gebhart/patrepeval huggingface dataset:
Therapy for Lyme arthritis: Strategies for the treatment of antibiotic‐refractory arthritis (2006)

Lyme arthritis, caused by the tick-borne spirochete Borrelia burgdorferi (1), typically causes intermittent or persistent arthritis in a few large joints, especially the knee, for several years (2). Treatment recommendations have changed over time. In the early 1980s, 3 intramuscular injections of benzathine penicillin or a 10-day course of high-dose intravenous (IV) penicillin cured only 35–55% of patients (3). In the late 1980s, treatment with IV ceftriaxone for 2 weeks was effective in 90% of patients (4,5); slightly better results were achieved with 4 weeks of therapy (6), but adverse events occurred more frequently. During the same period of time, a 4-week course of oral doxycycline or amoxicillin was also effective in 90% of patients with Lyme arthritis (7). However, joint swelling in some patients remained unresponsive to oral therapy and re-treatment with a 2-week course of IV ceftriaxone (7). To date, little information is available about therapy for such patients. One non–antibiotic-treated patient had resolution of joint swelling following hydroxychloroquine therapy (8). Sixteen of 20 patients with persistent arthritis despite antibiotic therapy experienced resolution after arthroscopic synovectomy (9). In 2000, an expert panel from the Infectious Diseases Society of America (IDSA) presented guidelines for the treatment of Lyme disease (10). The panel recommended initial treatment with oral doxycycline or amoxicillin for 4 weeks for patients with Lyme arthritis and no concomitant neurologic abnormalities. Results of a cost–benefit analysis suggested that such therapy is as effective as IV therapy, is safer than IV therapy, and is considerably less expensive (11). For patients in whom arthritis is persistent despite receiving 4 weeks of oral antibiotic therapy, the panel recommended re-treatment with another 4-week course of oral antibiotics or with a 2–4-week course of IV ceftriaxone. However, in a small percentage of patients, proliferative synovitis (12,13) persists for months to several years, even after 2 months of treatment with oral antibiotics, 1 month of treatment with IV antibiotics, or both, which we have termed antibiotic-refractory (or slowly resolving) Lyme arthritis.
Endovascular Aortic Repair Should Be the Gold Standard for Ruptured AAAs, and All Vascular Surgeons Should Be Prepared to Perform Them (2007)

When ruptured abdominal aortic aneurysms (AAAs) are not treated, they cause death. In addition, ruptured abdominal aortic aneurysms (RAAAs) have high mortality (35%-70%) and morbidity rates when treated by standard open surgical methods. These high perioperative mortality and morbidity rates have not been substantially reduced despite the introduction of many improvements in open operative technique or perioperative care. Endovascular approaches to treat AAAs introduced in the early 1990s provided an opportunity to substantially alter treatment outcomes when rupture occurred. This article details how these endovascular approaches, which include endovascular stented grafts, can be applied to the treatment of RAAAs, and what advantages these new catheter-based approaches to treatment offer.
Memory-enhancing effects of secreted forms of the β-amyloid precursor protein in normal and amnestic mice (1998)

When administered intracerebroventricularly to mice performing various learning tasks involving either short-term or long-term memory, secreted forms of the beta-amyloid precursor protein (APPs751 and APPs695) have potent memory-enhancing effects and block learning deficits induced by scopolamine. The memory-enhancing effects of APPs were observed over a wide range of extremely low doses (0.05-5,000 pg intracerebroventricularly), blocked by anti-APPs antisera, and observed when APPs was administered either after the first training session in a visual discrimination or a lever-press learning task or before the acquisition trial in an object recognition task. APPs had no effect on motor performance or exploratory activity. APPs695 and APPs751 were equally effective in the object recognition task, suggesting that the memory-enhancing effect of APPs does not require the Kunitz protease inhibitor domain. These data suggest an important role for APPss on memory processes.
Construction and use of a new vector/transposon, pLBT::mim-Tn10:lac:kan, to identify environmentally responsive genes in a marine bacterium (1996)

