gebhart/patrepeval huggingface dataset:
High dose intravenous iron, mineral homeostasis and intact FGF23 in normal and uremic rats (2013)

In non-iron depleted normal and uremic rats a single high dose of either of two intravenous iron preparations, iron isomaltoside 1000, and ferric carboxymaltose, had no effect on plasma levels of iFGF23 and phosphate for up to seven days.
High-resolution characterization of the pancreatic adenocarcinoma genome (2004)

The pancreatic adenocarcinoma genome harbors multiple amplifications and deletions, pointing to the existence of numerous oncogenes and tumor suppressor genes driving the genesis and progression of this lethal cancer. Here, array comparative genomic hybridization on a cDNA microarray platform and informatics tools have been used to define the copy number alterations in a panel of 24 pancreatic adenocarcinoma cell lines and 13 primary tumor specimens. This high-resolution genomic analysis has identified all known regional gains and losses as well as many previously uncharacterized highly recurrent copy number alterations. A systematic prioritization scheme has selected 64 focal minimal common regions (MCRs) of recurrent copy number change. These MCRs possess a median size of 2.7 megabases (Mb), with 21 (33%) MCRs spanning 1 Mb or less (median of 0.33 Mb) and possessing an average of 15 annotated genes. Furthermore, complementary expression profile analysis of a significant fraction of the genes residing within these 64 prioritized MCRs has enabled the identification of a subset of candidates with statistically significant association between gene dosage and mRNA expression. Thus, the integration of DNA and RNA profiles provides a highly productive entry point for the discovery of genes involved in the pathogenesis of pancreatic adenocarcinoma.
Characterization of Hydraulically-Induced Fracture Network Using Treatment and Microseismic Data in a Tight-Gas Formation: A Geomechanical Approach (2009)

Abstract Large amount of gas are being produced from unconventional tight-gas sand reservoirs (e.g., Cotton Valley Fm., Lobo Fm., Taylor Sand Fm. and, Wilcox Fm., etc.) and shale gas-bearing formations (e.g, Barnett, Fayetteville, Marcellus, Woodford, etc.). These plays are partly technology driven and partly economics driven. Modern well log evaluation techniques and completion methods are required to yield economic wells. In some cases microseismic monitoring campaigns are performed in these various low permeability environments to improve the understanding of the induced fracture network and to go beyond the simple assumption of a symmetric bi-wing fracture system. To better characterize the induced fracture network, a semi-analytical pseudo 3-D geomechanical model was developed based on considerations of the conservation of injected fluid mass and the mechanic interactions both between fractures and injected fluid as well as among the fractures. The hydraulically stimulated volume is represented by a horizontally expanding ellipse containing a simplified fracture network consisting of two sets of vertical planar fractures perpendicular to one another. This model provides a mathematically-equivalent description of the process of hydraulic fracture propagation and the characteristics of the induced fractures. Using microseismic datasets obtained during hydraulic treatments in several tight formations together with measured wellbore pressure and treatment parameters as the input, the modeling analysis yields information of the induced fracture network including fracture spacing and associated confining stress contrast. The results indicate a vertically contained developing fracture network with anisotropic spacing and moderate confining stress contrast. The fracture network extension toward the maximum horizontal stress is however limited. This information is then used as the input of the model to carry out forward simulations and provide detailed information of time-dependent fracture propagation including front location, fluid pressure, fracture width, induced porosity and permeability.
Reversible subband coding of images (1995)

Abstract In conventional 1D filter banks used for reversible subband coding of gray‐level still images, the high‐band signals are extrapolative or interpolative prediction error signals, the former using one side of the pixels alone and the latter using two sides of the pixels but with levels four times that of the input signals. This paper proposes a reversible subband coding method which has a high compression efficiency by reducing the entropy of the high‐band signal. This method employs 1D filter banks which use interpolative prediction error signals having levels twice that of the input signal as the high‐band signals. This paper also describes the design of non‐separable filter banks which predict a pixel in question by using four pixels around the point. The compression efficiency of the proposed method has been compared with the conventional method by using real images. The results show the following: the entropy of the proposed method is smaller than the conventional method by 0.1 to 0.5 bits/pel; some samples processed by the proposed method show a higher compression efficiency than those in the reversible predictive coding; the separable filter banks have a higher compression efficiency than the nonseparable filter banks (both based on the proposed method); and the reduced images using the proposed separable method with a lowpass filter have many taps to suppress aliasing.
Fabrication of long-period fiber gratings with 157-nm F2 laser radiation (2001)

