gebhart/patrepeval huggingface dataset:
First clinical results with Lu-177 PSMA-TUM1 for the treatment of castrate-resistant metastatic prostate cancer (2014)

10 Objectives EuK-Sub-KFF-DOTAGA (PSMA-TUM1) is a novel ligand targeting the prostate-specific membrane antigen (PSMA). We present the first clinical experience of treating metastatic castrate-resistant prostate cancer (PC) using Lu-177 PSMA-TUM1. Methods Radioligand therapy (RLT) with Lu-177 PSMA-TUM1 was performed in 6 PC patients with distant metastases and progressive disease, refractory to conventional treatment (including hormone, chemo- and radiation therapy). Ga-68 PSMA-HBED-CC PET/CT was performed in all patients 1-5 days prior to RLT, followed by one therapy cycle (mean administered activity 6.1±1.5 GBq, median 5.8, range 4.2 - 8.6 GBq) of Lu-177 PSMA-TUM1. In addition, early response was evaluated by means of Ga-68 PSMA-HBED-CC PET/CT in 3 patients. Results Intense PSMA expression by the extensive bone and lymph node metastases (n=4), lung metastases (n=1), residual/ locally recurrent PC (n=2) was confirmed by baseline Ga-68 PSMA-HBED-CC PET/CT. All lesions detected by PET/CT exhibited high Lu-177 PSMA-TUM1 uptake on post-therapy planar and SPECT images. Response evaluation by Ga-68 PSMA-HBED-CC PET/CT revealed excellent treatment response (partial remission) in 2 patients, with decrease in the SUVmax of the target lesion by 51 % and 89 % respectively, and disappearance of many of the previously noted PSMA-positive metastases. There was progression of skeletal metastases in 1 patient. The treatment was well tolerated by all patients without any significant adverse effects or alterations in any of the laboratory parameters. Conclusions Lu-177 PSMA-TUM1 is a novel and promising radioligand for the treatment of metastatic prostate cancer. Our initial results indicate that RLT is safe and effective, i.e. in combination with patient stratification by Ga-68 PSMA-HBED-CC PET/CT.
Short-Wavelength Sensitivity for the Direct Effects of Light on Alertness, Vigilance, and the Waking Electroencephalogram in Humans (2006)

Short-wavelength sensitivity to the acute alerting effects of light indicates that the visual photopic system is not the primary photoreceptor system mediating these responses to light. The frequency-specific changes in the waking EEG indicate that short-wavelength light is a powerful agent that immediately attenuates the negative effects of both homeostatic sleep pressure and the circadian drive for sleep on alertness, performance, and the ability to sustain attention.
NEGATIVE DOMINANT MUTATIONS OF THE <i>uidR</i> GENE IN <i>ESCHERICHIA COLI</i>: GENETIC PROOF FOR A COOPERATIVE REGULATION OF <i>uidA</i> EXPRESSION (1986)

The uidA gene is the first gene involved in the hexuronide-hexuronate pathway in Escherichia coli K-12 and is under the dual control of the uidR and uxuR encoded repressors. Point mutations affecting the uidR regulatory gene were sought to investigate the regulation of uidA. When the uidR mutant allele was on a multicopy plasmid and the wild-type allele was on the chromosome, some of the mutant phenotypes were dominant to the wild-type phenotype, indicating that the active form of the UidR repressor is multimeric. We have demonstrated that expression of the mutant phenotype is dependent on gene dosage. The dominance of the uidR allele was also sensitive to the presence of the wild-type uxuR allele in the cell. This behavior probably results from UidR-UxuR repressor interactions. A mechanism is proposed: we suggest that the UidR and UxuR repressors interact after their binding to the operator site of uidA; the binding of one regulatory molecule may facilitate the binding of the other one in a cooperative process.
Development of Highly Sensitive Fluorescent Probes for Detection of Intracellular Copper(I) in Living Systems (2010)

