gebhart/patrepeval huggingface dataset:
An improved Protein G with higher affinity for human/rabbit IgG Fc domains exploiting a computationally designed polar network (2014)

Protein G is an IgG binding protein that has been widely exploited for biotechnological purposes. Rosetta protein modeling identified a set of favorable polar mutations in Protein G, at its binding interface with the Fc domain of Immunoglobulin G, that were predicted to increase the stability and tighten the binding relative to native Protein G, with only a minor perturbation of the binding mode seen in the crystal structure. This triple mutant was synthesized and evaluated experimentally. Relative to the native protein G, the mutant showed a 3.5-fold enhancement in display level on the surface of yeast and a 5-fold tighter molar affinity for rabbit and human IgG. We attribute the improved affinity to a network of hydrogen bonds exploiting specific polar groups on human and rabbit Fc. The relative specificity increased as well since there was little affinity enhancement for goat and mouse Fc, while the affinity for rat Fc was poorer by half. This designed Protein G will be useful in biotechnological applications as a recombinant protein, where its improved affinity, display and specificity will increase antibody capture sensitivity and capacity. Furthermore, the display of this protein on the surface of yeast introduces the concept of the use of yeast as an affinity matrix.
Diabetic macular edema, Risk factors and concomitants (1999)

In this study, adult-onset DM, HBP, CVD, vitreomacular adhesion and advanced retinopathy were associated with increased risk of development of diffuse diabetic macular edema.
Time-Dependent Models in Collaborative Filtering Based Recommender System (2009)

In recent years, time information is more and more important in collaborative filtering (CF) based recommender system because many systems have collected rating data for a long time, and time effects in user preference is stronger. In this paper, we focus on modeling time effects in CF and analyze how temporal features influence CF. There are four main types of time effects in CF: (1) time bias, the interest of whole society changes with time; (2) user bias shifting, a user may change his/her rating habit over time; (3) item bias shifting, the popularity of items changes with time; (4) user preference shifting, a user may change his/her attitude to some types of items. In this work, these four time effects are used by factorized model, which is called TimeSVD. Moreover, many other time effects are used by simple methods. Our time-dependent models are tested on Netflix data from Nov. 1999 to Dec. 2005. Experimental results show that prediction accuracy in CF can be improved significantly by using time information.
Design and evaluation of a selective compressed memory system (2003)

This research explores any potential for an on-chip cache compression which can reduce not only cache miss ratio but also miss penalty, if main memory is also managed in compressed form. However, the decompression time causes a critical effect on the memory access time and variable-sized compressed blocks tend to increase the design complexity of the compressed cache architecture. This paper suggests several techniques to reduce the decompression overhead and to manage the compressed blocks efficiently which include selective compression, fixed space allocation for the compressed blocks, parallel decompression, the use of a decompression buffer, and so on. Moreover a simple compressed cache architecture based on the above techniques and its management method are proposed. The results from trace-driven simulation show that this approach can provide around 35% decrease in the on-chip cache miss ratio as well as a 53% decrease in the data traffic over the conventional memory systems. Also, a large amount of the decompression overhead can be reduced, and thus the average memory access time can also be reduced by maximum 20% against the conventional memory systems.
Lung Fibroblasts Improve Differentiation of Rat Type II Cells in Primary Culture (2001)

Epithelial-mesenchymal interactions mediate prenatal lung morphogenesis and differentiation, yet little is known about their effects in the adult. In this study we have examined the influence of cocultured lung fibroblasts on rat alveolar type II cell differentiation in primary culture. Type II cells that were co-cultured with lung fibroblasts showed significant increases in messenger RNA (mRNA) levels of surfactant protein (SP)-A, SP-B, SP-C, and SP-D. Metabolic labeling and immunohistochemistry demonstrated that these mRNAs were translated and processed. Addition of 10(-7) M dexamethasone (DEX) to cocultures antagonized the effects of the fibroblasts on SP-A and SP-C, but significantly augmented the effects on SP-B; expression of SP-D was unaffected. Coculture of type II cells with lung fibroblasts also increased acetate incorporation into phospholipids 10-fold, which was antagonized by DEX. Keratinocyte growth factor (KGF) mimicked the effects of lung fibroblasts on SP gene expression, but KGF neutralizing antibodies only partially reduced the effects of lung fibroblasts. KGF increased acetate incorporation into surfactant phospholipids, and the addition of DEX augmented this response. Together, our observations suggest that epithelial--mesenchymal interactions affect type II cell differentiation in the adult lung, and that these effects are partially mediated by KGF.
Amino-sugar glycosidase inhibitors: versatile tools for glycobiologists (1992)

