gebhart/patrepeval huggingface dataset:
Understanding Hydraulic Fracture Geometry and Interactions in the Horn River Basin through DFN and Numerical Modeling (2010)

Abstract In the Horn River Basin, evidence points to one of the key elements of a successful well completion being the effective connection of the hydraulic fracture into the natural fracture system, allowing the well to connect to a significantly enhanced drainage volume. However great uncertainty exists with respect to the nature of the natural fracture system and importantly how the hydraulic fracture interacts with it. To provide a framework to address these uncertainties, an approach has been developed within a Discrete Fracture Network (DFN) code. The DFN approach provides a platform to construct realistic fracture models of stochastically generated fracture elements constrained and conditioned by well and surface data. Simulation of hydraulic frac development through these DFN models using a rule based approach allows the rapid modelling of the interaction between the hydraulic frac and the natural fracture system with calibration of the model being provided by the generation of a simulated micro-seismic cloud. Comparison of the simulated micro-seismic pattern to field measurements increases confidence in the DFN approach and allows the tuning of key hydraulic properties as part of the calibration process. An additional challenge at this stage of the plays development however is that many of the developments are relatively data poor and therefore the rigorous simulation of detailed models conditioned to well data is often not possible. To address this, a number of simulations were run on more generic models where key properties such as fracture length, fracture aperture and intensity were varied and their impact on the resultant micro-seismic pattern observed. This more parametric approach allows well observations to be interpreted within a better constrained framework of fracture network knowledge. These DFN based simulations were supplemented by detailed geomechanical models using a hybrid FEM-DEM code that allowed the coupled stress-flow modelling of hydraulic frac interaction and pressure evolution, enabling certain stimulation design factors to be considered as well as testing the basis for the more stochastic modelling. The benefit of these combined simulations is that a framework is developed to integrate, interpret and test all the fracture related information, allowing more guided development decisions to be made as well as identifying critical data gaps to be addressed.
Copper-Catalyzed, Directing Group-Assisted Fluorination of Arene and Heteroarene C–H Bonds (2013)

We have developed a method for direct, copper-catalyzed, auxiliary-assisted fluorination of β-sp(2) C-H bonds of benzoic acid derivatives and γ-sp(2) C-H bonds of α,α-disubstituted benzylamine derivatives. The reaction employs a CuI catalyst, a AgF fluoride source, and DMF, pyridine, or DMPU solvent at moderately elevated temperatures. Selective mono- or difluorination can be achieved by simply changing reaction conditions. The method shows excellent functional group tolerance and provides a straightforward way for the preparation of ortho-fluorinated benzoic acids.
Entering the Era of Targeted Therapy for Chronic Lymphocytic Leukemia: Impact on the Practicing Clinician (2014)

Therapy for CLL has evolved significantly over the past decade with introduction of targeted therapy for CLL. This has the potential to completely transform how CLL is treated in the future.
X‐ray sources of medical linear accelerators: Focal and extra‐focal radiation (1993)

A computerized tomography (CT) reconstruction technique has been used to make quantitative measurements of the size and shape of the focal spot in medical linear accelerators. Using this technique, we have measured the focal spots in a total of nine accelerators, including (i) two Varian Clinac 2100c's, (ii) two Atomic Energy of Canada Ltd. (AECL) Therac-25's, (iii) two AECL Therac 6's, (iv) a Siemens KD-2, (v) a Varian Clinac 600c (4 MV), and (vi) an AECL Therac-20. Some of these focal spots were monitored for changes over a 2-yr period. It has been found that (i) the size and shape of the source spot varies greatly between accelerators of different design ranging from 0.5 to 3.4 mm in full width at half maximum (FWHM); and (ii) for accelerators of the same design, the focal spots are very similar. In addition to the measurements of the focal spot, a new technique for measuring the magnitude and distribution of extra-focal radiation originating from the linear accelerator head (flattening filter, primary collimator) has also been developed. The extra-focal radiation produced by a Varian Clinac 2100c accelerator was measured using this technique and it was found that the extra-focal radiation accounts for as much as 8% of the total photon fluence reaching the isocenter. The majority (75%) of this extra-focal radiation originates from within a circle 6 cm in diameter at the target plane. The source MTFs for each of the measured focal spots have been calculated in order to assess their influence on the spatial resolution of verification images. The limiting spatial resolution (i.e., 10% modulation) for all the source MTFs is 1.8 mm-1 or greater when used for transmission radiography at a magnification of 1.2. The extra-focal radiation, which produces a low-frequency drop in the source MTFs of up to 8%, changes with field size. As a result, the source MTFs of linear accelerators depend not only on the design of individual accelerators and image magnification, but also on the field size used when forming an image.
Label Refinement Network for Coarse-to-Fine Semantic Segmentation (2017)

