gebhart/patrepeval huggingface dataset:
Evolution of Porosity and Permeability in the Lower Cretaceous Travis Peak Formation, East Texas (1) (1992)

Porosity and permeability decrease significantly with depth in low-permeability, gas-bearing Travis Peak sandstones on the western flank of the Sabine arch, east Texas. The Travis Peak Formation is approximately 2000 ft (610 m) thick and is buried to depths of 6000-10,000 ft (1830-3050 m). Reservoirs consist chiefly of sandstones of fluvial and paralic origin. Thin-section and core-analysis data from a total of 3680 ft (1122 m) of core from 26 wells indicate that both depositional environment and diagenetic history influenced the present distribution of porosity and permeability. Porosity in clean sandstones decreases from an average (geometric mean) of 16.6% at 6000 ft (1830 m) to 5.0% at 10,000 ft (3050 m). Permeability is reduced four orders of magnitude over the same depth range, from an average (geometric mean) of 10 md at 6000 ft (1830 m) to 0.001 md at 10,000 ft (3050 m). Loss of porosity by mechanical compaction took place mainly within the first 3000 ft (900 m) of burial, prior to significant cementation. The observed decline in porosity and permeability with depth between 6000 and 10,000 ft (1830 and 3050 m) results from (1) increasing quartz cement, (2) decreasing secondary porosity, and (3) increasing overburden pressure that closes narrow pore throats. At any given depth, average permeability is 10 times higher in clean fluvial than in clean paral c sandstones. Clean fluvial and paralic sandstones contain similar volumes of quartz cement, but paralic sandstones are finer grained and contain an average of 7% more total cement.
Analysis of the Biochemical Mechanisms for the Endocrine Actions of Fibroblast Growth Factor-23 (2005)

Fibroblast growth factor (FGF)-23 has emerged as an endocrine regulator of phosphate and of vitamin D metabolism. It is produced in bone and, unlike other FGFs, circulates in the bloodstream to ultimately regulate phosphate handling and vitamin D production in the kidney. Presently, it is unknown which of the seven principal FGF receptors (FGFRs) transmits FGF23 biological activity. Furthermore, the molecular basis for the endocrine mode of FGF23 action is unclear. Herein, we performed surface plasmon resonance and mitogenesis experiments to comprehensively characterize receptor binding specificity. Our data demonstrate that FGF23 binds and activates the c splice isoforms of FGFR1-3, as well as FGFR4, but not the b splice isoforms of FGFR1-3. Interestingly, highly sulfated and longer glycosaminoglycan (GAG) species were capable of promoting FGF23 mitogenic activity. We also show that FGF23 induces tyrosine phosphorylation and inhibits sodium-phosphate cotransporter Npt2a mRNA expression using opossum kidney cells, a model kidney proximal tubule cell line. Removal of cell surface GAGs abolishes the effects of FGF23, and exogenous highly sulfated GAG is capable of restoring FGF23 activity, suggesting that proximal tubule cells naturally express GAGs that are permissive for FGF23 action. We propose that FGF23 signals through multiple FGFRs and that the unique endocrine actions of FGF23 involve escape from FGF23-producing cells and circulation to the kidney, where highly sulfated GAGs most likely act as cofactors for FGF23 activity. Our biochemical findings provide important insights into the molecular mechanisms by which dysregulated FGF23 signaling leads to disorders of hyper- and hypophosphatemia.
Changes in choriocapillaris and retinal pigment epithelium in age-related macular degeneration. (1999)

