gebhart/patrepeval huggingface dataset:
A single amino acid change in a myelin basic protein peptide confers the capacity to prevent rather than induce experimental autoimmune encephalomyelitis. (1991)

Experimental autoimmune encephalomyelitis (EAE) is an experimental demyelinating disease of rodents. In (PL/J x SJL) F1 mice, it is induced by immunization with the myelin basic protein peptide Ac1-11. Ac1-11 [4A], a myelin basic protein peptide analog with a single amino acid substitution, (i) binds to class II major histocompatibility complex molecules and stimulates encephalitogenic T cells in vitro better than Ac1-11, (ii) is nonimmunogenic and nonencephalitogenic in vivo in (PL/J x SJL)F1 mice, (iii) prevents EAE when administered before or at the time of immunization with Ac1-11, and (iv) prevents EAE when administered later, near the time of disease onset. Initial studies suggest that Ac1-11 [4A] does not prevent EAE by competitive inhibition or by activation of regulatory cells. Thus, substitution of a single amino acid in a myelin basic protein peptide confers the capacity to prevent rather than induce EAE, even after peptide-specific encephalitogenic T cells have been activated.
A Novel DNA Polymerase Family Found inArchaea (1998)

One of the most puzzling results from the complete genome sequence of the methanogenic archaeon Methanococcus jannaschii was that the organism may have only one DNA polymerase gene. This is because no other DNA polymerase-like open reading frames (ORFs) were found besides one ORF having the typical alpha-like DNA polymerase (family B). Recently, we identified the genes of DNA polymerase II (the second DNA polymerase) from the hyperthermophilic archaeon Pyrococcus furiosus, which has also at least one alpha-like DNA polymerase (T. Uemori, Y. Sato, I. Kato, H. Doi, and Y. Ishino, Genes Cells 2:499-512, 1997). The genes in M. jannaschii encoding the proteins that are homologous to the DNA polymerase II of P. furiosus have been located and cloned. The gene products of M. jannaschii expressed in Escherichia coli had both DNA polymerizing and 3'-->5' exonuclease activities. We propose here a novel DNA polymerase family which is entirely different from other hitherto-described DNA polymerases.
Expression of mRNAs for telomeric repeat binding factor (TRF)-1 and TRF2 in atypical adenomatous hyperplasia and adenocarcinoma of the lung. (2003)

These results are consistent with (but are not enough to confirm) the idea that high-grade AAH is closely related to BAC.
Ultrastructural changes seen after ALA‐IPL photorejuvenation: A pilot study (2005)

This small pilot study is the first to focus on the ultrastructural changes seen after ALA-IPL photorejuvenation. We found a greater shift toward type I collagen synthesis in the ALA-IPL group compared to the IPL group. The addition of ALA to IPL treatment for photorejuvenation may be superior to IPL alone.
A perceptually based physical error metric for realistic image synthesis (1999)

We introduce a new concept for accelerating realistic image synthesis algorithms. At the core of this procedure is a novel physical error metric that correctly predicts the perceptual threshold for detecting artifacts in scene features. Built into this metric is a computational model of the human visual system's loss of sensitivity at high background illumination levels, high spatial frequencies, and high contrast levels (visual masking). An important feature of our model is that it handles the luminance-dependent processing and spatiallydependent processing independently. This allows us to precompute the expensive spatially-dependent component, making our model extremely efficient. We illustrate the utility of our procedure with global illumination algorithms used for realistic image synthesis. The expense of global illumination computations is many orders of magnitude higher than the expense of direct illumination computations and can greatly benefit by applying our perceptually based technique. Results show our method preserves visual quality while achieving significant computational gains in areas of images with high frequency texture patterns, geometric details, and lighting variations.
Friedel–Crafts‐Type Mechanism for the Enzymatic Elimination of Ammonia from Histidine and Phenylalanine (2005)