Journal Article Amino-sugar glycosidase inhibitors: versatile tools for glycobiologists Get access Bryan Winchester, Bryan Winchester Search for other works by this author on: Oxford Academic PubMed Google Scholar George W.J. Fleet George W.J. Fleet 1Dyson Perrins Laboratory and Oxford Centre for Molecular SciencesSouth Parks Road, Oxford OX1 3QY, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Glycobiology, Volume 2, Issue 3, June 1992, Pages 199–210, https://doi.org/10.1093/glycob/2.3.199 Published: 01 June 1992 Article history Received: 20 March 1992 Accepted: 27 March 1992 Published: 01 June 1992
Lead in saliva and its relationship to blood in the residents of Klity Village in Thailand. (2005)

Lead concentrations in whole blood and saliva were examined in 16 females and 13 males living in Klity village, a highly contaminated area from lead mining, Thailand. The geometric mean for the lead content in the blood was 24.03 microg/dl (range 11.80-46.60 microg/dl) while the lead content in the saliva was 5.69 microg/dl (range 1.82-25.28 microg/dl). No significant differences were found between the concentrations of lead in blood and saliva in relation to the age of the subject. Males were found to have higher blood lead levels than females. The coefficient of correlation gamma between salivary and blood lead levels was -0.025. Our data suggests that saliva is not suitable material for biological monitoring with respect to lead exposure.
The Use of Acellular Dermal Matrices in Revisional Breast Reconstruction (2012)

Increased complications, including seroma formation, infection, wound dehiscence, and implant exposure, remain challenging problems. Long-term studies will be needed to prove the durability of acellular dermal matrices in breast revisional surgery.
A Limited Spectrum of Mutations Causes Constitutive Activation of the Yeast α-Factor Receptor (2000)

Activation of G protein coupled receptors (GPCRs) by binding of ligand is the initial event in diverse cellular signaling pathways. To examine the frequency and diversity of mutations that cause constitutive activation of one particular GPCR, the yeast alpha-factor receptor, we screened libraries of random mutations for constitutive alleles. In initial screens for mutant receptor alleles that exhibit signaling in the absence of added ligand, 14 different point mutations were isolated. All of these 14 mutants could be further activated by alpha-factor. Ten of the mutants also acquired the ability to signal in response to binding of desTrp(1)¿Ala(3)ălpha-factor, a peptide that acts as an antagonist toward normal alpha-factor receptors. Of these 10 mutants, at least eight alleles residing in the third, fifth, sixth, and seventh transmembrane segments exhibit bona fide constitutive signaling. The remaining alleles are hypersensitive to alpha-factor rather than constitutive. They can be activated by low concentrations of endogenous alpha-factor present in MATa cells. The strongest constitutively active receptor alleles were recovered multiple times from the mutational libraries, and extensive mutagenesis of certain regions of the alpha-factor receptor did not lead to recovery of any additional constitutive alleles. Thus, only a limited number of mutations is capable of causing constitutive activation of this receptor. Constitutive and hypersensitive signaling by the mutant receptors is partially suppressed by coexpression of normal receptors, consistent with preferential association of the G protein with unactivated receptors.
Suppressor T lymphocyte induction by a factor released from cultured blastocysts. (1985)

