gebhart/patrepeval huggingface dataset:
Comparison of DNA Double-strand Break Rejoining as Measured by Pulsed Field Gel Electrophoresis, Neutral Sucrose Gradient Centrifugation and Non-unwinding Filter Elution in Irradiated Plateau-phase CHO Cells (1991)

The initial (up to 30 min) rate of DNA double-strand break (dsb) rejoining was measured in irradiated plateau-phase CHO cells, in a set of parallel experiments using the same cell suspension, by means of non-unwinding filter elution, neutral sucrose gradient centrifugation, and two pulsed-field gel electrophoresis assays: asymmetric field inversion gel electrophoresis (AFIGE) and clamped homogeneous electric field (CHEF) gel electrophoresis. The rate of DNA dsb rejoining was compared to the rate of rejoining of chromatin breaks measured, also in the same cell population, using the technique of premature chromosome condensation (PCC). Two radiation exposures, 25 Gy and/or 50 Gy, were used and applied to the individual parts of the experiments according to the sensitivity of the assay under investigation. Similar values for the initial rate of DNA dsb rejoining were obtained with all assays used, with t 1/2 ranging between 10 and 12 min after exposure to 25 Gy and between 15 and 20 min after exposure to 50 Gy. The initial rate of rejoining of chromatin breaks was slower than that of DNA dsb and occurred with t 1/2 of 87 min. The results suggest that all major techniques currently used for assaying rejoining of DNA dsb give similar results despite their widely different biophysical basis, and indicate that more information is required before a direct correlation between rejoining of DNA dsb and rejoining of chromatin breaks can be established.
Pivotal Evaluation of the Accuracy of a Biomarker Used for Classification or Prediction: Standards for Study Design (2008)

Research methods for biomarker evaluation lag behind those for evaluating therapeutic treatments. Although a phased approach to development of biomarkers exists and guidelines are available for reporting study results, a coherent and comprehensive set of guidelines for study design has not been delineated. We describe a nested case-control study design that involves prospective collection of specimens before outcome ascertainment from a study cohort that is relevant to the clinical application. The biomarker is assayed in a blinded fashion on specimens from randomly selected case patients and control subjects in the study cohort. We separately describe aspects of the design that relate to the clinical context, biomarker performance criteria, the biomarker test, and study size. The design can be applied to studies of biomarkers intended for use in disease diagnosis, screening, or prognosis. Common biases that pervade the biomarker research literature would be eliminated if these rigorous standards were followed.
On the thru-reflect-line (TRL) numerical calibration and error analysis for parameter extraction of circuit model (2006)

In this work, a resistor standard is introduced into our previously proposed numerical thru-reflect-line (TRL) calibration procedure in order to determine the characteristic impedance of the line standard of calibration on the basis of a deterministic method of moments (MoM) algorithm. A comprehensive analytical derivation is presented with regards to electrical properties of such a resistor standard in comparison to other standards. In addition, an error analysis is detailed, which reveals correlations of characteristic parameters in connection with equivalent circuit model development from the conversions from field-based S-parameters to circuit-based Y- or Z-parameters. Interesting properties and criteria are derived, allowing accurate parameter extractions. To validate the proposed numerical TRL calibration procedure with this new resistor standard concept and the developed error analysis, the characteristic impedance of a microstrip line is extracted from a commercial software. In addition, a further example with microstrip discontinuity is shown and the effectiveness of the proposed technique is verified. © 2006 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2006.
Acoustic echo cancellation and doubletalk detection using estimated loudspeaker impulse responses (2005)

In this paper, we present a new approach to acoustic echo cancellation and doubletalk detection for a teleconferencing system including a loudspeaker for which an estimate of the loudspeaker impulse response is available. The approach is general in the sense that it may be applied to most existing acoustic echo cancellation and doubletalk detection algorithms. We show that the new approach reduces the computational complexity for both the echo cancellation and the doubletalk detection algorithms. Furthermore, the numerical examples show that the new approach also may increase the echo cancellation and doubletalk detection performances.
Direct-sequence spread-spectrum parallel acquisition in a fading mobile channel (1990)

