gebhart/patrepeval huggingface dataset:
BIOMASSETHANOL: Technical Progress, Opportunities, and Commercial Challenges (1999)

▪ Abstract Ethanol made from lignocellulosic biomass sources, such as agricultural and forestry residues and herbaceous and woody crops, provides unique environmental, economic, and strategic benefits. Through sustained research funding, primarily by the U.S. Department of Energy, the estimated cost of biomass ethanol production has dropped from ∼$4.63/gallon in 1980 to ∼$1.22/gallon today, and it is now potentially competitive for blending with gasoline. Advances in pretreatment by acid-catalyzed hemicellulose hydrolysis and enzymes for cellulose breakdown coupled with recent development of genetically engineered bacteria that ferment all five sugars in biomass to ethanol at high yields have been the key to reducing costs. However, through continued advances in accessing the cellulose and hemicellulose fractions, the cost of biomass ethanol can be reduced to the point at which it is competitive as a pure fuel without subsidies. A major challenge to realizing the great benefits of biomass ethanol remains to substantially reduce the risk of commercializing first-of-a-kind technology, and greater emphasis on developing a fundamental understanding of the technology for biomass conversion to ethanol would reduce application costs and accelerate commercialization. Teaming of experts to cooperatively research key processing steps would be a particularly powerful and effective approach to meeting these needs.
Latent class analysis permits unbiased estimates of the validity of DAT for the diagnosis of visceral leishmaniasis (1999)

LCA modelling proved a useful tool, as it gave consistent estimates of test characteristics and allowed for control of confounding factors and interaction effects. Since VL is a life-threatening disease for which expensive but effective and safe treatment exists, a clinical suspect in an endemic area should be treated on the basis of a positive DAT result.
The Immuno-Regulatory Protein CD200 Is Overexpressed in a Subset of B-Cell Chronic Lymphocytic Leukemias and Plays a Role in Down-Regulating the TH1 Immune Response (2004)

s for the 19th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer, San Francisco, California, November 4-7, 2004: Mechanisms of Escape/Resistance
Statistical experimental design in plasma etch modeling (1991)

The objective of this work is to obtain a comprehensive set of empirical models for plasma etch rates, uniformity, selectivity, and anisotropy. These models accurately represent the behavior of a specific piece of equipment under a wide range of etch recipes, thus making them ideal for manufacturing and diagnostic purposes. The response characteristics of a CCl/sub 4/-based plasma process used to etch doped polysilicon were examined via a 2/sup 6-1/ fractional factorial experiment followed by a Box-Wilson design. The effects of variation in RF power, pressure, electrode spacing, CCl/sub 4/ flow, He flow and O/sub 2/ flow on several output variables, including etch rate, selectivity, and process uniformity, were investigated. Etch anisotropy was also measured by scanning electron microscopy analysis on a 2/sup 6-2/ fraction of the original experiment. The screening factorial experiment was designed to isolate the most significant input parameters. Using this information as a platform from which to proceed, the subsequent phase of the experiment allowed the development of empirical models of etch behavior using response surface methodology (G. E. P. Box and N. D. Draper, 1987). The models were subsequently used to optimize the etch process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Some aspects of the electron impact induced fragmentation of diastereoisomeric thymidine cyclic 3′,5′‐phosphoranilidothioates (1980)

Abstract The similarities between the electron impact induced fragmentation of diastereoisomeric 4‐methyl‐2‐thio‐2 amino‐1,3,2‐dioxaphosphorinanes and thymidine cyclic 3′,5′‐phosphoranilidothioates are discussed.
Mechanisms of ATP release by human trabecular meshwork cells, the enabling step in purinergic regulation of aqueous humor outflow (2011)

