gebhart/patrepeval huggingface dataset:
A Proline-Hinge Alters the Characteristics of the Amphipathic α-helical AMPs (2013)

HP (2-20) is a 19-aa, amphipathic, a-helical peptide with antimicrobial properties that was derived from the N-terminus of Helicobacter pylori ribosomal protein L1. We previously showed that increasing the net hydrophobicity of HP (2-20) by substituting Trp for Gln 17 and Asp 19 (Anal 3) increased the peptide's antimicrobial activity. In hydrophobic medium, Anal 3 forms an amphipathic structure consisting of an N-terminal random coil region (residues 2-5) and an extended helical region (residues 6-20). To investigate the structure-activity relationship of Anal 3, we substituted Pro for Glu 9 (Anal 3-Pro) and then examined the new peptide's three-dimensional structure, antimicrobial activity and mechanism of action. Anal 3-Pro had an a-helical structure in the presence of trifluoroethanol (TFE) and sodium dodecyl sulfate (SDS). NMR spectroscopic analysis of Anal 3-Pro's tertiary structure in SDS micelles confirmed that the kink potential introduced by Pro 10 was responsible for the helix distortion. We also found that Anal 3-Pro exhibited about 4 times greater antimicrobial activity than Anal 3. Fluorescence activated flow cytometry and confocal fluorescence microscopy showed that incorporating a Pro-hinge into Anal 3 markedly reduced its membrane permeability so that it accumulated in the cytoplasm without remaining in the cell membrane. To investigate the translocation mechanism, we assessed its ability to release of FITC-dextran. The result showed Anal 3-Pro created a pore ,1.8 nm in diameter, which is similar to buforin II. Notably, scanning electron microscopic observation of Candida albicans revealed that Anal 3-Pro and buforin II exert similar effects on cell membranes, whereas magainin 2 exerts a different, more damaging, effect. In addition, Anal 3-Pro assumed a helix-hinge-helix structure in the presence of biological membranes and formed micropores in both bacterial and fungal membranes, through which it entered the cytoplasm and tightly bound to DNA. These results indicate that the bending region of Anal 3-Pro peptide is prerequisite for effective antibiotic activity and may facilitate easy penetration of the lipid bilayers of the cell membrane.
Effectiveness of a Nonselective ET<sub>A/B</sub>and a Selective ET<sub>A</sub>Antagonist in Rats With Monocrotaline-Induced Pulmonary Hypertension (2001)

Background —Both nonselective ET A/B receptor and selective ET A receptor antagonists can reduce pulmonary hypertension (PH) and right ventricular hypertrophy (RVH) in various animal models. Depending on their net effects after blockade of endothelial and smooth muscle ET B receptors, nonselective ET A/B antagonists could be more or less effective than selective ET A antagonists. Methods and Results —Two weeks after injection of saline or 60 mg/kg monocrotaline (MCT), rats received 50 mg · kg −1 · d −1 of a selective ( LU135252 ) or nonselective (BSF420627) antagonist for 3 weeks. This resulted in 4 groups: control (n=15), MCT (n=60), MCT+ET A (n=39), and MCT+ET A/B (n=40). Five-week survival was 35% in the MCT group; this was increased to 56% in the MCT+ET A group ( P =0.10) and to 67% in the MCT+ET A/B group ( P =0.0015). Drug administration was stopped 48 hours before hemodynamic measurements to evaluate the chronic effects of therapy: PH in the MCT group (RV systolic pressure 87±1 mm Hg) was improved similarly in both MCT+ET A and MCT+ET A/B groups (72±3 and 70±3 mm Hg, respectively, P <0.05). Severe RVH in the MCT group (RV/left ventricle+septum weight ratio 73±1%) was not affected by the selective antagonist (70±2%) but was reduced to 54±2% in the MCT+ET A/B group ( P <0.01). Pulmonary resistive properties, assessed from isolated lung pressure-flow relationships, were improved similarly in survivors from both treated groups. Conclusions —Both the nonselective ET A/B antagonist BSF420627 and the selective ET A antagonist LU135252 are effective in this model of PH. Similar direct comparative studies in other models of PH and with various dosage regimens are warranted to define the optimal pharmacological approach of PH when ET receptor antagonists are used.
A review of ionizing radiation effects in floating gate memories (2004)

