gebhart/patrepeval huggingface dataset:
Developmental expression of binding sites and messenger ribonucleic acid for vascular endothelial growth factor suggests a role for this protein in vasculogenesis and angiogenesis. (1993)

Vascular endothelial growth factor (VEGF) is an endothelial cell mitogen and angiogenic inducer produced by a variety of cell lines and tissues. As a soluble protein that exhibits a unique target cell specificity for vascular endothelial cells, VEGF has the potential to play an important role in the development of the vascular system. To better understand the role of VEGF in the processes of vasculogenesis and embryonic angiogenesis, patterns of mRNA expression and [125I]VEGF-binding sites were examined in sections of rat embryos and surrounding tissues during the early stages of development. In situ hybridization revealed the most intense hybridization of VEGF mRNA in the giant trophoblast cells and the mesometrium of early postimplantation specimens. In contrast, only low levels of expression were detected in the embryo until later in embryonic development. Possible embryonic targets for this secreted protein, as identified by displaceable [125I] VEGF binding, were found in association with the early egg sac at E8 and evident in hemangioblasts (blood islands) within the yolk sac at E8-E11. In addition, at all stages, binding was observed along the lumina of blood vessels, of both maternal and embryonic origin. These results provide evidence to support the hypothesis that VEGF plays an important role in the normal development of the embryo and supporting tissues. In the presence of ubiquitous and persistent high affinity binding sites on vascular endothelial cells and precursors, the growth of the vascular system may be regulated in early development by regional expression of VEGF by trophoblast and maternally derived cells, and later on by cells within the embryo as they develop their differentiated phenotype.
In vitro Uptake and Stability Study of pVEC and Its All-D Analog (2003)

A key step in the development of new hydrophilic pharmaceuticals is to get them through biological barriers. Cell-penetrating peptides, CPPs, have been shown previously to enter cells both in vitro and in vivo by a non-endocytotic mechanism and to be able to carry large cargo molecules with them. Recently, we showed that a small peptide, pVEC, from murine vascular endothelial cadherin, has the characteristics to be classified as a protein derived CPP. Here we have further investigated pVEC together with its all-D analog for cellular uptake, intra- and extracellular stability, and their enzymatic degradation. The two peptides, pVEC and all-D pVEC, translocate into aortic endothelial cells and murine fibroblasts by a non-endocytotic mechanism. In phosphate buffer, pVEC remains intact while the C-terminal lysine is quickly removed in human serum and serum-containing media. Both pVEC and pVEC without the C-terminal Lys were detected by mass spectrometry inside the two cell types tested. The pVEC half-life is 10.5 min in phosphate buffer containing 10 units of trypsin and 44.6 min in phosphate buffer containing 4.2 units of carboxypeptidase A and 18 units of carboxypeptidase B. In contrast topVEC, the all-D analog remains intact in serum and resists enzymatic degradation.
Thin-ribbon tapered coupler for dielectric waveguides (1994)

A recent discovery shows that a high-dielectric constant, low-loss, solid material can be made into a ribbon-like waveguide structure to yield an attenuation constant of less than 0.02 dB/m for single-mode guidance of millimeter/submillimeter waves. One of the crucial components that must be invented in order to guarantee the low-loss utilization of this dielectric-waveguide guiding system is the excitation coupler. The traditional tapered-to-a-point coupler for a dielectric rod waveguide fails when the dielectric constant of the dielectric waveguide is large. This article presents a new way to design a low-loss coupler for a high- or low-dielectric constant dielectric waveguide for millimeter or submillimeter waves.
On the role of macrophages in anthrax. (1993)

Bacillus anthracis, the causative agent of anthrax, produces systemic shock and death in susceptible animals, primarily through the action of its lethal toxin. This toxin, at high concentrations, induces lysis of macrophages in vitro but shows little or no effect on other cells. We found that when mice were specifically depleted of macrophages by silica injections, they became resistant to the toxin. Sensitivity could be restored by coinjection of toxin-sensitive cultured macrophages (RAW 264.7 cells) but not by coinjection of other cell lines tested. These results implied that macrophages mediate the action of lethal toxin in vivo and led us to investigate their role in death of the mammalian host. Sublytic concentrations of lethal toxin, orders of magnitude lower than those required to induce lysis of RAW 264.7 cells, were found to induce these cells to express interleukin 1 (IL-1) and tumor necrosis factor in vitro. Passive immunization against IL-1 or injection of an IL-1 receptor antagonist protected mice from toxin challenge, whereas anti-tumor necrosis factor provided little, if any, protection. These results imply that systemic shock and death from anthrax result primarily from the effects of high levels of cytokines, principally IL-1, produced by macrophages that have been stimulated by the anthrax lethal toxin.
Perceptual assessment of demosaicing algorithm performance (2002)