Our guiding hypothesis is that ecto-enzymatic conversion of extracellular ATP to adenosine activates A(1) adenosine receptors, reducing resistance to aqueous humor outflow and intraocular pressure. The initial step in this purinergic regulation is ATP release from outflow-pathway cells by mechanisms unknown. We measured similar ATP release from human explant-derived primary trabecular meshwork (TM) cells (HTM) and a human TM cell line (TM5). Responses to 21 inhibitors indicated that pannexin-1 (PX1) and connexin (Cx) hemichannels and P2X(7) receptors (P2RX(7) ) were comparably important in modulating ATP release induced by hypotonic swelling, whereas vesicular release was insignificant. Consistent with prior studies of PX1 activity in certain other cells, ATP release was lowered by the reducing agent dithiothreitol. Overexpressing PX1 in HEK293T cells promoted, while partial knockdown (KD) in both HEK293T and TM5 cells inhibited hypotonicity-activated ATP release. Additionally, KD reduced the pharmacologically defined contribution of PX1 and enhanced those of Cx and P2RX(7) . ATP release was also triggered by raising intracellular Ca(2+) activity with ionomycin after a prolonged lag time and was unaffected by the PX1 blocker probenecid, but nearly abolished by P2RX(7) antagonists. We conclude that swelling-stimulated ATP release from human TM cells is physiologically mediated by PX1 and Cx hemichannels and P2X(7) receptors, but not by vesicular release. PX1 appears not to be stimulated by intracellular Ca(2+) in TM cells, but can be modulated by oxidation-reduction state. The P2RX(7) -dependent component of swelling-activated release may be mediated by PX1 hemichannels or reflect apoptotic magnification of ATP release, either through itself and/or hemichannels.
Characterization of the Minimal Replicon of a Cryptic Deinococcus radiodurans SARK Plasmid and Development of Versatile Escherichia coli-D. radiodurans Shuttle Vectors (2000)

The nucleotide sequence of a 12-kb fragment of the cryptic Deinococcus radiodurans SARK plasmid pUE10 was determined, in order to direct the development of small, versatile cloning systems for Deinococcus. Annotation of the sequence revealed 12 possible open reading frames. Among these are the repU and resU genes, the predicted products of which share similarity with replication proteins and site-specific resolvases, respectively. The products of both genes were demonstrated using an overexpression system in Escherichia coli. RepU was found to be required for replication, and ResU was found to be required for stable maintenance of pUE10 derivatives. Gel shift analysis using purified His-tagged RepU identified putative binding sites and suggested that RepU may be involved in both replication initiation and autoregulation of repU expression. In addition, a gene encoding a possible antirestriction protein was found, which was shown to be required for high transformation frequencies. The arrangement of the replication region and putative replication genes for this plasmid from D. radiodurans strain SARK is similar to that for plasmids found in Thermus but not to that for the 45.7-kb plasmid found in D. radiodurans strain R1. The minimal region required for autonomous replication in D. radiodurans was determined by sequential deletion of segments from the 12-kb fragment. The resulting minimal replicon, which consists of approximately 2.6 kb, was used for the construction of a shuttle vector for E. coli and D. radiodurans. This vector, pRAD1, is a convenient general-purpose cloning vector. In addition, pRAD1 was used to generate a promoter probe vector, and a plasmid containing lacZ and a Deinococcus promoter was shown to efficiently express LacZ.
Molecular Mechanisms of Glioma Cell Motility (2017)

Gliomas are the most common intracranial tumors in humans. The most malignant among these tumors is glioblastoma (GBM), with an incidence of 3–5 out of 100,000 persons in Western countries. GBM arises either de novo (primary GBM) or develops from a lower grade glioma (secondary GBM). The prognosis is poor. GBMs are lethal tumors and even optimal surgical resection, followed by chemotherapy and irradiation, results in a median survival of about 12–15 months. One characteristic that is responsible for GBM malignancy, and its worse prognosis, is the highly infiltrative growth of GBM cells into the healthy brain. GBM cell migration and invasion is a very complex process that is regulated by several factors, which include changes in the migrating cell itself as well as the tumor microenvironment. This chapter provides an overview of routes of invasion of glioma cells, the signaling pathways that drive glioma cell motility, and the processes through which glioma cells modulate their surrounding environment.
Protéines messagères (2000)

Plusieurs protéines sont internalisées par des cellules vivantes grâce à un mécanisme distinct de l’endocytose classique. Elles ont ainsi accès direct au cytoplasme et au noyau des cellules. Ces mêmes protéines sont souvent sécrétées sans peptide signal. Des travaux récents portant sur ce mode original de signalisation intercellulaire ouvrent la voie à des interprétations nouvelles de plusieurs phénomènes développementaux et de certaines observations physiologiques. Ces travaux sont aussi à l’origine de développements biotechnologiques dans le domaine de la vectorisation.
Enhanced Cell Ingrowth and Proliferation through Three-Dimensional Nanocomposite Scaffolds with Controlled Pore Structures (2010)