The effects of ionizing radiation on microelectronics are traditionally a concern for devices intended for the space use, but they are becoming important even at ground level. Ionizing radiation effects can be broadly divided in two classes: total ionizing dose (progressive buildup of defects) and single event effects (macroscopic result of a single microscopic event). In both cases, ionizing radiation can lead to severe degradation of device performance, possibly resulting in device failure. This work is a review of literature results concerning both classes of ionizing radiation-related phenomena on floating gate memories. Regardless of its nature, ionizing radiation impacts two aspects of the performance and reliability of floating gate memories: the functionality and the adherence to specifications of the control circuitry, and the degradation of stored information in the array itself.
Nef and Gag Synthetic Peptide Priming of Antibody Responses to HIV Type 1 Antigens in Mice and Primates (1994)

T epitope mapping in human immunodeficiency virus proteins provides a useful tool for AIDS vaccine design. We have previously shown that four peptides selected from the Gag polyprotein of HIV-1 were able to prime mice for in vitro lymphoproliferative responses. These responses were shown to be MHC restricted, and a pool of these peptides was able to prime mice for a subsequent humoral response to HIV-1 Gag proteins. Here we show that two of these Gag peptides are able to prime the anti-HIV-1 IgG response to heat-inactivated HIV-1 in B10Sc.Cr mice. Furthermore, we extended this study in the nonhuman primate model, and show efficient priming of the IgG response to heat-inactivated HIV-1 using the pool of four Gag peptides in baboons. Further mapping of "nonself" peptides is extended to the HIV-1 Nef protein. Three potential Nef T epitopes located at positions 137-145, 98-107, and 81-95 are also shown to prime the IgG response to HIV-1 in the mouse model, although T cell proliferation to recall peptides in vitro was not detectable. Although they have not yet been defined as major helper T epitopes in humans, using classic in vitro stimulation assays, the fact that most of them are able to prime IgG responses in animals without detectable in vitro proliferative responses does not rule out their functional helper capacity in humans.
Static and electronic shaping of the radiated electromagnetic fields in radial arrays of substrate integrated leaky-wave antennas (2013)

This contribution describes how leaky waves can be malleably modulated in substrate integrated waveguide (SIW) antennas. It is the first time that such flexible and unconventional tapering of the leaky modes is demonstrated in a practical leaky-wave antenna (LWA) structure. The synthesis theory is based on the dispersion engineering of the radiative leaky mode. It is explained how this procedure provides, in a systematic and efficient manner, the requested modulation of the SIW geometry along its length. As a result, unseen shaping of the radiated fields with LWAs is achieved. This is demonstrated by several electrically-large designs at 15 GHz, to obtain highly focused radiation patterns both in near and far field regimes. Also, a radial-array configuration is described, which provides two-dimensional shaping of the radiated fields. Finally, it is anticipated how these antennas can be electronically controlled. In this way, it is foreseen a new type of high-gain, low-cost, single-layer, planar reconfigurable antennas, which are simply fed and directly integrated with the RF front-end.
Expression of p14ARF overcomes tumor resistance to p53. (2002)

Tumors without p53 mutation are often resistant to p53 gene therapy. We examined the mechanism using p53-resistant A549 cells and p53-sensitive H1299 cells. We found that p53 delivered by adenovirus is poorly expressed in A549 (ARF-null) cells but efficiently expressed in H1299 cells (ARF-positive). Strong p53 expression and apoptosis can be achieved in A549 cells using a p53 mutant resistant to degradation by MDM2 or by coexpression of ARF. The results suggest that enhanced MDM2 activity attributable to loss of ARF contributes to p53 resistance. Surprisingly, tumor cell lines with MDM2 gene amplification are still deficient for ARF expression, suggesting that MDM2 amplification does not substitute for ARF inactivation during tumor development.
Membrane-based sensor measures pollutants present in aqueous or gaseous environments (2008)