Record short wavelength F2 laser light was applied for the first time to rapidly form strong (&gt;20 dB) long-period gratings in hydrogen-free and hydrogen-loaded telecommunication fiber. In hydrogen-loaded fiber, 157-nm grating formation was 250-fold faster than with 248-nm KrF laser radiation.
Identification of a novel human fibroblast growth factor and characterization of its role in oncogenesis. (2001)

The fibroblast growth factor (FGF) family of signaling molecules has been implicated in normal developmental and physiological processes, as well as in human malignancy. Using a homology-based genomic DNA mining process, we identified a human gene encoding a novel member of the FGF family, that we designate FGF-20. The FGF-20 cDNA was isolated, and its sequence confirmed the gene prediction. FGF-20 is expressed in normal brain, particularly the cerebellum, and in some cancer cell lines. Recombinant FGF-20 protein induces DNA synthesis in a variety of cell types and is recognized by multiple FGF receptors. Ectopic expression of FGF-20 in NIH 3T3 cells renders the cells transformed in vitro and tumorigenic in nude mice. These results underscore the utility of mining genomic DNA databases and reveal FGF-20 to be a novel oncogene that may play a role in human cancer.
Elemental Diet‐Induced Immune Suppression Is Caused by Both Bacterial and Dietary Factors (1993)

Because it is unclear whether elemental diet-induced immune suppression is an indirect effect caused by the translocating bacteria or is directly caused by the elemental diet, we tested whether prevention of diet-induced bacterial translocation or disruption of the gut microflora ecology would prevent diet-induced impaired lymphocyte function in a rat elemental diet model. Prevention of diet-induced bacterial translocation was accomplished by the addition of cellulose fiber or oral antibiotics (penicillin and streptomycin) to the elemental diet feeding regimen. Control groups consisted of rat food-fed and elemental diet-fed (4.25% amino acids; 28% glucose) rats. Immune function was quantitated by measuring the mitogen-induced blastogenic response of peripheral blood or splenic mononuclear cells to the mitogens concanavalin A and phytohemagglutinin. Bacterial translocation from the gut to the mesenteric lymph node and cecal bacterial population levels were measured in all groups. Although the incidence of elemental diet-induced bacterial translocation was reduced from 100% to 25% (p < .01) by the addition of dietary fiber, fiber did not prevent diet-induced impaired lymphocyte function. Because fiber supplementation of the elemental diet did not completely prevent diet-induced intestinal bacterial overgrowth or bacterial translocation, the experiment was repeated in antibiotic-decontaminated rats. Antibiotic decontamination completely prevented diet-induced intestinal bacterial overgrowth and bacterial translocation. Although antibiotic decontamination reduced the magnitude of lymphocyte mitogen suppression (p < .05), it was not fully effective in reversing the diet-induced lymphocyte suppression. These results indicate that elemental diet-induced lymphocyte blastogenic suppression is related to both bacterial and dietary factors.
Automatic reconstruction of piecewise planar models from multiple views (2003)

A new method is described for automatically reconstructing 3D planar faces from multiple images of a scene. The novelty of the approach lies in the use of inter-image homographies to validate and best estimate the plane, and in the minimal initialization requirements-only a single 3D line with a textured neighbourhood is required to generate a plane hypothesis. The planar facets enable line grouping and also the construction of parts of the wireframe which were missed due to the inevitable shortcomings of feature detection and matching. The method allows a piecewise planar model of a scene to be built completely automatically, with no user intervention at any stage, given only the images and camera projection matrices as input. The robustness and reliability of the method are illustrated on several examples, from both aerial and interior views.
Phospholipases C and A2control lysosome-mediated IL-1β secretion: Implications for inflammatory processes (2004)