For the analysis of immunologic escape mechanisms of embryos during the implantation period in mice, the effects of culture supernatant of blastocysts on in vitro responsiveness to alloantigen of mice was investigated. Blastocyst-cultured conditioned medium was prepared by culturing late blastocysts of outbred ICR mice for 5 days. The addition of culture supernatant containing four or eight blastocysts to allogeneic mixed lymphocyte culture inhibited both the MLR responses and the generation of cytotoxic T lymphocytes (CTL). Preincubation of the culture supernatant with lymphocytes syngeneic to the responder cells of MLR induced potent suppressor cell activity in the MLR. The supernatant did not inhibit the activity of CTL at the effector phase, but preinduced suppressor cells obtained by incubation of splenocytes with the supernatant showed almost complete suppression of CTL activity at the effector phase. Both of the suppressor cells, active on MLR and at the generation phase of CTL as well as active at the effector phase, had a surface phenotype of Thy-1+ and Ig-. The suppressive material could be extracted from the eight-cell stage of fertilized ova or blastocysts but not from unfertilized ova, indicating that the production of the factor(s) is dependent on the stages of early embryogenesis. These results suggest that the active induction of suppressor T lymphocytes by the factor(s) released from implanted embryos is one of the protective mechanisms from maternal immunologic attack.
Transport of torsional stress in DNA (1999)

It is well known that transcription can induce torsional stress in DNA, affecting the activity of nearby genes or even inducing structural transitions in the DNA duplex. It has long been assumed that the generation of significant torsional stress requires the DNA to be anchored, forming a limited topological domain, because otherwise it would spin almost freely about its axis. Previous estimates of the rotational drag have, however, neglected the role of small natural bends in the helix backbone. We show how these bends can increase the drag several thousandfold relative to prior estimates, allowing significant torsional stress even in linear unanchored DNA. The model helps explain several puzzling experimental results on structural transitions induced by transcription of DNA.
La Crosse virus infection of mammalian cells induces mRNA instability (1988)

La Crosse virus infection of BHK cells leads to a dramatic shutoff of not only host protein synthesis but also viral protein synthesis later in infection. This shutoff can be accounted for by the loss of the cytoplasmic cellular and viral mRNAs. The induction of mRNA instability requires extensive virus replication, since when cycloheximide is added early in infection the preexisting viral and cellular mRNAs do not decrease upon incubation of the cultures. Pretreatment of the cultures with actinomycin D does not affect the ability of La Crosse virus infection to induce mRNA instability, and examination of the rRNAs shows no evidence of specific degradation due to activation of the interferon-associated latent RNase. The induction of mRNA instability therefore does not appear to operate through an interferon pathway. Viral mRNA synthesis, on the other hand, is not turned off during infection, and the cap-dependent endonuclease involved in viral mRNA initiation may be responsible for the mRNA instability.
Mobility support for universal plug and play (UPnP) devices using session initiation protocol (SIP) (2006)

Universal Plug and Play (UPnP) consists of a set of protocols that allow consumer electronic (CE) devices to discover, connect and access one another when they are on the same sub-network. However, UPnP does not provide support for device mobility in which devices are allowed to move from one IP networking domain to another without affecting their ability to interact with other devices. In this paper we propose a system level architecture to provide mobility support to UPnP devices and services by utilizing Session Initiation Protocol (SIP). We propose a new UPnP mime type for carrying UPnP data. We also propose a UPnP packet message forwarding architecture, which uses SIP signaling procedures and hides the mobility of UPnP capable devices from other devices in a network.
Large sensitive-area NbN nanowire superconducting single-photon detectors fabricated on single-crystal MgO substrates (2008)

We report on the performance of large area NbN nanowire superconducting single-photon detectors (SSPDs). 20×20μm2 area SSPDs with 80 and 100nm linewidths and 50% fill factor were fabricated in 4-nm-thick NbN films grown on single-crystal MgO substrates. The high quality of the devices was verified by electrical and optical testing and compares favorably to measurements of 10×10μm2 area SSPDs. Measurements of kinetic inductance versus bias current indicate that the constriction density is low. The fiber-coupled detection efficiency of the devices was 0.4%–3.5% at 100Hz dark count rate.
Energy‐Dispersive Spectrometry (2002)