The surprisingly high catalytic activity and selectivity of enzymes stem from their ability to both accelerate the target reaction and suppress competitive reaction pathways that may even be dominant in the absence of enzymes. For example, histidine and phenylalanine ammonia-lyases (HAL and PAL) trigger the abstraction of the nonacidic beta protons of these amino acids while leaving the much more acidic ammonium hydrogen atoms untouched. Both ammonia-lyases have a catalytically important electrophilic group, which was believed to be dehydroalanine for 30 years but has now been revealed by X-ray crystallography and UV spectroscopy to be a highly electrophilic 5-methylene-3,5-dihydroimidazol-4-one (MIO) group. Experiments suggest that the reaction is initiated by the electrophilic attack of MIO on the aromatic ring of the substrate. This incomplete Friedel-Crafts-type reaction leads to the activation of a beta proton and its stereospecific abstraction, followed by the elimination of ammonia and regeneration of the MIO group. The plausibility of such a mechanism is supported by a synthetic model. The application of the PAL reaction in the biocatalytic synthesis of enantiomerically pure alpha-amino beta-aryl propionates from aryl acrylates is also discussed.
Effect of Drilling Fluid Properties on Rate of Penetration (2009)

The scope of this work is to determine the effect of drilling fluid properties on penetration rate in a field using daily drilling reports. Based on our field studies the following drilling fluid properties affect penetration rate to varying degrees: mud weight, plastic viscosity and solid content. The result of this study shows that the net effect of drilling fluid properties on penetration rate is less than what it thought to be. Penetration rate is decreased by increasing plastic viscosity, solid content and mud weight. Decreasing the penetration rate is more attributed to increase of depth, because by increasing the depth, rock strength increases and porosity decreases.
GENETIC MANIPULATION OF MICROORGANISMS: POTENTIAL BENEFITS AND BIOHAZARDS (1976)

POTENTIAL BENEFITS . Introduction . Acquisition of Basic Knowledge . . . . ..... . . . . . . . . . Applications of Technology . . . . . . . POTENTIAL BIOHAZARDS . Introduction ... . . . . . . . . . . . . . . . ... . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . .... . . . . Factors Affecting the Probability of Escape oj Chimeric Microorganisms ... . . . . . . . . . . . Factors Affecting the Probability oj Survival and Perpetuation oj Recombinant DNA . . . . . . . . . Factors Affecting Probable Consequences oj Escape and Survival of Recombinant DNA Molecules . . . . . . . . . . . . . . . ..... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ......... . Estimating the Probability oj Manifestation oj Adverse Consequences by Recombinant DNA Molecules . . . .... .... . . .
Biochemical and Pharmacological Characterization of YM-60828, a Newly Synthesized and Orally Active Inhibitor of Human Factor Xa (1998)

YM-60828 was found to potently inhibit human factor Xa following oral administration. YM-60828 showed high affinity for factor Xa (Ki = 1.3 nM), but did not affect thrombin (Ki > 100 microM). YM-60828 doubled factor Xa clotting time, prothrombin time (PT) and activated partial thromboplastin time (APTT) at 0.10, 0.21, 0.24 microM, respectively. Importantly, it did not prolong thrombin time at 100 microM. YM-60828 also inhibited factor Xa in the prothrombinase complex with an IC50 value of 7.7 nM. In addition to its anticoagulant activity, YM-60828 inhibited platelet aggregation induced by various agonists (IC50 = 3 to 23 microM). Squirrel monkeys were used to study the ex vivo anticoagulant activity and pharmacokinetic properties of YM-60828. One hour after oral administration at 3 mg/kg, YM-60828 strongly prolonged PT and APTT by 4.8- and 1.9-fold, respectively, and plasma concentration reached 788 +/- 167 ng/ml. Bioavailability was calculated to be 20.3%. These results strongly suggest that YM-60828 will be a valuable orally active and potent anticoagulant agent showing potential antithrombotic activity.
Studies Dealing with Thionium Ion Promoted Mannich Cyclization Reactions (2000)

