gebhart/patrepeval huggingface dataset:
Engineered reciprocal chromosome translocations drive high threshold, reversible population replacement in Drosophila (2016)

Abstract Replacement of wild insect populations with transgene-bearing individuals unable to transmit disease or survive under specific environmental conditions provides self-perpetuating methods of disease prevention and population suppression, respectively. Gene drive mechanisms that require the gene drive element and linked cargo exceed a high threshold frequency to spread are attractive because they offer several points of control: they bring about local, but not global population replacement; and transgenes can be eliminated by reintroducing wildtypes into the population so as to drive the frequency of transgenes below the threshold required for drive. It has long been recognized that reciprocal chromosome translocations could, in principal, be used to bring about high threshold gene drive through a form of underdominance. However, translocations able to drive population replacement have not been reported, leaving it unclear if translocation-bearing strains fit enough to mediate gene drive can easily be generated. Here we use modeling to identify a range of conditions under which translocations should spread, and the equilibrium frequencies achieved, given specific introduction frequencies, fitness costs and migration rates. We also report the creation of engineered translocation-bearing strains of Drosophila melanogaster , generated through targeted chromosomal breakage and homologous recombination. By several measures translocation-bearing strains are fit, and drive high threshold, reversible population replacement in laboratory populations. These observations, together with the generality of the tools used to generate translocations, suggest that engineered translocations may be useful for controlled population replacement in many species.
Graceful degradation via versions (2007)

Correctness of a fault-tolerant system hinges on the failure model, which typically constrains the number of concurrent failures in the system. These assumptions are sometimes violated in practice, inevitably leading to degraded system behavior that deviates from the system's specification and even causing complete unavailability of the system.
Information representation and coding for flash memories (2009)

Flash memories are a very widely used type of non-volatile memory. Like magnetic recording and optical recording, flash memories have their own distinct properties. These distinct properties introduce very interesting information-representation and coding problems, which address many aspects of a successful storage system. In this paper, we survey recent results in this area. A focus is placed on rewriting codes and rank modulation.
Suture Suspension Arthroplasty Technique for Basal Joint Arthritis Reconstruction (2009)

Numerous techniques have been developed to address thumb basal joint arthritis. Many techniques include trapeziectomy with ligament reconstruction, most commonly performed by sacrificing a tendon that is used for ligament reconstruction and stabilization of the first metacarpal, with or without pin fixation. Harvesting a tendon for use in basal joint reconstruction is time-consuming and not without potential complications. Redirecting tendons via drill holes or anchoring tendons via suture anchors adds additional morbidity and time to the operative procedures. The authors introduce a novel technique of basal joint reconstruction, employing suture suspension for maintenance of joint arthroplasty space and stabilization of the base of the first metacarpal.
Synthesis and biological evaluation of aminoalkyloxy derivatives of 1, 3, 5(10) estratriene-like steroids as potential anti-cancer agents (2006)

1131 Breast cancer is second to cardiovascular disease in causing death in women between the ages of 35 and 55 years. It is also the second most common cause of death in women older than 55 years of age. Estrogens are important hormones in the female body. These steroids interact with multiple organ systems and make major impacts on the physiological events that occur throughout the female’s life. Among the estrogens, estradiol is the most potent because of its high binding affinity for the estrogen receptors. Tamoxifen, a therapeutically and clinically available SERM has been shown to be effective in the treatment of breast cancer. Nevertheless, tamoxifen have been associated with endometrial cancer due to its estrogenic activity within the uterus. Several chemically unrelated compounds have been found to demonstrate activities similar to that of SERMs through interaction with estrogen receptors. To synthesize compounds by combining a portion of the chemical features of tamoxifen, the aminoalkyloxy functional group, with the rigid structure of estradiol and compare the activity. Through modifying the 3-OH position on the Estradiol A-ring with different aminoalkyloxy derivatives; and opening the D-ring at the 17th position the synthesis of these compounds have been achieved. Receptor binding assays and gene proliferation studies will be done using MCF-7 cells, in vitro, to evaluate their effectiveness in treatment of breast cancer. The compounds have been successfully synthesized and their activity has been evaluated from the following studies: receptor binding studies, gene proliferation assays and gene expression. In synthesizing these specific types of compounds, it has been shown that have activity equal to or better than that of 4-hydroxytamoxifen, the active metabolite of Tamoxifen. Therefore, these compounds could be of use in the market for effectively treating patients affected by breast cancer.
Assay for Human Matrix Gla Protein in Serum (2000)