A parallel acquisition scheme for direct-sequence spread-spectrum systems is proposed, and its mean acquisition time performance is analyzed in both nonfading and Rayleigh-fading environments. An expression for the mean acquisition time is derived in terms of the probabilities of detection, missing, and false alarm. These parameters are first analyzed for a typical AWGN (additive white Gaussian noise) channel, then the Rayleigh-fading channel encountered in a typical UHF or microwave land mobile radio channel is studied. The channel is assumed frequency nonselective, and the effect of data modulation and code Doppler is not considered. The performance of the parallel system is compared to the corresponding serial system, and it is shown that a significant improvement can be achieved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Use of Selective Serotonin Reuptake Inhibitors in Children and Adolescents with Major Depression (2005)

Emerging data from several clinical trials show that the SSRIs have modest effects on childhood depression. In addition, SSRI treatment may be associated with behavioral activation, self-harm, and suicidal ideation. Appropriate use of SSRIs in children and adolescents requires careful diagnostic assessment, evaluation of co-occurring conditions, and diligent monitoring, especially within the first weeks of treatment.
<title>Automated visual quality evaluation of CVD film</title> (1992)

This study describes the implementation and performance of a new image analysis algorithm, ALOET, as applied to automatically distinguishing between acceptable and unacceptable chemical vapor deposition (CVD) diamond film. ALOET is a texture feature which measures the homogeneity of the edge orientations in a local window, and which is useful in differentially characterizing large and small polycrystalline structures. The analysis in this study includes a performance metric for film quality evaluation, numerical and visual performance results, and an example analytical model for determining the algorithm's control parameters.
Yeast Synthetic Biology Platform Generates Novel Chemical Structures as Scaffolds for Drug Discovery (2014)

Synthetic biology has been heralded as a new bioengineering platform for the production of bulk and specialty chemicals, drugs, and fuels. Here, we report for the first time a series of 74 novel compounds produced using a combinatorial genetics approach in baker's yeast. Based on the concept of "coevolution" with target proteins in an intracellular primary survival assay, the identified, mostly scaffold-sized (200-350 MW) compounds, which displayed excellent biological activity, can be considered as prevalidated hits. Of the molecules found, >75% have not been described previously; 20% of the compounds exhibit novel scaffolds. Their structural and physicochemical properties comply with established rules of drug- and fragment-likeness and exhibit increased structural complexities compared to synthetically produced fragments. In summary, the synthetic biology approach described here represents a completely new, complementary strategy for hit and early lead identification that can be easily integrated into the existing drug discovery process.
<i>Bacillus anthracis</i>Edema Toxin Suppresses Human Macrophage Phagocytosis and Cytoskeletal Remodeling via the Protein Kinase A and Exchange Protein Activated by Cyclic AMP Pathways (2009)

Bacillus anthracis, the etiological agent of anthrax, is a gram-positive spore-forming bacterium. It produces edema toxin (EdTx), a powerful adenylate cyclase that increases cyclic AMP (cAMP) levels in host cells. Because other cAMP-increasing agents inhibit key macrophage (MPhi) functions, such as phagocytosis, it was hypothesized that EdTx would exhibit similar suppressive activities. Our previous GeneChip data showed that EdTx downregulated MPhi genes involved in actin cytoskeleton remodeling, including protein kinase A (PKA). To further examine the role of EdTx during anthrax pathogenesis, we explored the hypothesis that EdTx treatment leads to deregulation of the cAMP-dependent PKA system, resulting in impaired cytoskeletal functions essential for MPhi activity. Our data revealed that EdTx significantly suppressed human MPhi phagocytosis of Ames spores. Cytoskeletal changes, such as decreased cell spreading and lowered F-actin content, were also observed for toxin-treated MPhis. Further, EdTx altered the protein levels and activity of PKA and exchange protein activated by cAMP (Epac), a recently identified cAMP-binding molecule. By using PKA- and Epac-selective cAMP analogs, we confirmed the involvement of both pathways in the inhibition of MPhi functions elicited by EdTx-generated cAMP. These results suggested that EdTx weakened the host immune response by increasing cAMP levels, which then signaled via PKA and Epac to cripple MPhi phagocytosis and interfered with cytoskeletal remodeling.
Washington Report (1974)

