gebhart/patrepeval huggingface dataset:
Improved depth resolution in near-infrared diffuse reflectance spectroscopy using obliquely oriented fibers (2009)

We demonstrate a significant improvement of depth selectivity when using obliquely oriented fibers for near-infrared (NIR) diffuse reflectance spectroscopy. This is confirmed by diffuse reflectance measurements of a two-layer tissue-mimicking phantom across the spectral range from 1,000 to 1,940 nm. The experimental proof is supported by Monte Carlo simulations. The results reveal up to fourfold reduction in the mean optical penetration depth, twofold reduction in its variation, and a decrease in the number of scattering events when a single fiber is oriented at an angle of 60 deg. The effect of reducing the mean optical penetration depth is enhanced by orienting both fibers inwardly. Using outwardly oriented fibers enables more selective probing of deeper layers, while reducing the contribution from surface layers. We further demonstrate that the effect of an inward oblique arrangement can be approximated to a decrease in fiber-to-fiber separation in the case of a perpendicular fiber arrangement. This approximation is valid in the weak- or absorption-free regime. Our results assert the advantages of using obliquely oriented fibers when attempting to specifically address superficial tissue layers, for example, for skin cancer detection, or in noninvasive glucose monitoring. Such flexibility could be further advantageous in a range of minimally invasive applications, including catheter-based interventions.
Ductal Carcinoma in Situ of the Breast (2004)

Ductal carcinoma in situ of the breast (also called intraductal carcinoma), a clonal proliferation of malignant-appearing cells within the mammary duct lumens without evidence of invasion beyond the epithelial basement membrane, is the precursor lesion of invasive breast cancer. In the past 20 years, concomitant with the wide use of screening mammography, its detected incidence has risen dramatically. Data from large cohort studies and randomized trials have emerged to guide treatment. This review summarizes progress in the understanding, pathogenesis, and treatment of ductal carcinoma in situ.
The future of CMOS wireless transceivers (2002)

Building blocks alone do not account for the current interest in CMOS for RF applications. The more compelling reason is the opportunities CMOS affords for large-scale integration. Modern wireless transceivers will increasingly blend digital blocks into conventional analog front-ends for frequency synthesis, adaptivity, multi-mode operation, and sophisticated detection. This raises questions such as how well digital CMOS circuits can co-exist on the same substrate as the radio front-end, or whether there is sufficient on-chip isolation in a low-cost package to guarantee stable operation of a receiver with more than 100 dB of baseband gain, or how the power amplifier modulates the on-chip local oscillator. The future of CMOS transceivers may well depend on satisfactory answers to these questions. This paper presents design techniques to mitigate these problems in a single-chip 900 MHz spread-spectrum transceiver implemented in 1 /spl mu/m CMOS, and measurements of the transceiver to validate their effectiveness.
Bandwidth extension in CMOS with optimized on-chip inductors (2000)

We present a technique for enhancing the bandwidth of gigahertz broad-band circuitry by using optimized on-chip spiral inductors as shunt-peaking elements. The series resistance of the on-chip inductor is incorporated as part of the load resistance to permit a large inductance to be realized with minimum area and capacitance. Simple, accurate inductance expressions are used in a lumped circuit inductor model to allow the passive and active components in the circuit to be simultaneously optimized. A quick and efficient global optimization method, based on geometric programming, is discussed. The bandwidth extension technique is applied in the implementation of a 2.125-Gbaud preamplifier that employs a common-gate input stage followed by a cascoded common-source stage. On-chip shunt peaking is introduced at the dominant pole to improve the overall system performance, including a 40% increase in the transimpedance. This implementation achieves a 1.6-k/spl Omega/ transimpedance and a 0.6-/spl mu/A input-referred current noise, while operating with a photodiode capacitance of 0.6 pF. A fully differential topology ensures good substrate and supply noise immunity. The amplifier, implemented in a triple-metal, single-poly, 14-GHz f/sub Tmax/, 0.5-/spl mu/m CMOS process, dissipates 225 mW, of which 110 mW is consumed by the 50-/spl Omega/ output driver stage. The optimized on-chip inductors consume only 15% of the total area of 0.6 mm/sup 2/.
Defining the optimal parameters for hairpin-based knockdown constructs (2007)