Matrix Gla protein (MGP) is synthesized in a vitamin K-dependent way in smooth muscle cells of the healthy vessel wall, and its mRNA transcription is substantially upregulated in atherosclerotic lesions. Here we report the preparation of a monoclonal antibody against human MGP and its use in an enzyme-linked immunosorbent assay. The intra-assay and interassay coefficients of variation in serum samples were 5.4% and 12.6%, respectively, and the lower detection limit was 8.5% of the normal serum value. Individual within-day variations were <11% and did not show a distinct circadian pattern. Day-to-day variations in fasting morning samples were <8%. In a first explorative survey, serum MGP concentrations were found to be significantly increased in patients with severe atherosclerosis, whereas these values were normal in those with low bone mass and osteoporosis. This finding is consistent with the high MGP mRNA expression observed in atherosclerotic vessels and plaques. More elaborate studies are required to assess the potential clinical utility of this newly developed assay.
Quality-driven disorder handling for concurrent windowed stream queries with shared operators (2016)

Handling timestamp-disorder among stream tuples is a basic requirement for data stream processing, and involves an inevitable tradeoff between the latency and the quality of stream query results. To meet the tradeoff requirements of diverse streaming applications, the approach of buffer-based, quality-driven disorder handling (QDDH) was proposed recently, which aims to minimize sizes of stream-sorting buffers, thus the result latency, while honoring user-specified result-quality requirements.
Determination of Polycyclic Aromatic Hydrocarbons in Water Using Nanoporous Material Prepared from Waste Avian Egg Shell (2012)

For the first time a biocompatible calcium carbonate vateritic polymorph was recrystallized from eggshell waste and its application for the extraction of polycyclic aromatic hydrocarbons in water samples was demonstrated. This nanoporous calcium carbonate was used as sorbent in dispersive micro‐solid‐phase extraction method. In this approach 50 mg of the calcium carbonate material having about 25 nm pores was placed in a 5 mL of water sample and ultrasonicated for 30 min. The cloudy sample was centrifuged at 13500 rpm for 2 min. The aqueous layer was then discarded and the CaCO 3 material was dabbed dry with a lint‐free tissue. The analytes were then desorbed with 100 μ L of dichloromethane by ultrasonication for 5 min. Finally, the extract was analyzed by gas chromatography flame ionization detector. Experimental parameters affecting the extraction recoveries were optimized. Using optimum extraction conditions, calibration curves were linear with correlation coefficients of 0.9853 to 0.9973 over the concentration range of 0.05 to 30 ng/mL. This method showed a detection limit as low as 0.004 ng/mL (at signal‐to‐noise ratio of 3). Performance of the dispersive micro‐solid‐phase extraction was compared with a previously optimized solid‐phase extraction technique. The developed method displayed good extraction recoveries (85 ± 8–110 ± 4%) with high enhancement factors (388–1433‐fold) and good repeatability (% RSD < 13) and involved the use of minimal solvents. Analysis of seawater from Dammam Port revealed the presence of the analytes at concentrations between 0.15 ± 0.01 and 13.43 ± 1.54 ng/mL.
DoWitcher: Effective Worm Detection and Containment in the Internet Core (2007)

