gebhart/patrepeval huggingface dataset:
Patient‐specific phosphorus mobilization clearance during nocturnal and short daily hemodialysis (2012)

The kinetics of plasma phosphorus during different hemodialysis (HD) modalities are incompletely understood. We recently demonstrated that a pseudo one-compartment kinetic model including phosphorus mobilization from various body compartments into extracellular fluids can describe intradialytic and postdialytic rebound kinetics of plasma phosphorus during conventional and short 2-hour HD treatments. In this model, individual patient differences in phosphorus kinetics were characterized by a single parameter, the phosphorus mobilization clearance (K(M)). In this report we determined K(M) in patients treated by in-center nocturnal HD (ICNHD) and short daily HD (SDHD) with low dialyzer phosphate clearance. In the ICNHD study, eight patients underwent 8-hour HD treatments where intradialytic and postdialytic plasma samples were collected; K(M) values were determined by nonlinear regression of plasma concentration as a function of time. In the SDHD study, five patients were studied during 28 treatments for approximately 3 hours. Here, K(M) was calculated using only predialytic and postdialytic plasma phosphorus concentrations. Dialyzer phosphate clearances were 134 ± 20 (mean ± SD) and 95 ± 16 mL/min during ICNHD and SDHD, respectively. K(M) values for the respective therapies were 124 ± 83 and 103 ± 33 mL/min, comparable to those determined previously during conventional and short HD treatments of 98 ± 44 mL/min. When results from ICNHD, SDHD, and previous HD modalities were combined, K(M) was directly correlated with postdialytic body weight (r = 0.38, P = 0.025) and inversely correlated with predialytic phosphorus concentration (r = -0.47, P = 0.005). These findings suggest that phosphorus kinetics during various HD modalities can be described by a pseudo one-compartment model.
Semantics of Ranking Queries for Probabilistic Data and Expected Ranks (2009)

When dealing with massive quantities of data, top-k queries are a powerful technique for returning only the k most relevant tuples for inspection, based on a scoring function. The problem of efficiently answering such ranking queries has been studied and analyzed extensively within traditional database settings. The importance of the top-k is perhaps even greater in probabilistic databases, where a relation can encode exponentially many possible worlds. There have been several recent attempts to propose definitions and algorithms for ranking queries over probabilistic data. However, these all lack many of the intuitive properties of a top-k over deterministic data. Specifically, we define a number of fundamental properties, including exact-k, containment, unique-rank, value-invariance, and stability, which are all satisfied by ranking queries on certain data. We argue that all these conditions should also be fulfilled by any reasonable definition for ranking uncertain data. Unfortunately, none of the existing definitions is able to achieve this. To remedy this shortcoming, this work proposes an intuitive new approach of expected rank. This uses the well-founded notion of the expected rank of each tuple across all possible worlds as the basis of the ranking. We are able to prove that, in contrast to all existing approaches, the expected rank satisfies all the required properties for a ranking query. We provide efficient solutions to compute this ranking across the major models of uncertain data, such as attribute-level and tuple-level uncertainty. For an uncertain relation of N tuples, the processing cost is O(N log N)-no worse than simply sorting the relation. In settings where there is a high cost for generating each tuple in turn, we provide pruning techniques based on probabilistic tail bounds that can terminate the search early and guarantee that the top-k has been found. Finally, a comprehensive experimental study confirms the effectiveness of our approach.
Chemical synthesis and characterization of maurocalcine, a scorpion toxin that activates Ca<sup>2+</sup> release channel/ryanodine receptors (2000)

