gebhart/patrepeval huggingface dataset:
Characterization of Opening Mode Fracture Systems in the Austin Chalk (2001)

ABSTRACT The Upper Cretaceous Austin Chalk is a low-permeability, fractured reservoir that has been the target of numerous horizontal wells in Texas. For wells to be successful, parameters such as well-bore azimuth, target horizon, and length must be optimized. Furthermore, information on fracture height and the storage volume potentially connected to the well bore is required. Two case studies are presented in which the height, aspect ratio, and vertical persistence of opening-mode fractures in the Austin Chalk have been examined, together with previously known attributes of fracture population attributes of orientation, aperture, effective aperture, spacing, aspect ratio, fracture fill, and fracture permeability. The studies are of an outcrop of the upper Austin Chalk near Waxahachie, North Central Texas (Grove Creek), and of a vertical segment and two horizontal laterals of a core in the Atco Member in Frio County, Pearsall Field (Kinlaw core). Large, potentially open fractures are commonly clustered, the distance between clusters ranging from ~1 to ~50 m. Aperture-size distributions follow power laws, and spacing-size distributions are negative-logarithmic or lognormal. The aperture size at which fractures are open to fluids is variable (0.14 to 11 mm). Fracture permeability, which is scale dependent, has been determined at 7.1 D (for 18 m of lower Austin Chalk core) and 286 D (for 300 m of upper Austin Chalk outcrop). Fractures may terminate at chalk-marl contacts, tip out within the marl, or pass through the marl layers. Fracture height is governed by truncation effects at marl horizons and pressure-solution seams, which in turn partly depend on fracture aperture and thickness of the inhibiting layer.
Differential elevation of matrix metalloproteinase expression in women exposed to levonorgestrel-releasing intrauterine system for a short or prolonged period of time (2008)

MMP-1, active MMP-2, MMP-3, MMP-7, MMP-9 and MMP-12 are more prevalent in the short-term LNG-IUS group, suggesting their important contribution to ECM breakdown and transient bleeding. The decrease in the percentage of women expressing MMP-2 and -3 might contribute to the decreased occurrence of unwanted spotting and bleeding in long-term LNG-IUS users.
Selective Deposition of Metals on Plastics Used in the Construction of Microanalytical Devices: Photo-Directed Formation of Metal Features on PMMA (2001)

We describe here, for the first time, the use of amine-terminated poly(methyl methacrylate), AT-PMMA, surfaces as a substrate for the electroless deposition of Au nanoparticle films (Au-EDNPFs), the adsorptive deposition of Au colloids, the laterally patterned formation of Au-EDNPFs, and the use of the patterned Au-EDNPFs to form electrolessly deposited Ag films with micrometer features. Au-EDNPFs were formed by chemical reduction of AuCl4- films coordinated to AT-PMMA sheets. The Au-EDNPFs act as autocatalytic substrates for the conventional electroless deposition of Ag. Such Ag films can be used in the construction of functional Ag/AgCl reference electrodes. In addition, sequentially deposited, multilayer Au colloid films formed on the AT-PMMA surfaces are shown to be effective electrochemical working electrodes in aqueous media. In the final portion of the work, laterally patterned (selective) deposition of Ag films was accomplished by photoremoval of photolabile protecting groups attached to the amine functionalities of AT-PMMA, followed by the Au-EDNPF formation process and subsequent electroless deposition of Ag onto the Au-EDNPF surface. The selectivity of the Au-EDNPF pattern formation process (deposition on only the deprotected amine sites and not the protected sites) is shown to be dictated by the pH of the AuCl4- solution in contact with the photodeprotected surfaces.
Chemotaxis of primitive hematopoietic cells in response to stromal cell–derived factor-1 (2000)

