gebhart/patrepeval huggingface dataset:
The Kinase Homology Domain of Receptor Guanylyl Cyclase C:  ATP Binding and Identification of an Adenine Nucleotide Sensitive Site (2006)

The role of the kinase homology domain (KHD) in receptor guanylyl cyclases is to regulate the activity of the catalytic guanylyl cyclase domain. The KHD lacks many of the amino acids required for phosphotransfer activity and, therefore, is not expected to possess kinase activity. Guanylyl cyclase activity of the receptor guanylyl cyclase C (GC-C) is modulated by ATP, and computational modeling showed that the KHD can adopt a structure similar to protein kinases, suggesting that the KHD is the site for ATP interaction. A monoclonal antibody, GCC:4D7, raised to the KHD of GC-C, fails to react with GC-C in the presence of ATP and ATP analogues that regulate GC-C catalytic activity, indicating that a conformational change occurs in the KHD on ATP binding. Mapping of the epitope of the antibody through the use of recombinant protein constructs and phage display showed that the epitope for GC-C:4D7 lies immediately C-terminal to a critical lysine residue (Lys516 in GC-C), required for ATP interaction in protein kinases. By employing a novel approach utilizing ATP-agarose affinity chromatography, we demonstrate that the intracellular domain of GC-C and the KHD bind ATP. Mutation of Lys516 to Ala abolishes ATP binding. Thus, this report is the first to show direct ATP binding to the pseudokinase domain of receptor guanylyl cyclase C, as well as to identify dramatic conformational changes that occur in this domain on ATP binding, akin to those seen in catalytically active protein kinases.
Superfluid-like Motion of a Small Absorbing Body in a Collisional Plasma (2008)

It is shown that the total frictional (drag) force acting on a slowly moving absorbing grain in a stationary weakly ionized high pressure plasma can be directed along its motion, causing the grain acceleration. At some velocity the forces associated with different plasma components balance each other, allowing free undamped superfluid motion of the grain.
Oregano: A potential prophylactic treatment for the intestinal microbiota (2019)

Prophylactic use of antibiotics in poultry diets has been identified as a problematic practice because of its potential to exacerbate the spread of antibiotic resistance to human pathogens. A range of countries have opted to completely ban the use of antibiotics in animal feed. The animal production industries are looking for alternative ways to effectively control pathogens while providing the performance benefits previously secured by antibiotics in feed. Here, we present evidence that oregano (<i>Origanum vulgare</i>) could be a potential alternative for pathogen control in the poultry industry. Broiler diets were supplemented with oregano powder (0%, 0.5%, 1%, and 2%) for six weeks. The capacity for pathogen control was estimated by microbiota profiling of the jejunum, ileum, and caecum content, and in the faeces, by 16S rRNA gene amplicon sequencing. The concentrations of short-chain fatty acids in the caecal content were also measured, as were villus/crypt parameters in the ileum. There were no differences among treatments in weight gain, feed intake, or the concentration of short-chain fatty acids. The height, width, and the surface area of villi in the ileum were not influenced by oregano addition. However, 1% and 2% of oregano produced a significant increase in the villus height to crypt depth ratio. There were no visible histopathological changes in the liver in control and treated groups. Although oregano had no significant effect on overall microbial diversity and gross composition, some specific genera, like <i>Proteus</i>, <i>Klebsiella</i> and <i>Staphylococcus</i>, which include known pathogens, were reduced in relative abundance by oregano treatment. <i>Bifidobacterium</i>, recognized as a beneficial and probiotic genus, was also suppressed by the oregano treatment.
Imitation Learning of Agenda-based Semantic Parsers (2015)

Semantic parsers conventionally construct logical forms bottom-up in a fixed order, resulting in the generation of many extraneous partial logical forms. In this paper, we combine ideas from imitation learning and agenda-based parsing to train a semantic parser that searches partial logical forms in a more strategic order. Empirically, our parser reduces the number of constructed partial logical forms by an order of magnitude, and obtains a 6x-9x speedup over fixed-order parsing, while maintaining comparable accuracy.
Inflammation and Airway Microbiota during Cystic Fibrosis Pulmonary Exacerbations (2013)