Membrane-based micro-sensors capable of measuring pollutants present in aqueous or gaseous environments are being developed in the USA at the Georgia Institute of Technology. Based on information available from the institute's Research News & Publications Office this brief feature article provides details of how these sensors work, the way in which they use polymer membranes, and potential applications.
Is durable macrochimerism key to achieving clinical transplantation tolerance? (2011)

aInstitute for Cellular Therapeutics bDepartment of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky, USA cComprehensive Transplant Center, Northwestern Memorial Hospital, Chicago, Illinois, USA Correspondence to Suzanne T. Ildstad, MD, Director, Institute for Cellular Therapeutics, Jewish Hospital, Distinguished Professor of Transplantation, Professor of Surgery, Physiology, Immunology, University of Louisville, 570 South Preston Street, Suite 404 Louisville, KY 40202-1760, USA Tel: +1 502 852 2080; fax: +1 502 852 2079; e-mail: [email protected]
MicroRNA-142-3p Negatively Regulates Canonical Wnt Signaling Pathway (2016)

Wnt/β-catenin signaling pathway plays essential roles in mammalian development and tissue homeostasis. MicroRNAs (miRNAs) are a class of regulators involved in modulating this pathway. In this study, we screened miRNAs regulating Wnt/β-catenin signaling by using a TopFlash based luciferase reporter. Surprisingly, we found that miR-142 inhibited Wnt/β-catenin signaling, which was inconsistent with a recent study showing that miR-142-3p targeted Adenomatous Polyposis Coli (APC) to upregulate Wnt/β-catenin signaling. Due to the discordance, we elaborated experiments by using extensive mutagenesis, which demonstrated that the stem-loop structure was important for miR-142 to efficiently suppress Wnt/β-catenin signaling. Moreover, the inhibitory effect of miR-142 relies on miR-142-3p rather than miR-142-5p. Further, we found that miR-142-3p directly modulated translation of Ctnnb1 mRNA (encoding β-catenin) through binding to its 3' untranslated region (3' UTR). Finally, miR-142 was able to repress cell cycle progression by inhibiting active Wnt/β-catenin signaling. Thus, our findings highlight the inhibitory role of miR-142-3p in Wnt/β-catenin signaling, which help to understand the complex regulation of Wnt/β-catenin signaling.
Prediction of catastrophes: An experimental model (2012)

Catastrophes of all kinds can be roughly defined as short-duration, large-amplitude events following and followed by long periods of "ripening." Major earthquakes surely belong to the class of "catastrophic" events. Because of the space-time scales involved, an experimental approach is often difficult, not to say impossible, however desirable it could be. Described in this article is a "laboratory" setup that yields data of a type that is amenable to theoretical methods of prediction. Observations are made of a critical slowing down in the noisy signal of a solder wire creeping under constant stress. This effect is shown to be a fair signal of the forthcoming catastrophe in two separate dynamical models. The first is an "abstract" model in which a time-dependent quantity drifts slowly but makes quick jumps from time to time. The second is a realistic physical model for the collective motion of dislocations (the Ananthakrishna set of equations for unstable creep). Hope thus exists that similar changes in the response to noise could forewarn catastrophes in other situations, where such precursor effects should manifest early enough.
Intron retention resulting from a silent mutation in the VWF gene that structurally influences the 5′ splice site (2016)

