gebhart/patrepeval huggingface dataset:
Polarized light imaging in biomedicine: emerging Mueller matrix methodologies for bulk tissue assessment (2015)

Polarized light point measurements and wide-field imaging have been studied for many years in an effort to develop accurate and information-rich tissue diagnostic methods. However, the extensive depolarization of polarized light in thick biological tissues has limited the success of these investigations. Recently, advances in technology and conceptual understanding have led to a significant resurgence of research activity in the promising field of bulk tissue polarimetry. In particular, with the advent of improved measurement, analysis, and interpretation methods, including Mueller matrix decomposition, new diagnostic avenues, such as quantification of microstructural anisotropy in bulk tissues, have been enabled. Further, novel technologies have improved the speed and the accuracy of polarimetric instruments for ex vivo and in vivo diagnostics. In this paper, we review some of the recent progress in tissue polarimetry, provide illustrative application examples, and offer an outlook to the future of polarized light imaging in bulk biological tissues.
Treatment of Depression Following Traumatic Brain Injury (2005)

Depression is a common consequence of traumatic brain injury (TBI), and is a source of substantial distress and disability for persons with TBI and their families. This article offers a practical approach to the evaluation and treatment of this condition. Diagnostic and etiologic considerations relevant to this issue are reviewed first. Next, somatic therapies for posttraumatic depression, including antidepressant medications and electroconvulsive therapy, are discussed. Use of these therapies is also considered in the context of the common medical and neurological comorbidities among persons with TBI. Finally, psychosocial interventions relevant to the care of persons with posttraumatic depression are presented.
Megakaryocyte-derived microparticles: direct visualization and distinction from platelet-derived microparticles (2008)

Platelet microparticles are a normal constituent of circulating blood. Several studies have demonstrated positive correlations between thrombotic states and platelet microparticle levels. Yet little is known about the processes by which platelet microparticles are generated in vivo. We now characterize microparticles derived directly from megakaryocytes. Video microscopy of live mouse megakaryocytes demonstrated that microparticles form as submicron beads along the lengths of slender, unbranched micropodia. These microparticles are CD41(+), CD42b(+), and express surface phosphatidylserine. Megakaryocyte microparticle generation is resistant to inhibition of microtubule assembly, which is critical to platelet formation, and augmented by inhibition of actin polymerization. To determine whether circulating microparticles are derived primarily from activated platelets or megakaryocytes, we identified markers that distinguish between these 2 populations. CD62P and LAMP-1 were found only on mouse microparticles from activated platelets. In contrast, full-length filamin A was found in megakaryocyte-derived microparticles, but not microparticles from activated platelets. Circulating microparticles isolated from mice were CD62P(-), LAMP-1(-) and expressed full-length filamin A, indicating a megakaryocytic origin. Similarly, circulating microparticles isolated from healthy volunteers were CD62P(-) and expressed full-length filamin A. Cultured human megakaryocytes elaborated microparticles that were CD41(+), CD42b(+), and express surface phosphatidylserine. These results indicate that direct production by megakaryocytes represents a physiologic means to generate circulating platelet microparticles.
2D Gel-Based Multiplexed Proteomic Analysis during Larval Development and Metamorphosis of the Biofouling Polychaete Tubeworm Hydroides elegans (2010)

Larval settlement and metamorphosis of a common biofouling polychaete worm, Hydroides elegans, involve remarkable structural and physiological changes during this pelagic to sessile habitat shift. The endogenous protein molecules and post-translational modifications that drive this larval transition process are not only of interest to ecologists but also to the antifouling paint industry, which aims to control the settlement of this biofouling species on man-made structures (e.g., ship hulls). On the basis of our recent proteomic studies, we hypothesize that rapid larval settlement of H. elegans could be mediated through changes in phosphorylation status of proteins rather than extensive de novo synthesis of proteins. To test this hypothesis, 2D gel-based multiplexed proteomics technology was used to monitor the changes in protein expression and phosphorylation status during larval development and metamorphosis of H. elegans. The protein expression profiles of larvae before and after they reached competency to attach and metamorphose were similar in terms of major proteins, but the percentage of phosphorylated proteins increased from 41% to 49% after competency. Notably, both the protein and phosphoprotein profiles of the metamorphosed individuals (adult) were distinctly different from that of the larvae, with only 40% of the proteins phosphorylated in the adult stage. The intensity ratio of all phosphoprotein spots to all total protein spots was also the highest in the competent larval stage. Overall, our results indicated that the level of protein phosphorylation might play a crucial role in the initiation of larval settlement and metamorphosis.
Hydrogel implants for the correction of myopia (1982)