Stromal cell-derived factor-1 (SDF-1) provides a potent chemotactic stimulus for CD34(+) hematopoietic cells. We cultured mobilized peripheral blood (PB) and umbilical cord blood (CB) for up to 5 weeks and examined the migratory activity of cobblestone area-forming cells (CAFCs) and long-term culture-initiating cells (LTC-ICs) in a transwell assay. In this system, SDF-1 or MS-5 marrow stromal cells placed in the lower chamber induced transmembrane and transendothelial migration by 2- and 5-week-old CAFCs and LTC-ICs in 3 hours. Transmigration was blocked by preincubation of input CD34(+) cells with antibody to CXCR4. Transendothelial migration of CB CAFCs and LTC-ICs was higher than that of PB. We expanded CD34(+) cells from CB in serum-free medium with thrombopoietin, flk-2 ligand, and c-kit ligand, with or without IL-3 and found that CAFCs cultured in the absence of IL-3 had a chemotactic response equivalent to noncultured cells, even after 5 weeks. However, addition of IL-3 to the culture reduced this response by 20-50%. These data indicate that SDF-1 induces chemotaxis of primitive hematopoietic cells signaling through CXCR4 and that the chemoattraction could be downmodulated by culture ex vivo.
Long-QT Syndrome Induced by the Antiaddiction Drug Ibogaine (2009)

A 31-year-old woman was admitted to the emergency department because of a seizure-like attack after a single 3.5-g dose of ibogaine. ECG showed a severe prolonged-QT interval of 548 msec and ventri...
<title>Shape analysis of pulmonary nodules based on thin-section CT images</title> (1997)

Shape characterization of small pulmonary nodules plays a significant role in differential diagnosis that discriminates malignant and benign nodules at early stages of pulmonary lesion development. This paper presents a method to characterize small pulmonary nodules based on the morphology of the development of lung lesions in thin section CT images. The feature extraction process focuses on the difference between the malignant and benign surface characteristics. Experiments to show its feasibility to improve the diagnostic accuracy are also demonstrated by applying the algorithm to eighteen cases including twelve malignant and six benign nodules.
Cloning and expression of a novel angiotensin II receptor subtype. (1992)

Angiotensin II (AII) is a major regulator of cardiovascular function and fluid homeostasis. Recently, the cDNA for an AII receptor (AT1) was cloned from rat smooth muscle and bovine adrenal. To search for AII receptor subtypes, we amplified rat adrenal cortex cDNA by PCR using primers based on the AT1 receptor. The product was distinct from the AT1 receptor as indicated by restriction enzyme analysis and DNA sequencing. A full-length cDNA clone (2.2 kilobase pairs) encoding a novel AII receptor (AT3) was obtained by screening an adrenal cortex library. The AT3 cDNA encodes a Mr 40,959 protein with 95% amino acid identity to the rat smooth muscle receptor, but the overall nucleotide similarity is 71% due to low homology in the 5'- (58%) and 3'- (62%) untranslated regions. Expressed AT3 receptors in Xenopus oocytes and COS-7 cells mediate agonist-induced Ca2+ mobilization but are pharmacologically distinct from the AT1 receptors. AT3 mRNA is most abundant in the adrenal cortex and pituitary and differs from AT1 mRNA in its tissue distribution. The structural features of the AT3 receptor, including two additional potential phosphorylation sites for protein kinase C, could be related to the distinctive binding properties of the adrenal and vascular receptors and to their differential regulation during altered sodium intake.
Vector quantized MBE with simplified V/UV division at 3.0 kbit/s (1993)

A speech coding algorithm for application to the Japan digital cellular half-rate coder has been developed based on the multiband excitation (MBE) algorithm using 3.0 kbit/s. The target performance is at the same level as that of a full-rate coder operating at 6.7 kbit/s. The quantization scheme for the spectral envelope of the MBE coder parameters is described. New features of the scheme include an efficient dimension converter, interframe coding of spectral envelope vectors, and multistage vector quantization with interpolative vector quantization. A simplified model of voiced/unvoiced division and a method of detecting/manipulating background noise have also been devised for MBE analysis. Informal listening tests indicate that, while the quality is slightly lower than that of a full-rate coder, it is nevertheless sufficiently high for digital telephony.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Turbo-codes and high spectral efficiency modulation (2002)

This paper presents a new coding scheme based on the association of a turbo-code with a bandwith efficient modulation. It is shown that the new coding scheme provides a substantial coding gain both on Gaussian channels and Rayleigh channels. On a Gaussian channel, it outperforms 64-state trellis-coded modulation (TCM) by 2.5 dB at the bit error rate (BER) of 10/sup -6/. On a Rayleigh fading channel, it outperforms 64-state TCM optimized for that environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Construction of a cellulase hyper-expression system in Trichoderma reesei by promoter and enzyme engineering (2012)