Maurocalcine is a novel toxin isolated from the venom of the chactid scorpion Scorpio maurus palmatus. It is a 33-mer basic peptide cross-linked by three disulfide bridges, which shares 82% sequence identity with imperatoxin A, a scorpion toxin from the venom of Pandinus imperator. Maurocalcine is peculiar in terms of structural properties since it does not possess any consensus motif reported so far in other scorpion toxins. Due to its low concentration in venom (0.5% of the proteins), maurocalcine was chemically synthesized by means of an optimized solid-phase method, and purified after folding/oxidation by using both C18 reversed-phase and ion exchange high-pressure liquid chromatographies. The synthetic product (sMCa) was characterized. The half-cystine pairing pattern of sMCa was identified by enzyme-based cleavage and Edman sequencing. The pairings were Cys3-Cys17, Cys10-Cys21, and Cys16-Cys32. In vivo, the sMCa was lethal to mice following intracerebroventricular inoculation (LD(50), 20 microg/mouse). In vitro, electrophysiological experiments based on recordings of single channels incorporated into planar lipid bilayers showed that sMCa potently and reversibly modifies channel gating behavior of the type 1 ryanodine receptor by inducing prominent subconductance behavior.
Structure-analysis method for electronic cleansing in cathartic and noncathartic CT colonography (2008)

Electronic cleansing (EC) is an emerging method for segmentation of fecal material in CT colonography (CTC) that is used for reducing or eliminating the requirement for cathartic bowel preparation and hence for improving patients' adherence to recommendations for colon cancer screening. In EC, feces tagged by an x-ray-opaque oral contrast agent are removed from the CTC images, effectively cleansing the colon after image acquisition. Existing EC approaches tend to suffer from the following cleansing artifacts: degradation of soft-tissue structures because of pseudo-enhancement caused by the surrounding tagged fecal materials, and pseudo soft-tissue structures and false fistulas caused by partial volume effects at the boundary between the air lumen and the tagged regions, called the air-tagging boundary (AT boundary). In this study, we developed a novel EC method, called structure-analysis cleansing, which effectively avoids these cleansing artifacts. In our method, submerged soft-tissue structures are recognized by their local morphologic signatures that are characterized based on the eigenvalues of a three-dimensional Hessian matrix. A structure-enhancement function is formulated for enhancing of the soft-tissue structures. In addition, thin folds sandwiched between the air lumen and tagged regions are enhanced by analysis of the local roughness based on multi-scale volumetric curvedness. Both values of the structure-enhancement function and the local roughness are integrated into the speed function of a level set method for delineating the tagged fecal materials. Thus, submerged soft-tissue structures as well as soft-tissue structures adhering to the tagged regions are preserved, whereas the tagged regions are removed along with the associated AT boundaries from CTC images. Evaluation of the quality of the cleansing based on polyps and folds in a colon phantom, as well as on polyps in clinical cathartic and noncathartic CTC cases with fluid and stool tagging, showed that our structure-analysis cleansing method is significantly superior to that of our previous thresholding-based EC method. It provides a cleansed colon with substantially reduced subtraction artifacts.
Novel Method For The Production Of Polyunsaturated Fatty Acids (Patent US 2006/0246556 A1) (2006)

The present invention relates to an improved process for the specific production of poly-unsaturated omega-3 and omega-6 fatty acids and a process for the production of triglycerides having an increased content of unsaturated fatty acids, in particular omega-3 and omega-6 fatty acids having at least two double bonds and a 20 or 22 carbon atom chain length. The invention relates to the production of a transgenic organism, preferably a transgenic plant or a transgenic microorganism, hav-ing an increased content of fatty acids, oils or lipids containing C20- or C22-fatty acids with a delta-5, 7, 8, 10 double bond, respectively due to the expression of a delta-8-desaturase and a delta-9-elon-gase from organisms such as plants preferably Algae like Isochrysis galbana or Euglena gracilis. In addition the invention relates to a process for the production of poly unsaturated fatty acids such as Eicosapentaenoic, Arachidonic, Docosapentaenoic or Doosahexaenoic acid through the co-expression of a delta-8-desaturase, a delta-9-elongase and a delta-5 desaturase in organisms such as microorganisms or plants. The invention additionally relates to the use of specific nucleic acid sequences encoding for the aforementioned proteins with delta-8-desaturase-, delta-9-elongase- or delta-5-desaturase-activity, nucleic acid constructs, vectors and organisms containing said nucleic acid sequences. The invention further relates to unsaturated fatty acids and triglycerides having an increased content of at least 1% by weight of unsaturated fatty acids and use thereof.
Can deep learning networks acquire the robustness of human recognition when faced with objects in visual noise? (2018)