Demosaicing is an important part of the image-processing chain for many digital color cameras. The demosaicing operation converts a raw image acquired with a single sensor array, overlaid with a color filter array, into a full-color image. In this paper, we report the results of two perceptual experiments that compare the perceptual quality of the output of different demosaicing algorithms. In the first experiment, we found that a Bayesian demosaicing algorithm produced the most preferred images. Detailed examination of the data, however indicated that the good performance of this algorithm was at least in part due to the fact that it sharpened the images while it demosaiced them. In a second experiment, we silenced image sharpness as a factor by applying a sharpening algorithm to the output of each demosaicing algorithm. The optimal amount of sharpening to be applied to each image was chosen using the results of a preliminary experiment. Once sharpness was equated in this way, an algorithm developed by Freeman based on bilinear interpolation combined with median filtering, gave the best results. An analysis of our data suggests that our perceptual results cannot be easily predicted using an image metric.
Unlocked nucleic acid – an RNA modification with broad potential (2011)

The first unlocked nucleic acid (UNA) monomer was described more than a decade ago, but only recent reports have revealed the true potential applications of this acyclic RNA mimic. UNA monomers enable the modulation of the thermodynamic stability of various nucleic acid structures such as RNA and DNA duplexes, quadruplexes or i-motifs. Moreover, UNA monomers were found to be compatible with RNase H activity, a property which is important for single stranded antisense constructs. Notably, UNA monomers can be applied in the design of superior siRNAs, combining potent gene silencing and dramatically reduced off-target effects.
Dispersed-pulse codebook and its application to a 4 kb/s speech coder (2002)

This paper presents a dispersed-pulse codebook for CELP coder. This codebook generates an excitation vector by convoluting dispersion vectors with signed pulses in an algebraic codevector. The dispersion vectors are obtained through training so the coding distortion to be reduced. An objective evaluation result shows that the coding distortion with this codebook is smaller than that with an algebraic codebook. The dispersed-pulse codebook is applied to a 4 kb/s CELP coder. Subjective evaluation results show that: (1) the fundamental performance of the 4 kb/s coder is equivalent to that of G.726 32 kb/s coder, and (2) the performances of the 4k b/s coder under some error and background noise conditions are equivalent to those of G.729 8 kb/s coder.
Chaperone therapy for homocystinuria: the rescue of CBS mutations by heme arginate (2014)

Classical homocystinuria is caused by mutations in the cystathionine β-synthase (CBS) gene. Previous experiments in bacterial and yeast cells showed that many mutant CBS enzymes misfold and that chemical chaperones enable proper folding of a number of mutations. In the present study, we tested the extent of misfolding of 27 CBS mutations previously tested in E. coli under the more folding-permissive conditions of mammalian CHO-K1 cells and the ability of chaperones to rescue the conformation of these mutations. Expression of mutations in mammalian cells increased the median activity 16-fold and the amount of tetramers 3.2-fold compared with expression in bacteria. Subsequently, we tested the responses of seven selected mutations to three compounds with chaperone-like activity. Aminooxyacetic acid and 4-phenylbutyric acid exhibited only a weak effect. In contrast, heme arginate substantially increased the formation of mutant CBS protein tetramers (up to sixfold) and rescued catalytic activity (up to ninefold) of five out of seven mutations (p.A114V, p.K102N, p.R125Q, p.R266K, and p.R369C). The greatest effect of heme arginate was observed for the mutation p.R125Q, which is non-responsive to in vivo treatment with vitamin B(6). Moreover, the heme responsiveness of the p.R125Q mutation was confirmed in fibroblasts derived from a patient homozygous for this genetic variant. Based on these data, we propose that a distinct group of heme-responsive CBS mutations may exist and that the heme pocket of CBS may become an important target for designing novel therapies for homocystinuria.
Single-Point FMR Linewidth Measurement by TE10Rectangular Transmission Cavity Perturbation (2016)