The previously described pLOFKm transposon delivery plasmid (J.Bacteriol. (1990) 172, 6557-6567) was engineered such that a promotorless lacZ gene was cloned within the transposon cassette, generating the vector pLBT. Using pLBT, stable insertion mutations were generated at high frequencies in Vibrio sp. S141 and Pseudomonas sp. S91, and the interrupted genes could be monitored for their pattern of regulation. Genetic screens isolated mutants defective in a variety of activities. We describe the construction and use of pLBT as a tool for reporter gene mutant analysis in bacteria other than well-characterized laboratory strains.
Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes (2014)

Extracting relevant information from large-scale data offers unprecedented opportunities in cancerology. We applied independent component analysis (ICA) to bladder cancer transcriptome data sets and interpreted the components using gene enrichment analysis and tumor-associated molecular, clinicopathological, and processing information. We identified components associated with biological processes of tumor cells or the tumor microenvironment, and other components revealed technical biases. Applying ICA to nine cancer types identified cancer-shared and bladder-cancer-specific components. We characterized the luminal and basal-like subtypes of muscle-invasive bladder cancers according to the components identified. The study of the urothelial differentiation component, specific to the luminal subtypes, showed that a molecular urothelial differentiation program was maintained even in those luminal tumors that had lost morphological differentiation. Study of the genomic alterations associated with this component coupled with functional studies revealed a protumorigenic role for PPARG in luminal tumors. Our results support the inclusion of ICA in the exploitation of multiscale data sets.
Implementation of an implantable joint-angle transducer. (2003)

An implantable joint-angle transducer (IJAT) was implemented to provide command-control information from the wrist for functional neuromuscular stimulation (FNS) neuroprostheses. The IJAT uses the Hall effect to sense joint angle. The objectives of this study were to evaluate (1) chronic functionality, (2) safety and biocompatibility, (3) repeatability of the implantation procedure, and (4) clinical feasibility. Accelerated bench testing projected an operating period of over 50 years. In chronic animal experiments, stable output was obtained from three of four IJATs for periods of 10 to 19 months. Histology revealed acceptable osseointegration of the implant. The device has been implanted in human subjects for over 2 years and provides an excellent control signal for hand grasp. We conclude that this device is safe and effective for chronic human use as a control input for an implanted hand neuroprosthesis.
Development of a New Performance Metric for Golf Clubs Using COR Maps and Impact Probability Data (2018)

Golf clubs are often evaluated by many methods to determine their performance. For drivers in particular, the primary performance indicator is ball speed, which is directly related to distance. Golf club manufacturers make many claims about how extra ball speed is achieved. For example, these may include: design features, face thickness, materials, center of gravity location, and moments of inertia. This paper proposes a new method to evaluate the performance of golf clubs from a single metric. With the benefits of modern launch monitors, accurate impact location data can be captured very efficiently. Using this, along with COR (coefficient of restitution) map testing, the Expected Value of COR can be calculated for a golfer or population of golfers. The “Expected COR” metric takes into account many engineering properties of a particular club that affect ball speed, along with the impact variation of the golfer, to give a single score for rating.
Anisotropic etching of SiO2 in low-frequency CF4/O2 and NF3/Ar plasmas (1984)

Anisotropic etching of SiO2 films is reported in low frequency (∼100 kHz), moderate-pressure (0.35 Torr) CF4/O2 and NF3/Ar plasmas. Rates up to 2000 Å/min were achieved with high selectivity over GaAs and InP substrates. The etching mechanism was studied with optical spectroscopy and downstream chemical titrations. Anisotropy is attributed to ion-enhanced reactivity of fluorine atoms with SiO2 at rates up to two hundred times larger than purely chemical etching by fluorine atoms. Damage and product sputter desorption models of this process were evaluated. These two models are nearly mathematically equivalent at steady state, and show that the effectiveness of ions in etching by enhanced reaction is roughly 15 times that in physical sputtering under these conditions.
High-Surface-Area Oxides Obtained by an Activated Carbon Route (2002)