We consider the problem of semantic image segmentation using deep convolutional neural networks. We propose a novel network architecture called the label refinement network that predicts segmentation labels in a coarse-to-fine fashion at several resolutions. The segmentation labels at a coarse resolution are used together with convolutional features to obtain finer resolution segmentation labels. We define loss functions at several stages in the network to provide supervisions at different stages. Our experimental results on several standard datasets demonstrate that the proposed model provides an effective way of producing pixel-wise dense image labeling.
Simultaneous optimization of spectrum, spatial coherence, gap, feature bias, and absorber thickness in synchrotron-based x-ray lithography (1993)

Of the many factors affecting the x-ray intensity distribution, the variables that can be controlled are the source spectrum, the proximity gap, the source spatial coherence, the mask linewidth bias, and the absorber thickness. To obtain the highest quality aerial image, all of these parameters must be optimized simultaneously. An optimization of the spectrum of the synchrotron Helios, located at IBM’s Advanced Lithography Facility is described. The optimum parameter space for proximity x-ray lithography at 0.1 μm minimum linewidth is then determined using the optimized spectrum by adjusting the free parameters. For maximum accuracy, a rigorous electromagnetic model that accounts for the dielectric properties of the absorber, the source partial coherence, and diffraction in the proximity gap is used to calculate the x-ray aerial image at the wafer. Descriptive figures-of-merit (FOMs) of the aerial image are the image contrast [(Imax−Imin)/(Imax+Imin)] and the exposure latitude. These two FOMs are maximized with respect to source spectrum, gap, source spatial coherence, feature size and bias, and mask absorber thickness. The global maximum of these FOMs is coarsely located in parameter space by determining the dependence of the FOMs on two variables at a time. The feature bias is then determined so that all feature types (gratings, lines, spaces) can be printed at the same dose with maximum average contrast and exposure latitude.
Heated ion implantation technology for highly reliable metal-gate/high-k CMOS SOI FinFETs (2013)

The impact of heated ion implantation (I/I) technology on metal-gate (MG)/high-k (HK) CMOS SOI FinFET performance and reliability has been thoroughly investigated. It was demonstrated that heated I/I brings perfect crystallization after annealing even in ultrathin Si channel. For the first time, it was found that heated I/I dramatically improves the characteristics such as I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> -I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> , V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> variability, and bias temperature instability (BTI) for both nMOS and pMOS FinFETs in comparison with conventional room temperature I/I.
Size, shape, and composition of luminescent species in oxidized Si nanocrystals and H-passivated porous Si (1995)

Near-edge and extended x-ray-absorption fine-structure measurements from a wide variety of oxidized Si nanocrystals and H-passivated porous Si samples, combined with electron microscopy, ir absorption, forward recoil scattering, and luminescence emission data, provide a consistent structural picture of the species responsible for the luminescence observed in these systems. For porous Si samples whose luminescence wavelengths peak in the visible region, i.e., at 700 nm, their mass-weighted-average structures are determined here to be particles (not wires) whose short-range character is crystalline and whose dimensions---typically 15 \AA{}---are significantly smaller than previously reported or proposed. Results are also presented which demonstrate that the observed visible luminescence is not related to either a photo-oxidized Si species in porous Si or an interfacial suboxide species in the Si nanocrystals. The structural and compositional findings reported here depend only on sample luminescence behavior, not on how the luminescent particles are produced, and thus have general implications in assigning quantum confinement as the mechanism responsible for the visible luminescence observed in both nanocrystalline and porous silicon.
Preparation of Highly Functionalized Grignard Reagents by an Iodine–Magnesium Exchange Reaction and its Application in Solid-Phase Synthesis (1998)

