gebhart/patrepeval huggingface dataset:
Engineering Synthetic Lipopeptide Antigen for Specific Detection of Mycobacterium avium subsp. paratuberculosis Infection (2021)

Unlike other MAC members, <i>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> (MAP) does not produce glycopeptidolipids (GPL) on the surface of the cell wall but a lipopentapeptide called L5P (also termed Lipopeptide-I or Para-LP-01) characterized in C-type (bovine) strains. This lipopeptide antigen contains a pentapeptide core, D-Phenylalanine-N-methyl-L-Valine-L-Isoleucine-L-Phenylalanine-L-Alanine, in which the N-terminal D-Phenylalanine is amido-linked with a fatty acid (C18-C20). The molecular and genetic characterization of this antigen demonstrated that L5P is unique to MAP. Knowledge of the structure of L5P enabled synthetic production of this lipopeptide in large quantities for immunological evaluation. Various studies described the immune response directed against L5P and confirmed its capability for detection of MAP infection. However, the hydrophobic nature of lipopeptide antigens make their handling and use in organic solvents unsuitable for industrial processes. The objectives of this study were to produce, by chemical synthesis, a water-soluble variant of L5P and to evaluate these compounds for the serological diagnosis of MAP using well-defined serum banks. The native L5P antigen and its hydrosoluble analog were synthesized on solid phase. The pure compounds were evaluated on collections of extensively characterized sera from infected and non-infected cattle. ROC analysis showed that L5P and also its water-soluble derivative are suitable for the development of a serological test for Johne's disease at a population level. However, these compounds used alone in ELISA have lower sensitivity (Se 82% for L5P and Se 62% for the water-soluble variant of L5P) compared to the Se 98% of a commercial test. Advantageously, these pure synthetic MAP specific antigens can be easily produced in non-limiting quantities at low cost and in standardized batches for robust studies. The fact that L5P has not been validated in the context of ovine paratuberculosis highlights the need to better characterize the antigens expressed from the different genetic lineages of MAP to discover new diagnostic antigens. In the context of infections due to other mycobacteria such as <i>M. bovis</i> or the more closely related species <i>M. avium</i> subsp. <i>hominissuis</i>, the L5P did not cross react and therefore may be a valuable antigen to solve ambiguous results in other tests.
Thrombin generation in whole blood (2008)

Tappenden et al (2007) reported the measurement of thrombin generation (TG) in native blood, using a method that was not essentially different from the one that we developed for the use in platelet poor and in platelet rich plasma (Hemker et al, 2002). Even though an essentially negative result, we feel that it is a necessary contribution to this developing field to report that, for several years, we have tried to measure TG in whole blood using this method with a large number of different modifications and that we essentially failed to obtain reproducible results. When copying the experimental setup of Tappenden et al (2007) our results were never better than those shown in Fig 1. Fluorescent traces obtained from whole blood. (A) Lower curves: fluorescence trace (±SD, n = 5) from 200 nmol/l (final concentration) of α2macroglobulin-thrombin in whole blood (left abscissa). Upper curves, the same in plasma (right abscissa). (B) Thick line: calibrator trace as in (A): traces from seven identical thrombin generation experiments in whole blood from the same donor. It is seen that: The fluorescent signals obtained were about 30× weaker than those from plasma and consequently showed a much higher signal to noise ratio, in fact so much that no useful first derivatives from the signal could be obtained. The curves obtained from whole blood were erratic and often showed higher fluorescence than the calibrator, rendering it impossible to convert fluorescence data into thrombin concentrations. In our experience the latter phenomenon is explained by clot formation and clot retraction together with shaking, which means that fluorescence is measured in small moving pools of serum, whereas the blood remains fluid in the calibrator well. We conclude that the method described by Tappenden et al (2007) cannot be repeated in our hands and surmise that one or more details of the experimental procedure are missing from the description.
Tunnel Field-Effect Transistors: Prospects and Challenges (2015)

