gebhart/patrepeval huggingface dataset:
Charge manipulation for improved mass determination of high‐mass species and mixture components by electrospray mass spectrometry (1998)

The manipulation of the charge states of high-mass ions can facilitate mass determination in electrospray (ES) mass spectrometry. Specifically, the reduction of charge (which leads to ions of higher mass-to-charge ratios) can significantly reduce peak overlap. Signals associated with various charge states of high-mass ions are more easily resolved at low charge states and chemical noise tends to be significantly lower at high mass-to-charge ratios than in the normal mass-to-charge window typically associated with electrospray. Algorithms that transform ES mass spectra to zero-charge spectra are most likely to yield unambiguous results when charge states are clearly resolved and when signal-to-noise ratios are relatively high. Charge manipulation can enhance the value of the transformation algorithms in cases in which compromises their utility. Such situations include ES mass spectra of high-mass species that yield charge states that are not baseline resolved, mixtures with many components and mixtures in which the signals from major components overwhelm signals from minor components. Examples of improved mass determination are illustrated for proteins using ion–ion chemistry as the means for charge state manipulation and the quadrupole ion trap as the mass analyzer. © 1998 John Wiley & Sons, Ltd.
Head-to-TOE Evaluation of High-Performance Sockets over Protocol Offload Engines (2005)

Despite the performance drawbacks of Ethernet, it still possesses a sizable footprint in cluster computing because of its low cost and backward compatibility to existing Ethernet infrastructure. In this paper, we demonstrate that these performance drawbacks can be reduced (and in some cases, arguably eliminated) by coupling TCP offload engines (TOEs) with 10-Gigabit Ethernet (10GigE). Although there exists significant research on individual network technologies such as 10GigE, InfiniBand (IBA), and Myrinet; to the best of our knowledge, there has been no work that compares the capabilities and limitations of these technologies with the recently introduced 10GigE TOEs in a homogeneous experimental testbed. Therefore, we present performance evaluations across 10GigE, IBA, and Myrinet (with identical cluster-compute nodes) in order to enable a coherent comparison with respect to the sockets interface. Specifically, we evaluate the network technologies at two levels: (i) a detailed micro-benchmark evaluation and (ii) an application-level evaluation with sample applications from different domains, including a bio-medical image visualization tool known as the Virtual Microscope, an iso-surface oil reservoir simulator, a cluster file-system known as the parallel virtual file-system (PVFS), and a popular cluster management tool known as Ganglia. In addition to 10GigE's advantage with respect to compatibility to wide-area network infrastructures, e.g., in support of grids, our results show that 10GigE also delivers performance that is comparable to traditional high-speed network technologies such as IBA and Myrinet in a system-area network environment to support clusters and that 10GigE is particularly well-suited for sockets-based applications
Free-space electro-optic sampling with a high-repetition-rate regenerative amplified laser (1997)

The use of a high-repetition-rate (250 kHz) regenerative amplified laser with μJ pulse energy in a free-space THz beam electro-optic sampling system has produced a significant improvement in both the signal-to-noise ratio (&amp;gt;105) and absolute probe beam photomodulation depth (&amp;gt;19%). Focal plane images of the electric field distribution (strength and polarity) in dipole and quadrupole planar photoconductive emitters are presented. Preliminary results of real-time 2D THz images of moving objects have also been obtained.
The Structure of the Vertebrate Lens (2004)

The cornea and the lens are the principal refractive elements of the eye responsible for, respectively, stationary and variable refraction. However, while both the cornea and the lens must be transparent to function properly, the basis of their transparency is quite different. In general, the cornea relies on the continuous pumping of interstitial fluid across its semipermeable surface membranes and a supramolecular organization of collagen fibrils for clarity. In contrast, lens transparency is presumed to be the result of a highly ordered arrangement of its unique fiberlike cells, or fibers, and a gradient of refractive index produced by a variable crystallin protein concentration within the fibers. However, while lens gross anatomy has a major role in determining lens optical quality (variable focusing power), lens ultrastructure is the principal factor in determining lens transparency. Furthermore, while all vertebrate lenses have a similar form, or structure, their anatomy is not identical, and thus their optical quality varies from species to species and as a function of age. In fact, on the basis of structure, four types of lenses can be distinguished. Key differences in lens morphology, caused during specific periods of development and growth, result in quantifiable variations in optical quality. Furthermore, lens structural anomalies, caused during the same periods of development and growth, result in quantifiable degradation in optical quality. Thus, vertebrate lenses are a prime example of form following function and malformation leading to malfunction.
The formation of hydrogen passivated silicon single-crystal surfaces using ultraviolet cleaning and HF etching (1988)