We describe here the new copper-selective fluorescent probes FluTPA1 and FluTPA2, in which the tetradentate ligand tris[(2-pyridyl)methyl]amine (TPA) is connected to a reduced form of a fluorescein platform through a benzyl ether linkage. These probes selectively react with copper ions in the presence of submillimolar glutathione and emit intense green fluorescence from the reaction product, O-methylfluorescein. Confocal images of live cells further show that FluTPA2 is membrane-permeable and allows visualization of CuI present in living cells.
Practical introduction to simulation optimization (2003)

The merging of optimization and simulation technologies has seen a rapid growth in recent years. A Google search on Simulation Optimization returns more than six thousand pages where this phrase appears. The content of these pages ranges from articles, conference presentations and books to software, sponsored work and consultancy. This is an area that has sparked as much interest in the academic world as in practical settings. In this paper, we first summarize some of the most relevant approaches that have been developed for the purpose of optimizing simulated systems. We then concentrate on the metaheuristic black-box approach that leads the field of practical applications and provide some relevant details of how this approach has been implemented and used in commercial software. Finally, we present an example of simulation optimization in the context of a simulation model developed to predict performance and measure risk in a real world project selection problem.
Subtractive chromatography for purification and recovery of nano-bioproducts (2005)

A novel polymer-coated adsorbent (subtractive adsorbent) has been manufactured and evaluated for the recovery of nanoparticle bioproducts. The core principle was to coat inert macroporous polymers (e.g. agarose) upon adsorbent beads of varied ligands. Here BSA nanoparticles, with an average nanoparticle diameter 95 nm, were fabricated and selected as feedstock for the demonstration of the principle. The adsorption of a mixture of fluorescently labelled BSA solution and BSA nanoparticles was investigated in a batch binding experiment upon polymer-coated Streamline DEAE and visualised by laser scanning confocal microscopy. The mechanistic design of such adsorbents and their basic application for the recovery of target nano-bioproducts from complex feedstock is strongly indicated.
An efficient magic state approach to small angle rotations (2016)

Standard error correction techniques only provide a quantum memory and need extra gadgets to perform computation. Central to quantum algorithms are small angle rotations, which can be fault-tolerantly implemented given a supply of an unconventional species of magic state. We present a low-cost distillation routine for preparing these small angle magic states. Our protocol builds on the work of Duclos-Cianci and Poulin [Phys. Rev. A, 91, 042315 (2015)] by compressing their circuit. Additionally, we present a method of diluting magic states that reduces costs associated with very small angle rotations. We quantify performance by the expected number of noisy magic states consumed per rotation, and compare with other protocols. For modest size angles, our protocols offer a factor 24 improvement over the best known gate synthesis protocols and a factor 2 over the Duclos-Cianci and Poulin protocol. For very small angle rotations, the dilution protocol dramatically reduces costs, giving several orders magnitude improvement over competitors. There also exists an intermediary regime of small, but not very small, angles where our approach gives a marginal improvement over gate synthesis. We discuss how different performance metrics may alter these conclusions.
Nanoengineered parabolic liquid mirrors (2006)

We give a progress report on an application of a new class of versatile optical elements pioneered by our laboratory: By coating liquids we create reflective surfaces that can be shaped by rotation into a parabolic mirror. Coated ferrofluids can also be shaped with magnetic fields. Low cost is what makes rotating mercury LM Telescopes interesting. However, they are limited by the fact that they cannot be tilted. We are now working on a new generation of LMs that can be tilted. The goal is to produce large inexpensive LMTs that can be tilted by at least twenty degrees. Early work demonstrated a tilted LM that used a high viscosity liquid. An extrapolation law, confirmed by our experiments, shows that it should be possible to tilt LMs by twenty degrees, assuming a liquid having a few times the viscosity of glycerin. Rotating nanoengineered LMTs are interesting even without tilting, since their lower weight would make then less costly than Hg mirrors and high viscosity makes them less sensitive to winds. We have made two major recent technological breakthroughs: We have made a robotic machine which is capable of producing the large quantities of coating material required for large mirrors. We have also developed a technique that allows us to coat the appropriate class of liquids by simply spraying the nanoengineered coating on them. In this contribution, we present optical tests of our liquids as well as optical shop tests of rotating mirrors.
Identification of an acidic fibroblast growth factor-like activity in a mesoblastic nephroma. (1989)

