gebhart/patrepeval huggingface dataset:
RS-Net: Regression-Segmentation 3D CNN for Synthesis of Full Resolution Missing Brain MRI in the Presence of Tumours (2018)

Accurate synthesis of a full 3D MR image containing tumours from available MRI (e.g. to replace an image that is currently unavailable or corrupted) would provide a clinician as well as downstream inference methods with important complementary information for disease analysis. In this paper, we present an end-to-end 3D convolution neural network that takes a set of acquired MR image sequences (e.g. T1, T2, T1ce) as input and concurrently performs (1) regression of the missing full resolution 3D MRI (e.g. FLAIR) and (2) segmentation of the tumour into subtypes (e.g. enhancement, core). The hypothesis is that this would focus the network to perform accurate synthesis in the area of the tumour. Experiments on the BraTS 2015 and 2017 datasets [1] show that: (1) the proposed method gives better performance than state-of-the-art methods in terms of established global evaluation metrics (e.g. PSNR), (2) replacing real MR volumes with the synthesized MRI does not lead to significant degradation in tumour and sub-structure segmentation accuracy. The system further provides uncertainty estimates based on Monte Carlo (MC) dropout [11] for the synthesized volume at each voxel, permitting quantification of the system's confidence in the output at each location.
Low complexity codes for writing a write-once memory twice (2010)

A write-once memory (wom) is a storage medium formed by a number of “write-once” binary cells, where each cell initially is in a `0' state and can be changed to a `1' state irreversibly. Examples of write-once memories include SLC flash memories and optical disks. This paper presents some low complexity codes for writing such write-once memories twice.
Indoor Positioning Based on Bluetooth Low-Energy Beacons Adopting Graph Optimization (2018)

Bluetooth Low-Energy (BLE) beacons-based indoor positioning is a promising method for indoor positioning, especially in applications of position-based services (PbS). It has low deployment cost and it is suitable for a wide range of mobile devices. Existing BLE beacon-based positioning methods can be categorized as range-based methods and fingerprinting-based methods. For range-based methods, the positions of the beacons should be known before positioning. For fingerprinting-based methods, a pre-requisite is the reference fingerprinting map (RFM). Many existing methods focus on how to perform the positioning assuming the beacon positions or RFM are known. However, in practical applications, determining the beacon positions or RFM in the indoor environment is normally a difficult task. This paper proposed an efficient and graph optimization-based way for estimating the beacon positions and the RFM, which combines the range-based method and the fingerprinting-based method. The method exists without need for any dedicated surveying instruments. A user equipped with a BLE-enabled mobile device walks in the region collecting inertial readings and BLE received signal strength indication (RSSI) readings. The inertial measurements are processed through the pedestrian dead reckoning (PDR) method to generate the constraints at adjacent poses. In addition, the BLE fingerprints are adopted to generate constraints between poses (with similar fingerprints) and the RSSIs are adopted to generate distance constraints between the poses and the beacon positions (according to a pre-defined path-loss model). The constraints are then adopted to form a cost function with a least square structure. By minimizing the cost function, the optimal user poses at different times and the beacon positions are estimated. In addition, the RFM can be generated through the pose estimations. Experiments are carried out, which validates that the proposed method for estimating the pre-requisites (including beacon positions and the RFM). These estimated pre-requisites are of sufficient quality for both range-based and fingerprinting-based positioning.
Combinatorial Screening and Rational Optimization for Hybridization to Folded Hepatitis C Virus RNA of Oligonucleotides with Biological Antisense Activity (1997)