Convolutional neural networks (CNNs) have attracted considerable attention for their remarkable performance at a variety of cognitive tasks, including visual object recognition. This has led to the proposal that deep learning networks may provide a biologically plausible model of human visual processing (e.g., Yamins et al., 2014; Khaligh-Razavi & Kriegeskorte, 2014). Here, we investigated whether these networks are robust to noisy viewing conditions. If not, are CNNs disrupted by visual noise in a manner that resembles human performance? To this end, we systematically compared the performance of humans and machines across a range of signal-to-noise ratios by presenting object images in varying levels of Gaussian pixel noise or Fourier phase-scrambled noise. Human performance proved far more robust to noise than state-of-the-art CNNs (AlexNet, VGG, and GoogLeNet). Moreover, CNNs were more severely impaired by Gaussian noise while humans had greater difficulty with spatially structured Fourier noise, implying that these CNNs process noisy objects in a qualitatively different manner. Next, we asked whether CNNs can acquire greater robustness by undergoing training with noisy object images. Noise-trained CNNs showed major improvements and successfully generalized to novel noisy images, demonstrating that noise invariance can be achieved by feedforward neural architectures through supervised learning. A layer-specific network analysis revealed that the middle and upper layers underwent the greatest change by acquiring representations that were more robust to visual noise following this training regime. Finally, we evaluated the patterns of error responses made by CNNs and humans by comparing their confusion matrices. After noisy image training, CNNs made patterns of errors that more strongly resembled those made by humans for objects in high levels of noise. Taken together, these results suggest that CNNs provide a promising model for gaining insight into the robustness of human object recognition performance. Meeting abstract presented at VSS 2018
Comparative genetic study of two sources of beta-tocopherol in sunflower (2005)

Two different sunflower lines with increased beta-tocopherol concentration in the seeds, LG-15 and T589, have been developed. The objective of the present research was to conduct a comparative genetic study of the increased beta-tocopherol concentration in both lines. Plants of LG-15 were reciprocally crossed with plants of T589 in 2003. The F1, F2, BC to LG-15 and BC to T589 seed generations were produced in the same environment in 2004 and analyzed for tocopherol profile. The results indicated a strong environmental effect on the increased levels of beta-tocopherol concentration in LG-15 and T589, which averaged 30.5% and 25.8%, respectively, in 2003 and 43.2% and 54.0%, respectively, in 2004. The comparison of individual plant means and standard errors of individual plant means for the F2 and BC generations with those in the non-segregating parental and F1 generations indicated no transgressive segregation for beta-tocopherol concentration in F2 or BC seeds. These results suggested that increased beta-tocopherol concentration in both lines is the result of genetic alterations at the same locus.
Supplementary Tables from Lisaftoclax (APG-2575) Is a Novel BCL-2 Inhibitor with Robust Antitumor Activity in Preclinical Models of Hematologic Malignancy (2023)

Supplementary Tables from Lisaftoclax (APG-2575) Is a Novel BCL-2 Inhibitor with Robust Antitumor Activity in Preclinical Models of Hematologic Malignancy
Actin Mutations in Dilated Cardiomyopathy, a Heritable Form of Heart Failure (1998)

To test the hypothesis that actin dysfunction leads to heart failure, patients with hereditary idiopathic dilated cardiomyopathy (IDC) were examined for mutations in the cardiac actin gene (ACTC). Missense mutations in ACTC that cosegregate with IDC were identified in two unrelated families. Both mutations affect universally conserved amino acids in domains of actin that attach to Z bands and intercalated discs. Coupled with previous data showing that dystrophin mutations also cause dilated cardiomyopathy, these results raise the possibility that defective transmission of force in cardiac myocytes is a mechanism underlying heart failure.
Diastereoselective microbial hydroxylation of milbemycin derivatives. (1989)