Enterprise networks are increasingly offloading the responsibility for worm detection and containment to the carrier networks. However, current approaches to the zero-day worm detection problem such as those based on content similarity of packet payloads are not scalable to the carrier link speeds (OC-48 and up-wards). In this paper, we introduce a new system, namely DoWitcher, which in contrast to previous approaches is scalable as well as able to detect the stealthiest worms that employ low-propagation rates or polymorphisms to evade detection. DoWitcher uses an incremental approach toward worm detection: First, it examines the layer-4 traffic features to discern the presence of a worm anomaly; Next, it determines a flow-filter mask that can be applied to isolate the suspect worm flows and; Finally, it enables full-packet capture of only those flows that match the mask, which are then processed by a longest common subsequence algorithm to extract the worm content signature. Via a proof-of-concept implementation on a commercially available network analyzer processing raw packets from an OC-48 link, we demonstrate the capability of DoWitcher to detect low-rate worms and extract signatures for even the polymorphic worms.
Stereo matching with transparency and matting (2002)

This paper formulates and solves a new variant of the stereo correspondence problem: simultaneously recovering the disparities, true colors, and opacities of visible surface elements. This problem arises in newer applications of stereo reconstruction, such as view interpolation and the layering of real imagery with synthetic graphics for special effects and virtual studio applications. While this problem is intrinsically more difficult than traditional stereo correspondence, where only the disparities are being recovered, it provides a principled way of dealing with commonly occurring problems such as occlusions and the handling of mixed (foreground/background) pixels near depth discontinuities. It also provides a novel means for separating foreground and background objects (matting), without the use of a special blue screen. We formulate the problem as the recovery of colors and opacities in a generalized 3-D (x, y, d) disparity space, and solve the problem using a combination of initial evidence aggregation followed by iterative energy minimization.
Design and performance of distributed helicon sources (2001)

Helicon plasma sources are known to be efficient generators of high-density plasma for materials processing applications. By using multiple sources, arbitrarily large substrates can in principle be covered uniformly with dense plasma. To test this idea, a seven-tube helicon source was constructed, and the plasma density and uniformity measured. Densities up to 1012 cm-3 over a 40 cm diameter area with ±3% uniformity were achieved.
Optical Combs and Photonic RF Oscillators with Whispering-Gallery Mode Microresonators (2011)

We demonstrate compact low-noise photonic oscillators with self-injection-locked semiconductor lasers and crystalline microresonators. We compare microwave feedback oscillators with electro-optic resonators, and latest optical Kerr comb generators.
An Automatic Computer-Aided Detection System for Meniscal Tears on Magnetic Resonance Images (2009)

Knee-related injuries including meniscal tears are common in both young athletes and the aging population, and require accurate diagnosis and surgical intervention when appropriate. With proper techniques and radiologists' experienced skills, confidence in detection of meniscal tears can be quite high. This paper develops a novel computer-aided detection (CAD) diagnostic system for automatic detection of meniscal tears in the knee. Evaluation of this CAD system using an archived database of images from 40 individuals with suspected knee injuries indicates that the sensitivity and specificity of the proposed CAD system are 83.87% and 75.19%, respectively, compared to the mean sensitivity and specificity of 77.41% and 81.39%, respectively, obtained by experienced radiologists in routine diagnosis without using the CAD. The experimental results suggest that the developed CAD system has great potential and promise in automatic detection of both simple and complex meniscal tears of the knee.
New Zno-Based Regenerable Sulfur Sorbents for Fluid-Bed/Transport Reactor Applications (2002)