The tunnel field-effect transistor (TFET) is considered a future transistor option due to its steep-slope prospects and the resulting advantages in operating at low supply voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> ). In this paper, using atomistic quantum models that are in agreement with experimental TFET devices, we are reviewing TFETs prospects at L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> = 13 nm node together with the main challenges and benefits of its implementation. Significant power savings at iso-performance to CMOS are shown for GaSb/InAs TFET, but only for performance targets which use lower than conventional V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> . Also, P-TFET current-drive is between 1× to 0.5× of N-TFET, depending on choice of I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> and V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</sub> . There are many challenges to realizing TFETs in products, such as the requirement of high quality III-V materials and oxides with very thin body dimensions, and the TFET's layout density and reliability issues due to its source/drain asymmetry. Yet, extremely parallelizable products, such as graphics cores, show the prospect of longer battery life at a cost of some chip area.
A radix-4 scalable design (2005)

Modular arithmetic operations are very important in cryptography. Modular multiplication is the most common arithmetic operation used in many cryptographic algorithms such as the Elliptic Curve Cryptography and the Diffie-Helman key exchange. The Montgomery Modular Multiplication algorithm (MM) has permitted cryptographic algorithms to speed up considerably. Multiplication is implemented by a series of multiprecision partial-product addition. The proposed multiple-word Radix-4 Montgomery Multiplication algorithm (R4MM) is extension of the Multiple-Word High-Radix (R2/sup k/) Montgomery Multiplication algorithm (MWR2/sup k/MM). There are two types of recoding applied in the R4MM. The architecture of the modular multiplier that implements the R4MM consists of three main blocks: the datapath (or kernel), the IO & memory and the control block. The computation in the R4MM algorithm takes place in the kernel. We show that a more elaborate design using two types of digit recoding makes the radix-4 design the best solution for the implementation of this scalable multiplier.
XTABLES: Bridging relational technology and XML (2002)

XML (Extensible Markup Language) has emerged as the standard data-exchange format for Internet-based business applications. These applications introduce a new set of data management requirements involving XML. However, for the foreseeable future, a significant amount of business data will continue to be stored in relational database systems. Thus, a bridge is needed to satisfy the requirements of these new XML-based applications while still using relational database technology. This paper describes the design and implementation of the XTABLES middleware system, which we believe achieves this goal. In particular, XTABLES provides a general framework to create XML views of relational data, query XML views, and store and query XML documents using a relational database system. Some of the novel features of the XTABLES architecture are that it 1) provides users with a single XML query language for creating and querying XML views of relational data, 2) executes queries efficiently by pushing most computation down to the relational database engine, c) allows users to query seamlessly over relational data and meta-data, and 4) allows users to write queries that span XML documents and XML views of relational data.
Novel Lipoprotein Subfraction and Size Measurements in Prediction of Mortality in Maintenance Hemodialysis Patients (2011)

Whereas conventional lipid profile cannot predict mortality in MHD patients, larger novel LDL particle diameter or higher large LDL particle concentrations appear predictive of greater survival, whereas higher very small LDL particle concentration is associated with higher death risk. Examining lipoprotein subfraction modulation in chronic diseases is indicated.
Detection and Characterization of Laryngeal Reflex Pathology in Mouse Models of Human Diseases (2014)