We present enhanced cell ingrowth and proliferation through cross-linked three-dimensional (3D) nanocomposite scaffolds fabricated using poly(propylene fumarate) (PPF) and hydroxyapatite (HA) nanoparticles. Scaffolds with controlled internal pore structures were produced from computer-aided design (CAD) models and solid freeform fabrication (SFF) technique, while those with random pore structures were fabricated by a NaCl leaching technique for comparison. The morphology and mechanical properties of scaffolds were characterized using scanning electron microscopy (SEM) and mechanical testing, respectively. Pore interconnectivity of scaffolds was assessed using X-ray microcomputed tomography (micro-CT) and 3D imaging analysis. In vitro cell studies have been performed using MC3T3-E1 mouse preosteoblasts and cultured scaffolds in a rotating-wall-vessel bioreactor for 4 and 7 days to assess cell attachment, viability, ingrowth depth, and proliferation. The mechanical properties of cross-linked nanocomposite scaffolds were not significantly different after adding HA or varying pore structures. However, pore interconnectivity of PPF/HA nanocomposite scaffolds with controlled pore structures has been significantly increased, resulting in enhanced cell ingrowth depth 7 days after cell seeding. Cell attachment and proliferation are also higher in PPF/HA nanocomposite scaffolds. These results suggest that cross-linked PPF/HA nanocomposite scaffolds with controlled pore structures may lead to promising bone tissue engineering scaffolds with excellent cell proliferation and ingrowth.
Regulation of Phosphatidylinositol 3,4,5-Trisphosphate 5′-Phosphatase Activity by Insulin (1996)

Polyphosphoinositides are thought to be mediators of cellular signaling pathways as well as regulators of cytoskeletal elements and membrane trafficking events. It has recently been demonstrated that a class of phosphatidylinositol (PI) 3,4,5-P3 5'-phosphatases contains SH2 domains and proline-rich regions, which are present in many signaling proteins. We report here that insulin stimulation of Chinese hamster ovary cells (CHO-T) expressing human insulin receptors causes an 8-10-fold increase in PI 3,4,5-P3 5'-phosphatase activity in anti-phosphotyrosine immunoprecipitates of the cell lysates. This insulin-sensitive polyphosphoinositide 5'-phosphatase did not catalyze dephosphorylation of PI 4,5-P2. No change in 5'-phosphatase activity was detected in insulin receptor or IRS-1 immune complexes in response to insulin. However, insulin treatment of CHO-T cells markedly increased the PI 3,4,5-P3 5'-phosphatase activity associated with Shc and Grb2. The insulin-regulated polyphosphoinositide 5'-phosphatase was not immunoreactive with antibody raised against the recently cloned SHIP 5'-phosphatase reported to associate with Shc and Grb2 in B lymphocytes. These data demonstrate that insulin causes formation of complexes containing a PI 3,4,5-P3 5'-phosphatase, and Shc or Grb2, or both, suggesting an important role of this enzyme in insulin signaling.
Transduction of a Mesenchyme-specific Gene Periostin into 293T Cells Induces Cell Invasive Activity through Epithelial-Mesenchymal Transformation (2006)

Tumor metastasis is a multistep pathological process involved in the final phase of tumor development. During this process, epithelium-derived tumor cells undergo fibroblast-like transformation, referred to as epithelial-mesenchymal transition (EMT), which contributes to aggressive behavior of tumors. We identify periostin, a mesenchyme-specific gene product, as a contributor to EMT and metastatic potential. Stable expression of a periostin transgene in tumorigenic but non-metastatic 293T cells caused cells to undergo fibroblast-like transformation accompanied by increased expressions of vimentin, epidermal growth factor receptor (EGFR), and matrix metalloproteinase-9. The cells expressing ectopic periostin increased cell migration, invasion, and adhesion by 2-9-fold. Invasive characteristics required signaling through integrin alpha(v)beta5 and EGFR. In addition, periostin-engineered 293T cells formed metastases in immunodeficient mice following either cardiac inoculation or injection into mammary fat pad. These data demonstrate an active role for periostin in EMT and metastasis that requires cross-talk between integrin and EGFR signaling pathways.
Identification and characterization of LTBP-2, a novel latent transforming growth factor-beta-binding protein. (1994)