An acidic fibroblast growth factor-like activity was detected in a primary mesoblastic nephroma. Identification was based upon Northern blot analysis of renal tumor RNA and by a biochemical characterization of the growth factor activity. The activity extracted from the tumor stimulated DNA synthesis in both mouse fibroblasts and bovine endothelial cells. This activity was heat-sensitive and enhanced in the presence of heparin. The extract activity bound to immobilized immobilized heparin, eluting at 1.2 M NaCl, and cross-reacted with antiserum to recombinant acidic fibroblast growth factor. We also present evidence for acidic fibroblast growth factor-like molecules in normal immature human kidney, although the amount of the activity detected is less than that in the mesoblastic nephroma. These data suggest that acidic fibroblast growth factor-like activity is present in the developing normal human kidney, and that some renal tumors can continue to express a similar activity.
Positive and Negative Sequence Control Strategies to Maximize the Voltage Support in Resistive–Inductive Grids During Grid Faults (2017)

Grid faults are one of the most severe perturbations in power systems. During these extreme disturbances, the reliability of the grid is compromised and the risk of a power outage is increased. To prevent this issue, distributed generation inverters can help the grid by supporting the grid voltages. Voltage support mainly depends on two constraints: the amount of injected current and the grid impedance. This paper proposes a voltage support control scheme that joins these two features. Hence, the control strategy injects the maximum rated current of the inverter. Thus, the inverter takes advantage of the distributed capacities and operates safely during voltage sags. Also, the controller selects the appropriate power references depending on the resistive-inductive grid impedance. Therefore, the grid can be better supported since the voltage at the point of common coupling is improved. Several voltage objectives, which cannot be achieved together, are developed and discussed in detail. These objectives are threefold: to maximize the positive sequence voltage; to minimize the negative sequence voltage; and to maximize the difference between positive and negative sequence voltages. A mathematical optimal solution is obtained for each objective function. This solution is characterized by a safe peak current injection, and by the optimization of the voltage profile in any type of grid connection. Therefore, the proposed control scheme includes advanced features for voltage support during voltage sags, which are applicable to different power facilities in different types of networks. Due to system limitations, a suboptimal solution is also considered, analyzed, and discussed for each of the optimization problems. Experimental results are presented to validate the theoretical solutions.
Discrimination and Quantitative Analysis of Wild Type and Point Mutant Early Region 1B Genes of Adenovirus Using Oligodeoxyribonucleotide Hybridization Probes (1987)

One of the cytocidal (cyt) mutants of adenovirus 2 (Ad2), cyt15, has been shown to have two point mutations separated by 36 bases in its early region 1B (E1B) gene that encodes the 19K (Mr, 19,000) protein. A part of the cyt15 E1B gene, including one of the point mutations, was probed with a 23-base long oligodeoxyribonucleotide (ME1B23). Another oligonucleotide probe of the same length was used for the corresponding region of the wild type (wt) E1B gene (E1B23). Over the 32P-end labeled oligonucleotide probe, a 25-fold molar excess of a competitor (1) (the unlabeled oligonucleotide of each counterpart) was added to the hybridization mixture. The E1B gene with or without a point mutation could easily be distinguished from its counterpart and quantitated in the presence of its counterpart under the hybridization conditions employed. Under the stringent wash conditions, the E1B gene of wt Ad2 could be completely discriminated from even a 100-fold molar excess of cyt15 E1B gene with the 32P-labeled E1B23 probe. The wt E1B gene could also be quantitated in the presence of a 100-fold molar excess of the mutant E1B gene.
Temperature-Sensitive Osmotic Remedial Mutants of <i>Escherichia coli</i> (1972)

