gebhart/patrepeval huggingface dataset:
ORFeome Cloning and Systems Biology: Standardized Mass Production of the Parts From the Parts-List (2004)

Together with metabolites, proteins and RNAs form complex biological systems through highly intricate networks of physical and functional interactions. Large-scale studies aimed at a molecular understanding of the structure, function, and dynamics of proteins and RNAs in the context of cellular networks require novel approaches and technologies. This Special Issue of Genome Research features strategies for the high-throughput construction and manipulation of complete sets of protein-encoding open reading frames (ORFeome), gene promoters (promoterome), and noncoding RNAs, as predicted from genome and transcriptome sequences. Here we discuss the use of a recombinational cloning system that allows efficiency, adaptability, and compatibility in the generation of ORFeome, promoterome, and other resources.
Pattern of ras and gsp oncogene mutations in radiation-associated human thyroid tumors. (1995)

The preferential activation of the Ki-ras oncogene in follicular radiation-associated human thyroid carcinomas, has been suggested by Wright et al. (1991). However, only 12 thyroid tumors were analysed in this study. In order to confirm if radiation favours, in human thyroid tumorigenesis, the appearance of a particular molecular lesion, we studied 33 benign and malignant human radiation-associated thyroid tumors. We used polymerase chain reaction (PCR) amplification and allele-specific hybridization with mutant-specific probes for the three ras genes and the gsp oncogene. Compared to 85 'spontaneous' human thyroid tumors, the radiation-associated cases: (1) show a similar overall frequency of ras and gsp mutations (about 30% and 6% respectively); (2) present a similar frequency of mutation of the three ras genes without any predominance in adenomas and papillary carcinomas and (3) all Ki-ras mutations were found in papillary carcinomas (4/15). ras and gsp genes were never found mutated simultaneously, suggesting an alternative role for both oncogenes in the thyroid tumorigenic radiation-associated process.
Variations on sweep algorithms: efficient computation of extended viewsheds and class intervals (1996)

Two novel applications of the plane sweep paradigm are demonstrated, namely, for the computation of extended viewsheds on gridded DEMs and for class interval selection on TIN-based DEMs. In both cases, the efficiency of the plane sweep algorithm is significantly better than a straightforward approach. The algorithms are presented by first giving the plane sweep method as a general approach that requires some ingredients to make it work well. Adaptations to minimize additional storage use are also presented. 1 Introduction One of the most important paradigms in the design of geometric algorithms is that of sweeping. In a plane sweep algorithm, an imaginary horizontal line traverses the plane from top to bottom, during which some property of the data is computed (a more clear description is given later). Plane sweep algorithms have been used for a variety of geometric problems like map overlay, Voronoi diagrams and hidden surface removal. The plane sweep approach is described in most te...
Alpine restoration: Identifying needs and determining priorities (2015)

Alpine plant communities are very sensitive to disturbance, being at the edge of their ecological range, geographically localised, and consisting of species that are poor reproducers due to their specific phenology and relatively low seed production (often with low viability).
An Animal Model of Autoimmune Emphysema (2004)

Although cigarette smoking is implicated in the pathogenesis of emphysema, the precise mechanisms of chronic progressive alveolar septal destruction are not well understood. We show, in a novel animal model, that immunocompetent, but not athymic, nude rats injected intraperitoneally with xenogeneic endothelial cells (ECs) produce antibodies against ECs and develop emphysema. Immunization with ECs also leads to alveolar septal cell apoptosis and activation of matrix metalloproteases MMP-9 and MMP-2. Anti-EC antibodies cause EC apoptosis in vitro and emphysema in passively immunized mice. Moreover, immunization also causes accumulation of CD4+ T cells in the lung. Adoptive transfer of pathogenic, spleen-derived CD4+ cells into naive immunocompetent animal also results in emphysema. This study shows for the first time that humoral- and CD4+ cell-dependent mechanisms are sufficient to trigger the development of emphysema, suggesting that alveolar septal cell destruction might result from immune mechanisms.
A methodology for integrating business process and information infrastructure models (1996)