Blocking the activity of IL-1 beta has entered the clinical arena of treating autoimmune diseases. However, a successful outcome of this approach requires a clear definition of the mechanisms controlling IL-1 beta release. These are still unclear as IL-1 beta, lacking a secretory signal peptide, follows a nonclassical pathway of secretion. Here, we analyze the molecular mechanism(s) undergoing IL-1 beta processing and release in human monocytes and provide a unifying model for the regulated secretion of the cytokine. Our data show that in a first step, pro-caspase-1 and endotoxin-induced pro-IL-1 beta are targeted in part to specialized secretory lysosomes, where they colocalize with other lysosomal proteins. Externalization of mature IL-1 beta and caspase-1 together with lysosomal proteins is then facilitated by extracellular ATP. ATP triggers the efflux of K(+) from the cell, followed by Ca(2+) influx and activation of three phospholipases: phosphatidylcholine-specific phospholipase C and calcium-independent and -dependent phospholipase A(2). Whereas calcium-independent phospholipase A(2) is involved in processing, phosphatidylcholine-specific phospholipase C and calcium-dependent phospholipase A(2) are required for secretion. Dissection of the events that follow ATP triggering allowed to demonstrate that K(+) efflux is responsible for phosphatidylcholine-specific phospholipase C induction, which in turn allows the rise in intracellular free calcium concentration required for activation of phospholipase A(2). This activation is ultimately responsible for lysosome exocytosis and IL-1 beta secretion.
Human embryonic stem cell differentiation into insulin secreting β‐cells for diabetes (2012)

hESC (human embryonic stem cells), when differentiated into pancreatic β ILC (islet-like clusters), have enormous potential for the cell transplantation therapy for Type 1 diabetes. We have developed a five-step protocol in which the EBs (embryoid bodies) were first differentiated into definitive endoderm and subsequently into pancreatic lineage followed by formation of functional endocrine β islets, which were finally matured efficiently under 3D conditions. The conventional cytokines activin A and RA (retinoic acid) were used initially to obtain definitive endoderm. In the last step, ILC were further matured under 3D conditions using amino acid rich media (CMRL media) supplemented with anti-hyperglycaemic hormone-Glp1 (glucagon-like peptide 1) analogue Liraglutide with prolonged t(½) and Exendin 4. The differentiated islet-like 3D clusters expressed bonafide mature and functional β-cell markers-PDX1 (pancreatic and duodenal homoeobox-1), C-peptide, insulin and MafA. Insulin synthesis de novo was confirmed by C-peptide ELISA of culture supernatant in response to varying concentrations of glucose as well as agonist and antagonist of functional 3D β islet cells in vitro. Our results indicate the presence of almost 65% of insulin producing cells in 3D clusters. The cells were also found to ameliorate hyperglycaemia in STZ (streptozotocin) induced diabetic NOD/SCID (non-obese diabetic/severe combined immunodeficiency) mouse up to 96 days of transplantation. This protocol provides a basis for 3D in vitro generation of long-term in vivo functionally viable islets from hESC.
Human μ opiate receptor (1994)

A human mu opiate receptor cDNA has been identified from a cerebral cortical cDNA library using sequences from the rat mu opiate receptor cDNA. The human mu opiate receptor (h mu OR1) shares 95% amino acid identity with the rat sequence. The expressed mu OR1 recognized tested opiate drugs and opioid peptides in a sodium- and GTP-sensitive fashion with affinities virtually identical to those displayed by the rat mu opiate receptor. Effects on cyclic AMP are similar to those noted for the rat mu opiate receptor. An 18 kb genomic clone hybridizing with the h mu OR1 cDNA contains 63 and 489 bp exonic sequences flanked by splice donor/acceptor sequences. Analysis of hybridization to DNA prepared from human rodent hybrid cell lines and chromosomal in situ hybridization studies indicate localization to 6q24-25. An MspI polymorphism, producing a 3.7 kb band, may prove useful in assessing this gene's involvement in neuropsychiatric disorders involving opiatergic systems.
ω-Amino Acid:Pyruvate Transaminase from Alcaligenes denitrificans Y2k-2: a New Catalyst for Kinetic Resolution of β-Amino Acids and Amines (2004)