A collection of temperature-sensitive mutants of Escherichia coli K-12 was examined for ability to grow at the restrictive temperature when the osmotic pressure of the medium was increased. Five of the fourteen mutants were found to be osmotic remedial. Four strains containing temperature-sensitive, osmotic-remedial mutations affecting aminoacyl-transfer ribonucleic acid synthetases were found to have altered permeability characteristics which may be attributable to changes in the lipopolysaccharide layer of the cell envelope at restrictive temperatures.
Skeletonization of Plant Point Cloud Data Using Stochastic Optimization Framework (2020)

Skeleton extraction from 3D plant point cloud data is an essential prior for myriads of phenotyping studies. Although skeleton extraction from 3D shapes have been studied extensively in the computer vision and graphics literature, handling the case of plants is still an open problem. Drawbacks of the existing approaches include the zigzag structure of the skeleton, nonuniform density of skeleton points, lack of points in the areas having complex geometry structure, and most importantly the lack of biological relevance. With the aim to improve existing skeleton structures of state-of-the-art, we propose a stochastic framework which is supported by the biological structure of the original plant (we consider plants without any leaves). Initially we estimate the branching structure of the plant by the notion of β-splines to form a <i>curve tree</i> defined as a finite set of curves joined in a tree topology with certain level of smoothness. In the next phase, we force the discrete points in the curve tree to move toward the original point cloud by treating each point in the curve tree as a center of Gaussian, and points in the input cloud data as observations from the Gaussians. The task is to find the correct locations of the Gaussian centroids by maximizing a likelihood. The optimization technique is iterative and is based on the Expectation Maximization (EM) algorithm. The E-step estimates which Gaussian the observed point cloud was sampled from, and the M-step maximizes the negative log-likelihood that the observed points were sampled from the Gaussian Mixture Model (GMM) with respect to the model parameters. We experiment with several real world and synthetic datasets and demonstrate the robustness of the approach over the state-of-the-art.
Localization of a chromosomal mutation affecting expression of extracellular lipase in Staphylococcus aureus (1992)

We describe a Tn551 chromosomal insertion in Staphylococcus aureus S6C that results in sharply reduced expression of extracellular lipase. With Tn917 as a probe, the insertion in the original mutant (KSI905) was localized to a 12.6-kb EcoRI DNA fragment. The 12.6-kb fragment was cloned and used as a probe to identify a 26-kb EcoRI fragment containing the Tn551 insertion site in the S6C parent strain. Restriction endonuclease analysis of the 12.6- and 26-kb EcoRI fragments confirmed that the Tn551 insertion in KSI905 was accompanied by a deletion of 18.7 kb of chromosomal DNA. Tn551 was transduced from KSI905 back into the S6C parent strain. All transductants exhibited the same lipase-negative (Lip-) phenotype and contained the same mutation with respect to both the insertion and the 18.7-kb deletion. The inability to produce lipase was not caused by disruption of the lipase structural gene, since all Lip- mutants carried intact copies of geh. Moreover, the Tn551 insertion was localized to a region of the staphylococcal chromosome at least 650 kb from geh. Taken together, these results suggest that the Tn551 insertion occurred in a region of the chromosome encoding a trans-active element required for the expression of extracellular lipase. A 20-bp oligonucleotide corresponding to a sequence within the region encoding RNA II near the Tn551 insertion site in ISP546 (H.L. Peng, R.P. Novick, B. Kreiswirth, J. Kornblum, and P. Schlievert, J. Bacteriol. 170:4365-4372, 1988) and a 1.75-kb DNA fragment representing the region encoding RNA III were used as gene probes to show that the Tn551 insertion did not occur in the agr locus. We conclude that the genetic element functions independently of agr or as an unrecognized part of that regulatory system.
metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data (2015)

The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs within whole-genome and targeted data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a two-dimensional statistical test allows the detection of DMRs in large methylation experiments with multiple groups of samples in minutes rather than days using off-the-shelf hardware. metilene outperforms other state-of-the-art tools for low coverage data and can estimate missing data. Hence, metilene is a versatile tool to study the effect of epigenetic modifications in differentiation/development, tumorigenesis, and systems biology on a global, genome-wide level. Whether in the framework of international consortia with dozens of samples per group, or even without biological replicates, it produces highly significant and reliable results.
Shock waves can enhance bacterial transformation with plasmid DNA (2004)