At −40°C aryl iodides that contain other functional groups can be selectively converted into Grignard reagents, which react with electrophiles such as benzaldehyde in the usual manner [Eq. (a)]. Aryl bromides and iodides that are immobilized as esters on a Wang resin behave analogously.
Phase I/II study of capecitabine and PHY906 in hepatocellular carcinoma (2008)

4610 PHY906, a Chinese medicine formula, has been used for 1,700 years for the treatment of diarrhea, vomiting, nausea, stomach cramps, and fever. PHY906 was found to potentiate the antitumor efficacy of capecitabine in hepatocellular carcinoma (HCC) xenografts. A Phase I/II, multicenter, open-label, dose-escalation, safety and efficacy study of capecitabine / PHY906 was initiated in patients with advanced HCC. Patients were required to have measurable, recurrent, metastatic, or unresectable HCC, Karnofsky status of 70% or above, and adequate organ and hematologic parameters. Study objectives were: Phase I - to determine the safety and tolerability of the two-drug combination; Phase II - to measure antitumor response and to assess patients’ quality of life (QoL). Patients were considered evaluable after two cycles of treatment. The initial dose regimen (capecitabine 1,000 mg/m2 BID; PHY906 1,000 mg BID) was found to have unfavorable toxicities. Thus, capecitabine was reduced to 750 mg/m2 BID and PHY906 to 600 mg BID. Subsequently, a new cohort of 750 mg/m2 BID capecitabine plus 800 mg BID PHY906 was added. Both latter regimens were well tolerated (N=4 for PHY906 600 mg BID, N=26 for PHY906 800 mg BID). The capecitabine 750 mg/m2 BID and PHY906 800 mg BID regimen was used for the Phase II study. Thirty-four patients participated in the Phase II study; 31 at US sites and 3 at Taiwan sites. Among the 27 evaluable patients at US sites, four (14.8%) achieved minor response (MR), 14(51.9%) had stable disease (SD), and 9(33.3%) exhibited progressive disease after two cycles of treatment. Median survival time was higher for the 20 Child-Pugh A patients (10.9 months vs. 9.2 months overall). Asian patients (N=12) had a higher overall 12-month survival rate (68%) than non-Asians (26%, N=15)[p=0.02]. Patients’ QoL did not appear to deteriorate significantly during treatment. Based on the results obtained with Child-Pugh A patients, additional Phase II studies in such patients in which the effectiveness of the capecitabine / PHY906 combination is compared to that of sorefinib (recently approved for the treatment of HCC) appear warranted. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration PhytoCeutica Inc. PhytoCeutica Inc. PhytoCeutica Inc.
Physical Layer Secure Communications over Wireless Channels via Common Zeros (2018)

Based on recent results on the challenges of identifiability in blind deconvolution and new methods for blind deconvolution with the knowledge of autocorrelation functions, a novel approach to secure communication over wireless channels is provided by using the Binary Modulation on Conjugated Zeros design. In particular, the blind deconvolution of a transmitted sequence via a wireless channel with Rayleigh fading is rendered impossible through the introduction of common zeros. A signal codebook design is provided as well as a decoding strategy with a shared secret key for the legitimate user. The probability of an eavesdropper guessing the correct key is computed and shown to converge to zero nearly exponentially with an increasing length of the key.
Engineering disulfide bridges to dissect antimicrobial and chemotactic activities of human β-defensin 3 (2003)