Retinal pigment epithelial cells (RPE) and the choriocapillaris are on opposite sides of Bruch's membrane and control transport in and out of the retina. In age-related macular degeneration (AMD), they may also be responsible for deposition of material in and on Bruch's membrane and the formation or regression of choroidal neovascularization (CNV). Indocyanine green (ICG) angiography can be used to visualize the choroidal vasculature and CNV. Filling of the choriocapillaris with ICG was delayed in subjects older than 50 years of age, and areas of hypofluorescence were observed in maculas of AMD subjects, often associated with CNV. Laser Doppler flowmetry of the choriocapillaris in the macula demonstrated that choroidal blood flow and volume are reduced in subjects older than 46 years of age and further decreased in subjects with AMD. The human choriocapillaris can be histologically studied in two dimensions by incubating the tissue for alkaline phosphatase activity, flat-embedding it in transparent polymer and sectioning it. Using this technique, choriocapillaris dropout was found to be associated with deposition of material in Bruch's membrane in diabetic subjects. When RPE are removed from Bruch's membrane, the choriocapillaris degenerates; the regeneration of choriocapillaris can be blocked by Genistein, a tyrosine kinase inhibitor. Finally, RPE cells may produce substances that both stimulate the formation and regression of CNV in animal models. These studies suggest that there may be a reduction in choriocapillaris flow in AMD, and this loss of choriocapillaris can be associated with the Bruch's membrane deposits that are hallmarks of AMD. Furthermore, RPE may stimulate the formation and regression of CNV and RPE loss can result in loss of choriocapillaris.
Anticonvulsant O-alkyl sulfamates. 2,3:4,5-Bis-O-(1-methylethylidene)-.beta.-D-fructopyranose sulfamate and related compounds (1987)

Novel sugar sulfamate 1 (McN-4853, topiramate) has been found to exhibit potent anticonvulsant activity analogous to that of phenytoin. In the maximal electroshock seizure test, orally at 2 h in mice, 1 had an ED50 of 39 mg/kg. Orally, 1 had a duration of action in excess of 8 h. Other aspects of the pharmacology of 1, as well as neurochemistry and carbonic anhydrase inhibition, are discussed. The conformational behavior of 1 in solution and in the solid state is discussed. A series of analogues of 1 were synthesized and examined for anticonvulsant properties.
948. Carcinogenic nitrogen compounds. Part XIII. Benzacridines, benzocarbazoles, and related compounds bearing ethyl and propyl groups (1952)

Ng. Ph. Buu-Hoï, R. Royer, B. Eckert and P. Jacquignon, J. Chem. Soc., 1952, 4867 DOI: 10.1039/JR9520004867
Class II-restricted T cell receptor engineeredin vitrofor higher affinity retains peptide specificity and function (2005)

The T cell receptor (TCR) alphabeta heterodimer determines the peptide and MHC specificity of a T cell. It has been proposed that in vivo selection processes maintain low TCR affinities because T cells with higher-affinity TCRs would (i) have reduced functional capacity or (ii) cross-react with self-peptides resulting in clonal deletion. We used the class II-restricted T cell clone 3.L2, specific for murine hemoglobin (Hb/I-E(k)), to explore these possibilities by engineering higher-affinity TCR mutants. A 3.L2 single-chain TCR (Vbeta-linker-Valpha) was mutagenized and selected for thermal stability and surface expression in a yeast display system. Stabilized mutants were used to generate a library with CDR3 mutations that were selected with Hb/I-E(k) to isolate a panel of affinity mutants with K(D) values as low as 25 nM. Kinetic analysis of soluble single-chain TCRs showed that increased affinities were the result of both faster on-rates and slower off-rates. T cells transfected with the mutant TCRs and wild-type TCR responded to similar concentrations of peptide, indicating that the increased affinity was not detrimental to T cell activation. T cell transfectants maintained exquisite hemoglobin peptide specificity, but an altered peptide ligand that acted as an antagonist for the wild-type TCR was converted to a strong agonist with higher-affinity TCRs. These results show that T cells with high-affinity class II reactive TCRs are functional, but there is an affinity threshold above which an increase in affinity does not result in significant enhancement of T cell activation.
Impact of optical enhancement techniques on the mask error enhancement function (MEEF) (2000)

Resolution, R, in optical lithography is often described by the Rayleigh equation: R equals k<SUB>1</SUB>(lambda) /NA. Since the 0.25 um generation there has been a trend of aggressive gate length reduction for high performance devices. Leading edge logic technologies require gate CDs equal to &frac12;to 2/3 the wavelength of the exposure system. Even with high NA steppers and scanners low k1 patterning is a requirement. Development of processes utilizing OPC and PSM technology is critical to achieving adequate process latitude and CD control. As k<SUB>1</SUB> factor falls below 0.5 the image quality and contrast degrades substantially. One result of low contrast images is that the CD variation in the photomask gives rise to larger than expected printed CD changes: the so-called MEEF. The MEEF can be simply defined as the ratio of the change of the resist feature width to the change in the mask feature width, assuming constant process and illumination conditions. For a 4x mask the MEEF can be calculated.
Improving the Estimation of Word Importance for News Multi-Document Summarization - Extended Technical Report (2014)