High-surface-area materials of various different compositions can be synthesized by a route involving impregnation of activated carbons with concentrated metal salt solutions and subsequent calcination to burn off the carbon material. This route allows the synthesis of a wide variety of different metal oxides, either as defined phases, if suitably chosen amounts of precursor salts are used, or as amorphous or partially crystalline multinary mixed-metal oxides. Typically, surface areas in the range between 50 and 200 m2/g are accessible, and in addition to crystalline binary oxides, several high-surface-area spinels and perovskites can also be prepared.
Riesz pyramids for fast phase-based video magnification (2014)

We present a new compact image pyramid representation, the Riesz pyramid, that can be used for real-time phase-based motion magnification. Our new representation is less overcomplete than even the smallest two orientation, octave-bandwidth complex steerable pyramid, and can be implemented using compact, efficient linear filters in the spatial domain. Motion-magnified videos produced with this new representation are of comparable quality to those produced with the complex steerable pyramid. When used with phase-based video magnification, the Riesz pyramid phase-shifts image features along only their dominant orientation rather than every orientation like the complex steerable pyramid.
Mapping the sensing spots of aerolysin for single oligonucleotides analysis (2018)

Nanopore sensing is a powerful single-molecule method for DNA and protein sequencing. Recent studies have demonstrated that aerolysin exhibits a high sensitivity for single-molecule detection. However, the lack of the atomic resolution structure of aerolysin pore has hindered the understanding of its sensing capabilities. Herein, we integrate nanopore experimental results and molecular simulations based on a recent pore structural model to precisely map the sensing spots of this toxin for ssDNA translocation. Rationally probing ssDNA length and composition upon pore translocation provides new important insights for molecular determinants of the aerolysin nanopore. Computational and experimental results reveal two critical sensing spots (R220, K238) generating two constriction points along the pore lumen. Taking advantage of the sensing spots, all four nucleobases, cytosine methylation and oxidation of guanine can be clearly identified in a mixture sample. The results provide evidence for the potential of aerolysin as a nanosensor for DNA sequencing.
Preparation and characterization of a biologic scaffold and hydrogel derived from colonic mucosa (2015)

Gastrointestinal pathologies, injuries, and defects affect millions of individuals each year. While there are diverse treatment options for these individuals, no ideal solution exists. The repair or replacement of gastrointestinal tissue, therefore, represents a large unmet clinical need. Biomaterials derived from extracellular matrix (ECM) scaffolds have been effectively used to repair or replace numerous tissues throughout the body in both preclinical and clinical studies. Such scaffolds are prepared from decellularized tissues, and the biochemical, structural, and biologic properties vary depending upon the source tissue from which the ECM is derived. Given the potential benefit of a site-specific ECM scaffold for some applications, the objective of this study was to prepare, characterize, and determine the in vitro and in vivo cell response to ECM derived from porcine colon. Results of this study show that porcine colon can be effectively decellularized while retaining biochemical and structural constituents of the source tissue. Two forms of colonic ECM, scaffold and hydrogel, were shown to be cell friendly and facilitate the polarization of macrophages toward an M2 phenotype both in vitro and in vivo. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 291-306, 2017.
Synthetic approaches towards CGA 293'343: a novel broad-spectrum insecticide (1999)

Synthetic approaches towards CGA 293'343 (ISO draft common name: thiamethoxam), a novel broad-spectrum insecticide from the class neonicotinoids, are described. 2-Chloro-5-chloromethylthiazole, an important synthetic intermediate, was prepared from five different precursors. Alternatively, CGA 293'343 was prepared via the intermediate 2-benzylmercapto-5-chloromethylthiazole, the synthesis of which is also described. © 1999 Society of Chemical Industry
Comparison of the Complete DNA Sequences of the Oka Varicella Vaccine and Its Parental Virus (2002)