Shock waves appear in nature whenever the different elements in a fluid approach one another with a velocity larger than the local speed of sound. Shock waves are strong perturbations in aerodynamics that propagate at supersonic speeds independent of the wave amplitude. Such disturbances occur in steady transonic or supersonic flow during explosions, lightening strokes and contact surfaces in laboratory devices. The typical thickness of the shock front in air is $~10^{\\mathrm{-7}}m$, very small compared to other characteristic lengths in fluid flow. Physically, the occurrence of shock waves is always characterized in a fluid flow by instantaneous changes in pressure, velocity and temperature.\n
Development of a scanning probe microscopy integrated atomic layer deposition system for <i>in situ</i> successive monitoring of thin film growth (2018)

A dual chamber system integrated with atomic layer deposition (ALD) and atomic force microscopy (AFM) was developed for the successive monitoring of nanoparticles to thin film growth process. The samples were fabricated in the ALD chamber. A magnetic transmission rod enabled sample transferring between the ALD and the AFM test chambers without breaking the vacuum, avoiding possible surface morphology change when frequently varying the growth condition and oxidation under ambient condition. The sample transmission also avoids deposition and contamination on the AFM tip during the successive testing. The sample stage has machined a group of accurate location pinholes, ensuring the 10 <i>μ</i>m<sup>2</sup> measurement consistency. As a demonstration, the platinum thin films with different thickness were fabricated by varying ALD cycles. The surface morphology was monitored successively during the deposition. Under vacuum with controlled oxygen partial pressure, the aging and sintering phenomenon of particles has been studied in the AFM testing chamber after high temperature treatment. The integrated AFM/ALD instrument is potentially a powerful system for monitoring the thin film preparation and characterization.
O‐Carboxymethylstarch Amine Polyampholytes as Papermaking Additives (1978)

Abstract Xanthated starch amine (XSA) polyampholytes, containing cationic amine and anionic xanthate substituents, improve both wet and dry strengths of paper when they are applied before formation of paper web. However, neither cationic starch amines nor starch xanthates, when applied individually, give the wet‐strength property. The potential for ampholytic starches, in general, to affect this important property was investigated. Multivalent cations (Fe +3 , Al +3 ) improved the paper wet strength independently of carboxymethylstarch amine derivates.
In the Middle: Creating a Middle Road Between U.S. and EU Data Protection Policies (2012)

The first section of this paper examines the historical differences that have led to the American approach to privacy and the European approach to privacy. The second section will examine the current U.S. model, and the third section will examine the EU model. Next, the fourth section will compare and contrast the two models. Finally, the last section will argue that the U.S. should have a regulatory agency and describe how that should look and run.
Hidradenitis Suppurativa (2003)

Background: Hidradenitis suppurativa is a clinically defined disease that causes considerable morbidity for patients. The results of recent studies, which have increased the understanding of this disease, are reviewed. Objective: The epidemiology, risk factors, pathogenesis, and treatment of this disease are summarized to help clinicians with practical patient management. Conclusion: Hidradenitis suppurativa remains a clinical challenge to patients and physicians alike. Physicians should be familiar with the impact this disease has on the patient and with the range of treatments available. Use of simple incisions as treatment is strongly discouraged. Additional pathogenic as well as therapeutic studies are necessary.
Inductively coupled plasma mass spectrometry with a quadrupole mass filter operated in the third stability region (1997)

An inductively coupled plasma mass spectrometer system is described in which the quadrupole mass filter is operated in the third stability region with Mathieu parameters (a, q)=(3, 3). Operation at the upper tip of this region is found to give generally better sensitivity and resolution than operation at the lower tip. A limiting resolution at half height of 4000 at m/z 59 is possible with operation at the upper tip. This resolution is insufficient to separate atomic ions from molecular ions of the same nominal mass except in favorable cases. However, operation at moderate resolution (R1/2=500 to 1000) is found to give very high abundance sensitivity (>107). The results suggest that the third stability region may be advantageous for specialized applications of inductively coupled plasma mass spectrometry.