In this paper, we propose a supervised model for ranking word importance that incorporates a rich set of features. Our model is superior to prior approaches for identifying words used in human summaries. Moreover we show that an extractive summarizer which includes our estimation of word importance results in summaries comparable with the state-of-the-art by automatic evaluation.
Allergenic and antigenic activity of peptide fragments in a whey hydrolysate formula (1998)

Our findings suggest that for skin reactivity peptides of > 1400 Da are needed. The minimal molecular mass for IgE binding in vitro appears to be situated between 1400 and 970 Da. Such peptides might be used to develop a safe formula for patients reacting to milk hydrolysates or even for tolerance induction.
Detection of extracellular proteases from microorganisms on agar plates (1996)

We present herein an improved assay for detecting the presence of extracellular proteases from microorganisms on agar plates. Using different substrates (gelatin, BSA, hemoglobin) incorporated into the agar and varying the culture medium composition, we were able to detect proteolytic activities from Pseudomonas aeruginosa, Micrococcus luteus and Serratia marcescens as well as the influence that these components displayed in the expression of these enzymes. For all microorganisms tested we found that in agar-BHI or yeast extract medium containing gelatin the sensitivity of proteinase detection was considerably greater than in BSA-agar or hemoglobin-agar. However, when BSA or hemoglobin were added to the culture medium, there was an increase in growth along with a marked reduction in the amount of proteinase production. In the case of M. luteus the incorporation of glycerol in BHI or yeast extract gelatin-agar induced protease liberation. Our results indicate that the technique described here is of value for detecting extracellular proteases directly in the culture medium, by means of a qualitative assay, simple, inexpensive, straight forward method to assess the presence of the proteolytic activity of a given microorganism colony with great freedom in substrate selection.
Bayesian shape recognition using Principle Component Analysis and Modified Chain Codes (2008)

This paper represents a shape recognition method using PCA (Principal Component Analysis) and Bayesian probability with MCC (Modified Chain Code). MCC is a shape descriptor which is invariant in 2D shape’s scale, translation and rotation. Shape prior information is analyzed by PCA using shape database. We recognized shapes by Bayesian probability with shape prior information. In this paper we describe traditional chain code to describe object features and using its modification version, PCA and Bayesian probabilistic analysis and classification are represented.
The Role of Ect2 Nuclear RhoGEF Activity in Ovarian Cancer Cell Transformation (2013)

Ect2, a Rho guanine nucleotide exchange factor (RhoGEF), is atypical among RhoGEFs in its predominantly nuclear localization in interphase cells. One current model suggests that Ect2 mislocalization drives cellular transformation by promoting aberrant activation of cytoplasmic Rho family GTPase substrates. However, in ovarian cancers, where Ect2 is both amplified and overexpressed at the mRNA level, we observed that the protein is highly expressed and predominantly nuclear and that nuclear but not cytoplasmic Ect2 increases with advanced disease. Knockdown of Ect2 in ovarian cancer cell lines impaired their anchorage-independent growth without affecting their growth on plastic. Restoration of Ect2 expression rescued the anchorage-independent growth defect, but not if either the DH catalytic domain or the nuclear localization sequences of Ect2 were mutated. These results suggested a novel mechanism whereby Ect2 could drive transformation in ovarian cancer cells by acting as a RhoGEF specifically within the nucleus. Interestingly, Ect2 had an intrinsically distinct GTPase specificity profile in the nucleus versus the cytoplasm. Nuclear Ect2 bound preferentially to Rac1, while cytoplasmic Ect2 bound to RhoA but not Rac. Consistent with nuclear activation of endogenous Rac, Ect2 overexpression was sufficient to recruit Rac effectors to the nucleus, a process that required a functional Ect2 catalytic domain. Furthermore, expression of active nuclearly targeted Rac1 rescued the defect in transformed growth caused by Ect2 knockdown. Our work suggests a novel mechanism of Ect2-driven transformation, identifies subcellular localization as a regulator of GEF specificity, and implicates activation of nuclear Rac1 in cellular transformation.
ATPase Activity of the Terminase Subunit pUL56 of Human Cytomegalovirus (2002)