We describe our initial application of a biochemical strategy, comprising combinatorial screening and rational optimization, which directly identifies oligonucleotides with maximum affinity (per unit length), specificity, and rates of hybridization to structurally preferred sites on folded RNA, to the problem of design of antisense oligonucleotides active against the hepatitis C virus (HCV). A fully randomized sequence DNA oligonucleotide (10-mer) library was equilibrated with each of two folded RNA fragments (200 and 370 nucleotides (nt)), together spanning the 5' 440 nt of an HCV transcript (by overlapping 130 nt), which were varied over a range of concentrations. The equilibrations were performed in solution under conditions determined to preserve RNA structure and to limit all RNA-DNA library oligonucleotide interactions to 1:1 stoichiometry. Subsequent Escherichia coli RNase H (endoribonuclease H: EC 3.1.26.4) cleavage analysis identified two preferred sites of highest affinity heteroduplex hybridization. The lengths and sequences of different substitute chemistry oligonucleotides complementary to these sites were rationally optimized using an iterative and quantitative analysis of binding affinity and specificity. Thus, DNA oligonucleotides that hybridized with the same affinity to the preferred sites in the folded RNA fragments found by screening as to short (< or = 25 nt) RNA complements were identified but were found to vary in length (10-18 nt) from site to site. Phosphorothioate (P=S) and 2'-fluoro (2'-F) uniformly substituted oligonucleotides also were found, which hybridized optimally to these sites, supporting the design of short (10-15-nt) and maximally specific oligonucleotides that are more nuclease-resistant (via P=S) and have higher affinity (via 2'-F) than DNA. Finally, the affinities of DNA and uniform 2'-F-, P=S-substituted 10-20-mer oligonucleotide complements for the best hybridization site, from HCV nt 355 to nt 364-374, closely corresponded to antisense mechanism inhibition activities in an in vitro translation assay and in a human cell-based HCV core protein expression assay, respectively. These results validate our strategy for the selection of hybridization-optimized and biologically active antisense oligonucleotides targeting HCV RNA and support the potential for utility in further applications.
Hydrolysis of Ionized Deoxycholic Acid in the Aqueous Phase and Rate Analysis for Transfer of Neutralized Deoxycholic Acid into the Benzene Phase across the Benzene/Water Interface (2008)

Sodium deoxycholate in water dissociates into sodium cation and deoxycholate anion in the aqueous phase, and then, the latter anions partially hydrolyze to form deionized deoxycholic acids. The acids move into the benzene phase, when liquid benzene is placed upon the aqueous phase, and finally the partition equilibrium is reached. The above processes were traced by pH change in the aqueous phase by a pH meter or the change in [OH-] with time, from which the rate for transfer of neutralized acid to the organic phase was analyzed. From the trace, the rate constants for hydrolysis of acid anion ( kf), neutralization of acid ( kb), transfer of neutralized acid from the aqueous phase to the organic phase ( kin*), and its back-transfer from the organic phase to the aqueous phase ( kut*) were evaluated; kf = 2.18 x 10 (-4) mol (-1) dm (3) min (-1), kb = 1.24 x 10 (5) mol (-1) dm (3) min (-1), kin* = 4.06 x 10 (-1) min (-1) cm (-2), and kout*) = 8.00 x 10 (-2) min (-1) cm (-2). The above values are supported by the partition constant of deoxycholic acid between the benzene phase and the aqueous phase.
In situ demonstration of intraepithelial lymphocyte adhesion to villus microvessels of the small intestine (2001)

The recirculation of lymphocytes through the intestinal mucosa is important for specific immune defense, but the origin and differentiation of intraepithelial lymphocytes (IEL) are not fully understood. The present study therefore used intravital microscopy to investigate the migration of IEL to the villus mucosa and Peyer's patches of the small intestine. IEL were separated from inverted murine small intestine and mesenteric lymph node (MLN) T cells were also isolated. The adhesion of fluorescence-labeled lymphocytes to postcapillary venules (PCV) of Peyer's patches and arcade microvessels of small intestinal villi was observed after injection. In some experiments, the effect of antibodies against adhesion molecules on cell kinetics were investigated. IEL time-dependently accumulated in villus microvessels of the small intestine, whereas few MLN cells did. Few IEL adhered to the PCV of Peyer's patches. IEL were shown to express alpha(E)beta(7)-integrin but not L-selectin. The accumulation of IEL in villus archade was significantly inhibited by antibody against beta(7)-integrin or mucosal addressin cell adhesion molecules (MAdCAM)-1, but not by alpha(E)-integrin. The combined blocking of beta(7)-integrin and MAdCAM-1 further attenuated the sticking of IEL in this area, although it did not entirely block the IEL adherence. The adherence of CD4(+) or TCRalphabeta IEL to villus microvessels was significantly greater than that of CD4(-) or TCRgammadelta IEL. It was demonstrated in situ for the first time that IEL adhered selectively to the villus microvessels of the small intestine partly via beta(7) and MAdCAM-1.
Impaired suppression of gluconeogenesis induced by overexpression of a noninsulin-responsive phosphoenolpyruvate carboxykinase gene (1993)