A method that allows the determination of magnetic permeability in magnetic bodies, as well as the ferromagnetic resonance (FMR) linewidth, by measuring only the quality factor and the resonant frequency of the perturbed microwave cavity at FMR is presented. The method is based on a set of equations derived for various types of magnetic media, including ferrites, single crystals, and polycrystalline materials. The evaluation of resonators containing magnetic medium is considered, and a detailed description of the spectrometer and the experimental procedure are presented. Independently measured yttrium iron garnet samples were used to validate the method.
Rationally Engineered AAV Capsids Improve Transduction and Volumetric Spread in the CNS (2017)

Adeno-associated virus (AAV) is the most common vector for clinical gene therapy of the CNS. This popularity originates from a high safety record and the longevity of transgene expression in neurons. Nevertheless, clinical efficacy for CNS indications is lacking, and one reason for this is the relatively limited spread and transduction efficacy in large regions of the human brain. Using rationally designed modifications of the capsid, novel AAV capsids have been generated that improve intracellular processing and result in increased transgene expression. Here, we sought to improve AAV-mediated neuronal transduction to minimize the existing limitations of CNS gene therapy. We investigated the efficacy of CNS transduction using a variety of tyrosine and threonine capsid mutants based on AAV2, AAV5, and AAV8 capsids, as well as AAV2 mutants incapable of binding heparan sulfate (HS). We found that mutating several tyrosine residues on the AAV2 capsid significantly enhanced neuronal transduction in the striatum and hippocampus, and the ablation of HS binding also increased the volumetric spread of the vector. Interestingly, the analogous tyrosine substitutions on AAV5 and AAV8 capsids did not improve the efficacy of these serotypes. Our results demonstrate that the efficacy of CNS gene transfer can be significantly improved with minor changes to the AAV capsid and that the effect is serotype specific.
A SMS normalization system integrating multiple grammatical resources (2012)

Abstract SMS language presents special phenomena and important deviations from natural language. Every day, an impressive amount of chat messages, SMS messages, and e-mails are sent all over the world. This widespread use makes important the development of systems that normalize SMS language into natural language. However, typical machine translation approaches are difficult to adapt to SMS language because of many irregularities that are shown by this kind of language. This paper presents a new approach for SMS normalization that combines lexical and phonological translation techniques with disambiguation algorithms at two different levels: lexical and semantic. The method proposed does not depend on big annotated corpus, which is difficult to build and is applied in two different domains showing its easiness of adaptation across different languages and domains. The results obtained by the system outperform some of the existing methods of SMS normalization despite the fact that the Spanish language and the corpus created have some features that complicate the normalization task.
Phorbol ester binding to protein kinase C requires a cysteine-rich zinc-finger-like sequence. (1989)

Protein kinase C normally has a tandem repeat of a characteristic cysteine-rich sequence in C1, the conserved region of the regulatory domain. These sequences resemble the DNA-binding zinc finger domain. For the gamma subspecies of rat brain protein kinase C, various deletion and point mutants in this domain were constructed, and the mutated proteins were expressed in Escherichia coli by using the T7 expression system. Radioactive phorbol 12,13-dibutyrate binding analysis indicated that a cysteine-rich zinc-finger-like sequence was essential for protein kinase C to bind phorbol ester and that one of two sequences was sufficient for the phorbol ester binding. Conserved region C2, another region in the regulatory domain, was apparently needed for the enzyme to require Ca2+ for phorbol ester binding activity.
A Gene Encoding an Antigen Recognized by Cytolytic T Lymphocytes on a Human Melanoma (1991)