Herpesviral DNA packaging is a complex process resulting in unit-length genomes packed into preformed procapsids. This process is believed to be mediated by two packaging proteins, the terminase subunits. In the case of double-stranded DNA bacteriophages, the translocation of DNA was shown to be an energy-dependent process associated with an ATPase activity of the large terminase subunit. In the case of human cytomegalovirus it was not known which protein has the ability to hydrolyze ATP. In this study we expressed human cytomegalovirus terminase subunits, pUL89 and the carboxyl-terminal half of pUL56, as GST fusion proteins and purified these by affinity chromatography. ATPase assays demonstrated that the enzymatic activity is exclusively associated with pUL56. The characterization of the ATP hydrolysis showed that the enzymatic reaction is a fast process, whereas the spontaneous ATP decay followed slow kinetics. Interestingly, although pUL89 did not show any ATPase activity, it was capable of enhancing the UL56-associated ATP hydrolysis. Furthermore, a specific association of in vitro translated pUL89 with the carboxyl-terminal half of GST-UL56C was detected. This interaction was confirmed by co-immunoprecipitations of infected cells. Our results clearly demonstrated that (i) both terminase subunits interact with each other and (ii) the subunit pUL56 has an ATPase activity.
Like a Bolt from the Blue: Phthalocyanines in Biomedical Optics (2011)

The purpose of this review is to compile preclinical and clinical results on phthalocyanines (Pcs) as photosensitizers (PS) for Photodynamic Therapy (PDT) and contrast agents for fluorescence imaging. Indeed, Pcs are excellent candidates in these fields due to their strong absorbance in the NIR region and high chemical and photo-stability. In particular, this is mostly relevant for their in vivo activation in deeper tissular regions. However, most Pcs present two major limitations, i.e., a strong tendency to aggregate and a low water-solubility. In order to overcome these issues, both chemical tuning and pharmaceutical formulation combined with tumor targeting strategies were applied. These aspects will be developed in this review for the most extensively studied Pcs during the last 25 years, i.e., aluminium-, zinc- and silicon-based Pcs.
Expression of Luteinizing Hormone/Human Chorionic Gonadotropin Receptor Gene in Benign Prostatic Hyperplasia and in Prostate Carcinoma in Humans (1997)

The findings that normal rat prostates express functional LH/hCG receptors led us to test the hypothesis that benign prostatic hyperplasia (BPH) and prostate carcinomas may also express this receptor gene. The data revealed the presence of LH/hCG receptor transcripts and receptor protein in normal and hyperplastic but not in atrophic glands present in BPH tissue. Smooth muscle and blood vessels in stroma of BPH tissue also contained receptors. Prostate carcinomas contain lower and more heterogeneous receptor levels than BPH tissue. Two human prostate cancer cell lines (LNCaP and DU 145) that were investigated showed the presence of a major 4.5-kilobase transcript and several minor transcripts and also the protein of LH/hCG receptors. However, androgen-sensitive LNCaP cells contained more receptors than androgen-insensitive DU 145 cells. In summary, we demonstrate for the first time that BPH and prostate cancer tissues and cell lines express LH/hCG receptor gene. These findings suggest that higher LH levels in aged men may play a role in BPH and/or prostate carcinomas.
Controlled field trial of a high-dose oral killed typhoid vaccine in India. (1977)

A controlled field trial of a modified vaccine containing Salmonella typhi, TY 2 strain, in a dose of 400 x 10(9) killed organisms per capsule, was carried out in schoolchildren aged 6-17 years. The children were followed up for 6-8 months. There were 66 cases of typhoid fever in the vaccine group (7312 children) and 54 in the control group (7292 children who had received a placebo). This difference is not statistically significant. The results confirm that, as found in earlier trials, oral typhoid vaccine, in the dosages used so far, gives no protection.
Role of SHIP1 in bone biology (2013)