Abstract Energy‐dispersive x‐ray spectrometry (EDS) is a technique for measuring the intensity of x‐ray emission as a function of the energy of the x‐ray photons. The excitation source for the x‐rays can be energetic electrons, photons, or ions, and the target can be solid, liquid, or gas, although solid targets are the norm in virtually all materials science applications. The measured x‐ray intensity can be related to the concentration (i.e., mass or atomic fraction) for each element present by performing physical/empirical matrix corrections to account for the interelement modification of the generated x radiation caused by (1) primary radiation stopping power and ionization effects, (2) attenuation of secondary characteristic x‐rays during their passage through matter, and (3) any inefficiencies in detection. In this article, various aspects of the process of obtaining high‐quality x‐ray spectra, the interpretation of spectra, and the accurate extraction of x‐ray intensities from spectra are considered. Materials analysis techniques that employ EDS include the following. Electron excitation : (1) electron probe x‐ray microanalysis (EPMA)/analytical scanning electron microscopy (ASEM), where EDS complements wavelength‐dispersive x‐ray spectroscopy (WDS); (2) analytical electron microscopy (AEM). Photon excitation: X‐ray fluorescence (XRF). Ion excitation: particle‐induced x‐ray emission (PIXE). This article will concentrate on EDS performed in electron‐beam instruments. The general principles of EDS x‐ray detection, processing, display, and spectral manipulation are similar for all analytical techniques regardless of the excitation source. The procedures for quantitative analysis depend in detail on the excitation process. Quantitative x‐ray microanalysis by electron excitation is considered in detail in the section on Electron Probe Microanalysis. Those aspects of quantitative x‐ray microanalysis that are particular to EDS spectral measurement are considered.
The Italian iron (1940)

Journal Article The Italian iron Get access Frederic Connett White Frederic Connett White Search for other works by this author on: Oxford Academic Google Scholar Notes and Queries, Volume 179, Issue 17, 26 October 1940, Page 295, https://doi.org/10.1093/nq/179.17.295d Published: 26 October 1940
Titanium-Mediated Diastereoselective Formation of (E)- or (Z)-2-Substituted 1-Vinylcyclopropanols: Scope and Limitation, Applications (2002)

Titanium-mediated cyclopropanation of α,β-unsaturated esters failed to provide 1-vinylcyclopropanol derivatives in useful yields, but (E)-2-substituted-1-vinylcyclopropanols were formed diastereoselectively from O-protected β-oxo- and β-halo esters, with the allylic double bond being created subsequently (Knoevenagel condensation or dehydrohalogenation). Titanium-mediated cyclopropanation of homoallyl alk-2-enoates, on the other hand, directly provided the corresponding Z diastereomers. Palladium(0)-catalysed azidation of their sulfonic esters (tosylate, mesylate), azide reduction, and subsequent double bond cleavage afforded (E)- or (Z)-2-alkyl-2,3-methanoamino acids, although improvements are required to perform the total asymmetric syntheses of molecules with three membered-rings by these methods. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
Regulation of the <i>gadd45β</i> Promoter by NF-κB (2002)

In addition to coordinating immune and inflammatory responses, NF-kappaB/Rel transcription factors control cell survival. The NF-kappaB antiapoptotic function is crucial to oncogenesis, cancer chemoresistance, and to antagonize tumor necrosis factor (TNF) receptor-induced killing. Recently, we have shown that the suppression of the c-Jun-N-terminal kinase (JNK) cascade is a pivotal protective mechanism by NF-kappaB, and that this suppression involves the upregulation of gadd45beta/myd118. Induction of gadd45beta by stress and cytokines requires NF-kappaB; however, the regulatory mechanisms underlying this induction are not known. Here, we report that, in HeLa cells, the NF-kappaB subunit RelA is sufficient to activate gadd45beta expression, whereas Rel and p50 are not. Activation of gadd45beta by RelA depends on three kappaB elements at positions -447/-438 (kappaB-1), -426/-417 (kappaB-2), and -377/-368 (kappaB-3) of the gadd45beta promoter. Each of these sites binds to NF-kappaB complexes in vitro, and is required for optimal promoter transactivation. The data establish the direct participation of NF-kappaB in the regulation of Gadd45beta, thereby providing important mechanistic insights into the control of apoptosis by the transcription factor.
From artificial red blood cells, oxygen carriers, and oxygen therapeutics to artificial cells, nanomedicine, and beyond (2012)