Induction of gene silencing using intracellularly expressed silencing triggers has been explored for large-scale loss-of-function screening, creation of knockdown cell lines or knockdown animals, and disease intervention. In all of these applications, the use of highly potent silencing constructs can maximize the possibility of obtaining target knockdown and thereby is intrinsically important for the chance of success. Several attempts have been made to improve the potency of a silencing construct. Results published in high profile journals such as Nature Biotechnology and Nature Genetics suggest that shRNAs with a 29-nucleotide (nt) stem is much more potent than shRNAs with a 19-nt stem, and miR30-based silencing constructs are much more potent than shRNA-based constructs. In this study, we systematically investigated several parameters, including the use of shRNA- or miR30-based scaffolds, the length of shRNA, and the selection of shRNA sequences for their impact on the knockdown efficiency of a silencing construct. Our studies revealed that the optimal configurations for a potent silencing trigger could be an shRNA with a 19-nt stem and a 9-nt loop. By comparing properties that favor the functional shRNAs and siRNAs using a set of 190 shRNAs against 19 targets and 360 siRNAs against four targets, we found that the functional shRNAs and siRNAs displayed similar but not identical nucleotide preferences. Based on the characteristic nucleotide preferences in the functional versus the nonfunctional shRNAs, we developed a computer program that outperforms an advanced siRNA selection algorithm for the enrichment of highly functional shRNAs.
Power limitation and high-power amplifier nonlinearities in on-board satellite communications systems (1993)

This paper discusses the problem of power limitation in onboard satellite communications systems. It considers the nonlinear characteristics of on-board high-power amplifiers and corresponding linearisation techniques. It is shown that, with the recent development of solid-state high-power amplifier designs and linearisation techniques for travelling wave-tube amplifiers, it is now possible to operate on-board amplifiers near to saturation without increasing their nonlinear effects.
Acyltransferases and Transacylases Involved in Fatty Acid Remodeling of Phospholipids and Metabolism of Bioactive Lipids in Mammalian Cells (1997)

Over 100 different phospholipid molecular species are known to be present in mammalian cells and tissues. Fatty acid remodeling systems for phospholipids including acyl-CoA: lysophospholipid acyltransferases, CoA-dependent and CoA-independent transacylation systems and lysophospholipase/transacylase are involved in the biosynthesis of these molecular species. Acyl-CoA:1-acyl-2-lysophospholipid acyltransferase prefers polyunsaturated fatty acyl-CoAs as acyl donors while acyl-CoA:2-acyl-1-lysophospholipid acyltransferase prefers saturated fatty acyl-CoAs. Therefore, the acyl-CoA:lysophospholipid acyltransferase system is involved in the synthesis of the phospholipid molecular species containing sn-1 saturated and sn-2 unsaturated fatty acids. The CoA-dependent transacylation system catalyzes the transfer of fatty acids esterified in phospholipids to lysophospholipids in the presence of CoA without the generation of free fatty acids. The CoA-dependent transacylation reaction in rat liver exhibits strict fatty acid specificity, i.e., three types of fatty acids (20:4, 18:2, and 18:0) are transferred. On the other hand, the CoA-independent transacylase catalyzes the transfer of C20 and C22 polyunsaturated fatty acids from diacyl phospholipids to various lysophospholipids, in particular, ether-containing lysophospholipids, in the absence of any cofactors. The CoA-independent transacylase is assumed to be involved in the accumulation of polyunsaturated fatty acids in ether-containing phospholipids and in the removal of deleterious ether-containing lysophospholipids. These acyltransferases and transacylases are involved in not only the remodeling of fatty acids but also the synthesis and degradation of some bioactive lipids and their precursors. In this review, the properties of these fatty acid remodeling systems and their possible roles in the biosynthesis of bioactive lipids are described.
Investigation of structural properties of carbon-epoxy composites using fiber-Bragg gratings (2003)