The bone marrow milieu comprising both hematopoietic and nonhematopoietic lineages has a unique structural organization. Bone undergoes continuous remodeling throughout life. This dynamic process involves a balance between bone-forming osteoblasts (OBs) derived from multipotent mesenchymal stem cells (MSCs) and bone-resorbing osteoclasts (OCs) derived from hematopoietic stem cells (HSCs). Src homology 2-domain-containing inositol 5'-phosphatase 1 (SHIP1) regulates cellular processes such as proliferation, differentiation, and survival via the PI3K/Akt signaling pathway initiated at the plasma membrane. SHIP1-deficient mice also exhibit profound osteoporosis that has been proposed to result from hyperresorptive activity by OCs. We have previously observed that SHIP1 is expressed in primary OBs, which display defective development in SHIP1-deficient mice. These findings led us to question whether SHIP1 plays a functional role in osteolineage development from MSC in vivo, which contributes to the osteoporotic phenotype in germline SHIP1 knockout mice. In this short review, we discuss our current understanding of inositol phospholipid signaling downstream of SHIP1 in bone biology.
Regional differences in retinoid release from embryonic neural tissue detected by an in vitro reporter assay (1992)

Retinoic acid and related retinoids have been suggested to contribute to the pattern of cell differentiation during vertebrate embryonic development. To identify cell groups that release morphogenetically active retinoids, we have developed a reporter assay that makes use of a retinoic acid inducible response element (RARE) to drive lacZ or luciferase reporter genes in stably transfected cell lines. This reporter gene assay allows detection of retinoids released from embryonic tissues over a range equivalent to that induced by femtomole amounts of retinoic acid. We have used this assay first to determine whether the floor plate, a cell group that has polarizing properties in neural tube and limb bud differentiation, is a local source of retinoids within the spinal cord. We have also examined whether the effects of exogenously administered retinoic acid on anteroposterior patterning of cells in the developing central nervous system correlate with differences in retinoid release from anterior and posterior neural tissue. We find that the release of morphogenetically active retinoids from the floor plate is only about 1.5-fold that of the dorsal spinal cord, which does not have neural tube or limb polarizing activity. These results suggest that the spatial distribution of retinoid release from spinal cord tissues differs from that of the neural and limb polarizing activity. This assay has also shown that retinoids are released from the embryonic spinal cord at much greater levels than from the forebrain. This result, together with previous observations that the development of forebrain structures is suppressed by low concentrations of retinoic acid, suggest that the normal development of forebrain structures is dependent on the maintenance of low concentrations of retinoids in anterior regions of the embryonic axis. This assay has also provided initial evidence that other embryonic tissues with polarizing properties in vivo release retinoids in vitro.
Dynamics near the Glass Temperature of Low Molecular Weight Cyclic Polystyrene (2001)

The segmental relaxation properties of a low molecular weight (4.6 kg/mol), cyclic polystyrene (PS) were characterized. The sample was obtained by fractionation using HPLC at the chromatographic critical condition, which yields a ring uncontaminated by its linear precursor. Both the glass temperature and the temperature dependence of the segmental relaxation times for the ring PS were equivalent to the high molecular weight limiting values for the linear polymer. These results are interpreted by considering the configurational mobility of a polymer lacking chain ends.
Iodine(V) Reagents in Organic Synthesis. Part 4. o-Iodoxybenzoic Acid as a Chemospecific Tool for Single Electron Transfer-Based Oxidation Processes (2002)

o-Iodoxybenzoic acid (IBX), a readily available hypervalent iodine(V) reagent, was found to be highly effective in carrying out oxidations adjacent to carbonyl functionalities (to form alpha,beta-unsaturated carbonyl compounds) and at benzylic and related carbon centers (to form conjugated aromatic carbonyl systems). Mechanistic investigations led to the conclusion that these new reactions are initiated by single electron transfer (SET) from the substrate to IBX to form a radical cation which reacts further to give the final products. Fine-tuning of the reaction conditions allowed remarkably selective transformations within multifunctional substrates, elevating the status of this reagent to that of a highly useful and chemoselective oxidant.
224. An experimental study of some potentially tautomeric 2- and 4(6)-substituted pyrimidines (1951)

J. R. Marshall and J. Walker, J. Chem. Soc., 1951, 1004 DOI: 10.1039/JR9510001004