Anaerobes identified from sputum by sequencing are associated with less inflammation and higher lung function compared to Pseudomonas at early exacerbation. CF PEx treatment results in variable changes of anaerobic genera suggesting the need for larger studies particularly of patients without traditional CF pathogens.
[Clinical study of cefotetan in obstetrics and gynecology]. (1983)

A new cephamycin antibiotic, cefotetan, was administered intramuscularly to 45 patients with female genital infections including 2 cases with abscess of Bartholin's gland, 14 cases with endometritis, 23 cases with adnexitis and 6 cases with pelvic peritonitis. The daily doses of the drug were 1 to 3 g, with 2 g daily being the most frequent regimen. The treatment was given twice daily in most patients. All cases responded to the drug, and marked response was seen in 22 cases and moderate response in 23. The eradication rate for causative organisms was 64.3%. In 16 cases of S. faecalis, it was rather low at 37.5%. Neither side effects nor abnormalities in clinical laboratory findings attributable to the drug were seen.
Risk Assessment: Controversies and Management of Moderate- to High-Risk Individuals (2005)

With the current understanding of sporadic and familial breast cancer, it is now possible to identify individuals who have a moderate or high risk of breast cancer. For these individuals, it is useful to perform formal cancer risk assessment and develop an individualized risk reduction plan, including a tailored plan for cancer screening, preventive therapy, and/or prophylactic surgery. Assessment using a predictive model such as the Gail model is particularly useful in individuals at increased risk for sporadic breast cancer. In addition, assessment of risk based on histologic appearance of benign or premalignant breast lesions can be used to identify individuals for whom more aggressive risk reduction strategies are warranted. For individuals who are at risk for familial cancer syndromes, other predictive models are more appropriate. For this extremely high-risk group, genetic testing for mutations in familial cancer susceptibility genes is helpful to identify individuals who would benefit from even more aggressive cancer risk reduction strategies. Strategies to identify the levels of risk for breast cancer, including the identification of moderate, high, or very high risk groups are discussed. Management options for these groups are presented, including who to consider for more aggressive screening, chemoprevention, or prophylactic surgery. Current recommendations for screening, chemoprevention, and surgery for each risk group are presented. The ability to identify individuals at high risk for breast cancer now enables clinicians to intervene to reduce the risk of breast cancer. Aggressive screening, preventive therapy, and prophylactic surgery in moderate- to high-risk individuals should, in the future, significantly reduce the incidence of invasive breast cancer.
Technology Scaling Roadmap for FinFET-Based FPGA Clusters Under Process Variations (2017)

The technology scaling impact on FinFET-based Field-Programmable Gate Array (FPGA) components (Flip-Flops and Multiplexers) and cluster metrics is evaluated for technology nodes starting from 20[Formula: see text]nm down to 7[Formula: see text]nm. Power consumption, delay and energy (Power Delay Product, or PDP) trends are reported with FinFET technology scaling. Cluster metrics are then evaluated based on three benchmarking circuits: 2-bit adder, 4-bit NAND and cascaded flip-flops chain. The study shows that power, delay and PDP of the FPGA cluster are improved as we scale down the technology. An example for improvement is that for 7[Formula: see text]nm 2-bit adder, circuit speed is 15% higher than its value at 20[Formula: see text]nm and PDP at 7[Formula: see text]nm is reduced by 43% compared to its value at 20[Formula: see text]nm. The impacts of temperature and threshold voltage variations on FPGA cluster performance are also reported after evaluating a 2-bit adder circuit as a benchmark which is then used to calculate the design constraints to meet 99.9% yield percentage.
Stability and Transient Dynamics of PLLs in Theory and Experiments (2020)

