-binding protein with adhesive and neurite outgrowth-promoting properties present at high levels in the developing rat central nervous system (Rauvala, H., and R. Pihlaskari. 1987 J. Biol. Chem. 262:16625-16635). Partial sequencing of p30 has revealed homology or identity with HMG-1 (Rauvala, H., J. Merenmies, R. Pihlaskari, M. Korkolainen, M.-L. Huhtala, and P. Panula. 1988. J. Cell Biol. 107:2292-2305), a 28-kD protein that was originally purified from the thymus (Goodwin, G.H., C. Sanders, and E. W. Johns. 1973. Eur. J. Biochem. 38:14-19) which binds DNA in vitro. We have analyzed the distribution of p30 in the developing rat peripheral nervous system (PNS). P30 was detected by immunohistochemistry and Western blot analysis using antibodies raised against intact p30 and against a synthetic peptide corresponding to the amino terminus of the p30 molecule. P30 was localized to nonnuclear compartments of neurons and peripheral glial cells (Schwann cells). P30 immunoreactivity of PNS neurons persisted into adulthood. In contrast, Schwann cell staining decreased after the second postnatal week and was not detectable in adult animals. Neuron-Schwann cell contact was correlated with diminished p30 levels in Schwann cells. Schwann cells of the normal adult sciatic nerve did not express p30; however, when deprived of axonal contact by nerve transection, the Schwann cells of the distal nerve stained intensely for p30. In addition, when Schwann cells and dorsal root ganglion neurons were grown in coculture, Schwann cells that were associated with neurites were not as intensely stained by anti-p30 as Schwann cells that were not in contact with neurons. The pattern of p30 expression during development and regeneration, and its apparent regulation by cell-cell contact suggests that p30 plays a role in the interaction between neurons and Schwann cells during morphogenesis of peripheral nerves.
Molecular Classification and Molecular Forecasting of Breast Cancer: Ready for Clinical Application? (2005)

Profiling breast cancer with expression arrays has become common, and it has been suggested that the results from early studies will lead to understanding of the molecular differences between clinical cases and allow individualization of care. We critically review two main applications of expression profiling; studies unraveling novel breast cancer classifications and those that aim to identify novel markers for prediction of clinical outcome. Breast cancer may now be subclassified into luminal, basal, and HER2 subtypes with distinct differences in prognosis and response to therapy. However, profiling studies to identify predictive markers have suffered from methodologic problems that prevent general application of their results. Future work will need to reanalyze existing microarray data sets to identify more representative sets of candidate genes for use as prognostic signatures and will need to take into account the new knowledge of molecular subtypes of breast cancer when assessing predictive effects.
Splicing of the Maize Sh1 First Intron Is Essential for Enhancement of Gene Expression, and a T-Rich Motif Increases Expression without Affecting Splicing (2002)

Certain plant and animal introns increase expression of protein-coding sequences when placed in the 5' region of the transcription unit. The mechanisms of intron-mediated enhancement have not been defined, but are generally accepted to be post- or cotranscriptional in character. One of the most effective plant introns in stimulating gene expression is the 1,028-bp first intron of the Sh1 gene that encodes maize (Zea mays) sucrose synthase. To address the mechanisms of intron-mediated enhancement, we used reporter gene fusions to identify features of the Sh1 first intron required for enhancement in cultured maize cells. A 145-bp derivative conferred approximately the same 20- to 50-fold stimulation typical for the full-length intron in this transient expression system. A 35-bp motif contained within the intron is required for maximum levels of enhancement but not for efficient transcript splicing. The important feature of this redundant 35-bp motif is T-richness rather than the specific sequence. When transcript splicing was abolished by mutations at the intron borders, enhancement was reduced to about 2-fold. The requirement of splicing for enhancement was not because of upstream translation initiation codons contained in unspliced transcripts. On the basis of our current findings, we conclude that splicing of the Sh1 intron is integral to enhancement, and we hypothesize that transcript modifications triggered by the T-rich motif and splicing may link the mRNA with the trafficking system of the cell.
High-Speed Chromosome Sorting (1987)