Alcaligenes denitrificans Y2k-2 was obtained by selective enrichment followed by screening from soil samples, which showed omega-amino acid:pyruvate transaminase activity, to kinetically resolve aliphatic beta-amino acid, and the corresponding structural gene (aptA) was cloned. The gene was functionally expressed in Escherichia coli BL21 by using an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible pET expression system (9.6 U/mg), and the recombinant AptA was purified to show a specific activity of 77.2 U/mg for L-beta-amino-n-butyric acid (L-beta-ABA). The enzyme converts various beta-amino acids and amines to the corresponding beta-keto acids and ketones by using pyruvate as an amine acceptor. The apparent K(m) and V(max) for L-beta-ABA were 56 mM and 500 U/mg, respectively, in the presence of 10 mM pyruvate. In the presence of 10 mM L-beta-ABA, the apparent K(m) and V(max) for pyruvate were 11 mM and 370 U/mg, respectively. The enzyme exhibits high stereoselectivity (E > 80) in the kinetic resolution of 50 mM D,L-beta-ABA, producing optically pure D-beta-ABA (99% enantiomeric excess) with 53% conversion.
Studies on structure and function of rhodopsin by use of cyclopentatrienylidene 11-cis-locked-rhodopsin (1984)

The photochemical reaction of cyclopentatrienylidene 11-cis-locked-rhodopsin derived from cyclopentatrienylidene 11-cis-locked-retinal and cattle opsin was spectrophotometrically studied. The difference absorption spectrum between the cyclopentatrienylidene 11-cis-locked-rhodopsin and its retinal oxime had its maximum at 495 nm (P-495). Irradiation of P-495 at -196 degrees C with either blue light or orange light caused no spectral change, supporting the cis-trans isomerization hypothesis for formation of bathorhodopsin. Upon irradiation of P-495 at 0 degree C with orange light, however, its absorption spectrum shifted to a shorter wavelength owing to formation of a hypsochromic product. The difference absorption spectrum between this product (P-466) and its retinal oxime showed its maximum at 466 nm. Analysis of retinal isomers by high-performance liquid chromatography showed that this spectral shift was not accompanied by photoisomerization of the chromophore. P-466 could almost completely be photoconverted to the original pigment (P-495) by irradiation at 0 degree C with blue light with little formation of the other isomeric form of its chromophore. The alpha-band of the circular dichroism spectrum of P-495 was very small in comparison with that of rhodopsin, while that of P-466 was comparable to it. These facts suggest that P-495 has a planar conformation in the side chain of the chromophore and that P-466 has a twisted one, probably at the C8-C9 single bond. Cyclic-GMP phosphodiesterase in frog rod outer segment was activated by neither P-495 nor P-466. This result suggests that the isomerization of the retinylidene chromophore of rhodopsin is indispensable in the phototransduction process.
The nature of the ADAS model based on the ISLM model (2006)

The aggregate demand and supply model (ADAS) is interpreted as a synthesis of the Keynesian and neoclassical models. It uses the ISLM model, without explaining its nature, to derive aggregate demand (AD). It is combined with an aggregate supply (AS) curve to explain price-inflation and output dynamics. This paper argues that neither the AD nor the AS curve is conceptually the same as its microeconomic counterpart and that ADAS is not a synthesis. In fact, ADAS implies that discretionary policy is necessary and that price changes do not perform their traditional negative feedback function.
Disk scrubbing in large archival storage systems (2004)

Large archival storage systems experience long periods of idleness broken up by rare data accesses. In such systems, disks may remain powered off for long periods of time. These systems can lose data for a variety of reasons, including failures at both the device level and the block level. To deal with these failures, we must detect them early enough to be able to use the redundancy built into the storage system. We propose a process called "disk scrubbing" in a system in which drives are periodically accessed to detect drive failure. By scrubbing all of the data stored on all of the disks, we can detect block failures and compensate for them by rebuilding the affected blocks. Our research shows how the scheduling of disk scrubbing affects overall system reliability, and that "opportunistic" scrubbing, in which the system scrubs disks only when they are powered on for other reasons, performs very well without the need to power on disks solely to check them.
N6-Allyladenosine: A New Small Molecule for RNA Labeling Identified by Mutation Assay (2017)