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Motion estimation using long-term motion vector prediction (1999)

Summary form only given. This paper presents a motion estimation technique for the coding of video sequences that is based on long-term temporal prediction. The motion vector of a moving object is tracked from one frame to another using a projection method. The traced motion vector is used as a starting point for the motion estimation search algorithm. The motion estimation algorithm used is based on an optimum fast block matching algorithm. Combinations of both spatial and temporal prediction are also used to obtain a more accurate estimate of the motion vector of the current macroblock. An inaccurately predicted motion vector can have a significant negative impact on the motion estimation algorithm. It can force the search algorithm to be trapped in a local minimum, or to spend unnecessary computations to find the optimum motion vector. The accuracy of the predicted motion vector is estimated using a reliability measure that allows the motion search algorithm to decide whether to use temporal motion vector predictor, spatial motion vector predictor, or both. As a reliability measure we used the mean squared error between the traced motion vectors in the current frame and in the previous frame. The reliability measure increases if the motion vector belongs to a moving object with constant speed. If the reliability measure is smaller than a certain threshold, then we abandon the temporal prediction and use spatial prediction. If both prediction methods fail, we abandon the fast motion search and perform full-search motion estimation in the low-resolution images. The experimental results show that long-term prediction reduces the number of computations performed by the motion search algorithm by up to 20%, while obtaining essentially the same quality.
Oxide nanostructures through self-assembly (2001)

A prominent theme in inorganic materials research is the creation of uniformly flat thin films and heterostructures over large wafers, which can subsequently be lithographically processed into functional devices. This letter proposes an approach that will lead to thin film topographies that are directly counter to the above-mentioned philosophy. Recent years have witnessed considerable research activity in the area of self-assembly of materials, stimulated by observations of self-organized behavior in biological systems. We have fabricated uniform arrays of nonplanar surface features by a spontaneous assembly process involving the oxidation of simple metals, especially under constrained conditions on a variety of substrates, including glass and Si. In this letter we demonstrate the pervasiveness of this process through examples involving the oxidation of Pd, Cu, Fe, and In. The feature sizes can be controlled through the grain size and thickness of the starting metal thin film. Finally, we demonstrate how such submicron scale arrays can serve as templates for the design and development of self-assembled, nanoelectronic devices.
Bacterial phospholipid hydrolysis enhances the destruction of Escherichia coli ingested by rabbit neutrophils. Role of cellular and extracellular phospholipases. (1990)