Fiber Bragg-gratings are embedded in carbon-epoxy laminates as well as bonded on the surface of composite wound pressure vessel. Structural properties of such composites are investigated. The measurements include stress-strain relation in laminates and Poisson's ratio in several specimens with varying orientation of the optical fiber Bragg-sensor with respect to the carbon fiber in an epoxy matrix. Additionally, fiber Bragg gratings are bonded on the surface of cylinders fabricated out of carbon-epoxy composites and longitudinal and hoop strain on the surface is measured.
Construction of validated, non-redundant composite protein sequence databases (1990)

A strategy has been developed for the construction of a validated, comprehensive composite protein sequence database. Entries are amalgamated from primary source data bases by a largely automated set of processes in which redundant and trivially different entries are eliminated. A modular approach has been adopted to allow scientific judgement to be used at each stage of database processing and amalgamation. Source databases are assigned a priority depending on the quality of sequence validation and commenting. Rejection of entries from the lower priority database, in each pairwise comparison of databases, is carried out according to optionally defined redundancy criteria based on sequence segment mismatches. Efficient algorithms for this methodology are embodied in the COMPO software system. COMPO has been applied for over 2 years in construction and regular updating of the OWL composite protein sequence database from the source databases NBRF-PIR, SWISS-PROT, a GenBank translation retrieved from the feature tables, NBRF-NEW, NEWAT86, PSD-KYOTO and the sequences contained in the Brookhaven protein structure databank. OWL is part of the ISIS integrated data resource of protein sequence and structure [Akrigg et al. (1988) Nature, 335, 745-746]. The modular nature of the integration process greatly facilitates the frequent updating of OWL following releases of the source databases. The extent of redundancy in these sources is revealed by the comparison process. The advantages of a robust composite database for sequence similarity searching and information retrieval are discussed.
Inhibition of Tumor Cell Motility by the Interferon-inducible GTPase MxA (2009)

To identify pathways controlling prostate cancer metastasis we performed differential display analysis of the human prostate carcinoma cell line PC-3 and its highly metastatic derivative PC-3M. This revealed that a 78-kDa interferon-inducible GTPase, MxA, was expressed in PC-3 but not in PC-3M cells. The gene encoding MxA, MX1, is located in the region of chromosome 21 deleted as a consequence of fusion of TMPRSS2 and ERG, which has been associated with aggressive, invasive prostate cancer. Stable exogenous MxA expression inhibited in vitro motility and invasiveness of PC-3M cells. In vivo exogenous MxA expression decreased the number of hepatic metastases following intrasplenic injection. Exogenous MxA also reduced motility and invasiveness of highly metastatic LOX melanoma cells. A mutation in MxA that inactivated its GTPase reversed inhibition of motility and invasion in both tumor cell lines. Co-immunoprecipitation studies demonstrated that MxA associated with tubulin, but the GTPase-inactivating mutation blocked this association. Because MxA is a highly inducible gene, an MxA-targeted drug discovery screen was initiated by placing the MxA promoter upstream of a luciferase reporter. Examination of the NCI diversity set of small molecules revealed three hits that activated the promoter. In PC-3M cells, these drugs induced MxA protein and inhibited motility. These data demonstrate that MxA inhibits tumor cell motility and invasion, and that MxA expression can be induced by small molecules, potentially offering a new approach to the prevention and treatment of metastasis.
Pokeweed mitogen-induced immunoglobulin secretion by peripheral blood lymphocytes from patients with primary intracranial tumors. Characterization of T helper and B cell function. (1985)