Human defensins form a family of small, cationic, and Cys-rich antimicrobial proteins that play important roles in innate immunity against invading microbes. They also function as effective immune modulators in adaptive immunity by selectively chemoattracting T lymphocytes and immature dendritic cells. On the basis of sequence homology and the connectivity of six conserved Cys residues, human defensins are classified into alpha and beta families. Structures of several beta-defensins have recently been characterized, confirming the disulfide connectivity conserved within the family, i.e., Cys1-Cys5, Cys2-Cys4, and Cys3-Cys6. We found that human beta-defensin 3 (hBD3), a recently described member of the growing beta family, did not fold preferentially into a native conformation in vitro under various oxidative conditions. Using the orthogonal protection of Cys1-Cys5 and of Cys1-Cys6, we chemically synthesized six topological analogs of hBD3 with predefined disulfide connectivities, including the (presumably) native beta pairing. Unexpectedly, all differently folded hBD3 species exhibited similar antimicrobial activity against Escherichia coli, whereas a wide range of chemotactic activities was observed with these analogs for monocytes and cells transfected by the chemokine receptor CCR6. Furthermore, whereas substitution of all Cys residues by alpha-aminobutyric acid completely abolished the chemotactic activity of hBD3, the bactericidal activity remained unaffected in the absence of any disulfide bridge. Our findings demonstrate that disulfide bonding in hBD3, although required for binding and activation of receptors for chemotaxis, is fully dispensable for its antimicrobial function, thus shedding light on the mechanisms of action for human beta-defensins and the design of novel peptide antibiotics.
A General Method for the Controlled Embedding of Nanoparticles in Silica Colloids (2006)

A novel method for the controlled embedding of multiple nanoparticles of various materials, such as gold nanoparticles, quantum dots, and magnetic nanoparticles, in silica colloids is presented. After adsorption of the amphiphilic polymer poly(vinylpyrrolidone) on hydrophobic or hydrophilic stabilized nanoparticles, these are adsorbed on silica spheres and covered by variable-thickness silica shells. This silica coating protects the embedded nanoparticles against chemical transformations, which is of crucial importance for the biocompatibility of particles containing toxic elements. Moreover, it is found that the optical properties of the nanoparticles are retained. Possible applications of multicore particles are briefly discussed.
Glycosaminoglycans of normal and malignant cultured human mammary cells. (1979)

Glycosaminoglycans have been characterized from a normal human breast cell line (HBL-100) and two different cell lines from human breast carcinoma (MDA-MB-231 and MCF-7). The glycosaminoglycans were labeled by exposure of cell cultures to [3H]glucosamine and [35S]sulfate and then isolated from both spent media and cells by pronase digestion and cetylpyridinium chloride fractionation. They were further characterized by (a) hexosamine composition, (b) controlled-pore glass exclusion chromatography, (c) reactivity with specific enzymes (hyaluronidase chondroitinase, heparitinase, and heparinase), (d) nitrous acid degradation, and (e) DEAD-Sephadex chromatography. The results indicate that the HBL-100 line synthesizes mainly hyaluronic acid, most of which is secreted into the medium. Chondroitin sulfate and heparan sulfate are the predominant glycosaminoglycans synthesized by the cancer lines; both are found mainly in the spent medium, but the hyaluronic acid synthesized by the MDA-MB-231 line remains cell associated. The cell-associated heparan sulfate had a molecular weight in excess of 13,000 and may contain linkages susceptible to testicular hyaluronidase. The MCF-7 cells produce significantly lower amounts of glycosaminoglycans than do the other two lines.
Human Blood Coagulation, Haemostasis and Thrombosis. (1973)

Book reviews together within one cover a very wide range of ideas and concepts in the investi- gation of rheumatic diseases.It will be a useful starting point for those wishing to probe restricted aspects of these diseases in more depth.However, most articles in themselves do not give sufficient informa- tion to allow critical evaluation of the results which are given.Inevitably, a book of this type rapidly becomes out of date, and one cannot avoid commenting on the delay in publication of these proceedings.Over two years elapsed between the meet- ing and publication, and although the cover flap says that the contributions have been written and revised so as to ensure the book is up to date, the extremely sparse scattering of 1975 references qualifies one's interpretation of this statement.It is useful to compare this publication with that of the 2nd World Congress in Immunology, which was held in August
Adaptation of Bordetella pertussis to Vaccination: A Cause for Its Reemergence? (2001)