This paper presents a generalization of the classical phase-locked loop (PLL) theory. It includes the effects of time-delays and mutual coupling between PLLs. Two methods for finding stable solutions to locked states and their transient dynamics are discussed. The theoretical predictions of these methods are verified by experimental measurements obtained of a classical PLL entrained by a clock. For entrainment the generalized and classical PLL theory overlap. The analysis correctly predicts the phase-relations of phase-locked states, the loop-gain dependency on the component characteristics and time-delays and the transient dynamics, i.e., perturbation decay rate and the frequency of perturbation decay. Thus the generalized theory allows a deeper understanding of a PLL's response. The model covers PLLs of arbitrary order and number of inputs.
The Effect of Robot-Assisted Therapy and Rehabilitative Training on Motor Recovery Following Stroke (1997)

These results suggest that robotic manipulation of the impaired limb may favorably add to recovery following stroke and that robotics may provide new strategies for neurologic rehabilitation.
Nature, Freedom, Ethics, and God (The Philosophy of Nature and the Philosophy of Spirit) (2005)

The Logic, as such, concludes with the Idea's comprehending its own self-comprehension, and thus ceasing to be a mere “content and object,” for itself, and becoming instead “science,” which knows itself (WL 6:572/GW 12:253,13/843). As such, however, it is still “enclosed within [eingeschlossen in] pure thought” or “subjectivity” (WL 6:572/ GW 12:253,15–19/843). But
Determination by the BI-RME method of entire-domain basis functions for the analysis of microstrip circuits (2003)

In this paper, we present a novel approach for the numerical determination of entire-domain basis functions for the analysis of shielded microstrip circuits, composed of arbitrarily shaped metallic patches with an arbitrary number of ports. This approach is based on the solution of Helmholtz and Laplace equations in the metallic areas with proper boundary condition by the Boundary Integral-Resonant Mode Expansion (BI-RME) method. Two examples validate the proposed method.
3D Multiclass Digital Core Models via microCT, SEM-EDS and Deep Learning (2023)

We describe an integrated methodology for constructing a 3D multiclass model of a rock sample, based on X-ray microtomography (microCT) and quantitative evaluation of minerals (QEMSCAN) by automated SEM-EDS (Scanning Electron Microscopy, Energy Dispersive Spectroscopy). We focus on building an automated operator-independent workflow, allowing to distinguish between voxels featuring substantially different physical properties, such as void, quartz, denser and less dense clay aggregates. The workflow is demonstrated using a set of five ⌀8 mm Berea sandstone miniplugs. For each miniplug, a ~4000 3 voxel microCT image is acquired. Next, each miniplug is cut into smaller pieces, and the 45 resulting polished surfaces are subjected to the QEMSCAN analysis, producing ~4000 2 pixel mineral maps. Each mineral map is automatically spatially registered with the corresponding microCT image using an in-house surface-based algorithm. Further, the ground truth images for the supervised multiclass segmentation are constructed from the mineral maps. We compare 3D and 2D convolutional neural network (CNN) architectures with the baseline Naïve Bayes classifier, which is roughly equivalent to the approaches commonly used in practice today. We find that supervised CNN-based segmentation is fairly stable, despite microCT image quality non-uniformness and achieves higher quality scores compared to feature based and baseline approaches.
Simultaneous enumeration of chromosomes 13, 18, 21, X, and Y in interphase cells for preimplantation genetic diagnosis of aneuploidy (1996)

A fluorescence in situ hybridization (FISH) protocol to simultaneously enumerate chromosomes 13, 18, 21, X, and Y in interphase cell nuclei for application in preimplantation genetic diagnosis (PGD) of aneuploidy was tested. Strict scoring criteria were developed to minimize recording errors. The protocol used optimized probes for chromosome-specific DNA repeat and single-copy loci and showed a significantly higher efficiency (95%) than previously published protocols. The other purpose of this study was to differentiate between two signals originating from a single split target or from two targets in close proximity. These criteria were based on the FISH results obtained from the analysis of all or most of the cells from 50 chromosomally normal or mosaic human embryos, 20 aneuploid embryos, and five polyploid embryos donated for research. Subsequently, 183 human embryos underwent PGD of aneuploidy in one of their cells. In 64 embryos that were not transferred back to the uterus, the rest of cells were also analyzed, and the previous results were confirmed in 91% of these embryos, with 0% (0/21) of the embryos classified as normal embryos being abnormal and 14% (6/43) of the embryos classified as abnormal being normal. Compared to previous protocols, these criteria minimize the risk of transferring abnormal embryos after PGD analysis.
Unmasking produced by combination tones (1979)