Latent transforming growth factor-beta (TGF-beta)-binding protein (LTBP) is a component of the latent TGF-beta complex in human platelets. LTBP is composed of two different cysteine-rich repeat sequences, i.e. epidermal growth factor (EGF)-like repeats and a repeat containing 8 cysteine residues. The overall structure of LTBP is similar to those of the microfibrillar proteins fibrillin-1 and fibrillin-2. Here we report the identification of a novel protein termed LTBP-2, which is structurally related to LTBP. cDNA for LTBP-2 was obtained from human foreskin fibroblast cDNA libraries using a fragment of the LTBP cDNA as a probe. LTBP-2 is composed of 20 EGF-like repeats and four copies of the 8-cysteine repeat. The amino acid sequence of LTBP-2 is 41% identical to that of LTBP and 25% identical to that of fibrillin-1. LTBP-2 is synthesized as a 240-kDa protein by human foreskin fibroblasts and also by COS cells transfected with the isolated LTBP-2 cDNA. Similar to LTBP, a considerable part of LTBP-2 was found to be associated with extracellular matrix. Co-transfection of cDNAs for LTBP-2 and TGF-beta 1 revealed that LTBP-2 forms a high molecular weight complex with the TGF-beta 1 precursor. The LTBP-2 gene was assigned to chromosome 14q24. These results indicate that different forms of latent TGF-beta complexes occur and suggest that the different associated proteins may function to target the complexes to specific sites.
Cloning and characterization of a second complementary DNA for human tryptase. (1990)

A second cDNA for human tryptase, called beta-tryptase, was cloned from a mast cell cDNA library in lambda ZAP. Its nucleotide sequence and corresponding amino acid sequence were determined and compared with those of a previously cloned tryptase cDNA, now called alpha-tryptase. The 1,142-base sequence of beta-tryptase encodes a 30-amino acid leader sequence of 3,089 D and a 245-amino acid catalytic region of 27,458 D. The amino acid sequence of beta-tryptase is 90% identical with that of alpha-tryptase, the first 20 amino acids of the catalytic portions being 100% identical. This identity, together with recognition of each recombinant protein by monoclonal antibodies directed against purified tryptase validate the tryptase identity of both alpha-tryptase and beta-tryptase cDNA molecules. Modest differences between the nucleic acid sequences of alpha- and beta-tryptase occurred throughout the cDNA molecules except in the 3' noncoding regions, which were identical. Although most highly conserved regions of amino acid sequence in the trypsin superfamily are conserved in both tryptase molecules, beta-tryptase has one carbohydrate binding site compared to two in alpha-tryptase, and one additional amino acid in the catalytic sequence. Regions of the substrate binding pocket in beta-tryptase (DSCQ, residues 218-221; SWG, residues 243-245) differ slightly from those in alpha-tryptase (DSCK, residues 217-220; SWD, residues 242-244). The presence of both alpha- and beta-tryptase sequences in each haploid genome was indicated by finding alpha- and beta-tryptase specific fragments after amplification by PCR of genomic DNA in 10 unrelated individuals. Localization of both alpha- and beta-tryptase sequences to human chromosome 16 was then performed by analysis of DNA preparations from 25 human/hamster somatic hybrids by PCR. It is now possible to assess the expression of each tryptase cDNA by mast cells and the relationship of each gene product to the active enzyme.
Crosslinked chitosan microspheres for encapsulation of diclofenac sodium: effect of crosslinking agent (2002)

Microspheres of chitosan crosslinked with three different crosslinking agents viz, glutaraldehyde, sulphuric acid and heat treatment have been prepared to encapsulate diclofenac sodium (DS). Chitosan microspheres are produced in a w/o emulsion followed by crosslinking in the water phase by one of the crosslinking methods. Encapsulation of DS has been carried out by soaking the already swollen crosslinked microspheres in a saturated solution of DS. Microspheres are further characterized by FTIR, x-RD and SEM. The in-vitro release studies are performed in 7.4 pH buffer solution. Microspheres produced are spherical and have smooth surfaces, with sizes ranging between 40-230 microm, as evidenced by SEM. The crosslinking of chitosan takes place at the free amino group in all the cases, as evidenced by FTIR. This leads to the formation of imine groups or ionic bonds. Polymer crystallinity increases after crosslinking, as determined by x-RD. The method adopted for drug loading into the microspheres is satisfactory, and up to 28-30% w/w loading is observed for the sulphuric acid-crosslinked microspheres, whereas 23-29 and 15-23% of loadings are obtained for the glutaraldehyde (GA)- and heat-crosslinked microspheres, respectively. Among all the systems studied, the 32% GA crosslinked microspheres have shown the sloxvest release i.e. 41% at 420 min, and a fastest release of 81% at 500 min is shown by heat crosslinking for 3 h. Drug release from the matrices deviates slightly from the Fickian process.
Immunological Functions of the Membrane Proximal Region of MHC Class II Molecules (2016)