We have previously demonstrated that patients with primary malignant brain tumors have impaired in vivo and in vitro cell-mediated immunity. The purpose of the present research was to employ pokeweed mitogen (PWM)-induced secretion of immunoglobulin (Ig) by peripheral blood lymphocytes (PBL) to further investigate impaired lymphocyte function in these patients. The PWM response of PBL from normal individuals averaged 8384 plaque-forming cells (PFC) per 10(6) cells, whereas the response of PBL from patients averaged 1590 PFC/10(6). The decreased PWM response of PBL patients could not be improved by varying the number of PBL placed in culture or employing different concentrations of PWM. Co-culture experiments to detect the presence of suppressor cells in PBL and purified T cell preparations from patients demonstrated that enhanced suppressor cell activity was not evident. Next, experiments were performed to assess the T-helper cell activity present in purified T cell preparations obtained from patients. The results demonstrated that T cells from patients lacked the ability to provide adequate helper activity in the PWM response. Moreover, studies with monoclonal antibodies directed against T cell subsets revealed that PBL from patients have a reduced percentage of T-helper cells (40%) as compared with normal values (55%). In concert with T-helper cell anomalies, B cell function in these patients also is diminished. Thus, these observations indicate that a combined T-helper and B cell defect may contribute to the broad impairment of host immunocompetence observed in patients with primary gliomas.
A high speed dual port memory with simultaneous serial and random mode access for video applications (1984)

A 64K/spl times/1 NMOS dynamic RAM which is interfaced in an on-chip 256-bit high-speed shift register is described. The device allows parallel transfer of 256 bits from a selected row in memory to the shift register in a normal RAS cycle time. Subsequently, the device provides simultaneous and asynchronous access from both the DRAM and the serial ports. The shift register can operate at a typical frequency of 33 MHz. When used in conjunction with multiple devices of the same design, a high-resolution bit-mapped video display system can be achieved with video bandwidths beyond 100 MHz. The dual-ported nature of the device allows a graphics processor to operate on the DRAM portion of the device while the shift register simultaneously provides a video data stream to a video display system.
Myocardial function, ischaemia and n-3 polyunsaturated fatty acids: a membrane basis (2007)

Long-chain n-3 polyunsaturated fatty acids (PUFAs) are selectively incorporated into cardiac cell membranes from the diet in a dose-related manner. Regular intake can slow the heart rate, reduce myocardial oxygen consumption, and increase coronary reserve. These properties contribute to preconditioning-like effects of resistance to myocardial ischaemic damage and improved post-ischaemic recovery. These effects can be demonstrated in isolated hearts independently of the effects of n-3 PUFAs on neural or blood parameters. The enrichment of myocardial membranes with n-3 PUFA also reduces vulnerability to cardiac arrhythmias, particularly ventricular fibrillation during myocardial ischaemia and reperfusion, and attenuates heart failure and cardiac hypertrophy. n-3 PUFA concentrations can increase from 7% to 15% in the myocardial membranes of rats (mainly in the form of docosahexaenoic acid [22: 6 n-3]) with dietary intakes of only 0.3% fish oil, equivalent to two meals of salmon per week in the human diet. Dietary fish oil produces changes in cardiac function that might contribute to cardiovascular health benefits in humans and does so by modifying cardiac membranes within a dose range achievable in the human diet.
Structure of hydrated oligonucleotides studied by in situ scanning tunneling microscopy. (1993)

We have used the scanning tunneling microscope (STM) to image several synthetic oligonucleotides adsorbed onto a positively charged Au(111) electrode. The molecules were deposited and imaged in aqueous electrolyte under potential control, a procedure that eliminated the problem of the substrate artifacts that had limited some previous STM studies. Experiments were carried out with two types of single-stranded molecules (11 and 20 bases long) and three types of double-stranded molecules (20 and 61 base pairs and 31 bases with 25 bases paired and 6-base "sticky" ends). The molecules lie along symmetry directions on the reconstructed (23 x square root of 3) gold surface, and length measurements indicate that they adopt simple base-stacked structures. The base stacking distances are, within experimental uncertainty, equal to the 0.33 nm measured for polymeric aggregates of stacked purines by direct imaging in identical conditions. The images show features consistent with helical structures. Double helices have a major-groove periodicity that is consistent with a 36 degrees twist. The single helices appear to be more tightly twisted. A simple tunneling model of STM contrast generates good agreement between measured and calculated images.
Decoding spectrotemporal features of overt and covert speech from the human cortex (2014)