Despite detailed knowledge of the regulation of individual steps in the gluconeogenic pathway, the relative importance of each step to the overall control of gluconeogenesis by insulin is not known. The aim of this study was to determine the role of phosphoenolpyruvate carboxykinase (PEPCK) in the regulation of gluconeogenesis by insulin. Clones of the rat hepatoma cell line H4IIE-C3 were produced, overexpressing a PEPCK gene, driven by a promoter not responsive to insulin. In these cells basal gluconeogenesis from 2-[14C]pyruvate was increased 2.1-fold compared to controls (4.63 +/- 0.49 nmol/10(5) cells vs. 2.21 +/- 0.24 nmol/10(5) cells after 3 h, P < 0.05, n = 5). Increased gluconeogenesis was associated with an increase in basal PEPCK mRNA levels (1.9-fold) and enzyme activity (2.8-fold). Insulin (10(-7) M) suppressed basal gluconeogenesis, PEPCK mRNA levels, and enzyme activity in control cells, but no detectable decrease was observed in PEPCK-transfected cells. These experiments provide direct evidence in intact cells that PEPCK is the rate-limiting enzyme in gluconeogenesis from pyruvate and show that insulin's action to inhibit gluconeogenesis is predominantly on the inhibition of PEPCK transcription.
Probability-based collision alerting logic for closely-spaced parallel approach (1997)

A prototype airborne collision alerting logic was developed for aircraft on approach to closely-spaced parallel runways. A novel design methodology was used based on collision probabilities instead of traditional spatial or temporal alerting criteria. With this technique, an alert is issued when the probability of a collision exceeds an acceptable threshold value. The logic was based on a hazard level corresponding to the current Precision Runway Monitor System of one accident in every one thousand worst-case blunders. Probability contours were constructed through Monte Carlo simulation over a range of aircraft position, speed, heading, and turn rate conditions. These contours were stored in look-up tables that were accessed in real time for evaluation during numerical simulation of approaches. Three runway spacings were investigated: 3,400, 2,500, and 1,700 ft. The results show that the unnecessary alert rate at 1,700 ft runway spacing was double that at 3,400 ft runway spacing. Additionally, the logic induced collisions in two low-closure-rate situations, suggesting that the worst case blunder may not be a drastic heading change. (Author)
High Temperature Sodium - Zinc Chloride Batteries With Sodium Beta - Alumina Solid Electrolyte (2007)

High Temperature energy storage systems are widely explored due to the increasing need of storage systems in the electric utility industry. With the use of such systems, load leveling can be achieved. The energy storage system of interest here is based on Sodium - β alumina solid electrolyte (BASE) with liquid sodium as anode and molten ZnCl2 as cathode. BASE is an excellent sodium ion conductor with a very high conductivity at 300oC. The discharge reaction: 2Na + ZnCl2 à 2NaCl + Zn OCV (350oC) = 2.4V Unlike sodium sulfur batteries, the volumetric power density of Na - ZnCl2 battery is higher due to the planar cell construction. If a cell fails, it develops a low resistance so that the other cells continue to deliver power in a normal manner. This paper will compare the Na - ZnCl2 batteries: planar design, construction and testing, with other high temperature storage batteries.
Image Compression Suitable for High Dynamic Range Image Rendering (2008)

In this paper, we propose a high dynamic range image coding method based on wavelet compression. In our method, we employ a pre-processing function to minimize errors between rendered (i.e. tone mapped) version of an original and compressed images. To enhance efficiency of the coding, we introduce the Hill function as the pre-processing. This function partially compresses the dynamic range of the HDR images based on the human visual system. The method implicitly assigns more bits to visually important luminance regions. We show the validity of our preprocessing by some experimental results.
Activation of the Hexosamine Pathway by Glucosamine<i>in Vivo</i>Induces Insulin Resistance in Multiple Insulin Sensitive Tissues<sup>1</sup> (1997)

