gebhart/patrepeval huggingface dataset:
Attenuated Rubella Virus (1966)

ALTHOUGH the need for an effective, safe rubella-virus vaccine has long been recognized it was not until 1962, when the virus was isolated and propagated in the laboratory,1 , 2 that development of a vaccine became theoretically possible. Interest in preventing rubella and associated teratogenesis was further intensified by observations made during the recent epidemic of 1963–1964. Although our early attempts to produce a killed-virus vaccine were unsuccessful, development of a live-virus vaccine seemed feasible, and approaches that had been used to attenuate other viruses were explored. In attempts to produce attenuation rubella viruses were subjected to protracted passage in tissue cultures. . . .
Structural modulations in Bi2Te3 (2008)

Bi 2 Te 3 is known for its large thermopower, a low thermal conductivity, and thereby a large thermoelectric figure of merit ZT at room temperature. Particularly, the low thermal conductivity is attributed to a high structural disorder. Electron probe microanalysis, transmission electron microscopy (TEM), and energy dispersive x-ray spectrometry in the TEM were applied on n-type Bi2(Te,Se)3 and p-type (Bi,Sb)2Te3 bulk materials for structural and chemical analysis. Significant variations in stoichiometry were found on the micrometer scale. Bulk materials showed a texture, grain sizes of 1−10 μm, and dislocations in the basal plane with a density of 109 cm−2 having a high mobility at room temperature. A structural modulation [natural nanostructure (nns)] was found on the nanometer scale. This nns was also observed in Bi2Te3 thin films and Bi2Te3/Bi2(Te,Se)3 superlattices and turned out to be of general character for Bi2Te3 materials. The nns was analyzed in detail by stereomicroscopy in the TEM and by image simulation. The nns was found to be a pure sinusoidal displacement field with (i) a displacement vector parallel to ⟨5,−5,1⟩ and an amplitude of about 10 pm and (ii) a wave vector parallel to {1,0,10} and a wavelength of 10 nm. Bi2Te3 samples from different batches produced under similar conditions showed different characteristics with respect to the nns: none, one, or two superimposed nns were observed. The nns is present in all parts of the sample with the same orientation. The formation of the nns is either bound to a certain stoichiometry range or to the thermal history of a sample and is related to the tendency of Te compounds to form amorphous phases. An ordered network of dislocations a few nanometers apart and chemical fluctuations on the nanometer scale as origins of the nns were ruled out. The displacement field of the nns is superimposed to the average structure and should significantly affect the thermoelectric properties. Particularly, the lattice thermal conductivity should be decreased due to phonon scattering on the sinusoidal strain field of the nns. Also, the nns should yield a one-dimensional or zero-dimensional behavior of the phonons and anisotropic transport coefficients in the basal plane.
Multisensor fusion for atrial and ventricular activity detection in coronary care monitoring (1999)

Information management for critical care monitoring is still a very difficult task. Medical staff is often overwhelmed by the amount of data provided by the increased number of specific monitoring devices and instrumentation, and the lack of an effective automated system. Specifically, a basic task such as arrhythmia detection still produce an important amount of undesirable alarms, due in part to the mechanistic approach of current monitoring systems. In this work, multisensor and multisource data fusion schemes to improve atrial and ventricular activity detection in critical care environments are presented. Applications of these schemes are quantitatively evaluated and compared with current methods, showing the potential advantages of data fusion techniques for event detection in noise corrupted signals.
PNA-PEG Modified Silicon Platforms as Functional Bio-Interfaces for Applications in DNA Microarrays and Biosensors (2009)