A new sorbent synthesis technique has been developed at GTI, based on sol−gel processing of inorganic and organic precursors, for the preparation of ZnO-based regenerable sulfur sorbents with unique properties that could not be attained with “conventional” sorbent preparation methods such as coprecipitation or solid-oxide mixing followed by extrusion, granulation, or spray drying. Unlike these techniques, which require very high calcination temperatures to impart physical strength to sorbents, sol−gel processing offers the unique capability of producing sintering at exceptionally low temperatures. As a result, materials with high surface areas, small pore sizes, and very high resistance to attrition can be synthesized. Sorbents prepared with this new technique demonstrated attrition indices that are well below the stringent requirement of the transport reactor of ≈4% and effective capacity for sulfur absorption exceeding 8 g of S/100 g of sorbent. In addition, these sorbents demonstrated regenerability at temperatures that are lower than those required by typical zinc titanates. On the basis of chemical analysis, physical characterization, attrition resistance determination, and evaluation of chemical reactivity and regenerability, the exceptional characteristics of this new class of zinc-based sorbents are demonstrated in this paper.
Volumetric spectroscopic imaging with spiral‐based <i>k</i>‐space trajectories (1998)

Spiral-based k-space trajectories were applied in a spectroscopic imaging sequence with time-varying readout gradients to collect volumetric chemical shift information. In addition to spectroscopic imaging of low signal-to-noise ratio (SNR) brain metabolites, the spiral trajectories were used to rapidly collect reference signals from the high SNR water signal to automatically phase the spectra and to aid the reconstruction of metabolite maps. Spectral-spatial pulses were used for excitation and water suppression. The pulses were designed to achieve stable phase profiles in the presence of up to 20% variation in the radiofrequency field. A gridding algorithm was used to resample the data onto a rectilinear grid before fast Fourier transforms. This method was demonstrated by in vivo imaging of brain metabolites at 1.5 T with 10 slices of 18 x 18 pixels each. Nominal voxel size was 1.1 cc, spectral bandwidth was 400 Hz, scan time was 18 min for the metabolite scan and 3 min for the reference scan.
A Microfabricated Near-Field Scanned Microwave Probe for Noncontact Dielectric Constant Metrology of Low-k Films (2006)

We have developed a non-contact method for quantitative measurements of permittivity, k, for low-k dielectric films of 0.1 to 1.5 mum in thickness deposited on up to 300-mm silicon wafers. It is based on a near-field scanned microwave probe formed by a microfabricated 4 GHz stripline resonator tapered down to a few-micron tip size. Probe calibration and measurements are performed at a unique tip-sample distance at which the probe resonant frequency exhibits a linear dependence on the parameter (k-1)/(k+1). The probe has about 10 micron sampling spot size and provides better than 0.3% precision and plusmn2% accuracy for k-value. Excellent correlation with mercury probe measurements is established using a variety of blanket low-k films
Metal‐Catalyzed One‐Pot Synthesis of Tetrazines Directly from Aliphatic Nitriles and Hydrazine (2012)

Der Weg ist frei: Das Fehlen einfacher Synthesemethoden stellte ein beträchtliches Hindernis für die breite Anwendung von 1,2,4,5-Tetrazinen in der bioorthogonalen Chemie und in funktionellen Materialien dar. Mit Lewis-sauren Metallkatalysatoren – allen voran NiII- und ZnII-Salzen – gelang nun die Synthese von 1,2,4,5-Tetrazinen direkt aus aliphatischen Nitrilen (siehe Schema).
Liquid-filled varifocal lens on a chip (2009)

In this study we developed a liquid-filled varifocal lens operated by electroactive polymer actuators. A silicon wafer was structured with micromachining processes to have four microfluidic chambers and a circular hole working as an aperture. The structured silicon wafer (opaque frame) was bonded to a glass wafer (transparent frame), and thus microfluidic channels were formed between them. Top surface of the main frame was covered with a transparent elastomer membrane, and the internal volume confined by the membrane and the two frames was filled with optical fluid. In order to operate this varifocal lens system, multilayered P(VDF-TrFE-CFE) [poly(vinylidene fluoride-trifluoroethylene-clorofluoroethylene)] polymer actuators were also developed, which show relaxor ferroelectric behavior, and thus produce large electrostrictive strain. When an electric field is applied, the multilayered P(VDF-TrFE-CFE) polymer actuators push the optical fluid so that the elastomer membrane together with the internal fluid changes their shape, which alters the light path of the varifocal lens. The original shape of the elastomer membrane is restored by the elastic recovery of the P(VDF-TrFE-CFE) actuators when an applied electric field is removed. We observed that with the applied voltage of 40 V the varifocal lens changes the optical power of more than 30 diopters within 20 ms. Optical analysis showed that the deformation shape of the optical membrane can be successfully used to design phone camera modules with auto-focus function.
Curcumin circumvents chemoresistance <i>in vitro</i> and potentiates the effect of thalidomide and bortezomib against human multiple myeloma in nude mice model (2009)