Dual-beam high-speed sorting has been developed to facilitate purification of chromosomes based on DNA staining with the fluorescent dyes Hoechst 33258 and chromomycin A3. Approximately 200 chromosomes per second of two types can be sorted from a suspension of chromosomes isolated from human lymphoblasts while fluorescent objects (chromosomes, debris fragments, chromosome clumps, and nuclei) are processed at the rate of about 20,000 per second. This sorting rate is approximately ten times that possible with conventional sorters. Chromosomes of a single type can be sorted with a purity of about 90 percent. DNA from the sorted chromosomes is suitable for construction of recombinant DNA libraries and for gene mapping.
Role of lysosomal and cytosolic pH in the regulation of macrophage lysosomal enzyme secretion (1990)

Rapid and parallel secretion of lysosomal beta-N-acetylglucosaminidase and preloaded fluorescein-labelled dextran was initiated in macrophages by agents affecting intracellular pH (methylamine, chlorpromazine, and the ionophores monensin and nigericin). In order to evaluate the relative role of changes in lysosomal and cytosolic pH, these parameters were monitored by using pH-sensitive fluorescent probes [fluorescein-labelled dextran or 2',7'-bis(carboxyethyl)-5(6)-carboxyfluorescein]. All agents except chlorpromazine caused large increases in lysosomal pH under conditions where they induced secretion. By varying extracellular pH and ion composition, the changes in lysosomal and cytosolic pH could be dissociated. Secretion was then found to be significantly modulated by changes in cytosolic pH, being enhanced by alkalinization and severely inhibited by cytosolic acidification. However, changes in cytosolic pH in the absence of stimulus were unable to initiate secretion. Dissociation of the effects on lysosomal and cytosolic pH was also achieved by combining stimuli with either nigericin or acetate. Further support for a role of intracellular pH in the control of lysosomal enzyme secretion was provided by experiments where bicarbonate was included in the medium. The present study demonstrates that an increase in lysosomal pH is sufficient to initiate lysosomal enzyme secretion in macrophages and provides evidence for a significant regulatory role of cytosolic pH.
A Convenient Procedure for Moderate-scale Rothemund Synthesis of Lipophilic Porphyrins: an Alternative to the Adler–Longo and Lindsey Methodologies (1998)

Rothemund synthesis of porphyrins is conveniently achieved using p-toluenesulfonic acid-catalysed reaction between pyrrole and aldehyde with azeotropic removal of the water formed in the reaction. These conditions are suitable for moderate-scale reactions and involve an easy work-up. In this way, 5,10,15,20-tetraheptylporphyrin (2), 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)porphyrin (3), 5,10,15,20-tetra-tert-butylporphyrin (4) and 5,10,15,20-[pyromellitoyl(tetrakis-o-oxyethoxyphenyl)]por-phyrin (5) were prepared in moderate to good yields.
The Tgif2 gene contains a retained intron within the coding sequence (2006)

These data demonstrate that the Tgif2 gene contains a retained intron, within the second coding exon. This retained intron is not removed from the human mRNA at a detectable level, but is spliced out in a significant proportion of mouse RNAs. This alternate splicing is dependent entirely on sequences within the mouse Tgif2 coding sequence, suggesting the presence of an exonic splicing enhancer. Both splice forms of mouse Tgif2 produce proteins which are functional transcriptional repressors.
In‐column field‐amplified sample stacking of biogenic amines on microfabricated electrophoresis devices (2003)

A novel method for performing in-column field-amplified sample stacking (FASS) in chip-based electrophoretic systems is presented. The methodology involves the use of a narrow sample channel (NSC) injector. NSC injectors allow sample plugs to be introduced directly into the separation channel, and subsequent stacking and separation can proceed without any need for leakage control. More importantly, stacking and separation occur in a single step negating the requirement for complex channel geometries and voltage switching to control sample plugs during the stacking procedure. The chip is composed of six paralleled systems. Using the NSC injector design, the number of reservoirs in the multiplexed chip is reduced to N + 2, where N is the number of paralleled systems. This design feature radically reduces the complexity in chip structures and associated chip operation. The approach is applied to the analysis of fluorescently labelled biogenic amines affording detection at concentrations down to 20 pM.
Solvent Selection for Whole Cell Biotransformations in Organic Media (1995)

