gebhart/patrepeval huggingface dataset:
Design challenges and performance of nested neutron mirrors for microfocusing on SNAP (2009)

Kirkpatrick–Baez (KB) neutron supermirrors can efficiently focus polychromatic neutron beams to micrometre dimensions. The ultimate size is determined mainly by the perfection of the mirrors and by the size of the beam needed to have sufficient experimental signal. Nested or Montel KB mirrors can collect ∼2.6 times more beam than standard sequential KB optics, but require good figure perfection at the edge of one mirror. This paper describes the characterization of the figure errors over the important reflective portions of the two mirrors needed for a Montel focusing pair. The measurements are placed in context with theoretical predictions and are used to predict mirror focusing performance. Strategies to improve on the focusing of this class of optics are suggested and early results from these mirrors installed on the Spallation Neutrons at Pressure (SNAP) Beamline 3 at the Spallation Neutron Source (SNS) at Oak Ridge are presented.
Nonlinear bulk elasticity imaging using dual frequency ultrasound (2019)

The nonlinear acoustic bulk properties of tissue, e.g., the coefficient of nonlinearity, β<sub>n</sub>, or the nonlinear bulk elasticity, β<sub>p</sub>=β<sub>n</sub>κ<sub>0</sub>, have been shown to be promising parameters for tissue characterization due to their sensitivity to tissue structure. Previously developed methods for imaging these parameters using single frequency ultrasound have shown success in a laboratory setting using the transmission mode. In the pulse-echo mode, however, unknown absorption, diffraction, and speckle produce unreliable estimates and instability, causing these methods to have achieved no clinical relevance. In this paper, a pulse-echo method for measurement of the nonlinear bulk elasticity is presented using a dual frequency approach. The method is less sensitive to diffraction and absorption due to a separate low frequency manipulation wave. The technique is tested in both simulations and in vitro in a heterogeneous phantom with two regions of different nonlinear properties. Both in simulations and in vitro, a spatial β<sub>p</sub> map is produced where the two regions are clearly distinguished. In addition, the quantitative estimates of β<sub>p</sub> obtained are close to the expected values, making the method a promising first step toward in vivo imaging of nonlinear bulk properties.
Eternal Packages: Liquid Metal Flip Chip Devices (2016)

Gallium liquid metal joints are described as an alternative to higher melting point tin-or lead-based solder joints in flip chip packages. A complete assembly process is described, including the bumping process with the electrodeposition of gallium on corrosion resistant bonding pad, a low-temperature and low bonding force chip joining process with a HCl flux, and an underfill process with a low stiffness material. An analysis of the projected reliability of Ga joints is presented, using known properties of Ga in its liquid and solid states, finite element models of flip chip modules, and preliminary experimental results on test modules. While experimental data suggest that damage to Ga joints produced in their solid state can disappear when the joints melt, adjustments to the elastic modulus of the underfill material are discussed to prevent plastic deformation and potential fatigue failure of the solid Ga joints.
Hydraulic method for the location of oil leaks from pressure-assisted 3-core and single-core cables (1987)

An investigation has been carried out into possible methods of oil-leak location in pressure-assisted cables. A hydraulic method of leak location, making use of the cable resistance to oil flow and involving measurements of pressure and flow at both ends of the cable is suggested as the most viable alternative to the present freezing technique on 3-core cables. The same principle can also be applied to single-core cables. The method was first tested in the laboratory using a long length of small-bore pipe to simulate a cable and the accuracy of location was repeatedly better than 1% of the total length. A small number of initial field trials on various types of cables provided useful information on the factors affecting the accuracy of locating actual leaks. Subsequent location tests on a wide variety of cables which developed leaks whilst in service, have proved highly successful. In most cases it was possible to correctly identify the leak position, without the need for freezing. The reasons for the variations in accuracy of test results together with practical problems are discussed.
Heparin affinity purification of extracellular vesicles (2015)