Many organizations today undertake Business Process Reengineering (BPR) and information infrastructure (i.e., network hardware, communications, and applications infrastructure) modernization efforts to drastically reduce costs and improve performance. While these efforts would appear to be mutually supportive and complementary in nature, they are rarely conducted jointly. Although it is known that changes to one of these two facets of the organization can produce significant impacts on the other, analysts and decision-makers have had only limited support for predicting the impacts of change to one or both of these two facets of the enterprise. BPR efforts are generally conducted using business process simulation tools. Information infrastructure modernization efforts are generally conducted using network simulation tools. What is lacking is an integrated method and the automated environment for studying the impacts of change to one of these two as pects of the enterprise on the other. This paper presents a simulation-based methodology enabling simultaneous consideration of changes to core business processes and the infrastructure mechanisms that support those processes.
Experiments on Stimulated Raman Scattering in S- and L-bands 16-QAM Signals for Ultra-Wideband Coherent WDM Systems (2018)

We experimentally evaluated stimulated Raman scattering (SRS) effect between S- and L-bands over 210-km SSMF 16-QAM transmission. SRS mainly induced power transition from S- to L-band, and was not the cause of nonlinear crosstalk penalty.
Dynamic programming based controllers to suppress stick-slip in a drilling system (2017)

During drilling operation, a wide range of undesirable vibrations can be induced by the nonlinear bit-rock interaction, which may cause fatigue failure of the drillstring, increase the bit wear rate, and reduce drilling efficiency. Among many undesirable drilling system dynamics, the stickslip vibration of a drillstring is most common and detrimental. In this paper, a two degree-of-freedom lumped model is established to capture the drilling system dynamics. At the bottom hole extremity, a bit-rock interaction model is developed to describe the nonlinear relationship between the bit angular speed and the torque on bit. In order to ease the stick-slip vibration, an optimal control policy is developed using the dynamic programming (DP) approach. Based on the features of the obtained policy, dimension reduction is achieved, which significantly improves the computational efficiency. According to the simulation results, the proposed DP based controller and the reduced-order controller can effectively suppress the stickslip vibration of the drillstring.
Parathyroid hormone induces protein kinase C but not adenylate cyclase in adult cardiomyocytes and regulates cyclic AMP levels via protein kinase C-dependent phosphodiesterase activity (1995)

Adult ventricular cardiomyocytes have been identified as target cells for parathyroid hormone (PTH) but little is known about its signal transduction in these cells. In the present study the influence of PTH on cyclic AMP accumulation and the activity of protein kinase C (PKC) in cardiomyocytes was evaluated. A mid-regional synthetic fragment of PTH, PTH-(28-48), which exerts a hypertrophic effect on cardiomyocytes, increased the activity of membrane-associated PKC in a dose-dependent manner (1-100 nM). Activated membranous PKC was dependent on Ca2+ and sensitive to an inhibitor of Ca(2+)-dependent isoforms of PKC. When adenylate cyclase was stimulated by the addition of isoprenaline, a beta-adrenoceptor agonist, PTH-(28-48) antagonized cyclic AMP accumulation. This antagonistic effect of PTH-(28-48) could be mimicked by activation of PKC with a phorbol ester and inhibited by isobutylmethylxanthine, a phosphodiesterase inhibitor. An N-terminal synthetic fragment, PTH-(1-34), which includes an adenylate cyclase-activating domain, did not stimulate the accumulation of cyclic AMP in cardiomyocytes. The results demonstrate that in adult cardiomyocytes PTH (1) is able to stimulate PKC, (2) is not able to cause accumulation of cyclic AMP and (3) functionally antagonizes the effect of beta-adrenoceptor stimulation to increase cellular cyclic AMP concentrations via PKC-dependent phosphodiesterase activity.
O3‐06‐07: GSI‐953 is a potent APP‐selective gamma‐secretase inhibitor for the treatment of Alzheimer's disease (2009)