Objectives: The laryngeal adductor reflex (LAR) is readily triggered in healthy, awake humans by delivering a puff of air to the laryngeal entrance via an endoscope passed through the nose into the throat. LAR impairment has been identified (but not well‐characterized) in people with amyotrophic lateral sclerosis (ALS) and is highly correlated with dysphagia. We propose to develop a nonsurgical approach for longitudinal investigation of the LAR in mice. Methods: We designed and constructed an elaborate prototype air pulse delivery system for use with mice. The system interfaces with a miniature endoscope that is small enough for oral insertion into the laryngeal entrance and contains a working channel through which calibrated puffs of air can be delivered, synchronized with rate and phase of the respiratory cycle. Results: We have successfully used this prototype system to evoke and video record (30 fps) the LAR in 10 healthy, C57BL/6 mice under light anesthesia, thus demonstrating proof of concept. Objective quantification of several LAR parameters is currently underway, including total LAR duration, duration of adduction versus abduction phases, and velocity of dorsal angle adduction and abduction. Conclusions: This study provides novel evidence that mice have an LAR similar to humans and that several parameters of the LAR can be objectively quantified in this small animal model. Additional research will include laryngeal brainstem response (LBR) recordings evoked by air pulse triggering of the LAR to elucidate pathological neural substrates in mouse models of ALS and other human diseases that cause dysphagia.
Memory efficient sanitization of a deduplicated storage system (2013)

Sanitization is the process of securely erasing sensitive data from a storage system, effectively restoring the system to a state as if the sensitive data had never been stored. Depending on the threat model, sanitization could require erasing all unreferenced blocks. This is particularly challenging in deduplicated storage systems because each piece of data on the physical media could be referred to by multiple namespace objects. For large storage systems, where available memory is a small fraction of storage capacity, standard techniques for tracking data references will not fit in memory, and we discuss multiple sanitization techniques that trade-off I/O and memory requirements. We have three key contributions. First, we provide an understanding of the threat model and what is required to sanitize a deduplicated storage system as compared to a device. Second, we have designed a memory efficient algorithm using perfect hashing that only requires from 2.54 to 2.87 bits per reference (98% savings) while minimizing the amount of I/O. Third, we present a complete sanitization design for EMC Data Domain.
A comprehensive fatigue failure criterion based on thermodynamic approach (2011)

In this work, stress curve and energy-based (linear elastic strain energy, and hysteresis loop energy) fatigue failure criteria are compared with a new, entropy-based model for the prediction of fatigue life in a woven glass/epoxy laminate. Extensive experimental results are reported that involve load-controlled tension–tension fatigue test with two different stress ratios as well as constant- and variable-loading of a woven glass/epoxy laminate with various load angles. The plot of fracture fatigue entropy vs. fatigue life is compared with the energy plotted vs. number of cycle and stress plotted vs. number of cycle (i.e., the so-called S–N curve) plots.
Automatic noninvasive measurement of systolic blood pressure using photoplethysmography (2009)

The photoplethysmographic-based technique for automatic measurement of systolic blood pressure, and the algorithm which was presented in this study, seems to be accurate.
Therapy of Acute Myeloid Leukemia in Adults (2003)

Treatment of acute myeloid leukemia (AML) begins with establishing a precise diagnosis. The term AML collectively refers to a mixture of distinct diseases that differ with regard to their pathogenetic evolution, genetic abnormalities, clinical features, response to therapy, and prognosis. Cytogenetic and molecular analyses have been instrumental in identifying disease entities among the mixed bag of AML subtypes, which are currently cataloged as suboptimally defined categories with widely different prognoses. These classifications are mainly based on cytogenetic knowledge. They provide leads in clinical decision making, e.g., with regard to treatment choice. The disclosure of genetic abnormalities may also offer potential targets for treatment intervention.
Development of angle-resolved spectroscopy system of electrons emitted from a surface with negative electron affinity state (2018)

We developed an angle-resolved photoemission spectroscopy system for the analysis of conduction-band electrons. By forming a negative electron affinity surface on a semiconductor surface, electrons in conduction bands are emitted into a vacuum and measured by using an analyzer. This method enables us to determine the energy and momentum of the conduction electrons. Furthermore, it can be used to determine unoccupied conduction band structures. The main challenges of this method are that the energies of the emitted electrons are extremely low and the trajectories of the electrons change due to various influences. We overcame these problems by placing the shielding mesh close to the sample and parallel to the sample surface. The entire chambers, including the shielding mesh, were grounded, and a negative bias voltage was applied only to the sample. This configuration realizes the acceleration of electrons while preserving the momentum component parallel to the sample surface. Another problem is the establishment of a method for converting a detected angle into the corresponding wavevector. We focused on the emission angle of electrons emitted from a sample and their minimum energy and then established an analytical method for converting detected angles into corresponding wavevectors on the basis of the minimum energy.
The recent developments of the fiber-optic bolometer (2021)