This study shows that optimizations of the promoter and linker for hybrid genes can dramatically improve the efficiency of heterologous expression of cellulase genes in T. reesei.
Speckle contrast optical spectroscopy, a non-invasive, diffuse optical method for measuring microvascular blood flow in tissue (2014)

We introduce a new, non-invasive, diffuse optical technique, speckle contrast optical spectroscopy (SCOS), for probing deep tissue blood flow using the statistical properties of laser speckle contrast and the photon diffusion model for a point source. The feasibility of the method is tested using liquid phantoms which demonstrate that SCOS is capable of measuring the dynamic properties of turbid media non-invasively. We further present an in vivo measurement in a human forearm muscle using SCOS in two modalities: one with the dependence of the speckle contrast on the source-detector separation and another on the exposure time. In doing so, we also introduce crucial corrections to the speckle contrast that account for the variance of the shot and sensor dark noises.
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information (2006)

We have developed MUMMALS, a program to construct multiple protein sequence alignment using probabilistic consistency. MUMMALS improves alignment quality by using pairwise alignment hidden Markov models (HMMs) with multiple match states that describe local structural information without exploiting explicit structure predictions. Parameters for such models have been estimated from a large library of structure-based alignments. We show that (i) on remote homologs, MUMMALS achieves statistically best accuracy among several leading aligners, such as ProbCons, MAFFT and MUSCLE, albeit the average improvement is small, in the order of several percent; (ii) a large collection (>10 000) of automatically computed pairwise structure alignments of divergent protein domains is superior to smaller but carefully curated datasets for estimation of alignment parameters and performance tests; (iii) reference-independent evaluation of alignment quality using sequence alignment-dependent structure superpositions correlates well with reference-dependent evaluation that compares sequence-based alignments to structure-based reference alignments.
Effect of purified eicosapentaenoate ethyl ester on fibrinolytic capacity in patients with stable coronary artery disease and lower extremity ischaemia (1996)

These findings indicate that the fibrinolytic capacity in patients with CAD and ASO is decreased by increased PAI activity, but that EPA may correct this fibrinolytic impairment by decreasing PAI activity via its inhibitory effect on atherogenic lipids.
Hydration of dA.cntdot.dT polymers: role of water in the thermodynamics of ethidium and propidium intercalation (1990)

We report differences in the interaction of two structurally similar phenanthroline intercalators, ethidium and propidium, with poly(dA).poly(dT) and poly[d(A-T)] as a function of ionic strength based on titration microcalorimetry, fluorescence titration, and hydrostatic pressure measurements. Both ethidium and propidium bind more strongly to poly[d(A-T)].poly[d(A-T)] than to poly(dA).poly(dT). Ethidium intercalation into the latter polymer displays titrations with positive cooperativity; this is not found with propidium. The enthalpy of intercalation (delta H degrees) is exothermic for both dyes with poly[d(A-T)].poly[d(A-T)]; however, the value of this parameter is nearly zero in the case of poly(dA).poly(dT). The molar volume change (delta V degrees) accompanying dye intercalation is negative under all conditions for poly[d(A-T)].poly[d(A-T)] whereas it is positive for poly(dA).poly(dT). The changes observed in delta V degrees correlate well with the entropy changes derived from the titration and calorimetric data for this reaction. The results, interpreted in terms of the relative hydration of these two polymers, are consistent with a higher extent of hydration of poly(dA).poly(dT) relative to poly[d(A-T)].poly[d(A-T)].
Architectural Heritage of Hahoe Village in Andong City, South Korea and Vigan City in Ilocos Sur, Philippines (2008)

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Abstract A nations' cultural heritage embodies its intellectual and spiritual contributions to its civilization of mankind. Cultural properties, whether tangible or intangible, represent both the essence and the basis of national cultures. Both the Philippines and South Korea's cultural heritages have survived various unfortunate chapters of their long histories. This study's purpose is to explore and evaluate the phenomenon of the architecture of Hahoe village in Andong city, Korea and Vigan city of Ilocos Sur, Philippines and to understand and cherish the cultural heritage of both countries. The historic city of Vigan has a unique architecture that blend Ilocano, Filipino, Chinese and Spanish styles in a tropical Asian setting, with a typical Spanish colonial urban layout as specified by the Ley Delas Indias. Hahoe village also represents a masterpiece of human creation and exhibit an important interchange of human values in architecture, monumental arts, town planning and landscape design. Though diverse in milieu, Hahoe village and Vigan city share a common phenomenon which is architecture that is called cultural heritage. ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Development of Photobase Generator with Benzoin Derivatives and Its Application to Photosensitive Materials (2014)