In the Netherlands, as in many other western countries, pertussis vaccines have been used extensively for more than 40 years. Therefore, it is conceivable that vaccine-induced immunity has affected the evolution of Bordetella pertussis. Consistent with this notion, pertussis has reemerged in the Netherlands, despite high vaccination coverage. Further, a notable change in the population structure of B. pertussis was observed in the Netherlands subsequent to the introduction of vaccination in the 1950s. Finally, we observed antigenic divergence between clinical isolates and vaccine strains, in particular with respect to the surface-associated proteins pertactin and pertussis toxin. Adaptation may have allowed B. pertussis to remain endemic despite widespread vaccination and may have contributed to the reemergence of pertussis in the Netherlands.
Cloning and characterization of platelet factor 4 cDNA derived from a human erythroleukemic cell line (1987)

We report the isolation of a platelet factor 4 (PF4) cDNA clone from a lambda gt11 expression cDNA library which was derived from a human erythroleukemic (HEL) cell line. The sequence of the DNA insert includes the 3'-untranslated region, the entire amino acid coding region for the mature PF4 protein, and a 5' region containing coding information for an additional 18 amino acids. In addition, supplemental genomic DNA sequencing shows that the full-length leader sequence is 30 amino acids long plus an initial methionine and codes for a hydrophobic signal-like sequence which is probably involved in transmembrane transport. A single species mRNA of approximately 800 nucleotides was detected on blots of HEL cell poly(A) + RNA using a labeled PF4 cDNA probe. The human PF4 leader sequence shares some DNA, but no amino acid, homology with the 15 amino acids at the N-terminus of mature bovine PF4, suggesting rapid divergence in this region of PF4 between these two species. Sequence comparison of the coding regions of mature PF4 and gamma IP-10, a protein induced in a variety of cells following treatment with gamma-interferon, shows a corrected divergence of 76%. The divergence of a common ancestor protein into PF4 and gamma IP-10 may have accompanied the development of sophisticated immune and coagulation systems in vertebrates. The availability of cDNA and genomic DNA information for these genes in other species will be useful in studying the evolution of the coagulation and immune systems.
Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase. (1995)

Escherichia coli RuvC protein is a specific endonuclease that resolves Holliday junctions during homologous recombination. Since the endonucleolytic activity of RuvC requires a divalent cation and since 3 or 4 acidic residues constitute the catalytic centers of several nucleases that require a divalent cation for the catalytic activity, we examined whether any of the acidic residues of RuvC were required for the nucleolytic activity. By site-directed mutagenesis, we constructed a series of ruvC mutant genes with similar amino acid replacements in 1 of the 13 acidic residues. Among them, the mutant genes with an alteration at Asp-7, Glu-66, Asp-138, or Asp-141 could not complement UV sensitivity of a ruvC deletion strain, and the multicopy mutant genes showed a dominant negative phenotype when introduced into a wild-type strain. The products of these mutant genes were purified and their biochemical properties were studied. All of them retained the ability to form a dimer and to bind specifically to a synthetic Holliday junction. However, they showed no, or extremely reduced, endonuclease activity specific for the junction. These 4 acidic residues, which are dispersed in the primary sequence, are located in close proximity at the bottom of the putative DNA binding cleft in the three-dimensional structure. From these results, we propose that these 4 acidic residues constitute the catalytic center for the Holliday junction resolvase and that some of them play a role in coordinating a divalent metal ion in the active center.
Laser-based mid-infrared reflectance imaging of biological tissues (2004)

Mid-infrared (MIR) (3-12 um) spectral imaging is a power analytical tool, but difficult in the back-reflectance mode for in-vivo diagnostics. Feasibility of MIR back-reflectance imaging is demonstrated using MIR semiconductor lasers. Transmittance through 500-microm thick films of water and blood showed a capability to resolve more than 6-OD signal dynamic range. Reflectance scanning imaging through a 150-microm thick film of blood showed negligible scattering effect, indicating the feasibility of optical coherent imaging. The result of coherent imaging of a plant leaf shows a MIR sub-surface image that would not be visible in white light. With two wavelengths, a similar result for a chicken skin subcutaneous tissue at different focal depths was obtained, showing blood vessels beneath a lipid layer. These results suggest that advanced multilaser wavelength systems in the fingerprint spectral region can be a useful tool for in-vivo spectral imaging in biomedical research and diagnostic applications.