We have tried to develop a new procedure to prepare the clean surface of a silicon single crystal. We successfully prepared the contamination free bare silicon surface with ultraviolet cleaning followed by HF dipping with low concentration HF obtained by dilution by organic free ultrapure water, at room temperature under the atmospheric condition. X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, and ultraviolet photoelectron spectroscopy measurements proved thus prepared surface has a hydrogen monoatomic layer terminating the dangling bonds of silicon. The hydrogen termination was found to have remarkable passivation effect against surface oxidation reaction. A silicon thin-film epitaxially grown on the prepared surface was confirmed to have perfect crystal structure and high-purity level by scanning electron microscopy, reflection high-energy electron diffraction, Raman spectroscopy and secondary ion mass spectroscopy.
Maspin Inhibits Cell Migration in the Absence of Protease Inhibitory Activity (2002)

Maspin is a member of the serpin family of protease inhibitors and is a tumor suppressor gene acting at the level of tumor invasion and metastasis. This in vivo activity correlates with the ability of maspin to inhibit cell migration in vitro. This behavior suggests that maspin inhibits matrix-degrading proteases, such as those of the plasminogen activation system, in a similar manner to the serpin PAI-1. However, there is controversy concerning the protease inhibitory activity of maspin. It is devoid of activity against a wide range of proteases, in common with other non-inhibitory serpins, but has recently been reported to inhibit plasminogen activators associated with cells and other biological surfaces (Sheng, S. J., Truong, B., Fredrickson, D., Wu, R. L., Pardee, A. B., and Sager, R. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 499-504; McGowen, R., Biliran, H., Jr., Sager, R., and Sheng, S. (2000) Cancer Res. 60, 4771-4778). We have compared the effects of maspin with those of PAI-1 in a range of situations in which plasminogen activation is potentiated, reflecting the biological context of this proteolytic system: urokinase-type plasminogen activator bound to its receptor on the surface of tumor cells, tissue-type plasminogen activator specifically bound to vascular smooth muscle cells, fibrin, and the prion protein. Maspin was found to have no inhibitory effect in any of these situations, in contrast to the efficient inhibition observed with PAI-1, but nevertheless maspin inhibited the migration of both tumor and vascular smooth muscle cells. We conclude that maspin is a non-inhibitory serpin and that protease inhibition does not account for its activity as a tumor suppressor.
High spectral purity Kerr frequency comb radio frequency photonic oscillator (2015)

Femtosecond laser-based generation of radio frequency signals has produced astonishing improvements in achievable spectral purity, one of the basic features characterizing the performance of an radio frequency oscillator. Kerr frequency combs hold promise for transforming these lab-scale oscillators to chip-scale level. In this work we demonstrate a miniature 10 GHz radio frequency photonic oscillator characterized with phase noise better than -60 dBc Hz(-1) at 10 Hz, -90 dBc Hz(-1) at 100 Hz and -170 dBc Hz(-1) at 10 MHz. The frequency stability of this device, as represented by Allan deviation measurements, is at the level of 10(-10) at 1-100 s integration time-orders of magnitude better than existing radio frequency photonic devices of similar size, weight and power consumption.
The influence of microstructure and monomer properties on the erosion mechanism of a class of polyanhydrides (1993)