We developed novel photobase generators (PBGs) that generate radicals and aliphatic amines simultaneously. We demonstrated that the PBGs induced radical polymerization and hydrolytic polycondensation. A film of poly[(methacryloxypropyl)silsesquioxane] (MA-PS) was cured in the presence of a PBG upon UV-light irradiation at 254 nm. This result showed that radical polymerization of methacryloyl groups of MA-PS with the photogenerated radicals and the crosslinking reactions based on the base-catalyzed condensation reactions of alkoxysilyl units of MA-PS proceeded. Furthermore, pencil hardness showed HB at 1.0 J cm−2 and 4H at 21.6 J cm−2 without heat treatment.
Structure of YciA from Haemophilus influenzae (HI0827), a Hexameric Broad Specificity Acyl-Coenzyme A Thioesterase, (2008)

The crystal structure of HI0827 from Haemophilus influenzae Rd KW20, initially annotated "hypothetical protein" in sequence databases, exhibits an acyl-coenzyme A (acyl-CoA) thioesterase "hot dog" fold with a trimer of dimers oligomeric association, a novel assembly for this enzyme family. In studies described in the preceding paper [Zhuang, Z., Song, F., Zhao, H., Li, L., Cao, J., Eisenstein, E., Herzberg, O., and Dunaway-Mariano, D. (2008) Biochemistry 47, 2789-2796], HI0827 is shown to be an acyl-CoA thioesterase that acts on a wide range of acyl-CoA compounds. Two substrate binding sites are located across the dimer interface. The binding sites are occupied by two CoA molecules, one with full occupancy and the second only partially occupied. The CoA molecules, acquired from HI0827-expressing Escherichia coli cells, remained tightly bound to the enzyme through the protein purification steps. The difference in CoA occupancies indicates a different substrate affinity for each of the binding sites, which in turn implies that the enzyme might be subject to allosteric regulation. Mutagenesis studies have shown that the replacement of the putative catalytic carboxylate Asp44 with an alanine residue abolishes activity. The impact of this mutation is seen in the crystal structure of D44A HI0827. Whereas the overall fold and assembly of the mutant protein are the same as those of the wild-type enzyme, the CoA ligands are absent. The dimer interface is perturbed, and the channel that accommodates the thioester acyl chain is more open and wider than that observed in the wild-type enzyme. A model of intact substrate bound to wild-type HI0827 provides a structural rationale for the broad substrate range.
THE SPECIFICATION OF DORSAL CELL FATES IN THE VERTEBRATE CENTRAL NERVOUS SYSTEM (1999)

The generation of distinct classes of neurons at defined positions within the developing vertebrate nervous system depends on inductive signals provided by local cell groups that act as organizing centers. Genetic and embryological studies have begun to elucidate the processes that control the pattern and identity of neuronal cell types. Here we discuss the cellular interactions and molecular mechanisms that direct neuronal cell fates in the dorsal half of the vertebrate central nervous system. The specification of dorsal neuronal cell fates appears to depend on a cascade of inductive signals initiated by cells of the epidermal ectoderm that flank the neural plate and propagated by roof plate cells within the neural tube. Members of the transforming growth factor-beta (TGF beta) family of secreted proteins have a prominent role in mediating these dorsalizing signals. Additional signals involving members of the Wnt and fibroblast growth factor (FGF) families may also contribute to the proliferation and differentiation of dorsal neuronal cell types.
Head and Neck Cancer (2001)

Head and neck cancers include neoplasms of the oral cavity, pharynx, and larynx. The risk of these cancers is strongly associated with smoking and alcohol ingestion. There have been important advances in understanding of the molecular pathogenesis and progression of head and neck cancer and also in approaches to therapy, which include innovations in surgery, radiation therapy, and cytotoxic-drug therapy.
Multifrequency operation technique for aperture coupled microstrip antennas (2002)