The synthesis and characterization of two types of silicon-based biofunctional interfaces are reported; each interface bonds a dense layer of poly(ethylene glycol) (PEG(n)) and peptide nucleic acid (PNA) probes. Phosphonate self-assembled monolayers were derivatized with PNA using a maleimido-terminated PEG(45). Similarly, siloxane monolayers were functionalized with PNA using a maleimido-terminated PEG(45) spacer and were subsequently modified with a shorter methoxy-terminated PEG(12) ("back-filling"). The long PEG(45) spacer was used to distance the PNA probe from the surface and to minimize undesirable nonspecific adsorption of DNA analyte. The short PEG(12) "back-filler" was used to provide additional passivation of the surface against nonspecific DNA adsorption. X-ray photoelectron spectroscopic (XPS) analysis near the C 1s and N 1s ionization edges was done to characterize chemical groups formed in the near-surface region, which confirmed binding of PEG and PNA to the phosphonate and silane films. XPS also indicated that additional PEG chains were tethered to the surface during the back-filling process. Fluorescence hybridization experiments were carried out with complementary and noncDNA strands; both phosphonate and siloxane biofunctional surfaces were effective for hybridization of cDNA strands and significantly reduced nonspecific adsorption of the analyte. Spatial patterns were prepared by polydimethylsiloxane (PDMS) micromolding on the PNA-functionalized surfaces; selective hybridization of fluorescently labeled DNA was shown at the PNA functionalized regions, and physisorption at the probe-less PEG-functionalized regions was dramatically reduced. These results show that PNA-PEG derivatized phosphonate monolayers hold promise for the smooth integration of device surface chemistry with semiconductor technology for the fabrication of DNA biosensors. In addition, our results confirm that PNA-PEG derivatized self-assembled carboxyalkylsiloxane films are promising substrates for DNA microarray applications.
Abstract W P93: Drag-Reducing Polymer Improves Microcirculation and Outcome after Permanent Middle Cerebral Artery Occlusion in Rats (2014)

Introduction: Current treatments for ischemia after stroke have not focused directly on the physiological effects of restoring or improving cerebral microvascular perfusion. Nanomolar concentrations of drag-reducing polymers (DRP) have been shown to improve hemodynamics and survival in animal models of the ischemic myocardium and peripheral circulation. We recently demonstrated that DRP improved microvascular perfusion in normal and traumatized rat brain. We hypothesized that DRP restores microvascular perfusion after focal ischemia and improves neurologic recovery in the rat. Methods: The suture permanent middle cerebral artery occlusion (MCAO) model in the rat was used. DRP was injected i.v. 90 minutes after MCAO. Controls were injected with an equal volume of saline. Using in vivo 2-photon laser scanning microscopy over the parietal cortex, we studied the acute effects of DRP on microvascular blood flow velocity, tissue oxygenation (NADH) and blood brain barrier (BBB) permeability for 5 hr after MCAO. Doppler cortical flow, rectal and cranial temperatures, arterial pressure, blood gases and electrolytes were monitored. Cerebral infarction was evaluated by triphenyltetrazolium chloride (TTC) staining 24 hr after MCAO and motor function by Rotarod at one week. Results: MCAO resulted in a progressive decrease in microvascular flow in the penumbra of the parietal cortex with hypoxia and increased BBB permeability during 5 hr monitored. DRP partially restored microvascular flow compared to control (21±6.7%, Mean ± SEM, p<0.05, n=4) and reduced the progression of ischemia and BBB permeability by 14±4.6 and 18±6.5%, respectively (p<0.05). Infarction volume was reduced by 24±8.1% in DRP treated rats (n=2, p<0.05). The Rotarod tests showed that one week after MCAO, DRP treated rats performed better than saline treated rats with times of 75.6±16.0% and 47.3±16.0%, respectively, as percent of normal rats. Conclusions: DRP restores cerebral microvascular flow after MCAO reducing tissue hypoxia and BBB damage. The improvement in flow is reflected by a reduction in infarct size 24 hours after MCAO and by improved motor neurological recovery at one week after MCAO. DRP can be a new effective therapy for ischemic stroke targeting microvascular perfusion.
Transplant of corneal epithelium to rabbit corneal wounds in vivo. (1985)

Sheets of corneal epithelium removed from 9-mm buttons of adult rabbit corneas using Dispase II were placed on abraded (basement membrane intact) or keratectomized corneas of anesthetized rabbits. Both types of wounds extended from limbus to limbus. The host animals were maintained under deep anesthesia for 3 hr, during which time culture medium was dripped onto the surface of the transplant. A soft contact lens then was placed over the cornea and the eye bandaged shut. Short-term experiments indicated that after 24 hr the transplanted epithelium was adherent to both abraded and keratectomized corneas (n = 4). Hemidesmosomes had formed between basal cells of donor epithelium and denuded host basement membrane, and cytoplasmic blebs had extended from donor epithelium into host keratectomized stroma. Seven transplants to abraded corneas and 17 transplants to keratectomized corneas were followed for longer time periods. Six of the seven transplants to abraded corneas were maintained until termination of the experiment (four at 4 weeks, one at 2 weeks, one at 1 week). Three of the 17 transplants to keratectomized corneas were maintained until termination (one at 4 weeks, one at 2 weeks, and one at 6 days). The remaining 14 sloughed between days 2 and 6. These data indicate that it is feasible to transplant corneal epithelial sheets and that they can be maintained most successfully if the host basement membrane is present.
Study of a two-level flow control scheme and buffering strategies (2002)