We summarized the developments of the fiber-optic bolometers including the bolometer fabrication, demodulation and performance with and without radiation. The bolometer showed a noise equivalent power density of 0.27 W/m 2 which was comparable with the resistive bolometer.
Human umbilical cord blood cells directly suppress ischemic oligodendrocyte cell death (2008)

Previous reports have shown that human umbilical cord blood cells (HUCBCs) administered intravenously 48 hr following middle cerebral artery occlusion reduce infarct area and behavioral deficits of rodents. This cellular therapy is potently neuroprotective and antiinflammatory. This study investigates the effect of HUCBC treatment on white matter injury and oligodendrocyte survival in a rat model of ischemia. Intravenous infusion of 10(6) HUCBCs 48 hr poststroke reduced the amount of white matter damage in vivo as seen by quantification of myelin basic protein staining in tissue sections. To determine whether HUCBC treatment was protective via direct effects on oligodendrocytes, cultured oligodendrocytes were studied in an in vitro model of oxygen glucose deprivation. Active caspase 3 immunohistochemistry and the lactate dehydrogenase assay for cytotoxicity were used to determine that HUCBCs provide protection to oligodendrocytes in vitro. Based on these results, it is likely that HUCBC administration directly protects oligodendrocytes and white matter. This effect is likely to contribute to the increased behavioral recovery observed with HUCBC therapy.
Copper-catalyzed [18F]fluorination of unsymmetrical diaryliodonium salts (2014)

156 Objectives In an initial report we described the rapid and efficient fluorination of unsymmetrical diaryliodonium salts under mild conditions in the presence of a copper salt (Sanford et al. Org. Lett. 2013, 15, 5134). A key facet of this initial work was the ability of the copper catalyzed process to demonstrate exquisite selectivity for the more sterically accessible aryl group. The reaction was also readily amenable to fluorination of electron-rich aryl groups. The aim of this project is to translate the copper-catalyzed fluorination of diaryliodonium salts to radiofluorination reactions using nucleophilic [18F]fluoride. Methods A wide range of reaction conditions have been evaluated to optimize the reaction for use with K[18F], including choice of copper catalyst and reaction temperature, time, solvent and stoichiometry. Additional experiments have been undertaken to determine substrate scope, the effect of different catalysts on the reaction outcome, and to demonstrate proof-of-concept through fluorination of clinically relevant targets. Results A range of fluorine-18 labeled arenes have been synthesized from the corresponding diaryliodonium salts. The methodology was tolerant of electron rich arenes, demonstrated through the reproducible synthesis of [18F]4-fluoroanisole in >70% radiochemical yield. Conclusions The copper-catalyzed fluorination of diaryliodonium salts has been adapted for radiofluorination reactions using nucleophilic [18F]fluoride. Radiochemical yields are excellent, and the methodology enables ready fluorination of electron rich arenes. Research Support Financial support of this work by NIBIB (T32EB005172-02) and NIGMS (1RO1 GM073836) is gratefully acknowledged.
Joint myocardial T1 and T2 mapping (2015)

Figure 1 a) The sequence diagram for the proposed technique. A saturation pulse is applied in every R-R interval to eliminate the magnetization history. The longitudinal magnetization then recovers for T sat . Subsequently a T 2 -prep with echo length TE prep is applied to generate the additional T 2 weighting, after which a single shot SSFP image is acquired. b) The mapping sequence acquires the first image with no magnetization preparation (corresponding to T sat = and TE prep = 0), followed by 12 images (3 are shown) acquired with different T sat and TE prep values. The major characteristics of the longitudinal magnetization signal curve are depicted under the pulse sequence diagram.
Neurotrophic factors in the therapy of peripheral neuropathy. (1995)