Major histocompatibility complex (MHC) class II molecules present exogenously derived antigen peptides to CD4 T cells, driving activation of naïve T cells and supporting CD4-driven immune functions. However, MHC class II molecules are not inert protein pedestals that simply bind and present peptides. These molecules also serve as multi-functional signaling molecules delivering activation, differentiation, or death signals (or a combination of these) to B cells, macrophages, as well as MHC class II-expressing T cells and tumor cells. Although multiple proteins are known to associate with MHC class II, interaction with STING (stimulator of interferon genes) and CD79 is essential for signaling. In addition, alternative transmembrane domain pairing between class II α and β chains influences association with membrane lipid sub-domains, impacting both signaling and antigen presentation. In contrast to the membrane-distal region of the class II molecule responsible for peptide binding and T-cell receptor engagement, the membrane-proximal region (composed of the connecting peptide, transmembrane domain, and cytoplasmic tail) mediates these "non-traditional" class II functions. Here, we review the literature on the function of the membrane-proximal region of the MHC class II molecule and discuss the impact of this aspect of class II immunobiology on immune regulation and human disease.
Coronary Arteries: Magnetization-prepared Contrast-enhanced Three-dimensional Volume-targeted Breath-hold MR Angiography (2001)

A volume-targeted contrast agent-enhanced breath-hold coronary magnetic resonance angiographic technique was optimized and evaluated in 16 volunteers. Substantial increases in coronary signal-to-noise ratio, contrast-to-noise ratio, lengths of depiction, and vessel sharpness were observed on enhanced images. The imaging approach with two 20-mL injections of contrast agent covers the left and right coronary arteries in two breath holds and is a promising method for coronary imaging.
Hydrated Electron Dynamics: From Clusters to Bulk (2004)

The electronic relaxation dynamics of size-selected (H2O)n-/(D2O)n[25 </= n </= 50] clusters have been studied with time-resolved photoelectron imaging. The excess electron (ec-) was excited through the ec-(p)<--ec-(s) transition with an ultrafast laser pulse, with subsequent evolution of the excited state monitored with photodetachment and photoelectron imaging. All clusters exhibited p-state population decay with concomitant s-state repopulation (internal conversion) on time scales ranging from 180 to 130 femtoseconds for (H2O)n- and 400 to 225 femtoseconds for (D2O)n-; the lifetimes decrease with increasing cluster sizes. Our results support the "nonadiabatic relaxation" mechanism for the bulk hydrated electron (eaq-), which invokes a 50-femtosecond eaq-(p)-->eaq-(s(dagger)) internal conversion lifetime.
An Efficient Technique for the Optimization of Submillimeter-wave Schottky-diode Harmonic Multipliers (2000)

A simple and efficient modified harmonic-balance technique is presented. This new algorithm is suitable for the large-signal time-dependent analysis of nonlinear millimeter wave circuits. The accurate design and successful implementation of very high frequency nonlinear circuits requires both a detailed understanding of the physical operation of the active devices and of how these nonlinear devices interact with the linear embedding circuit. This work addresses the specific task of establishing a robust simulation tool that combined this novel modified harmonic-balance circuit analysis technique with a physicsbased hydrodynamic transport model device simulator. A comparison with the accelerated fixed-point (AFP) harmonic-balance technique has been made through an evaluation of a Schottky-diode multiplier. The result shows that this approach can be used to realize improved multiplier operation with a minimal time of numerical computation. I.
The specification of neuronal identity by graded sonic hedgehog signalling (1999)

During the development of vertebrate nervous system, distinct classes of motor neurons and interneurons are generated at distinct dorsoventral positions in the ventral neural tube. The differentiation of these neuronal subtypes is directed by the secreted protein Sonic Hedgehog (Shh). Shh acts in a graded manner to establish different neural progenitor cell populations, defined by the expression of homeodomain transcription factors. These factors are critical for the interpretation of graded Shh signalling and act initially both to refine progenitor domain boundaries and to maintain their integrity. Subsequently, these factors direct the expression of genes that confer neuronal subtype identity to post-mitotic neurons.