Abstract The erosion of three different polyanhydrides consisting of sebacic acid (SA) and 1,3‐bis( p ‐carboxyphenoxy)propane (CPP) was investigated. Melt cast polymer matrices were prepared from the homopolymer p (SA) and two copolymers, p (CPP‐SA) 20 : 80 and p (CPP‐SA) 50 : 50. Particular attention was paid to the influence of the polymer matrix microstructure and of the monomers on erosion. Using polarized light microscopy we found that p (SA) and p (CPP‐SA) 20 : 80 matrices consist of spherulites. SEM investigations showed that their crystalline parts are more resistant to erosion than their amorphous areas. The matrices erode into highly porous devices, whose porosity is detectable by mercury porosimetry. Using wide‐angle x‐ray diffractometry we found that monomers crystallize inside the pores. DSC investigations showed a maximum of crystallized SA after 2–6 days and a continuous increase of CPP, which stays in the devices for weeks. We conclude that the microstructure and the monomer properties are the two main factors which determine the erosion of these polymers. The obtained data on changes in porosity, crystallinity, polymer matrix thickness, erosion front velocities, crystalline monomer content, and monomer release provides the basis for quantitatively describing the erosion process. © 1993 John Wiley &amp; Sons, Inc.
Correspondence (2002)

To the Editor:

The study of Elterman et al.1 is a significant advance in our understanding of the treatment of infantile spasms, particularly in the clear definition of response and relapse in terms of both the clinical and neurophysiological response, in its size, and in the use of actuarial curves (survival curves) for responders. There are, however, some weaknesses in the published data, and in their interpretation and analysis.

The results were reported on almost 80% (142/179) of children randomized to receive treatment rather than an intention-to-treat analysis of the 179 children allocated a treatment—as recommended in the CONSORT statement.2 The data show that 16 results are missing from those exposed to high-dose and 9 from the low-dose group; 2 cases were …
Establishment of a Persistent Escherichia coli Reservoir during the Acute Phase of a Bladder Infection (2001)

The vast majority of urinary tract infections are caused by strains of uropathogenic Escherichia coli that encode filamentous adhesive organelles called type 1 pili. These structures mediate both bacterial attachment to and invasion of bladder epithelial cells. However, the mechanism by which type 1 pilus-mediated bacterial invasion contributes to the pathogenesis of a urinary tract infection is unknown. Here we show that type 1-piliated uropathogens can invade the superficial epithelial cells that line the lumenal surface of the bladder and subsequently replicate, forming massive foci of intracellular E. coli termed bacterial factories. In response to infection, superficial bladder cells exfoliate and are removed with the flow of urine. To avoid clearance by exfoliation, intracellular uropathogens can reemerge and eventually establish a persistent, quiescent bacterial reservoir within the bladder mucosa that may serve as a source for recurrent acute infections. These observations suggest that urinary tract infections are more chronic and invasive than generally assumed.
Protein evolution with an expanded genetic code (2008)

We have devised a phage display system in which an expanded genetic code is available for directed evolution. This system allows selection to yield proteins containing unnatural amino acids should such sequences functionally outperform ones containing only the 20 canonical amino acids. We have optimized this system for use with several unnatural amino acids and provide a demonstration of its utility through the selection of anti-gp120 antibodies. One such phage-displayed antibody, selected from a naïve germline scFv antibody library in which six residues in V(H) CDR3 were randomized, contains sulfotyrosine and binds gp120 more effectively than a similarly displayed known sulfated antibody isolated from human serum. These experiments suggest that an expanded "synthetic" genetic code can confer a selective advantage in the directed evolution of proteins with specific properties.
Vaccine efficacy of Salmonella strains expressing glycoprotein 63 with different promoters (1997)