This paper proposes using an explicit rate control together with a simple window control for flow control in high-speed networks with resource reservations. The design justifications, the evaluation study, and the implementation results are presented. In particular, the idea of hard ACK and soft ACK in the context of end-to-end flow control is explored through simulation and the results are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Plasma fibrinogen and incident hypertension in the Atherosclerosis Risk In Communities (ARIC) Study (1998)

Despite a moderately strong positive association between fibrinogen levels and prevalent hypertension in both sexes, there was only a weak positive association between fibrinogen levels and incident hypertension in men and no association in women. Whether an elevated fibrinogen level is a risk factor for, or a consequence of, hypertension remains unclear.
Faster and improved 3-D head digitization in MEG using Kinect (2014)

Accuracy in localizing the brain areas that generate neuromagnetic activity in magnetoencephalography (MEG) is dependent on properly co-registering MEG data to the participant's structural magnetic resonance image (MRI). Effective MEG-MRI co-registration is, in turn, dependent on how accurately we can digitize anatomical landmarks on the surface of the head. In this study, we compared the performance of three devices-Polhemus electromagnetic system, NextEngine laser scanner and Microsoft Kinect for Windows-for source localization accuracy and MEG-MRI co-registration. A calibrated phantom was used for verifying the source localization accuracy. The Kinect improved source localization accuracy over the Polhemus and the laser scanner by 2.23 mm (137%) and 0.81 mm (50%), respectively. MEG-MRI co-registration accuracy was verified on data from five healthy human participants, who received the digitization process using all three devices. The Kinect device captured approximately 2000 times more surface points than the Polhemus in one third of the time (1 min compared to 3 min) and thrice as many points as the NextEngine laser scanner. Following automated surface matching, the calculated mean MEG-MRI co-registration error for the Kinect was improved by 2.85 mm with respect to the Polhemus device, and equivalent to the laser scanner. Importantly, the Kinect device automatically aligns 20-30 images per second in real-time, reducing the limitations on participant head movement during digitization that are implicit in the NextEngine laser scan (~1 min). We conclude that the Kinect scanner is an effective device for head digitization in MEG, providing the necessary accuracy in source localization and MEG-MRI co-registration, while reducing digitization time.
Trace chemical sensing of explosives (2007)

Foreword. Preface. List of Contributors. PART I: FUNDAMENTAL CONSIDERATIONS. Chapter 1. Chemical Sensing. Chapter 2. What to Detect? Chapter 3. Dangerous Innovations. Chapter 4. Where Should We Look For Explosive Molecules? Chapter 5. Structure of Turbulent Chemical Plumes. PART II: FIELD EXPERIENCE. Chapter 6. Detection of Trace Explosive Signatures in the Marine Environment. Chapter 7. Explosives Detection Using Ultrasensitive Electronic Vapor Sensors: Field Experience. Chapter 8. Reflections on Hunting Mines By Aroma Sensing. PART III: EXAMPLE SENSING TECHNOLOGIES. Chapter 9. Explosives Detection Based on Amplifying Fluorescence Polymers. Chapter 10. Ion Mobility Spectrometry. Chapter 11. Mass Spectrometry For Security Screening of Explosives. Chapter 12. Explosive Vapor Detection Using Microcantilever Sensors. Chapter 13. Lab-On-A-Chip Detection of Explosives. Chapter 14. Nanoscale Sensing Assemblies Using Quantum Dot-Protein Bioconjugates. Chapter 15. Remote Sensing of Explosive Materials Using Differential Reflection Spectroscopy. PART IV: SUPPLEMENTARY MATERIAL. Appendix : Organizations Involved in Searching For Hidden Explosives. Definitions, Symbols and Abbreviations. Explosives Definitions. Bibliography. Index.
Evaluation and design of filters using a Taylor series expansion (1997)