The first experimental artificial red blood cells have all three major functions of red blood cells (rbc). However, the first practical one is a simple polyhemoglobin (PolyHb) that only has an oxygen-carrying function. This is now in routine clinical use in South Africa and Russia. An oxygen carrier with antioxidant functions, PolyHb-catalase-superoxide dismutase, can fulfill two of the three functions of rbc. Even more complete is one with all three functions of rbc in the form of PolyHb-catalase-superoxide dismutase-carbonic anhydrase. The most advanced ones are nanodimension artificial rbc with either PEG-lipid membrane or PEG-PLA polymer membrane. Extensions into oxygen therapeutics include a PolyHb-tyrosinase that suppresses the growth of melanoma in a mice model. Another is a PolyHb-fibrinogen that is an oxygen carrier with platelet-like function. Research has now extended well beyond the original research on artificial rbc into many areas of artificial cells. These include nanoparticles, nanotubules, lipid vesicles, liposomes, polymer-tethered lipid vesicles, polymersomes, microcapsules, bioencapsulation, nanocapules, macroencapsulation, synthetic cells, and others. These are being used in nanotechnology, nanomedicine, regenerative medicine, enzyme/gene therapy, cell/stem cell therapy, biotechnology, drug delivery, hemoperfusion, nanosensers, and even by some groups in agriculture, industry, aquatic culture, nanocomputers, and nanorobotics.
Water and its relation to broken bond defects in fused silica (1976)

We have studied the effects of water and defects on the Raman spectrum of fused silica. Intensities of defect lines at 604 and 490 cm−1 were found to increase with fictive temperature and to decrease with increasing OH content. The results suggest that water in the melt is preferentially trapped at the defect sites. The increased sensitivity obtained by using an optical fiber as the sample enabled us to see for the first time the Si– (OH) stretching vibration at 970 cm−1. The Si–(OH) intensity agrees with that of the 1100 cm−1 dangling oxygen line in a silica fiber weakly doped with K2O. A comparison with other spectral features shows that the Raman cross section for the Si–O stretch is extremely weak. This weak cross section contributes to the weak Raman intensity of the 1100 cm−1 lines in both fused and crystalline SiO2 and also explains why the dangling oxygen stretching vibration is not observed by Raman scattering in neutron damaged silica. Measurements of the much stronger 3690 cm−1 OH stretching vibration in a series of bulk samples of known OH content suggest this line as a useful measure of OH in fibers. In addition we find a water induced low frequency (30 cm−1) band which is weakly Raman and strongly infrared active.
An Observation of Healthcare Knowledge Management (2014)

Healthcare within the U.S. is reaching a point where the facilities and doctors are collecting large amounts of patient and practice related information. The goal of cost savings is driving investment growth in healthcare technology. The introduction of knowledge management and the ability to leverage IT solutions can provide a means for which the healthcare industry can meet the demand for care that is growing with the increase of population and the gradual retirement of baby boomers. However, the advancements in health informatics along with knowledge management practices currently present challenges in terms of adoption. Therefore, this paper discusses the role of knowledge management and issues of knowledge management implementation in healthcare industry. Knowledge management practices have benefited many industries ranging from banking to retailing. It is widely believed that KM will also benefit the healthcare industry if KM implementation is properly planned and executed. KM may possibly change the way in which hospitals, doctors, and patients interact.
Spray cryotherapy for the treatment of glottic and subglottic stenosis (2010)

The use of spray cryotherapy alone or in conjunction with balloon dilation is a promising and effective therapeutic approach to treating glottic and subglottic narrowing.