The development of Salmonella vaccine vectors has been hindered by both the requirement for multiple doses to induce immune responses and a lack of plasmid stability. Direct comparisons of different promoter systems with the same antigen are necessary to address these important issues. We have previously described an AroA- AroD- deletion mutant of Salmonella typhimurium (GID101) which expresses the gene encoding the Leishmania major promastigote surface glycoprotein gp63 (GID101). While this construct provided significant protection against L. major challenge to highly susceptible BALB/c mice, this required at least two oral doses. We report here the use of two different inducible promoters, the nirB and osmC promoters, to improve vaccine efficacy. These constructs (termed GID105 and GID106, respectively) expressed gp63 in vitro under inducible conditions and colonized BALB/c mice after oral administration. GID105 demonstrated greater plasmid stability in vitro and in vivo than did either GID106 or GID101, which expresses gp63 constitutively. Spleen and lymph node cells from mice immunized with a single oral dose of GID105 proliferated in vitro in response to L. major and secreted gamma interferon, whereas cells from mice given the other constructs did not. Mice immunized with a single oral dose of GID1O5 or GID106 developed significantly smaller lesions upon challenge with L. major, whereas mice administered GID101 did not. Mice administered GID105 also showed considerable resistance to Leishmania donovani infection. These data provide a direct comparison of promoter systems and demonstrate that the use of inducible promoters such as the nirB promoter allows a considerable improvement over the previous vaccine construct in terms of protection against infection.
Lubricants and lubrications (2001)

List of Contributors. Foreword. A Word of Thanks. List of Abbreviations. Lubricants and their Market. Lubricants in the Tribological System. Rheology of Lubricants. Base Oils. Synthetic Base Oils. Additives. Lubricants in the Environment. Disposal of Used Lubricating Oils. Lubricants for Internal Combustion Engines. Gear Lubrication Oils. Hydraulic Oils. Compressor Oils. Turbine Oils. Metalworking Fluids. Forming Lubricants Lubricating Greases. Solid Lubrication. Laboratory Methods for Testing Lubricants. Mechanical--Dynamic Testing Methods for Lubricants. References. Subject Index.
Expression of C-terminal deleted p53 isoforms in neuroblastoma (2006)

The tumor suppressor gene, p53, is rarely mutated in neuroblastomas (NB) at the time of diagnosis, but its dysfunction could result from a nonfunctional conformation or cytoplasmic sequestration of the wild-type p53 protein. However, p53 mutation, when it occurs, is found in NB tumors with drug resistance acquired over the course of chemotherapy. As yet, no study has been devoted to the function of the specific p53 mutants identified in NB cells. This study includes characterization and functional analysis of p53 expressed in eight cell lines: three wild-type cell lines and five cell lines harboring mutations. We identified two transcription-inactive p53 variants truncated in the C-terminus, one of which corresponded to the p53beta isoform recently identified in normal tissue by Bourdon et al. [J. C. Bourdon, K. Fernandes, F. Murray-Zmijewski, G. Liu, A. Diot, D. P. Xirodimas, M. K. Saville and D. P. Lane (2005) Genes Dev., 19, 2122-2137]. Our results show, for the first time, that the p53beta isoform is the only p53 species to be endogenously expressed in the human NB cell line SK-N-AS, suggesting that the C-terminus truncated p53 isoforms may play an important role in NB tumor development.
Inhibition of insulitis and prevention of diabetes in nonobese diabetic mice by blocking L-selectin and very late antigen 4 adhesion receptors. (1993)

Leukocyte adhesion to the endothelial venules in the pancreatic islets is thought to be one of the initial steps in the development of insulin-dependent diabetes mellitus. It has been suggested that leukocyte adhesion to endothelium is a sequential multistep process involving various different homing receptors. We report here that blocking different homing receptors--namely, L-selectin and very late antigen 4 (VLA-4)--which function during different stages of the adhesion process, by specific monoclonal antibodies inhibits insulitis and prevents diabetes in mice. Moreover, leukocyte attachment to the inflamed vessels within pancreatic sections could be inhibited by anti-L-selectin and anti-VLA-4 antibodies. Interestingly, anti-L-selectin or anti-VLA-4 antibody did not appear to influence the autoimmune response to a panel of pancreatic beta-cell autoantigens. These data suggest that L-selectin and VLA-4 receptors are involved in mediating leukocyte homing to the islets and that intervention of these two adhesion pathways may provide a novel approach for treatment of autoimmune diseases such as insulin-dependent diabetes mellitus.
HCN Pacemaker Channels and Pain: A Drug Discovery Perspective (2009)