We attempted to induce corneal flattening in a baboon model by implanting donut-shaped hydrogel lenses in an intralamellar pocket created by a microkeratome. 7mm diameter hydrogels in five eyes produced corneal steepening from 3.4 to 22.5 diopters. Three to five months postoperatively the study was terminated and the corneas studied with correlative microscopy. There was an absence of inflammation, but the intralamellar pocket was lined with keratocytes, focal areas of epithelial implantation were found and the overlying corneal cap was normal.
Folate deficiency, biopterin and monoamine metabolism in depression (1992)

Seven (21%) of 34 patients with a severe DSM-III diagnosis of major depression had red-cell folate levels below 150 ng/ml. This subgroup with folate deficiency had significantly lower CSF 5-hydroxyindoleacetic acid (5HIAA) compared to neurological controls. For all depressed patients red-cell folate was significantly correlated with CSF 5HIAA and homovanillic acid (HVA). CSF tetrahydrobiopterin (BH4) was significantly correlated with CSF 5HIAA and HVA and red-cell folate. Our observations provide further evidence of the links between folate, biopterin and monoamine metabolism in depression.
Drain Current Centric Modality: Instrumentation and Evaluation of ISFET for Monitoring Myocardial Ischemia Like Variations in pH and Potassium Ion Concentration (2009)

Variations in concentrations of ions in biological systems can be important events in the onset of a physiological disorder. In an episode of myocardial ischemia, acidosis and elevation of potassium ion concentration has been observed in the extra-cellular matrix of the myocardium. As a spectrum of markers, they can help detect onset of ischemia as well as infarctions. In this study, Flexible Organic Ion-Sensitive Field-Effect Transistors (ISFETs) have been characterized to detect Ischemia-like variations in pH and potassium ion concentration. Detection capabilities, of the sensors, have been shown as pure chemical concentration to current signal transduction of the ISFET. Independent of peripheral amplifier-converter circuits, they are standalone sensors. The sensors have been evaluated for their sensitivity and signal resolution. Calibration expression, following a thermo-electric model for device operation, represents an explicit relations between transistor drain current and ion concentrations. Signal conditioning, by normalization, has been attempted to make the calibration expression explicit in ion-concentration. Finally a reliable detection strategy, in differential mode, is proposed for a reference electrode free device.
Rats Exposed to Isoflurane In Utero  during Early Gestation Are Behaviorally Abnormal as Adults (2011)

Rats exposed to isoflurane in utero at a time that corresponds to the second trimester in humans have impaired spatial memory acquisition and reduced anxiety, compared with controls. This suggests the fetal brain may be adversely affected by maternal anesthesia, and raises the possibility that vulnerability to deleterious neurodevelopmental effects of isoflurane begins much earlier in life than previously recognized.
Experimental generation and dynamical reconfiguration of different circular optical lattices for applications in atom trapping (2010)

Different configurations of optical lattices with circular cylindrical geometry have been recently studied in the context of atom trapping from a theoretical viewpoint, giving rise to a number of proposed applications. A common problem for testing theoretical predictions is the difficulty in the experimental realization of some of the necessary optical potentials. Here we discuss the experimental generation of four different circular optical lattices in an efficient and simple way using a single spatial light modulator. Our approach allows switching between different light configurations with a time resolution given by the response time of the light modulator.
A GPS sonobuoy localization system (2004)