Although they were used historically as antimicrobial agents, there is a modern requirement to devise organic solvent systems for exploitation in the biotransformation by intact cells of substrates that are poorly soluble in water. Water-immiscible solvents are normally less cytotoxic than are water-miscible ones. While a unitary mechanism is excluded, damage to the membrane remains the likeliest major mechanism of cytotoxicity, and may be conveniently assessed using an electronic biomass probe. Studies designed to account for the mechanisms of action of general anesthetics and of uncouplers parallel those designed to account for the cytotoxicity of organic solvents. Although there are hundreds of potential physical descriptors of solvent properties, many are broadly similar to each other, such that the intrinsic dimensionality of solvent space is relatively small (< 10). This opens up the possibility of providing a rational biophysical basis for the optimization of the solvents used for biotransformations. The widely used descriptor of solvent behavior, log P (the octanol:water partition coefficient), is a composite of more fundamental molecular descriptors; this explains why there are rarely good correlations between cytotoxicity and log P when a wide variety of solvents is studied. Although the intrinsic dimensionality of solvent space is relatively small, pure solvents still populate it rather sparsely. Thus, mixtures of solvents can and do provide the opportunity of obtaining a solvent optimal for a biotransformation of interest.
Immediate and delayed VEGF‐mediated NO synthesis in endothelial cells: Role of PI3K, PKC and PLC pathways (2002)

1. The mechanism(s) by which vascular endothelial growth factor (VEGF) induces endothelial nitric oxide synthase (eNOS) activation remain(s) unclear up to a certain extent. Therefore, we sought to evaluate the contribution of numerous pathways in VEGF-induced nitric oxide (NO) synthesis by measuring cGMP production. In addition, as VEGF induces the synthesis of NO and platelet-activating factor (PAF), we wanted to assess if the induction of PAF and NO is contributing to the synthesis of each other. 2. Herein, we show that a treatment of endothelial cells with a phospholipase C (PLC) inhibitor (U73122), a calmodulin antagonist (W-7) or with intracellular calcium chelators (EGTA/AM, BAPTA/AM) prevented VEGF-mediated eNOS Ser(1177)-phosphorylation and NO synthesis measured by cGMP production. 3. Pretreatment with phosphatidylinositol 3-kinase (PI3K) (Wortmannin, LY294002) or protein kinase C (PKC) (GF109203X, Ro318220) inhibitors attenuated eNOS Ser(1177)-phosphorylation mediated by VEGF, but did not alter immediate (0-10 min) cGMP synthesis induced by VEGF, but abrogated by up to 84% the delayed (10-30 min) cGMP synthesis. 4. Pretreatment with PAF synthesis inhibitors or with PAF receptor antagonists did not abrogate neither eNOS Ser(1177)-phosphorylation nor cGMP synthesis mediated by VEGF. 5. In conclusion, VEGF induces an immediate cGMP synthesis through the PLC-Ca2+/CaM pathway, and that the induction of delayed cGMP synthesis implies Akt and PKC activity.
Report from a workshop on multianalyte microsphere assays (2002)

Multiplexed assays using fluorescent microspheres is an exciting technique that has been gaining popularity among researchers, particularly those in the public health field. Part of its popularity is due to its flexibility, as both immunoassays and oligonucleotide hybridization assays can be developed on this platform. This report summarizes a workshop held by the Centers for Disease Control and Prevention that discussed issues surrounding these assays and the Luminex 100 xMAP instrument. Topics included instrumentation, assay design, sample matrix and volume, quality control, and development of commercial applications.
Recent advances in silage microbiology (2013)

Recent advances in silage microbiology are reviewed. Most new techniques in silage microbiology use the polymerase chain reaction (PCR) to make copies of a portion of the DNA in microorganisms. These techniques allow us to identify and quantify species as well as do community analysis. The PCR-based techniques are uncovering new species, both bacteria and fungi, during storage and feeding. Silage inoculants are widely available, but of greater interest has been research investigating why inoculants are so successful. Various inoculant strains have been found to produce bacteriocins and other compounds that inhibit other bacteria and fungi, improving their chances for success. In vitro ruminal fermentation research is showing that some inoculated silages affect rumen microorganisms, reducing methane in some cases and increasing microbial biomass production in others. Better understanding of silage microbiology will allow us to better manage silos and develop better inoculants to improve silage quality.
Do Banks Respond Asymmetrically to the Global Crisis? Evidence From Turkey (2015)