Disease-associated silent mutations are considered to affect the accurate pre-messenger RNA (mRNA) splicing either by influencing regulatory elements, leading to exon skipping, or by creating a new cryptic splice site. This study describes a new molecular pathological mechanism by which a silent mutation inhibits splicing and leads to intron retention. We identified a heterozygous silent mutation, c.7464C>T, in exon 44 of the von Willebrand factor (VWF) gene in a family with type 1 von Willebrand disease. In vivo and ex vivo transcript analysis revealed an aberrantly spliced transcript, with intron 44 retained in the mRNA, implying disruption of the first catalytic step of splicing at the 5' splice site (5'ss). The abnormal transcript with the retained intronic region coded a truncated protein that lacked the carboxy-terminal end of the VWF protein. Confocal immunofluorescence characterizations of blood outgrowth endothelial cells derived from the patient confirmed the presence of the truncated protein by demonstrating accumulation of VWF in the endoplasmic reticulum. In silico pre-mRNA secondary and tertiary structure analysis revealed that this substitution, despite its distal position from the 5'ss (85 bp downstream), induces cis alterations in pre-mRNA structure that result in the formation of a stable hairpin at the 5'ss. This hairpin sequesters the 5'ss residues involved in U1 small nuclear RNA interactions, thereby inhibiting excision of the pre-mRNA intronic region. This study is the first to show the allosteric-like/far-reaching effect of an exonic variation on pre-mRNA splicing that is mediated by structural changes in the pre-mRNA.
Lactate in human sweat: a critical review of research to the present day (2012)

This review provides a critical overview of the literature published in the area of lactate in human sweat between 1934 and the present. The first section summarizes the relevant pieces of literature, the second evaluates the literature across a range of topics and the third presents potential applications for sweat lactate measurements. Key factors that may affect sweat lactate are discussed in detail in the second section of this review. Both acetylcholine and catecholamine hormonal signals can trigger sweating independently of one another; differences in sweat output and lactate concentrations are compared. The primary triggers for sweating, exercise and heat are also compared, with exercise-induced sweating being further examined with respect to the exercise intensity. This review examines the significant variations in sweat lactate between bodily sites as well the relationship to physiological parameters such as gender, age and physical fitness, along with the effect of climate adaptation on sweat lactate concentrations.
Manifold learning for image-based breathing gating in MRI (2011)

Respiratory motion is a challenging factor for image-guided procedures in the abdominal region. Target localization, an important issue in applications like radiation therapy, becomes difficult due to this motion. Therefore, it is necessary to detect the respiratory signal to have a higher accuracy in planning and treatment. We propose a novel image-based breathing gating method to recover the breathing signal directly from the image data. For the gating we use Laplacian eigenmaps, a manifold learning technique, to determine the low-dimensional manifold embedded in the high-dimensional space. Since Laplacian eigenmaps assign each 2D MR slice a coordinate in a low-dimensional space by respecting the neighborhood relationship, they are well suited for analyzing the respiratory motion. We perform the manifold learning on MR slices acquired from a fixed location. Then, we use the resulting respiratory signal to derive a similarity criterion to be used in applications like 4D MRI reconstruction. We perform experiments on liver data using one and three dimensions as the dimension of the manifold and compare the results. The results from the first case show that using only one dimension as the dimension of the manifold is not enough to represent the complex motion of the liver caused by respiration. We successfully recover the changes due to respiratory motion by using three dimensions. The proposed method has the potential of reducing the processing time for the 4D reconstruction significantly by defining a search window for a subsequent registration approach. It is fully automatic and does not require any prior information or training data.
Likelihood methods for MPSK modulation classification (1995)

New algorithms based on the likelihood functional (LF) and approximations thereof are proposed for the problem of classifying MPSK modulations in additive white Gaussian noise. Previously introduced classifiers for this problem are theoretically interpreted as simplified versions of the ones in here. The performance of a single-term approximation to the optimal LF classifier is evaluated analytically and is shown to be very close to that of the optimal. Furthermore, recursive algorithms for the implementation of this new quasi-log-likelihood-ratio (qLLR) classifier are derived which imply no significant increase in classifier complexity. The present method of generating classification algorithms can be generalized to arbitrary two-dimensional signal constellations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<title>Cylindrical large computer-generated holograms and hidden-point removal process</title> (1996)