The DNA sequences of the Oka varicella vaccine virus (V-Oka) and its parental virus (P-Oka) were completed. Comparison of the sequences revealed 42 base substitutions, which led to 20 amino acid conversions and length differences in tandem repeat regions (R1, R3, and R4) and in an origin of DNA replication. Amino acid substitutions existed in open reading frames (ORFs) 6, 9A, 10, 21, 31, 39, 50, 52, 55, 59, 62, and 64. Of these, 15 base substitutions, leading to eight amino acid substitutions, were in the gene 62 region alone. Further DNA sequence analysis showed that these substitutions were specific for V-Oka and were not present in nine clinical isolates. The immediate-early gene 62 product (IE62) of P-Oka had stronger transactivational activity than the mutant IE62 contained in V-Oka in 293 and CV-1 cells. An infectious center assay of a plaque-purified clone (S7-01) from the V-Oka with 8 amino acid substitutions in ORF 62 showed smaller plaque formation and less-efficient virus-spreading activity than did P-Oka in human embryonic lung cells. Another clone (S-13) with only five substitutions in ORF 62 spread slightly faster than S7-01 but not as effectively as P-Oka. Moreover, transient luciferase assay in 293 cells showed that transactivational activities of IE62s of S7-01 and S7-13 were lower than that of P-Oka. Based on these results, it appears that amino acid substitutions in ORF 62 are responsible for virus growth and spreading from infected to uninfected cells. Furthermore, the Oka vaccine virus was completely distinguishable from P-Oka and 54 clinical isolates by seven restriction-enzyme fragment length polymorphisms that detected differences in the DNA sequence.
Enhanced TOF-SIMS Imaging of a Micropatterned Protein by Stable Isotope Protein Labeling (2000)

Patterning of biomolecules on surfaces is an increasingly important technological goal. Because the fabrication of biomolecule arrays often involves stepwise, spatially resolved derivatization of surfaces, spectroscopic imaging of these arrays is important in their fabrication and optimization. Although imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a powerful method for spatially resolved surface analysis, TOF-SIMS images of micropatterned proteins on organic substrates can be difficult to acquire, because of the lack of high intensity, protein-specific molecular ions that are essential for imaging under static conditions. In contrast, low-mass ions are of suitable intensity for imaging, but can originate from different chemical species on the surface. A potential solution to this problem is to utilize stable isotope labeled proteins, an approach that has heretofore not been explored in TOF-SIMS imaging of micropatterned proteins and peptides. To investigate the feasibility of stable isotope enhanced TOF-SIMS imaging of proteins, we synthesized 15N-labeled streptavidin by labeling of the protein during expression from a recombinant gene. The spatial distribution of streptavidin bound to biotin micropatterns, fabricated on a polymer and on a self-assembled monolayer on gold, was imaged by TOF-SIMS. Imaging of high-intensity, low-m/z secondary ions (e.g., C15N-) unique to streptavidin enabled unambiguous spatial mapping of the micropatterned protein with a lateral resolution of a few micrometers. TOF-SIMS imaging of micropatterned 15N-labeled streptavidin also illustrated the exquisite sensitivity of TOF-SIMS to low fractional coverage of protein (5 A effective thickness) in the background regions of the protein micropattern.
Electrooptically tunable folded arrayed waveguide grating multiplexer (2004)

Channel tunability of 10 GHz has been demonstrated in a 40-channel 50-GHz-spaced folded silica-on-silicon arrayed waveguide grating (AWG) multiplexer using quadratic nonlinearity in phosphorous-doped glass and a specially shaped electrode. Such AWG can be stabilized and tuned around ITU grid without power-consuming thermoelectric coolers.
Orientation tracking for outdoor augmented reality registration (1999)

Our work stems from a program focused on developing tracking technologies for wide-area augmented realities in unprepared outdoor environments. Other participants in the Defense Advanced Research Projects Agency (Darpa) funded Geospatial Registration of Information for Dismounted Soldiers (Grids) program included University of North Carolina at Chapel Hill and Raytheon. We describe a hybrid orientation tracking system combining inertial sensors and computer vision. We exploit the complementary nature of these two sensing technologies to compensate for their respective weaknesses. Our multiple-sensor fusion is novel in augmented reality tracking systems, and the results demonstrate its utility.
Experimental study of the effects of size variations on piezoelectrically transduced MEMS resonators (2010)