Curcumin (diferuloylmethane), a yellow pigment in turmeric, has been shown to inhibit the activation of nuclear factor-kappaB (NF-kappaB), a transcription factor closely linked to chemoresistance in multiple myeloma cells. Whether curcumin can overcome chemoresistance and enhance the activity of thalidomide and bortezomib, used to treat patients with multiple myeloma, was investigated in vitro and in xenograft model in nude mice. Our results show that curcumin inhibited the proliferation of human multiple myeloma cells regardless of their sensitivity to dexamethasone, doxorubicin, or melphalan. Curcumin also potentiated the apoptotic effects of thalidomide and bortezomib by down-regulating the constitutive activation of NF-kappaB and Akt, and this correlated with the suppression of NF-kappaB-regulated gene products, including cyclin D1, Bcl-xL, Bcl-2, TRAF1, cIAP-1, XIAP, survivin, and vascular endothelial growth factor. Furthermore, in a nude mice model, we found that curcumin potentiated the antitumor effects of bortezomib (P<0.001, vehicle versus bortezomib+curcumin; P<0.001, bortezomib versus bortezomib+curcumin), and this correlated with suppression of Ki-67 (P<0.001 versus control), CD31 (P<0.001 versus vehicle), and vascular endothelial growth factor (P<0.001 versus vehicle) expression. Collectively, our results suggest that curcumin overcomes chemoresistance and sensitizes multiple myeloma cells to thalidomide and bortezomib by down-regulating NF-kappaB and NF-kappaB-regulated gene products.
Reactive distillation process for the production of furfural using solid acid catalysts (2014)

A novel continuous reactive distillation process with solid acid catalysts is demonstrated for the production of furfural from synthetic and pre-hydrolysate liquor feeds containing xylose.
Bulk-Like Laminated Nitride Metal/Semiconductor Superlattices for Thermoelectric Devices (2013)

Bulk-like thermionic energy conversion devices have been fabricated from nanostructured nitride metal/semiconductor superlattices using a novel lamination process. 5-μm thick (Hf <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.5</sub> Zr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.5</sub> )N (6-nm)/ScN (6-nm) metal/semiconductor superlattices with a 12 nm period were deposited on 100-silicon substrates by reactive magnetron sputtering followed by a selective tetra methyl ammonium hydroxide substrate etching and a gold-gold lamination process to yield 300 μm × 300 μm × 290 μm microscale thermionic energy conversion elements with 16,640 superlattice periods. The thermionic element had a Seebeck coefficient of -120 μV/K at 800 K, an electrical conductivity of ~2500 Ω <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> at 800 K, and a thermal conductivity of 2.9 and 4.3 W/m-K at 300 and 625 K, respectively. The temperature dependence of the Seebeck coefficient from 300 to 800 K suggests a parallel parasitic conduction path that is dominant at low temperature, and the temperature independent electrical conductivity indicates that the (Hf <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.5</sub> Zr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.5</sub> )N/gold interface contact resistivity currently dominates the device. The thermal conductivity of the laminate was significantly lower than the thermal conductivity of the individual metal or semiconductor layers, indicating the beneficial effect of the metal/semiconductor interfaces toward lowering the thermal conductivity. The described lamination process effectively bridges the gap between the nanoscale requirements needed to enhance the thermoelectric figure of merit ZT and the microscale requirements of real-world devices.