A multiple frequency operation technique is proposed for a microstrip antenna, in which the structure is fed by a microstrip line through an aperture coupling. The technique is general and can also be applied to microstrip antennas with other feed types. It allows the antenna to operate at several discrete frequencies over a wide frequency band.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Titanium Tetrachloride in Organic Synthesis [New synthetic methods (21)] (1977)

Abstract Titanium tetrachloride can accelerate numerous organic reactions. Valuable syntheses of, e.g. , allyl sulfides, amides, enamines, and ketones are based upon transformations of functional groups with TiCl 4 . Particular mention should also be made of carbon‐carbon linkage with TiCl 4 which permits the synthesis of hydroxy ketones and carbonyl compounds of the Michael adduct type. TiCl 4 reduced in situ is suitable for the reduction of chloroarenes or the linkage of two aldehyde molecules to give an alkene.
Complex amplitude correlation for compensation of large in-plane motion in digital speckle pattern interferometry (2006)

The use of complex amplitude correlation to compensate for large in-plane motion in digital speckle pattern interferometry is investigated. The result is compared with experiments where digital speckle photography (DSP) is used for compensation. An advantage of using complex amplitude correlation instead of intensity correlation (as in DSP) is that the phase change describing the deformation is retrieved directly from the correlation peak, and there is no need to compensate for the large movement and then use the interferometric algorithms. A discovered drawback of this method is that the correlation values drop quickly if a phase gradient larger than pi is present in the subimages used for cross correlation. This means that, for the complex amplitude correlation to be used, the size of the subimages must be well chosen or a third parämeter in the cross-correlation algorithm that compensates for the phase variation is needed. Correlation values and wrapped phase maps from the two techniques (intensity and complex amplitude correlation) are presented.
Tumor-specific transgene expression from the human telomerase reverse transcriptase promoter enables targeting of the therapeutic effects of the Bax gene to cancers. (2000)

Human telomerase reverse transcriptase (hTERT) is the catalytic subunit of telomerase, which is highly active in immortalized cells and >85% of human cancers but is quiescent in most normal somatic cells. To test the feasibility of using the hTERT promoter to induce tumor-specific transgene expression in cancer gene therapy, we constructed an adenoviral vector expressing a LacZ reporter gene driven by the hTERT core promoter and evaluated its activity in vitro and in vivo. The hTERT promoter could drive high-level expression of LacZ in tumor cells but not in normal cells and normal mouse tissues. Using a binary adenoviral system that can induce Bax gene expression, we showed that induction of the Bax gene expression via the hTERT promoter elicited tumor-specific apoptosis in vitro, suppressed tumor growth in nude mice, and prevented the toxicity of the Bax gene in vitro and in vivo. Thus, the hTERT promoter is apparently a strong and tumor-selective promoter with potential application in targeted cancer gene therapy.
Persistent improvement in synaptic and cognitive functions in an Alzheimer mouse model after rolipram treatment (2004)

Evidence suggests that Alzheimer disease (AD) begins as a disorder of synaptic function, caused in part by increased levels of amyloid beta-peptide 1-42 (Abeta42). Both synaptic and cognitive deficits are reproduced in mice double transgenic for amyloid precursor protein (AA substitution K670N,M671L) and presenilin-1 (AA substitution M146V). Here we demonstrate that brief treatment with the phosphodiesterase 4 inhibitor rolipram ameliorates deficits in both long-term potentiation (LTP) and contextual learning in the double-transgenic mice. Most importantly, this beneficial effect can be extended beyond the duration of the administration. One course of long-term systemic treatment with rolipram improves LTP and basal synaptic transmission as well as working, reference, and associative memory deficits for at least 2 months after the end of the treatment. This protective effect is possibly due to stabilization of synaptic circuitry via alterations in gene expression by activation of the cAMP-dependent protein kinase (PKA)/cAMP regulatory element-binding protein (CREB) signaling pathway that make the synapses more resistant to the insult inflicted by Abeta. Thus, agents that enhance the cAMP/PKA/CREB pathway have potential for the treatment of AD and other diseases associated with elevated Abeta42 levels.