The diastereoselective hydroxylation of milbemycin A4 (1) at the 13β-position (→2) was performed by cultures of Streptomyces violascens (ATCC 31560). 14, 15-epoxymilbemycin A4 (3) was formed via a parallel reaction as a byproduct. The conversion and the product ratio, 2/3, were improved by the addition of organic solvents. The best results, i.e., 91% conversion with 92% 2 and 8% 3, were obtained by adding 2.5% DMSO to the culture broth. Oxime 7 was also hydroxylated at the 13β-position by S. violascens under similar conditions. In the case of milbemycin A3 (9) and D (10), the main products after treatment with S. violascens were the corresponding 14, 15-epoxides, 13 and 14, respectively.
An inversion approach to separating sources in marine simultaneous shooting acquisition – application to a Gulf of Mexico data set (2012)

ABSTRACT The simultaneous firing of marine sources can provide a significant uplift in terms of acquisition efficiency and data quality enhancement. However, the seismic interference resulting from one or more ‘other’ sources needs to be well understood and the appropriate processing strategies need to be developed for the method to fulfil its promise. In this paper, a modified inversion approach is presented for the effective separation of sources in marine simultaneous shooting acquisition. The method aims to distribute all energy in the simultaneous shot records by reconstructing the individual shot records at their respective locations. The method is applied to a wide azimuth data set acquired in the Gulf of Mexico where two sources out of four in total were fired simultaneously. Results demonstrate that the individual sources can be separated satisfactory, both at the prestack and post‐stack level.
Quantification of Banding, Streaking and Grain in Flat Field Images. (2000)

In this paper, we discuss techniques for the quantification of random and periodic noise present in flat field images. The types of noise studied are: (1) One-dimensional periodic noise (banding); (2) One-dimensional random noise (streaking) and, (3) Two-dimensional random noise (grain). A spectral separation technique was developed which allows the estimation of the individual noise power spectrum (NPS) of each artifact, based on the original flat field data. We proceed by assuming that the components are additive. First, the one-dimensional periodic components are identified, quantified, and removed from the flat field scan. Then the residual one-dimensional and two-dimensional random noise components are estimated via analysis of the twodimensional NPS. This technique is useful in the characterization of digital cameras, printers, and scanners.
Interactive Sound Rendering on Mobile Devices using Ray-Parameterized\n Reverberation Filters (2018)

We present a new sound rendering pipeline that is able to generate plausible\nsound propagation effects for interactive dynamic scenes. Our approach combines\nray-tracing-based sound propagation with reverberation filters using robust\nautomatic reverb parameter estimation that is driven by impulse responses\ncomputed at a low sampling rate.We propose a unified spherical harmonic\nrepresentation of directional sound in both the propagation and auralization\nmodules and use this formulation to perform a constant number of convolution\noperations for any number of sound sources while rendering spatial audio. In\ncomparison to previous geometric acoustic methods, we achieve a speedup of over\nan order of magnitude while delivering similar audio to high-quality\nconvolution rendering algorithms. As a result, our approach is the first\ncapable of rendering plausible dynamic sound propagation effects on commodity\nsmartphones.\n
Pulmonary nodules: computer-aided detection in digital chest images. (1990)

Currently, radiologists fail to detect pulmonary nodules in up to 30% of cases with actually positive findings. Diagnoses may be missed due to camouflaging effects of anatomic background, subjective and varying decision criteria, or distractions in clinical situations. We developed a computerized method to detect locations of lung nodules in digital chest images. The method is based on a difference-image approach and feature-extraction techniques, including growth, slope, and profile tests. Computer results were used to alert 12 radiologists to possible nodule locations in 60 clinical cases. Preliminary results suggest that computer aid can improve the detection performance of radiologists.
Dynamic resource control for high-speed downlink packet access wireless channel (2004)

It is a challenging task to provide Quality of Service (QoS) control for a shared high-speed downlink packet access (HSDPA) wireless channel. In this paper, we first propose a new dynamic resource control framework integrated with adaptive modulation and coding (AMC) and hybrid automatic repeat request (H-ARQ) to support class-based multimedia applications over HSDPA wireless channels. Then we present a new scheduling algorithm, Delay-sensitive Dynamic Fair Queueing (DSDFQ), to meet delay requirements of multimedia applications as well as maintain high network efficiency. The proposed approach can easily adapt to load fluctuations of different traffic classes and varying wireless channel conditions caused by user mobility, fading and shadowing. Performance evaluation shows the advantage of our proposed approach.
Genetic Algorithm Reveals Energy-Efficient Waveforms for Neural Stimulation (2009)