A GPS localization system is described that uses the precision navigation signal but does not require a SAASM decoding unit in the sonobuoy. The system operates by retransmitting a selected 1 MHz portion of the GPS L1 or L2 signal spectrum from the sonobuoy to a Master Control Station (MCS). By offsetting the selected spectrum about 2 MHz from the center frequency of the GPS band, both the current P(Y) signal and the new M-code signal can be accommodated. By cross-correlating the retransmitted signal with the same signal received at a remote site a differential delay can be computed for each visible satellite. This delay defines a prolate spheroid with one focus at the satellite and the other at the remote site. The intersection of the measured prolate spheroid with the oblate spheroid approximation of the sea surface defines a closed curve on the surface of the ocean on which the sonobuoy lies. Two additional satellite measurements or two additional measurements of the same satellite from a moving remote site such as an airplane then locates the sonobuoy uniquely.
What is the future of targeted therapy in rheumatology: biologics or small molecules? (2014)

Biologic therapeutics and small-molecule inhibitors both have significant advantages and disadvantages in the therapy of rheumatic diseases. The future of targeted therapies is one of the most exciting questions of current rheumatology research and therapy.
Medium access control for power line communications: an overview of the IEEE 1901 and ITU-T G.hn standards (2011)

Power lines are becoming increasingly popular for high-speed communications, while at the same time reliable communications over them poses several unique challenges. Recently, two standardization bodies, the Institute of Electrical and Electronics Engineers (IEEE) and the International Telecommunication Union (ITU), addressed in their IEEE 1901 and ITU-T G.hn standards, respectively, both the medium access control and the physical layer specifications of power line communications. In this article, we provide an overview of these standards from the media access control technology perspective, and the similarities and dissimilarities between the IEEE 1901 and ITU-T G.hn standards are discussed, as well as potential performance issues. We use a top-down approach to analyze the features and technologies of the standards.
Gel polymer electrolyte with semi‐IPN fabric for polymer lithium‐ion battery (2011)

Abstract A new type of semi‐IPN gel electrolyte was prepared by thermal polymerization in this article. At first, the crosslinkable PEG200 (MXPEG) was prepared by condensation reaction, then the crosslinkable components were blent with PMMA and heated under vacuum to form polymer blends with semi‐IPN fabric. Differential scanning calorimetry and X‐ray diffraction spectroscopy were used to investigate the thermal properties and crystalline/amorphous structure of the prepared polymer blends. With semi‐IPN fabric, they present amorphous absolutely. For semi‐IPN gel electrolyte, the mechanical and the electrochemical properties are varied with the quantity of absorbed liquid electrolyte. Ion‐conductivity behavior for semi‐IPN gel electrolyte measured by means of AC impedance spectrum showed that the best data was 1.62 × 10 −3 S cm −1 at room temperature, and Arrhenius‐type relationship was obeyed in the temperature dependence of ionic conductivity. In addition, the electrochemical stability window of the semi‐IPN gel electrolyte was 4.6 V. All the properties showed that the prepared semi‐IPN gel electrolyte was expected to have applications of electrolyte for lithium‐ion polymer secondary batteries. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Fast finite difference time domain analysis of microstrip patch antennas (2002)

Although the finite-difference-time-domain method has been successfully used to model microstrip-fed patch antennas, this has been achieved using uniform grids. The authors show that by using nonuniform grids, in conjunction with first-order absorbing boundaries and broadband excitation, a drastic reduction in computation time can be achieved. Comparison with published data shows no loss in accuracy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Ultrathin&lt;tex&gt;$hbox Al_2hbox O_3$&lt;/tex&gt;and&lt;tex&gt;$hboxHfO_2$&lt;/tex&gt;Gate Dielectrics on Surface-Nitrided Ge (2004)