Treatment of several amido-substituted thioacetals with dimethyl(methylthio)sulfonium tetrafluoroborate (DMTSF) produces synthetically useful thionium ions that are intercepted by the adjacent nitrogen atom to afford both five- and six-membered alkylthio-substituted lactams as transient intermediates. Further reaction of the alkylthio-substituted lactam with DMTSF generates an N-acyliminium ion, which undergoes cyclization with the tethered aromatic ring to produce an azapolycyclic ring system. Related cyclization sequences occur when amido thioacetals possessing simple olefinic tethers were used. The overall procedure represents an efficient one-pot approach toward various nitrogen-containing ring systems. The cyclization reaction was employed for a synthesis of the core skeleton of the erythrina alkaloid family.
Thin Film Structure of Triisopropylsilylethynyl‐Functionalized Pentacene and Tetraceno[2,3‐b]thiophene from Grazing Incidence X‐Ray Diffraction (2010)

The specific molecular arrangement of triisopropylsilylethynyl (TIPS)-functionalized acenes is widely considered to be the origin of the high performance of TIPS-pentacene thin film devices. However, detailed information on the molecular packing is so far only available for bulk single crystals, and the molecular packing of TIPS-functionalized acenes in thin films has not been directly determined to date. A combination of ultrabright synchrotron grazing incidence X-ray diffraction (GIXD) and crystallographic refinement calculations is utilized to obtain precise information about the molecular packing of two high-performance TIPS-functionalized semiconductors, TIPS- tetraceno[2,3-b]thiophene and TIPS-pentacene, in thin films on silicon oxide. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Bacterial Adhesion to Oral Tissues: A Model for Infectious Diseases (1989)

The majority of bacteria which colonize humans display sharp host and tissue tropisms; consequently, relatively little is known about how they initiate colonization on mucosal surfaces. The mouth has a variety of features which have enabled it to serve as a useful model for the discovery of basic principles of host-parasite interactions occurring in mucosal environments. Early studies demonstrated that indigenous bacteria attach to surfaces of the mouth in a highly selective manner; attachment was often observed to correlate with colonization. These studies led to the recognition that bacterial attachment is an essential step for colonization in environments which contain surfaces exposed to a fluid flow. Bacterial adhesion has subsequently grown into a major area of infectious disease research. Many bacteria have been found to possess proteinaceous components, called "adhesins", on their surfaces which bind in a stereochemically specific manner to complementary molecules, or "receptors", on the tissue surface. Adhesins are often lectins which bind to saccharide receptors, but some adhesins are thought to bind to proteinaceous receptors. Studies of components of human saliva, which adsorb to hydroxyapatite (HA) surfaces similar to those of teeth, and promote the attachment of prominent plaque bacteria, have revealed that the acidic proline-rich proteins (PRPs) promote the attachment of several important bacteria. These include strains of Actinomyces viscosus, Bacteroides gingivalis, some strains of Streptococcus mutans, and others. The salivary PRP's are a unique family of molecules. However, segments of PRPs are structurally related to collagen. This may be significant, since B. gingivalis and certain cariogenic streptococci bind to collagenous substrata, and such interactions may facilitate their invasion into gingival tissues, or into dentin or cementum, respectively. Another unexpected observation was that although A. viscosus and other bacteria bind avidly to PRPs adsorbed onto apatitic surfaces, they do not interact with PRPs in solution. PRP molecules evidently undergo a conformational change when they adsorb to HA, and adhesins of A. viscosus recognize cryptic segments which are only exposed in adsorbed molecules. This provides the bacteria with a mechanism for efficiently attaching to teeth while suspended in saliva. It also offers a molecular explanation for their sharp tropisms for human teeth. It has proven convenient to refer to such hidden receptors for bacterial adhesins as "cryptitopes" (from cryptic, meaning hidden, and topo, meaning place).(ABSTRACT TRUNCATED AT 400 WORDS)
Chromosome arm 20q gains and other genomic alterations in esophageal squamous cell carcinoma, as analyzed by comparative genomic hybridization and fluorescence in situ hybridization. (2004)