This article reviews evidence that hyperpolarization-activated, cation nonselective (HCN) channels, the molecular basis of the Ih current, potentially represent valid targets for novel analgesic agents. Ih is a prominent current in many peripheral sensory nerves, with highest current density typically found in large diameter neurons. Recent data suggest that Ih may represent a valid target for the treatment of spontaneous pain and allodynia associated with nerve injury. The majority of available electrophysiological and molecular evidence suggests that fast activating, weakly cyclic adenosine monophosphate (cAMP) sensitive HCN1-based channels may make a significant contribution to Ih, especially in large diameter, mechanosensitive fibers, where the Ih current appears to support abnormal spontaneous firing after nerve injury. In contrast, HCN4 channels seem to play the predominant role in cardiac pacemaker tissue. These observations raise the possibility that HCN1 selective blockers may inhibit pain associated with nerve injury without dramatic effects on heart rate. Development of novel HCN blocking analgesics presents a number of significant technical challenges. Although a number of HCN blockers are available, such as ZD-7288, ivabradine, and others, these drugs inhibit all HCN isoforms with the same potency. As a result, these compounds have powerful effects on heart rate, severely limiting their utility for non-cardiac indications such as pain. Selectivity challenges, mechanisms of compound interaction with the channel, and assay methods are described in detail.
Functional Protein Microarrays in Drug Discovery (2007)

As central actors in most biological functions, proteins are the subject of intense study. This has driven the development of increasingly sophisticated approaches for the study of proteins, which has extended to proteomic level methodologies. Yet currently no book has addressed all aspects of functional microarrays in a coherent and integrated fas
Presence of 4‐hydroxynonenal in cerebrospinal fluid of patients with sporadic amyotrophic lateral sclerosis (1998)

A marker of lipid peroxidation 4-hydroxynonenal (HNE) was elevated in the cerebrospinal fluid (CSF) of a patient with sporadic amyotrophic lateral sclerosis (sALS) compared with that of most patients with other neurological diseases. Such elevations of HNE were sufficient to kill cyclic adenosine monophosphate (cAMP)-differentiated motor neuron hybrid cells in vitro, and anti-oxidants prevented this HNE-dependent cell death. These data suggest that oxidative stress and lipid peroxidation are associated with and may promote motor neuron degeneration in sALS.
Hepatitis C Virus E2 Has Three Immunogenic Domains Containing Conformational Epitopes with Distinct Properties and Biological Functions (2004)

Mechanisms of virion attachment, interaction with its receptor, and cell entry are poorly understood for hepatitis C virus (HCV) because of a lack of an efficient and reliable in vitro system for virus propagation. Infectious HCV retroviral pseudotype particles (HCVpp) were recently shown to express native E1E2 glycoproteins, as defined in part by HCV human monoclonal antibodies (HMAbs) to conformational epitopes on E2, and some of these antibodies block HCVpp infection (A. Op De Beeck, C. Voisset, B. Bartosch, Y. Ciczora, L. Cocquerel, Z. Y. Keck, S. Foung, F. L. Cosset, and J. Dubuisson, J. Virol. 78:2994-3002, 2004). Why some HMAbs are neutralizing and others are nonneutralizing is looked at in this report by a series of studies to determine the expression of their epitopes on E2 associated with HCVpp and the role of antibody binding affinity. Antibody cross-competition defined three E2 immunogenic domains with neutralizing HMAbs restricted to two domains that were also able to block E2 interaction with CD81, a putative receptor for HCV. HCVpp immunoprecipitation showed that neutralizing and nonneutralizing domains are expressed on E2 associated with HCVpp, and affinity studies found moderate-to-high-affinity antibodies in all domains. These findings support the perspective that HCV-specific epitopes are responsible for functional steps in virus infection, with specific antibodies blocking distinct steps of virus attachment and entry, rather than the perspective that virus neutralization correlates with increased antibody binding to any virion surface site, independent of the epitope recognized by the antibody. Segregation of virus neutralization and sensitivity to low pH to specific regions supports a model of HCV E2 immunogenic domains similar to the antigenic structural and functional domains of other flavivirus envelope E glycoproteins.