Extracellular vesicles (EVs) are lipid membrane vesicles released by cells. They carry active biomolecules including DNA, RNA, and protein which can be transferred to recipient cells. Isolation and purification of EVs from culture cell media and biofluids is still a major challenge. The most widely used isolation method is ultracentrifugation (UC) which requires expensive equipment and only partially purifies EVs. Previously we have shown that heparin blocks EV uptake in cells, supporting a direct EV-heparin interaction. Here we show that EVs can be purified from cell culture media and human plasma using ultrafiltration (UF) followed by heparin-affinity beads. UF/heparin-purified EVs from cell culture displayed the EV marker Alix, contained a diverse RNA profile, had lower levels of protein contamination, and were functional at binding to and uptake into cells. RNA yield was similar for EVs isolated by UC. We were able to detect mRNAs in plasma samples with comparable levels to UC samples. In conclusion, we have discovered a simple, scalable, and effective method to purify EVs taking advantage of their heparin affinity.
Tunable interchannel broad-band dispersion-slope compensation for 10-Gb/s WDM systems using a nonchannelized third-order chirped FBG (2003)

We demonstrate tunable dispersion-slope compensation using a single broad-band nonchannelized fiber Bragg grating. Tunability of the dispersion slope is achieved by stretching the grating, which has a third-order time-delay variation with wavelength, thereby causing a second-order variation in dispersion. Although this nonlinear dispersion characteristic causes some inherent mismatch between the grating and real fiber links, the induced errors are negligible in 10-Gb/s systems. Dispersion-slope tunability of /spl sim/65 ps/nm/sup 2/ is achieved using a grating with dispersion variation of up to 400 ps/nm over a 3.5-nm usable bandwidth. Using this grating, we show over 10-dB improvement in the worst-case channel in a 10-Gb/s return-to-zero system. Two gratings are cascaded in order to double the dispersion values that can be compensated by the grating.
Selective killing of tumor cells by RNAi-Silencing of BORIS (2008)

AACR Annual Meeting-- Apr 12-16, 2008; San Diego, CA

2700 

Background: Brother of the Regulator of Imprinted Sites (BORIS) is an epigenetically acting transcription factor that displaces the tumor suppressor protein CTCF in cancer cells resulting in upregulation of numerous proteins associated with oncogenesis. Previous studies have demonstrated vaccination against BORIS results in the generation of cytolytic immune responses against histologically-diverse tumors. In this study, RNAi induction was assessed as an alternative approach to induction of selective tumor cell killing. Materials and Methods: Short interfering RNA nucleotides targeting either specific zinc finger or non-zinc finger portions of BORIS, as well as scrambled control siRNA, were generated and administered to non-malignant epithelial and endothelial cells, and to several tumor cell lines representing breast cancer, glioma, and hepatoma. BORIS expression, and silencing thereof, was assessed by Western Blot analysis. TUNEL, MTT and Caspase 3/7 assays were performed to ascertain the effects of the siRNAs on proliferation and apoptosis of non-malignant and cancer cells. Results: BORIS expression was found in all cancer cell lines tested, but not control non-malignant cells, with highest expression in the MDA-231 breast cancer cell line. Treatment with 1.7nM of BORIS-specific siRNA, but not scrambled control siRNA, led to a significant reduction in BORIS expression and a profound induction of cell death in MDA-231 cells. Cell death was concentration dependent and peaked between 48 to 72 hours post treatment. Apoptosis was confirmed as the mechanism of cell death by TUNEL staining and Caspase 3/7 activation. Conclusion: This is the first unequivocal validation that the BORIS transcription factor represents an important target in the development of cancer therapeutics.
Updates Through Views: A New Hope (2006)

Database views are extensively used to represent unmaterialized tables. Applications rarely distinguish between a materialized base table and a virtual view, thus, they may issue update requests on the views. Since views are virtual, update requests on them need to be translated to updates on the base tables. Existing literature has shown the difficulty of translating view updates in a side-effect free manner. To address this problem, we propose a novel approach for separating the data instance into a logical and a physical level. This separation allows us to achieve side-effect free translations of any kind of update on the view. Furthermore, deletes on a view can be translated without affecting the base tables. We describe the implementation of the framework and present our experimental results
Synthesis and benzodiazepine receptors affinity of 2,3-dihydro-9-phenyl-1H-pyrrolo[3,4-b]quinolin-1-one and 3-carbethoxy-4-phenylquinoline derivatives. (1992)