We determined the effect of infusion of glucosamine (GlcN), which bypasses the rate limiting reaction in the hexosamine pathway, on insulin-stimulated rates of glucose uptake and glycogen synthesis in vivo in rat tissues varying with respect to their glutamine:fructose-6-phosphate amidotransferase (GFA) activity. Three groups of conscious fasted rats received 6-h infusions of either saline (BAS), insulin (18 mU/kg x min) and saline (INS), or insulin and GlcN (30 micromol/ kg x min, GLCN). [3-(3)H]glucose was infused to trace whole body glucose kinetics and glycogen synthesis, and rates of tissue glucose uptake were determined using a bolus injection of [1-(14)C]2-deoxyglucose at 315 min. GlcN decreased insulin-stimulated glucose uptake (315-360 min) by 49% (P < 0.001) at the level of the whole body, and by 31-53% (P < 0.05 or less) in the heart, epididymal fat, submandibular gland and in soleus, abdominis and gastrocnemius muscles. GlcN completely abolished glycogen synthesis in the liver. GlcN decreased insulin-stimulated glucose uptake similarly in the submandibular gland (1.3 +/- 0.2 vs. 2.0 +/- 0.3 nmol/mg protein x min, GLCN vs. INS, P < 0.05) and gastrocnemius muscle (1.4 +/- 0.3 vs. 3.1 +/- 0.5 nmol/mg protein x min), although the activity of the hexosamine pathway, as judged from basal GFA activity, was 10-fold higher in the submandibular gland (286 +/- 35 pmol/mg protein x min) than in gastrocnemius muscle (27 +/- 3 pmol/mg protein x min, P < 0.001). These data raise the possibility that overactivity of the hexosamine pathway may contribute to glucose toxicity not only in skeletal muscle but also in other insulin sensitive tissues. They also imply that the magnitude of insulin resistance induced between tissues is determined by factors other than GFA.
Software Fault Tolerance: A Tutorial (2000)

Because of our present inability to produce error-free software, software fault tolerance is and will continue to be an important consideration in software systems. The root cause of software design errors is the complexity of the systems. Compounding the problems in building correct software is the difficulty in assessing the correctness of software for highly complex systems. After a brief overview of the software development processes, we note how hard-to-detect design faults are likely to be introduced during development and how software faults tend to be state-dependent and activated by particular input sequences. Although component reliability is an important quality measure for system level analysis, software reliability is hard to characterize and the use of post-verification reliability estimates remains a controversial issue. For some applications software safety is more important than reliability, and fault tolerance techniques used in those applications are aimed at preventing catastrophes. Single version software fault tolerance techniques discussed include system structuring and closure, atomic actions, inline fault detection, exception handling, and others. Multiversion techniques are based on the assumption that software built differently should fail differently and thus, if one of the redundant versions fails, it is expected that at least one of the other versions will provide an acceptable output. Recovery blocks, N-version programming, and other multiversion techniques are reviewed.
Male Accessory Gland Factors Elicit Change From ‘Virgin’ to ‘Mated’ Behaviour in the Female Corn Earworm Moth <i>Helicoverpa Zea</i> (1993)

ABSTRACT After mating, the females of many species of moths become depleted of sex pheromone, calling behaviour is terminated, and they become transiently or permanently unreceptive to additional matings. In the corn earworm moth, Helicoverpa zea, we have found that the male accessory gland/duplex is required for evoking the post-mating depletion of sex pheromone but apparently not for the cessation of calling. The latter change requires the receipt of a spermatophore or a chemical messenger derived from non-accessory gland/duplex sources. Desalted extracts of combined accessory glands and duplexes caused a depletion of pheromone in injected females. Proteinaceous components in extracts purified by fractionation in cation-exchange cartridges and by reverse-phase high-performance liquid chromotography retain their pheromonostatic activity. In addition, this fractionated material shuts off calling behaviour and prevents mating in injected females, raising the possibility that redundant mechanisms exist in eliciting the different components of ‘mated’ behaviour.
ChemInform Abstract: One‐Pot Synthesis of Allylamine Derivatives by Iodine‐Catalyzed Three‐Component Reaction of N‐Heterocycles, Paraformaldehyde and Styrenes. (2013)