Escherichia coli ingested by PMN are promptly growth arrested but undergo limited destruction. We have studied bacterial phospholipid hydrolysis as a possible limiting factor in the disassembly of ingested E. coli, comparing the fates, during phagocytosis by rabbit peritoneal exudate PMN, of three isogenic strains, differing in their content of the pldA gene encoding the principal E. coli phospholipase A (PLA), i.e., pldA-, pldA+, pldA (the latter strain bearing the pldA gene in a multicopy plasmid resulting in a 20-fold increase in PLA content). Ingestion and growth inhibition (greater than 99% within 15 min) were the same for the three strains, but phospholipid degradation differed according to bacterial PLA content: pldA up to 60%, pldA+ up to 30%, and pldA- up to 20%. Since the pldA- strain has no activatable PLA, phospholipid degradation in this strain demonstrates the action of a PMN PLA. Added PLA2-rich ascitic fluid (AF) or purified AF PLA2 increased the rate and extent of degradation of the pldA- strain, provided the enzyme was added before ingestion was complete. 125I-AF-PLA2 binds to both E. coli and PMN and thus can enter the vacuole during phagocytosis. Although up to 50-fold more AF-PLA2 than the PLA2 content of the PMN could be loaded into the PMN in this way, degradation of pldA- E. coli did not exceed 30%. Increased phospholipid degradation had no effect on the degradation of bacterial macromolecules. In contrast, bacterial disassembly manifest as structural disorganization, release of bacterial protein derived material, and inhibition of protein synthesis were markedly enhanced when greater than 50% of prelabelled bacterial phospholipids were degraded. These findings reveal a link between envelope phospholipid degradation and overall bacterial destruction, suggesting therefore that factors limiting PLA action limit the destruction of E. coli ingested by PMN.
Evidence for Oncolytic Virotherapy: Where Have We Got to and Where Are We Going? (2015)

The last few years have seen an increased interest in immunotherapy in the treatment of malignant disease. In particular, there has been significant enthusiasm for oncolytic virotherapy, with a large amount of pre-clinical data showing promise in animal models in a wide range of tumour types. How do we move forward into the clinical setting and translate something which has such potential into meaningful clinical outcomes? Here, we review how the field of oncolytic virotherapy has developed thus far and what the future may hold.
Spontaneous and Evoked Activity of Substantia Nigra Pars Reticulata Neurons during High-Frequency Stimulation of the Subthalamic Nucleus (2003)

The subthalamic nucleus (STN), a major component of the basal ganglia, exerts an excitatory influence on the output structures of this system i.e., the substantia nigra pars reticulata (SNR) and the internal segment of the globus pallidus. High-frequency stimulation of the STN is a method currently used to treat parkinsonian symptoms. The aim of the present study was to analyze the effects of STN high-frequency stimulation on the activity of SNR neurons and to investigate its impact on the transfer of information between the cerebral cortex and the SNR. During STN high-frequency stimulation, the activity of SNR cells was decreased at low-intensity stimulation, whereas it was increased at a higher intensity. The decrease in the discharge of SNR cells likely results from the activation of a GABAergic transmission in the SNR because this effect was blocked by local application of bicuculline. The increased activity likely results from the activation of the glutamatergic subthalamonigral projection because the latency of the evoked excitations was consistent with the conduction time of the subthalamonigral neurons. Finally, during STN high-frequency stimulation, the transmission of cortical information along the direct trans-striatal pathway was preserved, whereas the functionality of the trans-subthalamic pathways was partly preserved or completely blocked depending on the stimulation intensity. The present data indicate that STN high-frequency stimulation influences the activity of SNR cells through activation of their excitatory and inhibitory synaptic afferent pathways as well as antidromic activation of the projection neurons.
Energy Efficient Resource Allocation for Wireless Power Transfer Enabled Collaborative Mobile Clouds (2016)

In order to fully enjoy high rate broadband multimedia services, prolonging the battery lifetime of user equipment is critical for mobile users, especially for smartphone users. In this paper, the problem of distributing cellular data via a wireless power transfer enabled collaborative mobile cloud (WeCMC) in an energy efficient manner is investigated. WeCMC is formed by a group of users who have both functionalities of information decoding and energy harvesting, and are interested for cooperating in downloading content from the operators. Through device-to-device communications, the users inside WeCMC are able to cooperate during the downloading procedure and offload data from the base station to other WeCMC members. When considering multi-input multi-output wireless channel and wireless power transfer, an efficient algorithm is presented to optimally schedule the data offloading and radio resources in order to maximize energy efficiency as well as fairness among mobile users. Specifically, the proposed framework takes energy minimization and quality of service requirement into consideration. Performance evaluations demonstrate that a significant energy saving gain can be achieved by the proposed schemes.
Cell-Specific Delivery of Polymeric Nanoparticles to Carbohydrate-Tagging Cells (2007)