A series of 2,3-dihydro-9-phenyl-1H-pyrrolo[3,4-b]quinolin-1-one derivatives and related compounds were tested for their ability to bind benzodiazepine receptors (BZRs). Most of the synthesized compounds showed micromolar affinity for BZR peripheral type, but not for the central one, with the exception of compound 4m which displayed an IC50 = 0.407 microM, only 2 fold higher than IC50 for chlordiazepoxide.
The Design, Synthesis, and Evaluation of C7 Diversified Bryostatin Analogs Reveals a Hot Spot for PKC Affinity (2008)

The first series of systematically varied C7-functionalized bryostatin analogs (12 members in all) have been synthesized through an efficient and convergent route. A new hotspot for PKC affinity, not present in the natural products, has been discovered, allowing for affinity control and potentially for selective regulation of PKC isozymes. Several analogs exhibit single-digit nanomolar affinity to PKC and display superior activity compared to bryostatin against the leukemia cell line K562.
Engineered Mannose‐Binding Lectin (FcMBL) Decreases Macrophage Phagocytosis (2016)

Mannose‐binding lectin (MBL) is an innate immune system opsonin that binds a large variety of pathogen‐associated molecular patterns (PAMPs) on bacteria, fungi, viruses, parasites and toxins, leading to the activation of the lectin compliment pathway, coagulation, and opsonization of pathogens for phagocytosis. Due to its opsonizing abilities, MBL can be used to diagnose and treat blood‐borne infections, including sepsis. We have engineered a recombinant protein (FcMBL) by fusing the Fc domain of IgG1 to the pathogen‐binding domains of MBL. FcMBL preserves the capabilities of wild‐type MBL to recognize and bind pathogen, while avoiding the subsequent immune responses normally produced by wild‐type MBL, such as complement activation, coagulation, and inflammation. In the present study, we have differentiated THP‐1 acute monocytic leukemia cells into monocyte‐derived macrophages (MDM) using 12‐O‐tetradecanoylphorbol‐13‐acetate (PMA) and used these to test MBL‐dependent phagocytosis. Phagocytosis levels were determined using flow cytometry by measuring the fluorescent signal of pHrodo® Red E. coli BioParticles®, which fluoresce upon macrophage ingestion due to a change in pH from the extracellular environment (pH 7.4) to the inside of a phagosome (pH 5). Characterizing FcMBL as an effective opsonin capable of recognizing and binding to a diverse range of pathogens but without activating an immune response typical of wild‐type MBL will provide useful information about the use of FcMBL as a therapeutic protein. Support or Funding Information This work was supported by Defense Advance Research Projects Agency (DARPA) Grant N66001‐11‐1‐4180 and Contract HR0011‐13‐C‐0025 and the Wyss Institute for Biologically Inspired Engineering at Harvard University.
The Effect of Growth Regulators and Antibiotics on Eggplant Transformation (1997)

A protocol with a high rate of transformation and regeneration of `Hibush' eggplant ( Solanum melongena L.) has been developed. This protocol used leaves of in vitro-grown seedlings as a source of explants. The shoot regeneration culture medium contained 0.1 μ m thidiazuron (TDZ) combined with 10 to 20 μ m N 6 -[isopentyl] adenine (2iP). Adding TDZ significantly improved regeneration efficiency and produced a mean of 15 buds and 3 to 4 shoots per explant. When explants were cocultivated with Agrobacterium tumefaciens strains Q10, Q20, Q30, Q40, Q201, Q202, Q203, or Q204 containing the native cryIIIB Bacillus thuringiensis (Bt) , neomycin phosphotransferase ( NPTII ), and β-glucuronidase ( uidA ) genes, a callus/bud regeneration frequency of 38.8% was observed on the selection medium. Kanamycin at 50 μg·mL -1 was most effective in selecting for transgenic buds and shoots. Augmentin at 300 μg·mL -1 was used to eliminate A. tumefaciens. Augmentin also enhanced shoot proliferation. A transformation/regeneration efficiency of 20.8% was observed for shoot production. More than 400 putative transgenic plants have been produced with this method. From 50 putative transgenic plants, gene integration has been confirmed with Southern blot analysis and progeny tests.
On the Construction and Decoding of Concatenated Polar Codes (2013)