Gamma secretase is responsible for the intramembraneous cleavage of the Alzheimer's Precursor Protein (APP), the Notch receptor, and several other substrates. While inhibition of this protease results in potentially therapeutic reductions in the neurotoxic Abeta peptide, severe side effects might result from inhibiting Notch processing. We report a novel thiophene sulfonamide gamma-secretase inhibitor, GSI-953, that selectively inhibits cleavage of APP while sparing Notch processing. In vitro assays of Abeta production and Notch function, measurements of Abeta levels in plasma and brain of Tg2576 mouse, and assessments of cognitive function using the contextual fear conditioning model are described, as well as human plasma Abeta levels and initial biomarker data. This compound inhibits Abeta production with low nM potency in vitro in cellular and cell-free assays. Cellular assays of Notch cleavage reveal that this compound is >15-fold selective for the inhibition of APP cleavage. In the Tg2576 transgenic mouse, this compound causes a robust reduction in brain and plasma Abeta levels and reverses memory deficits that are correlated with Abeta load. A lowering of plasma Abeta levels in human demonstrates target engagement. These data demonstrate that GSI-953 is a potent and selective gamma-secretase inhibitor with potential for therapeutic utility in Alzheimer's Disease. For these reasons, GSI-953 has been advanced into human clinical trials.
Transcranial Doppler evaluation of syncope: an application in aerospace physiology. (1991)

A non-invasive method which combines the simultaneous measurement of mean arterial blood pressure (MBP), heart rate (HR) and mean cerebral blood flow velocity (MFV) was used to monitor patients with history of syncope, in horizontal and vertical posture tilt at 80 degrees. MFV in the right middle cerebral artery was measured using a transcranial Doppler instrument (TCD). MFV decreased concurrently with the onset of symptoms, and at the time of syncope reached an average of 68% below pre-tilt values. At the same time MBP showed an average decline of 25%, and HR increased by 38%. There was no correlation between MBP and MFV, at the onset of tilt, presyncope and syncope. MFV, but not HR or MBP, showed significant transition from one condition to the other. These data suggest that there may be a useful application of TCD measurements of MFV in aeromedical evaluation of syncope or syncopal tendency. These measurements would necessarily be used in conjunction with a tilt-table procedure. The possibility exists that MFV might be useful to preclude the actual occurrence of syncope in test subjects, or to show an abnormal tendency toward syncope, but will require more extensive testing than that carried out in the present study.
Experimental studies on AC dielectric barrier corona discharge reactors for NO/sub x//SO/sub x/ decompositions (1997)

Summary form only given. The interest in the AC dielectric barrier corona discharge (DBCD) is growing rapidly because of their successful application to the decomposition of air pollutants such as NO/sub x//SO/sub x/. DBCD has a configuration of inserted dielectric barrier between highly non-uniform metal electrodes in the form of either cylinder-wire or pins-plate arrangement. Geometrical configuration of DBCD is of great importance for optimal design of flue gas purification reactors. In this work, two types of DBCD reactors, cylinder-wire and pins-plate, are designed and experimented, and their decomposition efficiencies of NO/sub x/ and SO/sub x/ are compared. The powered electrodes of either tungsten wire or pins having a radius of curvature of 1 mm are fixed at 20 mm away from dielectric barriers of pyrex tube or acryl plate with a thickness of 2 mm. Stainless steel tube and plate of 100 mm in length are used as a grounded electrode of both type reactors, respectively.
Reordering of amorphous layers of Si implanted with 31P, 75As, and 11B ions (1977)

The effect of impurities on the epitaxial regrowth of Si from amorphous layers created by ion implantation into 〈100〉 and 〈111〉 Si was studied by channeling effect measurements with 2-MeV 4He ions. The Si wafers were first implanted at −180 °C with 28Si ions to form amorphous layers approximately 4000 Å thick and then were implanted with 31P, 75As, or 11B ions to concentration levels of about 0.2–0.5 at.%. For these layers with impurity species the growth rate is found to be significantly higher than for those without. The measured regrowth rate at 500 °C for 〈100〉 Si with an impurity concentration of ∼2×1020 cm−3 of 31P or 75As is a factor of 6 greater, and of 11B a factor of 20 greater, than the regrowth rate in amorphous layers without impurities. For the case of 31P implanted 〈100〉 Si the activation energy of regrowth is close to that (2.35 eV) found for impurity-free amorphous layers and for 11B implanted samples the energy is 1.9 eV. For 〈111〉 31P implanted Si specimens there is an increase in growth rate over that found in impurity-free samples and a high level of residual disorder.
Learning Representations using Spectral-Biased Random Walks on Graphs (2020)