This paper tests whether Turkish banks respond asymmetrically to the global crisis with respect to their ownership using bank-level data during 2002Q4-2013Q3 period and employing panel estimation techniques. The dependent variables are selected financial ratios on capital adequacy, asset quality, liquidity, profitability, balance sheet and income-expenditure structure. Main determinants are bank-specific control variables on overdue loans, overhead costs, FX open position and bank size as well as dummy variables for bank listing and bank age. Other determinants include GDP growth, inflation, exchange rate, policy rate and required reserves, which reflect the impact of macroeconomic conditions and the monetary policy on bank structure. Estimation results suggest that Turkish banks respond asymmetrically to the global crisis with respect to their ownership. This result can be attributed to structural, institutional and historical factors, which cause macroeconomic and policy-related explanatory variables to have uneven effects on banks before and after the global crisis. Meanwhile, the impacts of bank-specific determinants are also observed to be disproportionate across different ownership categories between the pre-crisis and the post-crisis periods. These findings highlight the importance of analyzing the Turkish banking sector by an ownership breakdown in order to detect the asymmetric response and the paper also emphasizes the need to perform the analysis by sub-periods to be able to capture the effect of the global crisis.
Complementary and Coordinated Roles of the VEGFs and Angiopoietins during Normal and Pathologic Vascular Formation (2002)

Mammalian organisms depend on their vasculature todeliver nutrients and oxygen to all of their tissues, totransport products (such as hormones and antibodies)from certain cells to distant parts of the body, and to carryaway waste products. The development of a functioningvasculature, as well as its proper integration into the tissues it serves, depends on myriad interactions and communications between the many cell types involved. Although a large number of signals are involved inmediating these intercellular communications, a greatdeal of focus has been directed to growth factors that aremembers of either the vascular endothelial growth factor(VEGF) family or the angiopoietin family. Why the focuson these two families of growth factors? First of all, thesetwo families of growth factors are unique in that they actvia receptors that are largely restricted to the vasculatureendothelium—this very restricted distribution of their receptors indicates that these two families of growth factorsevolved to play very particular roles specifically involving the vasculature. Moreover, genetic approaches—involving gene knockouts and transgenic overexpression inmice—have spectacularly confirmed the very critical andvery specific roles played by members of these twogrowth factor families during vascular development.Thus, the focus on the VEGFs and angiopoietins seemswell-placed based on their action via vascular-specific receptors and the confirmation of their critical and specificvascular roles based on genetic studies in mice. Since theVEGFs have been extensively dealt with in a number ofexcellent reviews (Eriksson and Alitalo 1999; Ferrara1999; Yancopoulos et al. 2000; Carmeliet et al. 2001),this review highlights work from our laboratory regarding the angiopoietins, although much of this work is presented in the context of the complementary and reciprocal actions of the angiopoietins as compared to theVEGFs...
The amino terminus of G protein alpha subunits is required for interaction with beta gamma. (1988)

The guanine nucleotide-binding proteins (G proteins), which transduce hormonal and light signals across the plasma membrane, are heterotrimers composed of alpha, beta, and gamma subunits. Activation of G proteins by guanine nucleotides is accompanied by dissociation of the heterotrimer: G + alpha.beta.gamma in equilibrium alpha G + beta.gamma. Brain contains several G proteins of which the most abundant are alpha 39.beta.gamma and alpha 41.beta.gamma. We have used proteolysis by trypsin to study the functional domains of the alpha subunits. In the presence of guanosine 5'-(3-O-thio)triphosphate, trypsin removes a 2-kDa peptide from the amino terminus of these proteins (Hurley, J. B., Simon, M. I., Teplow, D. B., Robishaw, J. D., and Gilman, A. G. (1984) Science 226, 860-862; Winslow, J. W., Van Amsterdam, J. R., and Neer, E. J. (1986) J. Biol. Chem. 261, 7571-7579). Tryptic cleavage does not affect the GTPase activity of the truncated molecule nor the apparent Km for GTP. However, removal of the 2-kDa amino-terminal peptide prevents association of the alpha subunits with beta.gamma. Since the apparent substrate for pertussis toxin-catalyzed ADP-ribosylation is the alpha.beta.gamma heterotrimer, the trypsin-cleaved alpha subunit is not a substrate for the toxin. Digestion of the carboxyl terminus of alpha 39 with carboxypeptidase A prevents ADP-ribosylation by pertussis toxin but does not interfere with the formation of alpha 39.beta.gamma heterotrimers. We do not yet know whether the amino-terminal region of alpha 39 interacts with beta gamma directly or whether it is necessary to maintain a conformation of alpha 39 which is required for heterotrimer formation. Further studies are needed to define the nature of the contracts between alpha and beta gamma subunits since understanding the structural basis for their reversible interaction is fundamental to understanding their function.
Temperature response of biological materials to pulsed non‐ablative CO2 laser irradiation (1991)