A scheme for concatenating the recently invented polar codes with interleaved block codes is considered. By concatenating binary polar codes with interleaved Reed-Solomon codes, we prove that the proposed concatenation scheme captures the capacity-achieving property of polar codes, while having a significantly better error-decay rate. We show that for any $ε> 0$, and total frame length $N$, the parameters of the scheme can be set such that the frame error probability is less than $2^{-N^{1-ε}}$, while the scheme is still capacity achieving. This improves upon $2^{-N^{0.5-\eps}}$, the frame error probability of Arikan's polar codes. We also propose decoding algorithms for concatenated polar codes, which significantly improve the error-rate performance at finite block lengths while preserving the low decoding complexity.
Reduced-parts-count multilevel rectifiers (2002)

Multilevel power converters have gained much attention in recent years due to their high power quality, low switching losses, and high-voltage capability. These advantages make the multilevel converter a candidate topology for the next generation of naval ship prolusion systems. The primary disadvantage of these systems is the large number of semiconductors involved. This paper presents a reduced-parts-count rectifier which is well suited for naval rectifier applications where bidirectional power flow is not required. The proposed converter is analyzed and experimentally verified on an 18-kW four-level rectifier/inverter system.
Optical geometry calibration method for free-form digital tomosynthesis (2016)

Digital tomosynthesis is a type of limited angle tomography that allows 3D information to be reconstructed from a set of x-ray projection images taken at various angles using an x-ray tube, a mechanical arm to rotate the tube about the object, and a digital detector. Tomosynthesis reconstruction requires the precise location of the detector with respect to each x-ray source, forcing all current clinical tomosynthesis systems to use a physically coupled source and detector so the geometry is always known and is always the same. This limits the imaging geometries and its large size is impractical for mobile or field operations. To counter this, we have developed a free form tomosynthesis with a decoupled, free-moving source and detector that uses a novel optical method for accurate and real-time geometry calibration to allow for manual, hand-held tomosynthesis and even CT imaging. We accomplish this by using a camera, attached to the source, to track the motion of the source relative to the detector. Attached to the detector is an optical pattern and the image captured by the camera is then used to determine the relative camera/pattern position and orientation by analyzing the pattern distortion and calculating the source positions for each projection, necessary for 3D reconstruction. This allows for portable imaging in the field and also as an inexpensive upgrade to existing 2D systems, such as in developing countries, to provide 3D image data. Here we report the first feasibility demonstrations of free form digital tomosynthesis systems using the method.
Method for improved CMP pad conditioning performance (2010)

A new pad conditioning arm design enables the use of closed-loop control (CLC) to improve conditioning performance throughout the life of a pad and disk pair. Measured pad conditioner torque is used to monitor and control the conditioning and polish processes in situ and in real time. The CLC system maintains process performance throughout pad life by adjusting the conditioner down force to compensate for process drift, such as the loss of diamond aggressiveness as the disk ages.
African swine fever: A re-emerging viral disease threatening the global pig industry (2018)

African swine fever (ASF) recently has spread beyond sub-Saharan Africa to the Trans-Caucasus region, parts of the Russian Federation and Eastern Europe. In this new epidemiological scenario, the disease has similarities, but also important differences, compared to the situation in Africa, including the substantial involvement of wild boar. A better understanding of this new situation will enable better control and prevent further spread of disease. In this article, these different scenarios are compared, and recent information on the pathogenesis of ASF virus strains, the immune response to infection and prospects for developing vaccines is presented. Knowledge gaps and the prospects for future control are discussed.
ASSOCIATED ANTIGENS FOR IMMUNOSCINTIGRAPHY IN PATIENTS WITH MELANOMA (1988)