Auditory perception and auditory imagery have been shown to activate overlapping brain regions. We hypothesized that these phenomena also share a common underlying neural representation. To assess this, we used electrocorticography intracranial recordings from epileptic patients performing an out loud or a silent reading task. In these tasks, short stories scrolled across a video screen in two conditions: subjects read the same stories both aloud (overt) and silently (covert). In a control condition the subject remained in a resting state. We first built a high gamma (70-150 Hz) neural decoding model to reconstruct spectrotemporal auditory features of self-generated overt speech. We then evaluated whether this same model could reconstruct auditory speech features in the covert speech condition. Two speech models were tested: a spectrogram and a modulation-based feature space. For the overt condition, reconstruction accuracy was evaluated as the correlation between original and predicted speech features, and was significant in each subject (p < 10(-5); paired two-sample t-test). For the covert speech condition, dynamic time warping was first used to realign the covert speech reconstruction with the corresponding original speech from the overt condition. Reconstruction accuracy was then evaluated as the correlation between original and reconstructed speech features. Covert reconstruction accuracy was compared to the accuracy obtained from reconstructions in the baseline control condition. Reconstruction accuracy for the covert condition was significantly better than for the control condition (p < 0.005; paired two-sample t-test). The superior temporal gyrus, pre- and post-central gyrus provided the highest reconstruction information. The relationship between overt and covert speech reconstruction depended on anatomy. These results provide evidence that auditory representations of covert speech can be reconstructed from models that are built from an overt speech data set, supporting a partially shared neural substrate.
Nutritional Implications Of Resistant Starch (1996)

An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the 'Save PDF' action button.
Characterization of a glial cell line persistently infected with borna disease virus (BDV): influence of neurotrophic factors on BDV protein and RNA expression (1993)

Borna disease virus (BDV) infects cells of the nervous system in a wide range of species. Previous work suggests that there are differences in BDV replication in neuronal cells and glial cells. Many neurons are lysed by the immunopathologic response to BDV; lysis of dentate gyrus neurons in the absence of encephalitis is seen in rats inoculated with BDV as neonates. In contrast, persistently BDV-infected astrocytes increase over the course of BDV infection. Therefore, we compared BDV replication in neuronal (SK-N-SH and SK-N-SHEP) and astrocytic (C6) cell lines. While SK-N-SH cells produced more infectious virions per cell, the C6 cells contained more BDV proteins and RNA. BDV sequences in the supernatants of both cell types were identified, despite low titers of infectious virus, suggesting the release of incomplete virions into the medium. C6 cells secreted a factor or factors into the medium that enhanced the production of BDV proteins and RNA in other cell lines. In addition, nerve growth factor treatment produced the same enhancement. Thus, BDV replication in certain neural cells in vitro may be linked to the production of cell-specific factors which affect viral replication.
Temporal patterns for the derivation of PMPDF and PMF estimates in the GTSM region of Australia (2005)

The Bureau of Meteorology has recently revised the Probable Maximum Precipitation (PMP) estimates for the Generalised Tropical Storm Method (GTSM) region of Australia. The revision process has involved the application of the more technically rigorous Generalised Southeast Australia Method (GSAM), which was previously developed for the southern part of Australia, to a much larger data set of large tropical storms. This has generally led to an increase in the total GTSM PMP depths. At times, however, an even bigger increase to the Probable Maximum Precipitation Design Flood (PMPDF) and the Probable Maximum Flood (PMF) has been caused by changes to the temporal patterns. The paper discusses the derivation of the revised GTSM temporal patterns and demonstrates their application in estimating both the PMPDF and the PMF using Keepit Dam in NSW.
Severity of spatial learning impairment in aging: Development of a learning index for performance in the Morris water maze. (2015)

The Morris water maze task was originally designed to assess the rat's ability to learn to navigate to a specific location in a relatively large spatial environment. This article describes new measures that provide information about the spatial distribution of the rat's search during both training and probe trial performance. The basic new measure optimizes the use of computer tracking to identify the rat's position with respect to the target location. This proximity measure was found to be highly sensitive to age-related impairment in an assessment of young and aged male Long-Evans rats. Also described is the development of a learning index that provides a continuous, graded measure of the severity of age-related impairment in the task. An index of this type should be useful in correlational analyses with other neurobiological or behavioral measures for the study of individual differences in functional/biological decline in aging.