Several state-of-the-art neural graph embedding methods are based on short random walks (stochastic processes) because of their ease of computation, simplicity in capturing complex local graph properties, scalability, and interpretibility. In this work, we are interested in studying how much a probabilistic bias in this stochastic process affects the quality of the nodes picked by the process. In particular, our biased walk, with a certain probability, favors movement towards nodes whose neighborhoods bear a structural resemblance to the current node's neighborhood. We succinctly capture this neighborhood as a probability measure based on the spectrum of the node's neighborhood subgraph represented as a normalized Laplacian matrix. We propose the use of a paragraph vector model with a novel Wasserstein regularization term. We empirically evaluate our approach against several state-of-the-art node embedding techniques on a wide variety of real-world datasets and demonstrate that our proposed method significantly improves upon existing methods on both link prediction and node classification tasks.
Approximate nonlinear control for a two degree of freedom overhead crane: theory and experimentation (2005)

In this paper, we develop nonlinear algorithms for accurately controlling the payload position for a two-degree of freedom overhead crane system. Since this model does not lend itself to nonlinear control design in a straightforward manner, we develop an approximate model of the system which facilitates the construction of error systems suitable for the development of back-stepping type controllers. A Lyapunov-like argument is then applied to the approximate model under the proposed control to elucidate payload positioning performance. Experimental results are used to validate the performance of the control approach. A discussion of cable flexibility and actuator dynamics is also presented.
Laser-driven scanning tunneling microscope (1991)

New modes of operation of a scanning tunneling microscope (STM) with laser radiation coupled into the tip of the tunneling junction are demonstrated. The dc current generated by rectifying the laser light and the difference-frequency signal produced in the STM by two laser beams are used to obtain atomic-resolution surface images of graphite, as well as to control the tip-sample distance. Such a laser-driven STM can generate surface images without external bias voltage and, when the difference-frequency signal is used for the distance control, even without any dc current between the tip and the sample. This mode of operation may also allow insulators to be studied.
Parallel WaveGAN: A fast waveform generation model based on generative adversarial networks with multi-resolution spectrogram (2019)

We propose Parallel WaveGAN, a distillation-free, fast, and small-footprint waveform generation method using a generative adversarial network. In the proposed method, a non-autoregressive WaveNet is trained by jointly optimizing multi-resolution spectrogram and adversarial loss functions, which can effectively capture the time-frequency distribution of the realistic speech waveform. As our method does not require density distillation used in the conventional teacher-student framework, the entire model can be easily trained. Furthermore, our model is able to generate high-fidelity speech even with its compact architecture. In particular, the proposed Parallel WaveGAN has only 1.44 M parameters and can generate 24 kHz speech waveform 28.68 times faster than real-time on a single GPU environment. Perceptual listening test results verify that our proposed method achieves 4.16 mean opinion score within a Transformer-based text-to-speech framework, which is comparative to the best distillation-based Parallel WaveNet system.
Slowness: An Objective for Spike-Timing–Dependent Plasticity? (2007)