This experiment investigated some interactions between combination tones (CT) and unmasking. Data were obtained from nine normal-hearing listeners in a forward-masking paradigm in which a 2000-Hz, 35-dB SPL masker preceded a 2000-Hz test signal. An adaptive, three-interval forced-choice procedure was employed to estimate the threshold for the test signal. This measurement provided a baseline. When a second sinusoid, the suppressor, of variable frequency and 55 dB SPL was presented concurrently with the masker, the amount of masking could be less than in the baseline condition. This two-tone unmasking was observed when the suppressor was approximately 2300 Hz. In the cubic difference tone (CDT) condition, two higher-frequency sinusoids of 80 dB SPL (with the lower frequency fixed at 2800 Hz) were added to the masker. In the difference tone (DT) condition, two higher-frequency sinusoids of 100 dB SPL (with the lower frequency fixed at 3500 Hz) were added to the masker. None of these sinusoids produced unmasking when presented individually, but when the CDT and DT were approximately 2300 Hz, unmasking was observed. The unmasking produced by the CTs was similar in its frequency characteristics to that of the single, suppressor tone. These results indicate that unmasking can be produced by CTs, just as if CTs were present in the stimulus. These data indirectly support the notion that CTs may be present in the form of traveling waves propagated along the basilar membrane.
Body Mass Index in Adolescence in Relation to Total Mortality: 32-Year Follow-up of 227,000 Norwegian Boys and Girls (2003)

A large number of studies have explored the relation between body mass index (BMI) and mortality in adults. The relation between BMI in adolescence and mortality has been investigated to a lesser extent. It has been suggested that all-cause mortality is elevated among those who were overweight during adolescence, but the limitation of previous studies has been study size. The present study explored this relation in a Norwegian cohort of 227,003 boys and girls, aged 14-19 years, whose height and weight were measured during tuberculosis screening in 1963-1975. These persons were followed for an average of 31.5 years (about 7.2 million person-years). A total of 7,516 deaths were registered. Multivariate Cox proportional hazards regression models were used in the analyses. An increasing risk of death by increasing BMI in adolescence was observed. Mortality among males whose baseline BMI was between the 85th and 95th percentiles and above the 95th percentile in the US reference population was 30% and 80% higher, respectively, than that among those whose baseline BMI was between the 25th and 75th percentiles. The corresponding rates among females were 30% and 100%. The excess mortality among adolescents whose BMI was high was not clearly manifested before they reached their thirties. Hence, BMI in adolescence is predictive of adult mortality.
Visualization of supercomputer simulations in physics (1989)

Recent advances in computer graphics hardware and software have resulted in major improvements in our ability to experience computer simulations of physics by viewing dynamic three-dimensional scenes representing the simulations. This paper describes the hardware and software tools ana' techniques in use at NASA's Numerical Aerodynamic Simulation Facility for visualization of computational fluid dynamics. The visualization process is illustrated by video tapes and stereo pictures (available from the authors).
LiSP: Lightweight security protocols for wireless sensor networks. (2005)