Energy consumption is an important consideration for battery-powered implantable stimulators. We used a genetic algorithm (GA) that mimics biological evolution to determine the energy-optimal waveform shape for neural stimulation. The GA was coupled to NEURON using a model of extracellular stimulation of a mammalian myelinated axon. Stimulation waveforms represented the organisms of a population, and each waveform's shape was encoded into genes. The fitness of each waveform was based on its energy efficiency and ability to elicit an action potential. After each generation of the GA, waveforms mated to produce offspring waveforms, and a new population was formed consisting of the offspring and the fittest waveforms of the previous generation. Over the course of the GA, waveforms became increasingly energy-efficient and converged upon a highly energy-efficient shape. The resulting waveforms resembled truncated normal curves or sinusoids and were 3-74% more energy-efficient than several waveform shapes commonly used in neural stimulation. If implemented in implantable neural stimulators, the GA optimized waveforms could prolong battery life, thereby reducing the costs and risks of battery-replacement surgery.
Stretchable Conductive Composites Based on Metal Wools for Use as Electrical Vias in Soft Devices (2015)

Soft devices can be bent, stretched, and compressed reversibly, but conventional wires are rigid. This work describes stretchable composites that are easily fabricated with simple tools and commodity materials, and that can provide a strategy for electrical wiring that meets certain needs of soft devices. These composites are made by combining metal wool and elastomeric polymers. Embedding fine (average fiber width ≈25 μm) steel wool (or other metal wools) in a silicone polymer creates an electrically conductive path through the nonconductive elastomer. This composite is flexible, stretchable, compressible, inexpensive, and simple to incorporate into the bodies of soft devices. It is also electrically anisotropic, and shows maximum conductivity along the majority axis of the fibers, but maximum extension perpendicular to this axis. The utility of this composite for creating an electrically conductive path through an elastomer was demonstrated in several devices, including: a soft, solderless breadboard, a soft touch sensor, and a soft strain gauge.
Group VIII metal complexes as catalysts for halogen exchange between alkyl halides (1975)

J. E. Lyons, J. Chem. Soc., Chem. Commun., 1975, 418 DOI: 10.1039/C39750000418
Low loss optical interlayer coupling using reflector-enhanced grating couplers (2013)

We demonstrate improved optical interlayer coupling based on grating couplers with backside metal reflectors. Losses of 1.5dB and 2.0dB are achieved with 145nm and 220nm grating etch depth on a 130nm SOI CMOS platform, respectively.
Sizing in Virtualized Data Centers (2011)

In this paper, we undertake the problem of server consolidation in virtualized data centers from the perspective of approximation algorithms. We formulate server consolidation as a stochastic bin packing problem, where the server capacity and an allowed server overflow probability p are given, and the objective is to assign VMs to as few physical servers as possible, and the probability that the aggregated load of a physical server exceeds the server capacity is at most p. We propose a new VM sizing approach called effective sizing, which simplifies the stochastic optimization problem by associat­ ing a VM's dynamic load with a fixed demand. Effective sizing decides a VM's resource demand through statistical multiplexing principles, which consider various factors impacting the aggre­ gated resource demand of a host where the VM may be placed. Based on effective sizing, we design a suite of polynomial time VM placement algorithms for both VM migration cost-oblivious and migration cost-aware scenarios. Through analysis, we show that our algorithm is 0(1)­ approximation for the stochastic bin packing problem when the VM loads can be modeled as all Poisson or all normal distributions. Through evaluations driven by a real data center load trace, we show that our consolidation solution can achieve an order of reduction on physical server requirement compared to that before consolidation; the consolidation result is only 24% more than the optimal solution. With efl'ective sizing, our server consolidation solution achieves 10% to 23% more energy savings than state-of-the-art approaches.