Carbohydrates on cell surfaces contribute a variety of communications between the cell and its environment, and they have been assumed to act as markers for cellular recognition. In this research, 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer nanoparticles, which can react with specific carbohydrates of target cells, were newly prepared to serve as novel drug carriers. A water-soluble MPC polymer bearing hydrazide groups (PMBH) was synthesized by conventional radical polymerization. The MPC polymer showed amphiphilic nature and worked as an emulsifier to form nanoparticles. The nanoparticles covered with PMBH were prepared by the solvent evaporation method and exhibited monodispersity. They were approximately 200 nm in diameter and -2.0 mV in surface potential. According to a surface analysis of the nanoparticles, phosphorylcholine and hydrazide groups were observed, and the surface was fully covered with PMBH. Unnatural carbohydrates having ketone groups on human cervical carcinoma cell (HeLa) surfaces were expressed by treatment with levulinoyl mannosamine (ManLev). When the PMBH nanoparticles were in contact with the ManLev-treated HeLa cells, they accumulated in the cells. In contrast, the nanoparticles were not observed in native HeLa cells (without unnatural carbohydrates). These results indicate that the hydrazide groups of the nanoparticles selectively reacted to the ketone groups of the carbohydrates on the cell surface. The PMBH nanoparticles immobilized with anticancer drugs such as doxorubicin or paclitaxel were in contact with either ManLev-treated or untreated HeLa cells. The viability of the ManLev-treated HeLa cells was effectively reduced, but that of the untreated cells was preserved. This indicated that the anticancer drugs were selectively delivered to the ManLev-treated cells. Nonspecific cellular uptake of the nanoparticles was effectively reduced by MPC polymer coating. Furthermore, the immobilization processes of the drugs differed because of the solubility of the drugs. In conclusion, cellular-specific drug delivery by means of the novel nanoparticles was demonstrated with the selective reaction between unnatural carbohydrates on the cell surface and the hydrazide groups bearing the phosphorylcholine polymer nanoparticles.
A simplified method for monitoring heparin therapy at the bedside: The activated whole blood clotting time (1981)

Twelve patients receiving heparin during hemodialysis had coagulation parameters monitored using the whole blood clotting time (WBCT), activated partial thromboplastin time (APTT), plasma heparin levels and activated whole blood clotting time (AWBCT). The AWBCT, performed with a battery-powered portable incubator/timer, correlated with both the corresponding WBCT and the plasma heparin levels. However, the correlation between the AWBCT and the APTT was quite poor. This assay is simply performed, inexpensive, and reproducible. It is recommended as an excellent method for monitoring heparin therapy.
On Nebuchadnezzar in <i>Pseudo-Sirach</i> (2009)

Pseudo-Sirach is arguably a pseudepigraphon, even though Ben Sira, the protagonist, is referred to in the third person. It is an early medieval Hebrew-language homiletical collection, structured as exchanges between the child prodigy Ben Sira (Jeremiah’s son), and King Nebuchadnezzar. This article offers a general discussion of the structure of the frame-story, in which Nebuchadnezzar and Ben Sira are interlocutors. It contrasts this to another source poking fun at Nebuchadnezzar. Then, the difference between this treatment of the destroyer of the First Temple and how early rabbinic sources treated Vespasian and Titus is considered. The only such locus which comes close to the pattern in Pseudo-Sirach is the subnarrative about how R. Joḥanan ben Zakkai comes to the rescue of Vespasian as the latter, having been informed, while having put on a shoe, that the Romans made him their king, is unable to put on the other shoe. In contrast, the appearance of the Pseudo Nero shaped the early rabbinic narrative about Nero, and if we are to find a Nero parallel to Jewish derisive treatments of Nebuchadnezzar, it is in the Latin Commenta Bernensia to Lucan’s Pharsalia that we can find them.