Neurotrophic factors are proteins that promote the survival and differentiation of specific populations of neurones. With the successful cloning and large-scale production of many different neurotrophic factors, it has become practical to consider their application in the treatment of neurological disease. Several groups of neurotrophic factors hold particular promise for the therapy of peripheral nervous system disease in the near future. These include the neurotrophin gene family, cytokines such as CNTF and the IGF family. Evidence is accumulating that an abnormal availability of some of these factors may contribute towards the pathophysiology of some types of neuropathy, most notably diabetic neuropathy. Pre-clinical studies in animal models have demonstrated the likely efficacy of factors such as NGF for small-fibre sensory neuropathy, BDNF, CNTF and IGF-I for motor neurone disease, and NT-3 for large-fibre neuropathy. Clinical trials of several growth factors are currently underway for the treatment of peripheral nerve disease, and other clinical trials are currently being planned.
Ultrahigh-resolution adaptive optics - optical coherence tomography: toward isotropic 3 μm resolution for in vivo retinal imaging (2007)

Ultrahigh axial resolution in adaptive optics - optical coherence tomography (AO-OCT) is fundamentally limited by the intrinsic chromatic aberrations of the human eye. Variation in refractive index of the ocular media with wavelength causes the spectral content of broadband light sources to focus at different depths in the retina for light entering the eye and at the imaging detector for light exiting. This effect has not been previously reported for ultrahigh-resolution OCT (without AO) likely because the effect is masked by the relatively long depth of focus dictated by the small pupils used in these systems. With AO, the pupil size is much larger and depth of focus substantially narrower. As such the chromatic aberrations of the eye can counteract the lateral resolution benefit of AO when used with broadband light sources. To more fully tap the potential of AO-OCT, compensation of the eye's chromatic and monochromatic aberrations must occur concurrently. One solution is to insert an achromatizing lens in front of the eye whose chromatic aberrations are equal but opposite in sign to that of the eye. In this paper we evaluate the efficacy of a novel design that uses a custom achromatizing lens placed near the fiber collimating optic. AO-OCT images are acquired on several subjects with and without the achromatizing lens and in combination with two light sources of different spectral width. The combination of the achromatizing lens and broadband light source yielded the sharpest images of the retina and the smallest speckle.
Visual Benefit of Correcting Higher Order Aberrations of the Eye (2000)

There is currently considerable debate concerning the visual impact of correcting the higher order aberrations of the eye. We describe new measurements of a large population of human eyes and compute the visual benefit of correcting higher order aberrations. We also describe the increase in contrast sensitivity when higher order aberrations are corrected with an adaptive optics system. All these results suggest that many, though not all, observers with normal vision would receive worthwhile improvements in spatial vision from customized vision correction, at least over a range of viewing distances and particularly when the pupils are large. Keratoconic patients or patients suffering from spherical aberration as a result of laser refractive surgery as it is presently performed would especially benefit. These results encourage the development of methods to correct higher order aberrations.
Lossless and Low-Power Image Compressor for Wireless Capsule Endoscopy (2011)

We present a lossless and low-complexity image compression algorithm for endoscopic images. The algorithm consists of a static prediction scheme and a combination of golomb-rice and unary encoding. It does not require any buffer memory and is suitable to work with any commercial low-power image sensors that output image pixels in raster-scan fashion. The proposed lossless algorithm has compression ratio of approximately 73% for endoscopic images. Compared to the existing lossless compression standard such as JPEG-LS, the proposed scheme has better compression ratio, lower computational complexity, and lesser memory requirement. The algorithm is implemented in a 0.18 μm CMOS technology and consumes 0.16 mm × 0.16 mm silicon area and 18 μW of power when working at 2 frames per second.