Many human melanoma tumors express antigens that are recognized in vitro by cytolytic T lymphocytes (CTLs) derived from the tumor-bearing patient. A gene was identified that directed the expression of antigen MZ2-E on a human melanoma cell line. This gene shows no similarity to known sequences and belongs to a family of at least three genes. It is expressed by the original melanoma cells, other melanoma cell lines, and by some tumor cells of other histological types. No expression was observed in a panel of normal tissues. Antigen MZ2-E appears to be presented by HLA-A1; anti-MZ2-E CTLs of the original patient recognized two melanoma cell lines of other HLA-A1 patients that expressed the gene. Thus, precisely targeted immunotherapy directed against antigen MZ2-E could be provided to individuals identified by HLA typing and analysis of the RNA of a small tumor sample.
Effects of growth factors in vivo. I. Cell ingrowth into porous subcutaneous chambers. (1987)

Growth factors secreted by platelets and macrophages may play roles in atherogenesis and in wound repair. The multiple biologic effects of these factors are being studied extensively in vitro, but their roles in vivo are relatively unexplored. The cellular responses to platelet-derived growth factor (PDGF), transforming growth factor beta (TGF beta), basic fibroblast growth factor (bFGF), and epidermal growth factor (EGF) were examined in a wound chamber model in rats. Growth factors were emulsified in bovine dermal collagen suspensions, placed in 1 X 30-mm porous polytetrafluoroethylene tubes, inserted subcutaneously, and removed after 10 days. The presence of PDGF (400 ng), TGF beta (200 ng), or bFGF (100 ng) increased the DNA content of the chambers two- to sixfold, compared with controls. Regardless of dose, EGF (100-800 ng) did not affect the DNA content. The increases in DNA observed for PDGF, TGF beta, or bFGF resulted from accumulations of varying numbers of fibroblasts, capillaries, macrophages, and leukocytes in 10-day chambers. The addition of 250 micrograms/ml heparin to the collagen suspension potentiated the response to PDGF and bFGF, but not to TGF beta or EGF. The clearance of 125I-labeled growth factors from the chambers was biphasic. After an initial rapid phase, the remaining growth factor was slowly cleared. The half-life of the initial phase was rapid for PDGF (12 hours) and bFGF (9 hours) and somewhat slower for TGF beta (22 hours). There was no difference in the rate of clearance between collagen and collagen/heparin matrices for any of the growth factors examined. These studies demonstrate that PDGF, bFGF, and TGF beta can induce granulation tissue development in normal animals. The similarity in cellular responses to three peptides with differing in vitro actions suggests that the responses observed at 10 days reflect a secondary process, possibly mediated by effector cells such as macrophages, lymphocytes, or granulocytes that are attracted into the chamber by each growth factor, rather than a direct effect of the factors themselves.
Characterization of a high-affinity antiserum specific for the amino-terminal sequence of human parathyroid hormone. (1987)

1. The present paper describes a detailed study of the specificity of high-affinity antibodies obtained from the yolk of eggs laid by a chicken successfully immunized with synthetic human parathyroid hormone (hPTH)-(1-34). 2. Using 125I-labelled bovine parathyroid hormone (bPTH)-(1-84) purified by high performance liquid chromatography (HPLC) as tracer, and hPTH-(1-34) as reference, we found superimposable curves with hPTH-(13-34), bPTH-(13-34) and bPTH-(1-34); the [Asp-76]hPTH-(1-84) peptide showed a molar percent cross-reactivity (calculated at 50% B/BO) of 73% and the bovine sequence 1-84 of 15%. 3. Studying amidated [Tyr-34] bovine PTH fragments we found the highest cross-reactivity with the peptide 7-34 (33%) followed by 20-34 (1.7%) and 25-34 (0.4%). The bovine sequence 1-25 showed a low reactivity (0.7%) and the 1-12 sequence none at all. Rat parathyroid hormone (rPTH)-(1-34) showed low cross-reactivity (3.1%), the same occurring with peptide [Tyr-34, Norleu-8,18] bPTH-(1-34) (1.5%). 4. The data suggest that the antibodies studied recognize epitopes in or near amino acids 18 to 25 of the sequence of the hPTH molecule. This region of the molecule is coincident with the antigenic determinant predicted by the analysis of the hydrophilicity plot of the hPTH-(1-34) peptide.
Intra-Articular Injections for the Treatment of Osteoarthritis (2011)