This paper presents surface temperature responses of various tissue phantoms and in vitro and in vivo biological materials in air to non-ablative pulsed CO2 laser irradiation, measured with a thermocamera. We studied cooling off behavior of the materials after a laser pulse, to come to an understanding of heat accumulation and related thermal damage during (super) pulsed CO2 laser irradiation. The experiments show a very slow decay of temperatures in the longer time regime. This behavior is well predicted by a simple model for one-dimensional heat flow that considers the CO2 laser radiation as producing a heat flux on the material surface. The critical pulse repetition frequency for which temperature accumulation is sufficiently low is estimated at about 5 Hz. Although we have not investigated the ablative situation, our results suggest that very low pulse frequencies in microsurgical procedures may be recommended.
Integrated DNA, cDNA, and protein studies in Becker muscular dystrophy show high exception to the reading frame rule (2008)

Becker muscular dystrophy (BMD) is a milder form of X-linked Duchenne muscular dystrophy (DMD). Here, we report a study of 75 patients with immunoblot and/or immunostaining findings of muscle biopsy consistent with BMD (abnormal dystrophin). We utilized multiplex ligation dependent probe amplification (MLPA) on genomic DNA (gDNA) to screen all 79 exons for both deletions and duplications. A total of 19 patients testing negative for MLPA mutations were tested for mRNA splicing abnormalities using cDNA-MLPA on muscle biopsy. Complete cDNA sequencing was done on MLPA-negative patients. We identified disease-causing mutations in 66 (88%) of the patients. Of the mutation-positive patients, 42 (64%) showed deletions of one or more exons, 14 (21%) showed duplications, and 10 (15%) showed various mutations detected by cDNA-MLPA and sequencing studies. We found a high rate of "exceptions" to the reading frame rule in this BMD series (out-of-frame BMD; 17/56 deletions/duplications; 30%). This was partly explained by the high incidence of 5' gene deletions in BMD patients (a region known to be a hotspot for exceptions), and due to complex splicing patterns in which a subset of transcripts showed deletions larger than gDNA (exon-skipping). Comparing our findings in BMD to previously published DMD data, BMD patients have higher proportions of duplications, a different distribution of mutations, and higher exception to the reading frame rule.
Development of a Peptide Nucleic Acid Array Platform for the Detection of Genetically Modified Organisms in Food (2005)

Two previously developed platforms, a multiplex polymerase chain reaction (PCR) and a peptide nucleic acid (PNA) array, the former allowing for the simultaneous detection of five transgenes and two endogenous controls in food and feed matrices and the latter for the assessment of the identity of amplified PCR products, were combined in order to develop a PNA array device for the screening of genetically modified organisms (GMOs) in food. PNA probes were opportunely designed, synthesized, and deposited on commercial slides. The length of the probes as well as the distance of the probes from the surface were evaluated and found to be critical points. The most suitable probes were found to be 15-mer PNAs linked to the slide surface by means of two 2-(2-aminoethoxy)ethoxyacetic acids as spacers. The device was tested on a model system constituted by flour samples containing a mixture of standards at known concentrations of transgenic material, in particular Roundup Ready soybean and Bt11, Bt176, Mon810, and GA21 maize: The DNA was amplified using the specific multiplex PCR method and tested on the PNA array. The method proposed was found to be able to correctly identify every GMO present in the tested samples.