We have studied ultrathin Al/sub 2/O/sub 3/ and HfO/sub 2/ gate dielectrics on Ge grown by ultrahigh vacuum-reactive atomic-beam deposition and ultraviolet ozone oxidation. Al/sub 2/O/sub 3/-Ge gate stack had a t/sub eq//spl sim/23 /spl Aring/, and three orders of magnitude lower leakage current compared to SiO/sub 2/. HfO/sub 2/-Ge allowed even greater scaling, achieving t/sub eq//spl sim/11 /spl Aring/ and six orders of magnitude lower leakage current compared to SiO/sub 2/. We have carried out a detailed study of cleaning conditions for the Ge wafer, dielectric deposition condition, and anneal conditions and their effect on the electrical properties of metal-gated dielectric-Ge capacitors. We show that surface nitridation is important in reducing hysteresis, interfacial layer formation and leakage current. However, surface nitridation also introduces positive trapped charges and/or dipoles at the interface, resulting in significant flatband voltage shifts, which are mitigated by post-deposition anneals.
Human collagen isolated from adipose tissue (2012)

Collagen, the most abundant protein in vertebrates, is a useful biomaterial in pharmaceutical and medical industries. So far, most collagen has been extracted from animals and cadavers. Herein, we suggest human adipose tissue, which is routinely abandoned after liposuction, as a plentiful source of human collagen. In this study, human collagen was obtained from adipose tissue through two successive major steps: (i) extraction of the extracellular matrix (ECM) by pulverization, centrifugation, alkaline, and alcohol treatment; (ii) isolation of collagen from ECM by pepsin treatment in dilute acetic acid. The purified human adipose-derived collagen was characterized by Fourier transform infrared spectroscopy, polyacrylamide gel electrophoresis, amino acid analysis, and circular dichroism spectroscopy. The extracted collagen showed a typical triple helix structure, good thermal stability due to abundant imino acids, and high solubility at acidic pH. The collagen greatly facilitated the adhesion and proliferation of human adipose-derived stem cells and normal human dermal fibroblasts on polystyrene plates. These results suggest that human adipose tissue obtained by liposuction can provide human collagen for use in cosmetics, pharmaceutics, and medicine.
Beam Position Monitor System for Storage Rings (1985)

Beam position monitors (BPM) for synchrotron light storage rings usually consist of beam pickup electrodes, coaxial relays and a narrowband receiver. While accurate, these systems are slow and of limited use in the commissioning of an accelerator. A beam position monitor is described which is intended to be a principal diagnostic during debug and routine running of a storage ring. It is capable of measuring the position of a single bunch on the first or nth orbit to an accuracy of a few percent. Stored beam position is more accurately measured with averaging techniques. Beam position changes can be studied in a bandwidth from DC to a few MHz. The beam monitor electronics consist of a separate amplification, detection, and sampling channel for each beam pickup electrode. Fast switches in each channel permit selection of the nth turn for measurement (single bunch mode). A calibration pulse is injected into each channel after beam measurement to permit gain offsets to be measured and removed from the final data. While initially more costly than the usual beam position monitor system, this system will pay for itself in reduced storage ring debug and trouble shooting time.
Computation of Recommender System Using Localized Regularization (2015)

Online and offline targeting and recommendations are major topics in ecommerce. The topic is treated as “Matrix Completion”, “Missing Values” and “Matrix Imputations” in statistics. The main goal in all of these fields is to compute the unknown (missing) values in the data matrix. In computing or recovering the unknown entries of the matrix, overfitting may happen which is due to the lack of sufficient information and thus some penalization of the objective function in the form of regularization becomes necessary. This work is based on a different view of regularization, i.e., a localized regularization technique which leads to improvement in the estimation of the missing values.
Serum fructosamine and glycated haemoglobin measurements in diabetic control. (1986)