Osteoarthritis (OA), also called degenerative joint disease, is the most frequently occurring chronic musculoskeletal disease, particularly affecting the aging population. The use of viscosupplementation, i.e. intra-articular (IA) hyaluronic acid (HA) drug therapy, to treat OA, is growing worldwide, due to important results obtained from several clinical trials, which reported IA HA-related improvements in functional activity and pain management. This review is an update of the IA use of this compound in the treatment of OA, with clinical evidence from the last few years being discussed and used to delineate new trends for the future.
Robust phase unwrapping by convex optimization (2014)

The 2-D phase unwrapping problem aims at retrieving a “phase” image from its modulo 2π observations. Many applications, such as interferometry or synthetic aperture radar imaging, are concerned by this problem since they proceed by recording complex or modulated data from which a “wrapped” phase is extracted. Although 1-D phase unwrapping is trivial, a challenge remains in higher dimensions to overcome two common problems: noise and discontinuities in the true phase image. In contrast to state-of-the-art techniques, this work aims at simultaneously unwrap and denoise the phase image. We propose a robust convex optimization approach that enforces data fidelity constraints expressed in the corrupted phase derivative domain while promoting a sparse phase prior. The resulting optimization problem is solved by the Chambolle-Pock primal-dual scheme. We show that under different observation noise levels, our approach compares favorably to those that perform the unwrapping and denoising in two separate steps.
Epidemiological Expansion, Structural Studies, and Clinical Challenges of New β-Lactamases from Gram-Negative Bacteria (2010)

β-Lactamase evolution presents to the infectious disease community a major challenge in the treatment of infections caused by multidrug-resistant gram-negative bacteria. Because over 1,000 of these naturally occurring β-lactamases exist, attempts to correlate structure and function have become daunting. Although new enzymes in the extended-spectrum β-lactamase (ESBL) families are frequently identified, the older CTX-M-14 and CTX-M-15 enzymes have become the most prevalent ESBLs in global surveillance. Carbapenemases with either serine-based or zinc-facilitated hydrolysis mechanisms are posing some of the most critical problems. Most geographical regions now report KPC serine carbapenemases and the metallo-β-lactamases VIM, IMP, and NDM-1, even though NDM-1 was only recently identified. The rapid emergence of these newer enzymes, with multiple β-lactamases appearing in a single organism, makes the design of new β-lactamase inactivators or β-lactamase-stable β-lactams all the more difficult. Combination therapy will likely be required to counteract the continuing evolution of these insidious enzymes in multidrug-resistant pathogens.
Drugs for Parkinson's disease (2001)

Levodopa is the most effective drug available for treating the motor symptoms of idiopathic Parkinson's disease. It is usually combined with a peripheral dopa decarboxylase inhibitor. Early treatment with dopamine agonists can reduce the risk of developing dyskinesia. Dopamine agonists and catechol-O-methyltransferase inhibitors can significantly reduce motor fluctuations. Amantadine reduces the severity of dyskinesia in some patients. No treatment has been proven to delay disease progression.
Population ecology and fishery of Cittarium pica (Gastropoda: Trochidae) on the Caribbean coast of Costa Rica. (2003)

The West Indian Topshell Cittarium pica is artisanally collected on rocky shores along the Caribbean Coast of Costa Rica. There are neither data on the state of its exploitation nor exist any regulation of the fishery From October 2000 to March 2001, the population dynamics of this species were studied at an unexploited and two exploited sites to determine the present impact of the fishery on the resource. Average population density with 14 ind./m2 about three times higher at the unexploited than at the exploited sites. Length-frequency histograms showed a strong shift towards smaller specimens at the exploited sites, which is also reflected in significantly higher rates of total mortality (Z = 4.05 and 4.47) when compared to the unexploited site (Z = 1.47). Von Bertalanffy growth parameters were estimated as k = 0.19-0.28 (yr-1) and L infinity = 104 mm. No significant differences were found among sites. From these values a range of the growth performance index phi was computed (phi = 3.31-3.48) which lies at the lower end of the values reported for other tropical marine gastropods. The size at first maturity for both sexes combined was estimated as 29.20 +/- 1.14 mm. Exploitation rates > 0.6 for both exploited sites and a large fraction of small specimens (< 30 mm) in the catches suggest overexploitation and recruitment overfishing. Based on the estimated maximum sustainable yield we recommend regulative measures for the fishery such as a control of a minimum landing size of 40 mm and a closure of the fishery during its reproductive period (from July to November).