We describe a new method for analyzing, classifying, and evaluating filters that can be applied to interpolation filters as well as to arbitrary derivative filters of any order. Our analysis is based on the Taylor series expansion of the convolution sum. Our analysis shows the need and derives the method for the normalization of derivative filter weights. Under certain minimal restrictions of the underlying function, we are able to compute tight absolute error bounds of the reconstruction process. We demonstrate the utilization of our methods to the analysis of the class of cubic BC-spline filters. As our technique is not restricted to interpolation filters, we are able to show that the Catmull-Rom spline filter and its derivative are the most accurate reconstruction and derivative filters, respectively, among the class of BC-spline filters. We also present a new derivative filter which features better spatial accuracy than any derivative BC-spline filter, and is optimal within our framework. We conclude by demonstrating the use of these optimal filters for accurate interpolation and gradient estimation in volume rendering.
Quantification of Angiogenesis due to Basic Fibroblast Growth Factor in a Modified Rabbit Corneal Model (1992)

The rabbit corneal angiogenesis assay was modified to allow quantification of the neovascular response induced by growth factors. Basic Fibroblast Growth Factor (bFGF) was used for this experiment. bFGF was diluted in phosphate buffer solution (PBS) in such a way that 2 microliter of solution contained concentrations ranging from 17 to 1,200 ng. Each drop was absorbed by a 1 x 2 mm particle of a dried 70% hydratable hydrogel and implanted into a mid-stroma corneal pocket, 2 mm from the limbus. Iodinated bFGF was used to measure growth factor diffusion in the cornea, which was found to be isotropic. Autoradiography showed that bFGF was stored in the cornea at both epithelial and endothelial level. Corneal neovascularization occurred on the second day after implantation and was maximal on the 7th day. At this time the neovascular surface was measured by planimetry on corneal photographs and compared with controls. This method allows precise definition of the dose of any substance to be implanted into the cornea and induces a rapid neovascular response, thus allowing quantitative evaluation of neovascularization within one week. A neovascular response was detectable for doses as low as 35 ng of bFGF and increased proportionally to the dose of bFGF implanted.
MPISec I/O: Providing Data Confidentiality in MPI-I/O (2009)

Applications performing scientific computations or processing streaming media benefit from parallel I/O significantly, as they operate on large data sets that require large I/O. MPI-I/O is a commonly used library interface in parallel applications to perform I/O efficiently. Optimizations like collective-I/O embedded in MPI-I/O allow multiple processes executing in parallel to perform I/O by merging requests of other processes and sharing them later. In such a scenario, preserving confidentiality of disk-resident data from unauthorized accesses by processes without significantly impacting performance of the application is a challenging task. In this paper, we evaluate the impact of ensuring data-confidentiality in MPI-I/O on the performance of parallel applications and provide an enhanced interface, called MPISec I/O, which brings an average overhead of only 5.77% over MPI-I/O in the best case, and about 7.82% in the average case.
Attachment styles and fear of personal death: A case study of affect regulation. (1990)

The relation between attachment styles and fear of personal death was assessed. We classified a sample of Israeli undergraduate students into secure, ambivalent, and avoidant attachment groups and assessed the extent of, and the meaning attached to, overt fear of personal death as well as the extent of fear at a low level of awareness. Ambivalent subjects exhibited stronger overt fear of death than did secure and avoidant subjects, and both ambivalent and avoidant subjects showed stronger fear of death at a low level of awareness than secure subjects. Ambivalent subjects were also more likely to fear the loss of their social identity in death, and avoidant subjects were more likely to fear the unknown nature of their death. Results are discussed in terms of the effects of attachment styles on affect regulation. According to Bowiby's (1973) attachment theory, when an individual is confident that an attachment figure will be available to him whenever he desires it, that person will be much less prone to either intense or chronic fear than will an individual who for any reason has no such confidence (p. 202). Whereas most attachment research has focused on the fear of separation from a loved person, no attention has been paid to the fear of the ultimate separation: personal death. The purpose of the present study was to examine the relation between attachment styles and fear of personal death.
Substance P enhances cytokine-induced vascular cell adhesion molecule-1 (VCAM-1) expression on cultured rheumatoid fibroblast-like synoviocytes (1998)