Analysis of human melanoma cells with murine monoclonal antibodies has identified a number of antigens which are associated with the malignant transformation of melanocytes (for review, see 1 ,2). These antigens are referred to as melanoma associated antigens (MAA). Most of them, if not all of them, are detectable in melanocytes which are cultured in-vitro and are likely to be differentiation antigens. The MAA thus far identified with monoclonal antibodies display marked differences in their tissue distribution, molecular structure, chemical composition and antigenic profile. Immunohistochemical studies and clinical investigations have already evaluated the usefulness of many MAA in the area of immunodiagnosis and immunotherapy. MAA have been identified which can differentiate nevocellular nevi from malignant melanomas (13), which provide useful information about the biology of melanoma cells and the clinical course of melanoma (3-5), which represent useful markers to radioimage melanoma lesions with radiolabeled monoclonal antibodies (6,7) and which represent appropriate targets to develop immunotherapy to melanoma {6,8-16). We have focused our investigations on the high molecular weight­ melanoma associated antigen (HMW-MAA), since it meets the criteria to be a useful marker to radioimage lesions with radiolabeled monoclonal antibodies and to be an appropriate target to develop immunotherapy to melanoma.
Towards metabolic mapping of the human retina (2007)

Functional alterations are first signs of a starting pathological process. A device that measures parameter for the characterization of the metabolism at the human eye-ground would be a helpful tool for early diagnostics in stages when alterations are yet reversible. Measurements of blood flow and of oxygen saturation are necessary but not sufficient. The new technique of auto-fluorescence lifetime measurement (FLIM) opens in combination with selected excitation and emission ranges the possibility for metabolic mapping. FLIM not only adds an additional discrimination parameter to distinguish different fluorophores but also resolves different quenching states of the same fluorophore. Because of its high sensitivity and high temporal resolution, its capability to resolve multi-exponential decay functions, and its easy combination with laser scanner ophthalmoscopy, multi-dimensional time-correlated single photon counting was used for fundus imaging. An optimized set up for in vivo lifetime measurements at the human eye-ground will be explained. In this, the fundus fluorescence is excited at 446 or 468 nm and the time-resolved autofluorescence is detected in two spectral ranges between 510 and 560 nm as well as between 560 and 700 nm simultaneously. Exciting the fundus at 446 nm, several fluorescence maxima of lifetime t1 were detected between 100 and 220 ps in lifetime histograms of 40 degrees fundus images. In contrast, excitation at 468 nm results in a single maximum of lifetime t1 = 190 +/- 16 ps. Several fundus layers contribute to the fluorescence intensity in the short-wave emission range 510-560 nm. In contrast, the fluorescence intensity in the long-wave emission range between 560 and 700 nm is dominated by the fluorescence of lipofuscin in the retinal pigment epithelium. Comparing the lateral distribution of parameters of a tri-exponential model function in lifetime images of the fundus with the layered anatomical fundus structure, the shortest component (t1 = 190 ps) originates from the retinal pigment epithelium and the second lifetime (t2 = 1,000 ps) from the neural retina. The lifetime t3 approximately 5.5 ns might be influenced by the long decay of the fluorescence in the crystalline lens. In vitro analysis of the spectral properties of expected fluorophores under the condition of the living eye lightens the interpretation of in vivo measurements. Taking into account the transmission of the ocular media, the excitation of NADH is unlikely at the fundus.
Oxygen Isotope Analysis of Saline Solutions by a Carbonic anhydrase-Catalyzed CO<sub>2</sub>–H<sub>2</sub>O Equilibration Method (C<sup>3</sup>HEM) with an Improved Drying Technique (2020)

The recently introduced carbonic anhydrase-catalyzed CO2–H2O equilibration method (or C3HEM) for oxygen isotopes of aqueous samples has remarkably improved the analytical efficiency of the classic and most popular stable isotope analytical method in geochemistry. However, the applicability of this novel analytical method has not yet been tested for saline/hypersaline solutions despite their significance in various scientific problems. In this study, 1 m chloride and sulfate solutions of geochemical importance were used to investigate the kinetics of oxygen isotope exchange between CO2 and H2O at 25 °C. For these saline solutions, oxygen isotope equilibrium times (EQTs), rate constants, and oxygen isotope salt effects (OISEs) were determined with 4 or 16 μm carbonic anhydrase (CA). Our experimental results reveal that EQTs, ranging from 0.73 to 4.48 h, were much shorter than the typical EQT, confirming the greatly improved analytical efficiency of the C3HEM for saline solutions. In addition, a new simpler CA drying technique was developed, further improving the analytical efficiency of the C3HEM by significantly reducing the required labor time for sample vial preparation. Detailed analytical protocols and practical guidelines of the C3HEM are provided for prospective users.