These findings provide evidence for a number of previously unknown genomic aberrations in esophageal squamous cell carcinoma, suggesting the existence of target regions relevant to its progression. Esophageal squamous cell carcinoma with 20q gain showed extensive lung metastases, pleural effusion and liver metastases and poorer prognosis compared to cases without 20q gain. Our results suggest that amplification of BTAK or E2F1 are likely to lead to an increase in the number of malignant phenotypes of esophageal squamous cell carcinoma and that these aberrations can be expected to be useful as markers of poor prognosis.
Diarrheal deaths in American children. Are they preventable? (1988)

We reviewed national mortality data for 1973 through 1983 to assess the importance of diarrheal diseases as a cause of preventable childhood death in the United States. An average of 500 children aged 1 month to 4 years died each year with diarrhea reported as the cause of death. These diarrheal deaths were most common among children who were younger than 1 year of age, black, and living in the South, and were most common during the winter. In Mississippi, review of fatal cases of diarrhea identified maternal factors--black race, young age, unmarried status, low level of education, and little prenatal care--to be most associated with diarrheal death in the child. Fifty percent of these deaths occurred after a child had reached a medical facility. Our findings suggest that diarrheal deaths may be preventable and that targeted interventions could contribute to improved child survival in the United States.
An advanced demultiplexing system for physiological stimulation (1997)

A CMOS very large scale integration (VLSI) chip has been designed and built to implement a scheme developed for multiplexing/demultiplexing the signals required to operate an intracortical stimulating electrode array. Because the use of radio telemetry in a proposed system utilizing this chip may impose limits upon the rate of data transmission to the chip, the scheme described herein was used to reduce the amount of digital information which must be sent to control a large quantity (up to several hundred) of stimulating electrodes. By incorporating multiple current sources on chip, many channels may be stimulated simultaneously. By incorporating on-chip timers, control over pulse timing is assigned to the chip, reducing by up to fourfold the amount of control data which must be sent. By incorporating on-chip RAM, information associated with the desired stimulus amplitude and pulse timing can be stored on chip. In this manner, it is necessary to send control information to the chip only when the information changes, rather than at the stimulus repeat rate for each channel. This further reduces the data rate by a factor of five to ten times or more. The architecture described here, implemented as an eight-channel stimulator, is scalable to a 625-channel stimulator while keeping data transmission rates under 2 Mbps.
Patulin induces pro-survival functions via autophagy inhibition and p62 accumulation (2013)

Patulin (PAT) is one of the most common mycotoxins found in moldy fruits. Skin contact is one of the most likely exposure routes of PAT. Investigation of dermal toxicity of PAT is clearly needed and has been highlighted by WHO. In the present study, using human keratinocyte HaCaT cells as a model, we found that treatment with PAT caused an increased autophagosome accumulation. Measurements of autophagic flux demonstrated that the accumulation of autophagosomes by PAT was not directly due to enhanced autophagosome formation but due to inhibition of autophagosome degradation. Reductions in the activities of the lysosomal enzymes cathepsin B and cathepsin D by PAT might contribute to this inhibitory effect. Consistent with this, inhibition of autophagosome degradation by PAT resulted in accumulation of p62 that functioned as a pro-survival signal. The pro-survival function of p62 was found to be attributed to reactive oxygen species-mediated cytoprotective endoplasmic reticulum (ER) stress response. ER stress exerted cytoprotective effect via extracellular signal-regulated kinase1/2-dependent B-cell CLL/lymphoma 2-associated agonist of cell death inhibitory phosphorylation. Given the critical role of autophagy and its substrate p62 in carcinogenesis, our findings may have important implications in PAT-induced skin carcinogenesis.
1.55 µm vertical-cavity surface-emitting laserswith wafer-fused InGaAsP/InP-GaAs/AlAs DBRs (1996)

The authors propose a novel 1.55 µm vertical-cavity surface-emitting laser (VCSEL) structure with wafer-fused InGaAsP/InP-GaAs/AlAs distributed Bragg reflectors. The resonant-cavity wavelength before water fusion is in exact accord with the emission wavelength, and a 25 µm diameter VCSEL exhibits CW operation at 27°C.
Chalcogenide holey fibres (2000)