We have been making researches on 3D displays using computer-generated holograms (CGHs). Our CGHs are binary Fresnel holograms that reconstruct point light sources and are recorded by using high resolution laser printers (image setters). The image setters have the resolution of 3600 or 5080 dots per inch (7.1 or 5.0 micron dot width). The resolution is lower than that of photo reduction, but it has wide drawing area, and it is not expensive to draw large CGH patterns on a high contrast film. In this paper, we present an approach to making cylindrical large CGHs and hidden-point removal process. The number of reconstructible point light sources is considered to be restricted due to the low resolution of the printer. To improve this restriction and to make larger displays, we propose a method arranging plural CGHs cylindrically that reconstruct divided objects. For improving the depth of the objects reconstructed from the CGHs, we consider it is necessary to apply hidden-point removal process to our CGH calculation. Whether a certain point object is visible or not from a point of view depends on the existence of the interference fringes on the CGH plane.
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags (2010)

Intense interest centers on the role of the human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study of methods for surveying bacterial communities in human feces using 454/Roche pyrosequencing of 16S rRNA gene tags. We analyzed fecal samples from 10 individuals and compared methods for storage, DNA purification and sequence acquisition. To assess reproducibility, we compared samples one cm apart on a single stool specimen for each individual. To analyze storage methods, we compared 1) immediate freezing at -80 degrees C, 2) storage on ice for 24 or 3) 48 hours. For DNA purification methods, we tested three commercial kits and bead beating in hot phenol. Variations due to the different methodologies were compared to variation among individuals using two approaches--one based on presence-absence information for bacterial taxa (unweighted UniFrac) and the other taking into account their relative abundance (weighted UniFrac). In the unweighted analysis relatively little variation was associated with the different analytical procedures, and variation between individuals predominated. In the weighted analysis considerable variation was associated with the purification methods. Particularly notable was improved recovery of Firmicutes sequences using the hot phenol method. We also carried out surveys of the effects of different 454 sequencing methods (FLX versus Titanium) and amplification of different 16S rRNA variable gene segments. Based on our findings we present recommendations for protocols to collect, process and sequence bacterial 16S rDNA from fecal samples--some major points are 1) if feasible, bead-beating in hot phenol or use of the PSP kit improves recovery; 2) storage methods can be adjusted based on experimental convenience; 3) unweighted (presence-absence) comparisons are less affected by lysis method.
Monitoring irrigation water application with computerized controllers (2009)

Presented at Proceedings of the 23rd annual Central Plains irrigation conference held in Burlington, Colorado on February 22-23, 2011.
Cross-Presentation of the Long-Lived Lymphocytic Choriomeningitis Virus Nucleoprotein Does Not Require Neosynthesis and Is Enhanced via Heat Shock Proteins (2005)

Many viral proteins that contain MHC class I-restricted peptides are long-lived, and it is elusive how they can give rise to class I epitopes. Recently, we showed that direct presentation of an epitope of the long-lived lymphocytic choriomeningitis virus nucleoprotein (LCMV-NP) required neosynthesis in accordance with the defective ribosomal products hypothesis. In this study, we report that LCMV-NP can be cross-primed in mice using either LCMV-NP-transfected human HEK293 or BALB/c-derived B8 cells as Ag donor cells. In addition, we establish that contrary to direct presentation, cross-presentation required accumulation of the mature LCMV-NP and could not be sustained by the newly synthesized LCMV-NP protein, intermediate proteasomal degradation products, or the minimal NP396 epitope. Nevertheless, NP cross-presentation was enhanced by heat shock and was blunted by inhibitors of heat shock protein 90 and gp96. We propose that cross-presentation has evolved to sustain the presentation of stable viral proteins when their neosynthesis has ceased in infected donor cells.
Endoquiz (2006)

Bei einer 29-jährigen Patientin bestanden seit Monaten Schmerzen beim Schlucken, die bereits zu einer deutlichen Gewichtsabnahme geführt hatten.
Estimating the albedo map of a face from a single image (2005)

This paper describes how a facial albedo map can be recovered from a single image using a statistical model that captures variations in surface normal direction. We fit the model to intensity data using constraints on the surface normal direction provided by Lambert's law and then use the differences between observed and reconstructed image brightness to estimate the albedo map. We show that this process is stable under varying illumination and use the process to render images under novel illumination.