RNA labeling is crucial for the study of RNA structure and metabolism. Herein we report N<sup>6</sup>-allyladenosine (a<sup>6</sup>A) as a new small molecule for RNA labeling through both metabolic and enzyme-assisted manners. a<sup>6</sup>A behaves like A and can be metabolically incorporated into newly synthesized RNAs inside mammalian cells. We also show that human RNA N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) methyltransferases METTL3/METTL14 can work with a synthetic cofactor, namely allyl-SAM (S-adenosyl methionine with methyl replaced by allyl) in order to site-specifically install an allyl group to the N<sup>6</sup>-position of A within specific sequence to generate a<sup>6</sup>A-labeled RNAs. The iodination of N<sup>6</sup>-allyl group of a<sup>6</sup>A under mild buffer conditions spontaneously induces the formation of N<sup>1</sup>,N<sup>6</sup>-cyclized adenosine and creates mutations at its opposite site during complementary DNA synthesis of reverse transcription. The existing m<sup>6</sup>A in RNA is inert to methyltransferase-assisted allyl labeling, which offers a chance to differentiate m<sup>6</sup>A from A at individual RNA sites. Our work demonstrates a new method for RNA labeling, which could find applications in developing sequencing methods for nascent RNAs and RNA modifications.
2 Molecular Basis of Mammalian Egg Activation (1995)

The chapter discusses signal transduction mechanisms in the activation of mammalian eggs, primarily in the mouse, and explains the sequence of events that accompanies fertilization in the mouse. This information provides a framework within which to examine known and proposed signaling mechanisms that regulate egg activation, helps understand the role of several possible second messengers in egg activation, and helps describe the sperm–egg interaction that may result in the production of second messengers. In the mammal, the first interaction between the sperm and egg is at the level of the zona pellucida (ZP), an extracellular coat that surrounds all mammalian eggs. In the mouse, the ZP is composed of three glycoproteins: ZP1, ZP2, and ZP3. Although acrosome-intact sperm establishes primary binding with ZP3 through an O-linked carbohydrate moiety, the identity of this moiety is controversial. Following sperm binding, ZP3 induces the acrosome reaction of the bound sperm.
The chemistry of silica and its potential health benefits. (2007)

There is considerable interest in the effects of silica on human health in contrast to prior research which focused solely on the toxic effects of inhaled crystalline silica. However, multiple forms of silica exist in nature and silicon, a component, is the second most prevalent element after oxygen. Silica has widespread industrial applications including use as a food additive, i.e., anti-caking agent, as a means to clarify beverages, control viscosity, as an anti-foaming agent, dough modifier, and as an excipient in drugs and vitamins. Chemically, silica is an oxide of silicon, viz., silicon dioxide, and is generally colorless to white and insoluble in water. When associated with metals or minerals the family of silicates is formed. There are several water soluble forms of silica referred collectively to as silicic acid (ortho, meta, di, and tri-silicates), which are present in surface and well water in the range of 1--100 mg/L. Orthosilicic acid is the form predominantly absorbed by humans and is found in numerous tissues including bone, tendons, aorta, liver and kidney. Compelling data suggest that silica is essential for health although no RDI has been established. However, deficiency induces deformities in skull and peripheral bones, poorly formed joints, reduced contents of cartilage, collagen, and disruption of mineral balance in the femur and vertebrae. Very little toxicity data exist regarding aqueous silica consumption due, in part, to the lack of anecdotal reports of toxicity and general presumption of safety. However, a few rodent studies have been conducted, which indicate a No Observed Adverse Effects Level (NOAEL) of 50,000 ppm (mg/L) for dietary silica. In conclusion, many forms of silica exist in nature and compelling data support myriad beneficial effects of silica in water.