The fabrication of the first non-silica holey or microstructured optical fibre is reported. The chalcogenide glass gallium lanthanum sulphide was used. Applications of such fibres include optical switching, high power-delivery, acousto-optic devices, air-guiding fibres, fibre sensors, mid-IR devices, amongst others. In addition, holey fibre technology provides an improved route towards fabricating singlemode compound glass fibres.
A MODEL FOR SIMULATING RESIDENTIAL DEVELOPMENT (1965)

Abstract This article is the outgrowth of a long period of experimentation with models of residential and other development which focus on the individual decision-maker—the householder in search of a home, and the builder attempting to cater to his desires. The first part of the paper describes the means by which this process is simulated in a computer. Later parts of the paper indicate how this view of consumer behavior has led naturally into a consideration of households' activity patterns and into research on these patterns. In conclusion the author indicates by implication that the integration of these two approaches may lead in the direction of measurements of accessibility and of taking account of the competition fm desirable sites, of consequent increases in the intensity of utilization, and of the rents of these sites. Thus this article, in conjunction with others, illustrates a remarkable convergence between research starting at the level of individual decision units and coming to consider the larger framework, and research starting from gross changes in the metropolitan configuration and coming to give increasing consideration to the actual decision process.
Modeling the Endosomal Escape of Cell-Penetrating Peptides:  Transmembrane pH Gradient Driven Translocation across Phospholipid Bilayers (2005)

Cell-penetrating peptides (CPPs) are able to mediate the efficient cellular uptake of a wide range of cargoes. Internalization of a number of CPPs requires uptake by endocytosis, initiated by binding to anionic cell surface heparan sulfate (HS), followed by escape from endosomes. To elucidate the endosomal escape mechanism, we have modeled the process for two CPPs: penetratin (pAntp) and the N-terminal signal peptide of the unprocessed bovine prion protein (bPrPp). Large unilamellar phospholipid vesicles (LUVs) were produced encapsulating either peptide, and an ionophore, nigericin, was used to create a transmembrane pH gradient (DeltapH(mem), inside acidic) similar to the one arising in endosomes in vivo. In the absence of DeltapH(mem), no pAntp escape from the LUVs is observed, while a fraction of bPrPp escapes. In the presence of DeltapH(mem), a significant amount of pAntp escapes and an even higher degree of bPrPp escape takes place. These results, together with the differences in kinetics of escape, indicate different escape mechanisms for the two peptides. A minimum threshold peptide concentration exists for the escape of both peptides. Coupling of the peptides to a cargo reduces the fraction escaping, while complexation with HS significantly hinders the escape. Fluorescence correlation spectroscopy results show that during the escape process the LUVs are intact. Taken together, these results suggest a model for endosomal escape of CPPs: DeltapH(mem)-mediated mechanism, following dissociation from HS of the peptides, above a minimum threshold peptide concentration, in a process that does not involve lysis of the vesicles.
Design, development, and performance evaluation of a low-cost, low-power wake-up radio system for wireless sensor networks (2013)

Energy-efficient operation is a challenge for wireless sensor networks (WSNs). A common method employed for this purpose is duty-cycled operation, which extends battery lifetime yet incurs several types of energy wastes and challenges. A promising alternative to duty-cycled operation is the use of wake-up radio (WuR), where the main microcontroller unit (MCU) and transceiver, that is, the two most energy-consuming elements, are kept in energy-saving mode until a special signal from another node is received by an attached, secondary, ultra-low power receiver. Next, this so-called wake-up receiver generates an interrupt to activate the receiver node's MCU and, consequently, the main radio. This article presents a complete wake-up radio design that targets simplicity in design for the monetary cost and flexibility concerns, along with a good operation range and very low power consumption. Both the transmitter (WuTx) and the receiver (WuRx) designs are presented with the accompanying physical experiments for several design alternatives. Detailed analysis of the end system is provided in terms of both operational distance (more than 10 m) and current consumption (less than 1 μA). As a reference, a commercial WuR system is analyzed and compared to the presented system by expressing the trade-offs and advantages of both systems.