Our nervous system can efficiently recognize objects in spite of changes in contextual variables such as perspective or lighting conditions. Several lines of research have proposed that this ability for invariant recognition is learned by exploiting the fact that object identities typically vary more slowly in time than contextual variables or noise. Here, we study the question of how this "temporal stability" or "slowness" approach can be implemented within the limits of biologically realistic spike-based learning rules. We first show that slow feature analysis, an algorithm that is based on slowness, can be implemented in linear continuous model neurons by means of a modified Hebbian learning rule. This approach provides a link to the trace rule, which is another implementation of slowness learning. Then, we show analytically that for linear Poisson neurons, slowness learning can be implemented by spike-timing-dependent plasticity (STDP) with a specific learning window. By studying the learning dynamics of STDP, we show that for functional interpretations of STDP, it is not the learning window alone that is relevant but rather the convolution of the learning window with the postsynaptic potential. We then derive STDP learning windows that implement slow feature analysis and the "trace rule." The resulting learning windows are compatible with physiological data both in shape and timescale. Moreover, our analysis shows that the learning window can be split into two functionally different components that are sensitive to reversible and irreversible aspects of the input statistics, respectively. The theory indicates that irreversible input statistics are not in favor of stable weight distributions but may generate oscillatory weight dynamics. Our analysis offers a novel interpretation for the functional role of STDP in physiological neurons.
The Intelligent surfer: Probabilistic Combination of Link and Content Information in PageRank (2001)

The PageRank algorithm, used in the Google search engine, greatly improves the results of Web search by taking into account the link structure of the Web. PageRank assigns to a page a score proportional to the number of times a random surfer would visit that page, if it surfed indefinitely from page to page, following all outlinks from a page with equal probability. We propose to improve Page-Rank by using a more intelligent surfer, one that is guided by a probabilistic model of the relevance of a page to a query. Efficient execution of our algorithm at query time is made possible by precomputing at crawl time (and thus once for all queries) the necessary terms. Experiments on two large subsets of the Web indicate that our algorithm significantly outperforms PageRank in the (human-rated) quality of the pages returned, while remaining efficient enough to be used in today’s large search engines. 1
Flow Cytometric Analysis of Macrophages and Dendritic Cell Subsets in the Mouse Lung (2013)

The lung hosts multiple populations of macrophages and dendritic cells, which play a crucial role in lung pathology. The accurate identification and enumeration of these subsets are essential for understanding their role in lung pathology. Flow cytometry is a mainstream tool for studying the immune system. However, a systematic flow cytometric approach to identify subsets of macrophages and dendritic cells (DCs) accurately and consistently in the normal mouse lung has not been described. Here we developed a panel of surface markers and an analysis strategy that accurately identify all known populations of macrophages and DCs, and their precursors in the lung during steady-state conditions and bleomycin-induced injury. Using this panel, we assessed the polarization of lung macrophages during the course of bleomycin-induced lung injury. Alveolar macrophages expressed markers of alternatively activated macrophages during both acute and fibrotic phases of bleomycin-induced lung injury, whereas markers of classically activated macrophages were expressed only during the acute phase. Taken together, these data suggest that this flow cytometric panel is very helpful in identifying macrophage and DC populations and their state of activation in normal, injured, and fibrotic lungs.
On the analysis of orthogonal chirp division multiplexing for shallow water underwater acoustic communication (2017)

This paper describes the use of the novel Orthogonal Chirp Division Multiplex (OCDM) waveform for an end-to-end high data rate underwater acoustic transmission system. The described OCDM based transmission is evaluated over a realistic underwater acoustic (UWA) channel and compared fairly against the conventional orthogonal frequency division multiplex (OFDM). By efficiently exploiting multi-paths diversity of the channel, OCDM is shown to provide better robustness than OFDM especially in case of a underloaded configuration when only a subset of N chirp waveforms are modulated leading to an interesting trade-off between spectral efficiency and robustness against UWA channel impairments.
Digoxin-specific Fab fragments impair renal function in the rabbit (1992)

A 2 mg kg-1 intravenous bolus dose of digoxin-specific Fab fragments produced a 28% reduction in creatinine clearance in rabbits after 24 h. Urine output was reduced, while plasma and urinary creatinine concentrations were unaffected and increased, respectively. By 5 days the creatinine clearance had returned to normal. The fractional excretion of Na+ was nearly halved, indicating that the tubular reabsorption of Na+ increased to compensate for the reduced glomerular filtration rate, suggesting that tubular (as opposed to glomerular) function was not impaired.
A New Framework for Building Participation in the Arts (2001)

RAND’s landmark study explores why people become involved in the arts and how arts organizations can influence their participation.