Abstract An efficient reaction to the title compounds with high stereo‐ and regioselectivities is described.
Evaluation of storage phosphor imaging for quantitative analysis of 2-D gels using the Quest II system. (1993)

The advent of storage phosphor technology has been of considerable benefit to the imaging of gel-separated radiolabeled proteins due to the rapid and quantitative nature of the data acquisition process. Previously, times over one month were required to obtain fluorographs of the same gel to yield data of sufficient dynamic range for quantitative analysis of high-resolution two-dimensional (2-D) gels. As we are in the process of building a human 2-D gel protein database, and therefore have a high throughput of 2-D gels both to image and quantitate using the Quest II software, we undertook an evaluation of a storage phosphor imager, including an evaluation of signal fade. The results of this evaluation demonstrate the feasibility of using such a system, and we describe the procedures that allow us to use this technique for quantitative analysis of many complex 2-D gel patterns. These procedures include a useful batch printing program that allows printing of many images in a non-interactive mode. Examples will be presented of how autoradiography, using storage phosphor plates and the Quest II system, have enabled us to begin building a human 2-D gel protein database including posttranslational modification information, without the previous time constraints associated with such a project.
Properties and application of a multichannel integrated circuit for low-artifact, patterned electrical stimulation of neural tissue (2012)

Using a high-density MEA stimulation/recording system, we effectively stimulated individual retinal ganglion cells (RGCs) and recorded the neuronal responses with minimal distortion, even on the stimulating electrodes. We independently stimulated a population of RGCs in rat retina, and using a complex spatio-temporal pattern of electrical stimulation pulses, we replicated visually evoked spiking activity of a subset of these cells with high fidelity. Significance. Compared with current state-of-the-art MEA systems, the Stimchip is able to stimulate neuronal cells with much more complex sequences of electrical pulses and with significantly reduced artifacts. This opens up new possibilities for studies of neuronal responses to electrical stimulation, both in the context of neuroscience research and in the development of neuroprosthetic devices.
Single-Needle Lateral Sacroplasty Technique (2018)

Sacral insufficiency fractures result in significant morbidity, and percutaneous sacroplasty has emerged as a promising technique for their treatment. We present a technical note regarding our method of treating these fractures using a "single-needle" lateral technique with a combination of conebeam CT and biplane fluoroscopy. We treated 10 patients, in whom the median Visual Analog Scale pain score decreased from 7.0 to 0 (<i>P</i> < .001). We concluded that single-needle sacroplasty is feasible and safe using this technique.
Mucin mRNA Expression in Normal and Vasomotor Inferior Turbinates (1997)

Mucins are the major glycoprotein component of respiratory tract secretions. Little is known about their expression in the upper respiratory tract. In order to define this expression, in situ hybridization was performed on 19 normal and 4 vasomotor rhinitis (VMR) inferior turbinates to identify mucin mRNA. MUC1, MUC2, MUC4, MUC5AC, MUC5B, and MUC7 were expressed in both the normal and VMR turbinates. MUC4 and MUC5AC were the most highly expressed mucins. MUC1, MUC2, MUC4, and MUC5AC were expressed mainly by the epithelial border, whereas MUC5B and MUC7 were expressed by the submucosal glands. MUC1 and MUC4 exhibited a diffuse expression by multiple cell types along the mucosal border, whereas MUC2 and MUC5AC expression appeared to be limited to a subpopulation of epithelial cells, most likely goblet cells. Although MUC1, MUC4, and MUC5AC showed sporadic submucosal glandular expression, MUC5B and MUC7 appeared to be the predominant submucosal gland mucins in the inferior turbinates. MUC3 and MUC6 expression, which have been found primarily in the gastric mucosa, were not seen in any of the inferior turbinate samples examined. The only difference seen between normal and VMR turbinates was a slight decrease in MUC1 expression in the VMR group. The variety of mucins expressed and the diversity of their expression patterns may have significance in terms of the rheologic and particle clearance properties of nasal secretions. Understanding the expression patterns in normal turbinates will serve as the foundation for further study of these mucins in disease states.