Rheumatoid arthritis (RA) is an autoimmune disease characterized by inflammation of the synovial membrane of multiple joints. This inflammatory microenvironment allows fibroblast-like synoviocytes (FLS) to express or enhance several adhesion or costimulatory molecules. This phenotypic shift, under proinflammatory cytokines, seems to be related to functional consequences for antigen presentation to T cells. The sensory neuropeptide substance P (SP), present at high levels, is able to act on FLS proliferation and enzyme secretion. These data led us to investigate whether SP could also provoke a phenotypic change of FLS. Using flow cytometry and a three-step cellular ELISA method, we determined whether SP has an influence on the expression of MHC class II, intercellular adhesion molecule-1 (ICAM-1), VCAM-1, LFA-3, CD40, B7.1 or B7.2 molecules on RA FLS incubated with interferon-gamma (IFN-gamma) or IL-1beta or tumour necrosis factor-alpha (TNF-alpha) with or without SP. Our results indicate that SP potentiates the effect of proinflammatory cytokines on the expression of VCAM-1 on RA FLS. We verified the presence of specific SP (NK1) receptor mRNA. Using reverse transcription-polymerase chain reaction, we showed that RA FLS of patients express NK1 receptor mRNA. These results suggest that SP increase of cytokine-induced VCAM-1 expression acts via this specific SP receptor. Thus, during chronic inflammation RA FLS are at the interface between the immune and the nervous systems.
Beyond <i>DSM</i> : Seeking a Brain-Based Classification of Mental Illness (2010)

Harnessing knowledge gained from modern research in neuroscience and genetics to improve the diagnosis of psychiatric disorders was a major impetus for undertaking a revision of the Diagnostic and Statistical Manual of Mental Disorders ( DSM ).
Optimal Shift Scheduling with Multiple Break Windows (1996)

This paper presents a new integer programming model for optimal shift scheduling with multiple rest and lunch breaks, and break windows. A set-covering approach for this problem was originally developed by Dantzig (1954). Since then, a number of set-covering-based formulations have been proposed in the literature. These formulations require an integer variable for every shift type, shift start time, and rest/lunch break placement combination. Unfortunately, the number of integer variables required is rather large, making them impractical to solve for an optimal solution in most applications. We present a new approach in which a set of break variables is introduced for every shift-break type combination to determine the break placements. This approach leads to a significantly improved integer programming model requiring substantially smaller number of variables and computer memory. We tested the proposed approach with 40 test problems involving between 1,728 and 8,640 shift variations, and five demand patterns. Our results showed that the proposed formulation is very useful in solving large shift scheduling problems optimally.
Probing the substrate binding site of <i>Candida tenuis</i> xylose reductase (AKR2B5) with site-directed mutagenesis (2005)

Little is known about how substrates bind to CtXR (Candida tenuis xylose reductase; AKR2B5) and other members of the AKR (aldo-keto reductase) protein superfamily. Modelling of xylose into the active site of CtXR suggested that Trp23, Asp50 and Asn309 are the main components of pentose-specific substrate-binding recognition. Kinetic consequences of site-directed substitutions of these residues are reported. The mutants W23F and W23Y catalysed NADH-dependent reduction of xylose with only 4 and 1% of the wild-type efficiency (kcat/K(m)) respectively, but improved the wild-type selectivity for utilization of ketones, relative to xylose, by factors of 156 and 471 respectively. Comparison of multiple sequence alignment with reported specificities of AKR members emphasizes a conserved role of Trp23 in determining aldehyde-versus-ketone substrate selectivity. D50A showed 31 and 18% of the wild-type catalytic-centre activities for xylose reduction and xylitol oxidation respectively, consistent with a decrease in the rates of the chemical steps caused by the mutation, but no change in the apparent substrate binding constants and the pattern of substrate specificities. The 30-fold preference of the wild-type for D-galactose compared with 2-deoxy-D-galactose was lost completely in N309A and N309D mutants. Comparison of the 2.4 A (1 A=0.1 nm) X-ray crystal structure of mutant N309D bound to NAD+ with the previous structure of the wild-type holoenzyme reveals no major structural perturbations. The results suggest that replacement of Asn309 with alanine or aspartic acid disrupts the function of the original side chain in donating a hydrogen atom for bonding with the substrate C-2(R) hydroxy group, thus causing a loss of transition-state stabilization energy of 8-9 kJ/mol.