Sensor networks, usually built with a large number of small, low-cost sensor devices, are characterized by their large-scale and unattended deployment that invites many critical attacks, thereby necessitating high-level security support for their intended applications and services. However, making sensor networks secure is challenging due mainly to the fact that sensors are battery-powered and it is often very difficult to change or recharge their batteries. To address this challenge, we design, develop and evaluate <bolditalic> Li</bolditalic><italic>ghtweight</italic> <bolditalic>S</bolditalic><italic> ecurity</italic> <bolditalic>P</bolditalic><italic>rotocols</italic> (LiSP) that cooperatively build a unified, energy-efficient security framework for sensor networks. We present two (group-based and distributed) key management/sharing schemes that are tailored to local and remote transactions, respectively. While the group-based scheme achieves efficient and robust re-keying via key broadcasting/authentication/recovery, distributed key sharing enables the development of attack-tolerant routing protocols capable of gracefully resisting device compromises as well as replacing resource-expensive, public-key-cipher-based protocols with a purely symmetric-cipher-based alternative. The problem of attack-tolerance is further investigated for the development of a secure localization protocol. The proposed protocol uses mutual collaboration among sensors to achieve high-level attack-tolerance in terms of detecting/identifying/rejecting sources of attacks, if present. Accordingly, it plays the role of an anomaly-based intrusion detection system tailored to localization that safeguards the network from localization-targeted attacks. As a countermeasure against physically tampering with sensors, we develop a novel soft tamper-proofing technique that verifies integrity of the program residing in each sensor device whenever it joins the network, or is suspected to have been compromised. Unlike other techniques unsuitable for low-cost, resource-limited sensors, our technique augments such sensors to be usable for applications that require high-level security. Finally, the benefits of our protocols are demonstrated via analysis and evaluation of their capability to defeat known security attacks, and their performance in terms of processing, communication and memory overheads.
Upgrading metallurgical grade (MG) silicon for use as solar grade feedstock (2002)

The most attractive approach to upgrade metallurgical-grade (MG) silicon is to chemically refine impurities, especially boron (B) and phosphorus (P), in the molten state followed by directional solidification. The most problematic impurity is B as it has the highest segregation coefficient. A simple refining process of blowing gas through the melt was developed to reduce B in MG silicon effectively, and the process has been scaled up to charge sizes up to 150 kg. The B reduction has been maintained with increase in charge sizes and confirmed by using it on B-doped silicon at ten times the concentration. The simplicity of the refining process when adapted to a commercial MG silicon plant is expected to produce solar grade (SoG) silicon at low cost.
Synthesis, In Vitro Degradation, and Mechanical Properties of Two-Component Poly(Ester Urethane)Urea Scaffolds: Effects of Water and Polyol Composition (2007)

The development of minimally invasive therapeutics for orthopedic clinical conditions has substantial benefits, especially for osteoporotic fragility fractures and vertebral compression fractures. Poly(ester urethane)urea (PEUUR) foams are potentially useful for addressing these conditions because they cure in situ upon injection to form porous scaffolds. In this study, the effects of water concentration and polyester triol composition on the physicochemical, mechanical, and biological properties of PEUUR foams were investigated. A liquid resin (lysine diisocyanate) and hardener (poly(epsilon-caprolactone-co-glycolide-co-DL-lactide) triol, tertiary amine catalyst, anionic stabilizer, and fatty acid-derived pore opener) were mixed, and the resulting reactive liquid mixture was injected into a mold to harden. By varying the water content over the range of 0.5 to 2.75 parts per hundred parts polyol, materials with porosities ranging from 89.1 to 95.8 vol-% were prepared. Cells permeated the PEUUR foams after 21 days post-seeding, implying that the pores are open and interconnected. In vitro, the materials yielded non-cytotoxic decomposition products, and differences in the half-life of the polyester triol component translated to differences in the PEUUR foam degradation rates. We anticipate that PEUUR foams will present compelling opportunities for the design of new tissue-engineered scaffolds and delivery systems because of their favorable biological and physical properties.
Mapping the rotational diffusion of fluorophores in cells with time-resolved wide-field fluorescence anisotropy imaging (2005)

We demonstrate time-resolved fluoroescence anistropy imaging with simultaneous acquistion of the parallel and perpendicular polarization of a fluoroescence image. This allows imaging of the viscosity in cells.
103. Are renal ??-adrenoceptor alterations a major cause of genetic hypertension in the spontaneously hypertensive rat? (1991)

The journal consistently attracts the most important and highly innovative papers from the current research; our commitment to rapid publication ensures that these are published in the fastest time possible. In addition to primary papers from world-renowned experts, the Journal contains authoritative reviews that summarize and evaluate the most significant recent developments. Also included are special reports, original short papers containing innovative and time-sensitive information. Submitted articles undergo a preliminary review by the editor. Some articles may be returned to authors without further consideration. Those being considered for publication will undergo further assessment and peer-review by the editors and those invited to do so from a reviewer pool. ​ Official Journal of the: International Society of Hypertension European Society of Hypertension