Serum fructosamine and glycated haemoglobin (HbA1) were measured in capillary samples from diabetic children and compared with samples from non-diabetic children. Glycaemic control was assessed clinically and by average daily glucose values recorded by home monitoring. Fructosamine correlated with HbA1 and with average glucose values measured over 30 days. HbA1 also correlated with average glucose values measured over 60 days. Changes in fructosamine with time tended to parallel those of HbA1, and advance indication of deteriorating or improving glycaemic control was possible by observing changes in these. Fructosamine has many advantages over HbA1 measurement such as speed, technical ease, and low cost, and is a reliable alternative to HbA1 estimation as an indication of glycaemic control.
The rate of metabolism in marine animals: environmental constraints, ecological demands and energetic opportunities (2007)

The rates of metabolism in animals vary tremendously throughout the biosphere. The origins of this variation are a matter of active debate with some scientists highlighting the importance of anatomical or environmental constraints, while others emphasize the diversity of ecological roles that organisms play and the associated energy demands. Here, we analyse metabolic rates in diverse marine taxa, with special emphasis on patterns of metabolic rate across a depth gradient, in an effort to understand the extent and underlying causes of variation. The conclusion from this analysis is that low rates of metabolism, in the deep sea and elsewhere, do not result from resource (e.g. food or oxygen) limitation or from temperature or pressure constraint. While metabolic rates do decline strongly with depth in several important animal groups, for others metabolism in abyssal species proceeds as fast as in ecologically similar shallow-water species at equivalent temperatures. Rather, high metabolic demand follows strong selection for locomotory capacity among visual predators inhabiting well-lit oceanic waters. Relaxation of this selection where visual predation is limited provides an opportunity for reduced energy expenditure. Large-scale metabolic variation in the ocean results from interspecific differences in ecological energy demand.
A Taxonomy of Computer Program Security Flaws, with Examples (1994)

Abstract : An organized record of actual flaws can be useful to designers, implementors, and evaluators of computer systems. This paper provides a taxonomy for computer program security flaws together with an appendix that carefully documents 50 actual security flaws. These flaws have all been described previously in the open literature, but in widely separated places. For those new to the field of computer security, they provide a good introduction to the characteristics of security flaws and how they can arise. Because these flaws were not randomly selected from a valid statistical sample of such flaws, we make no strong claims concerning the likely distribution of actual security flaws within the taxonomy. However, this taxonomy can be used to organize and abstract more representative samples. Data organized this way could be used to focus efforts to remove security flaws and prevent their introduction.
The Mitochondrial Effects of Small Organic Ligands of BCL-2 (2006)

We have investigated the mitochondrial effects of BH3I-2', Chelerythrine, and HA14-1, small organic molecules that share the ability to bind the BH3 domain of BCL-2. All compounds displayed a biphasic effect on mitochondrial respiration with uncoupling at low concentrations and respiratory inhibition at higher concentrations, the relative uncoupling potency being BH3I-2' (half-maximal uncoupling at about 80 nm) > Chelerythrine (half-maximal uncoupling at about 2 microm) > HA14-1 (half-maximal uncoupling at about 20 microm). At concentrations lower than required for uncoupling all compounds sensitized the permeability transition pore (PTP) to opening both in isolated mitochondria and intact cells. To assess whether the effects on BCL-2 binding, PTP induction and respiration could be due to different structural determinants we have tested a set of HA14-1 analogs from the Hoffmann-La Roche chemical library. We have identified 5-(6-chloro-2,4-dioxo-1,3,4,10-tetrahydro-2H-9-oxa-1,3-diaza-anthracen-10-yl)-pyrimidine-2,4,6-trione (EM20-25) as a molecule devoid of effects on respiration that is able to induce PTP opening, to disrupt the BCL-2/BAX interactions in situ and to activate caspase-9 in BCL-2-overexpressing cells. EM20-25 neutralized the antiapoptotic activity of overexpressed BCL-2 toward staurosporine and sensitized BCL-2-expressing cells from leukemic patients to the killing effects of staurosporine, chlorambucil, and fludarabine. These results provide a proof of principle that the potentially toxic effects of BCL-2 ligands on mitochondrial respiration are not essential for their antiapoptotic activity and represent an important step forward in the development of tumor-selective drugs acting on BCL-2.