We report results of a parametric study on a set of single-crystal-silicon plate resonators, whose lateral dimensions are varied so that the main resonance mode occurs at a range of f = 13...30 MHz. The resonator transduction is based on a piezoelectric AlN thin film. Measurements spanning >1000 devices and two wafers indicate that with certain device dimensions the square extensional resonance mode and a higher-order extensional mode are excited with a relatively low frequency scatter of Δf ~ 2 000 ppm (full range). Other resonance modes typically have a frequency scatter larger than 15 000 ppm, which we interpret to be an indication of their flexural character. Additionally, we observe a splitting of the main resonance mode branch at intermediate device dimensions.
Diffusion of light in turbid material (1989)

This paper discusses some of the present knowledge of the mathematical techniques used to describe light diffusion in turbid material such as tissues. Attention will be paid to the usefulness and limitations of various techniques. First, we review the transport theory, radiance, radiant energy fluence rate, phase functions, boundary conditions, and measurement techniques. We then discuss the first-order solution, multiple scattering, diffusion approximation, and their limitations. The plane wave, spherical wave, beam wave, and pulse wave excitations are discussed followed by a brief review of the surface scattering effects due to rough interfaces.
Clinical efficacy of zanolimumab (HuMax-CD4): two phase 2 studies in refractory cutaneous T-cell lymphoma (2007)

The efficacy and safety of zanolimumab in patients with refractory cutaneous T-cell lymphoma (CTCL) have been assessed in two phase 2, multicenter, prospective, open-label, uncontrolled clinical studies. Patients with treatment refractory CD4(+) CTCL (mycosis fungoides [MF], n = 38; Sézary syndrome [SS], n = 9) received 17 weekly infusions of zanolimumab (early-stage patients, 280 and 560 mg; advanced-stage patients, 280 and 980 mg). The primary end point was objective response (OR) as assessed by composite assessment of index lesion disease activity score. Secondary end points included physician's global assessment (PGA), time to response, response duration, and time to progression. ORs were recorded for patients in both CTCL types (MF, 13 ORs; SS, 2 ORs). In the high-dose groups (560 and 980 mg dose groups), a response rate of 56% was obtained with a median response of 81 weeks. Adverse events reported most frequently included low-grade infections and eczematous dermatitis. Zanolimumab showed marked clinical efficacy in the treatment of patients with refractory MF, with early onset of response, high response rate, and durable responses. The treatment was well tolerated with no dose-related toxicity other than the targeted depletion of peripheral T cells. A pivotal study has been initiated based on these findings.
Effect of thermal aging on board level drop reliability for Pb-free BGA packages (2004)

The drive for Pb-free solders in the microelectronics industry presents several new reliability challenges. Examples include package compatibility with higher process temperatures, new solder compound failure mechanisms, and the selection of the proper Pb-free alloy to maximize product lifetime. In addition to the challenges posed by the Pb-free material conversion, the migration of market focus from desktop computing to portable applications is changing the critical system failure mode of interest from conventional temperature cycling (T/C) induced solder fatigue opens to drop impact induced solder joint fracture. In this paper a study was conducted to investigate the influence of intermetallic compound (IMC) growth on the solder joint reliability of Pb-free ball grid array (BGA) packages under drop loading conditions. Thermal aging at homologous temperatures between 0.76 and 0.91 with microstructural analysis was conducted to analyze the solid phase IMC growth at the solder to BGA pad interface. Component level,ball shear and pull tests were also conducted to investigate the aging effect on solder joint strength. A key finding from this work is that Kirkendall voids formed at the bulk solder to package bare Cu pad interface under relative low 100/spl deg/C aging. Void formation and coalesce is shown to be the dominant mechanism for solder joint strength and board level drop reliability degradation.
White Light Emission from Organic LEDs Utilizing Spiro Compounds with High-Temperature Stability (2000)

Bright white light emission in rubrene-doped organic LEDs has been demonstrated using spiro compounds—such as spiro-TAD, shown in the Figure—with high glass transition temperatures. These materials show high morphological stability for hole transport and emission of blue light, and thus still operate at temperatures well above 100 °C. The devices give a maximum luminance of 11800 cd/m2.