gebhart/patrepeval huggingface dataset:
High-Sensitivity Ion Mobility Spectrometry/Mass Spectrometry Using Electrodynamic Ion Funnel Interfaces (2005)

The utility of ion mobility spectrometry (IMS) for separation of mixtures and structural characterization of ions has been demonstrated extensively, including in biological and nanoscience contexts. A major attraction of IMS is its speed, several orders of magnitude greater than that of condensed-phase separations. Nonetheless, IMS combined with mass spectrometry (MS) has remained a niche technique, substantially because of limited sensitivity resulting from ion losses at the IMS-MS junction. We have developed a new electrospray ionization (ESI)-IMS-QTOF MS instrument that incorporates electrodynamic ion funnels at both front ESI-IMS and rear IMS-QTOF interfaces. The front funnel is of the novel "hourglass" design that efficiently accumulates ions and pulses them into the IMS drift tube. Even for drift tubes of 2-m length, ion transmission through IMS and on to QTOF is essentially lossless across the range of ion masses relevant to most applications. The rf ion focusing at the IMS terminus does not degrade IMS resolving power, which exceeds 100 (for singly charged ions) and is close to the theoretical limit. The overall sensitivity of the present ESI-IMS-MS system is comparable to that of commercial ESI-MS, which should make IMS-MS suitable for analyses of complex mixtures with ultrahigh sensitivity and exceptional throughput.
CHEMISTRY FLOWS LIKE CLOCKWORK (2003)

RETURN TO ISSUEPREVNewsNEXTCHEMISTRY FLOWS LIKE CLOCKWORKFlow system used to make simple devices for time-dependent studiesMITCH JACOBYCite this: Chem. Eng. News 2003, 81, 8, 5Publication Date (Print):February 24, 2003Publication History Published online13 November 2010Published inissue 24 February 2003https://pubs.acs.org/doi/10.1021/cen-v081n008.p005https://doi.org/10.1021/cen-v081n008.p005newsACS PublicationsCopyright © 2003 AMERICAN CHEMICAL SOCIETYArticle Views20Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options SUBJECTS:Biotechnology,Chemical reactions,Fluid dynamics,Polymerization kinetics Get e-Alerts
Cowpox Virus Evades CTL Recognition and Inhibits the Intracellular Transport of MHC Class I Molecules (2007)

Orthopoxviruses evade host immune responses by using a number of strategies, including decoy chemokine receptors, regulation of apoptosis, and evasion of complement-mediated lysis. Different from other poxviral subfamilies, however, orthopoxviruses are not known to evade recognition by CTL. In fact, vaccinia virus (VV) is used as a vaccine against smallpox and a vector for eliciting strong T cell responses to foreign Ags. and both human and mouse T cells are readily stimulated by VV-infected APC in vitro. Surprisingly, however, CD8(+) T cells of mice infected with cowpox virus (CPV) or VV recognized APC infected with VV but not APC infected with CPV. Likewise, CD8(+) T cells from vaccinated human subjects could not be activated by CPV-infected targets and CPV prevented the recognition of VV-infected APC upon coinfection. Because CD8(+) T cells recognize viral peptides presented by MHC class I (MHC I), we examined surface expression, total levels, and intracellular maturation of MHC I in CPV- and VV-infected human and mouse cells. Although total levels of MHC I were unchanged, CPV reduced surface levels and inhibited the intracellular transport of MHC I early during infection. CPV did not prevent peptide loading of MHC I but completely inhibited MHC I exit from the endoplasmic reticulum. Because this inhibition was independent of viral replication, we conclude that an early gene product of CPV abrogates MHC I trafficking, thus rendering CPV-infected cells "invisible" to T cells. The absence of this immune evasion mechanism in VV likely limits virulence without compromising immunogenicity.
Characterization of a soluble ternary complex formed between human interferon‐β‐1a and its receptor chains (1999)

Abstract The extracellular portions of the chains that comprise the human type I interferon receptor, IFNAR1 and IFNAR2, have been expressed and purified as recombinant soluble His‐tagged proteins, and their interactions with each other and with human interferon‐β‐1a (IFN‐β‐1a) were studied by gel filtration and by cross‐linking. By gel filtration, no stable binary complexes between IFN‐β‐1a and IFNAR1, or between IFNAR1 and IFNAR2 were detected. However, a stable binary complex formed between IFN‐β‐1a and IFNAR2. Analysis of binary complex formation using various molar excesses of IFN‐β‐1a and IFNAR2 indicated that the complex had a 1:1 stoichiometry, and reducing SDS‐PAGE of the binary complex treated with the cross‐linking reagent dissucinimidyl glutarate (DSG) indicated that the major cross‐linked species had an apparent M r consistent with the sum of its two individual components. Gel filtration of a mixture of IFNAR1 and the IFN‐β‐1a/IFNAR2 complex indicated that the three proteins formed a stable ternary complex. Analysis of ternary complex formation using various molar excesses of IFNAR1 and the IFN‐β‐1a/IFNAR2 complex indicated that the ternary complex had a 1:1:1 stoichiometry, and reducing SDS‐PAGE of the ternary complex treated with DSG indicated that the major cross‐linked species had an apparent M r consistent with the sum of its three individual components. We conclude that the ternary complex forms by the sequential association of IFN‐β‐1a with IFNAR2, followed by the association of IFNAR1 with the preformed binary complex. The ability to produce the IFN‐β‐1a/IFNAR2 and IFN‐β‐1a/IFNAR1/IFNAR2 complexes make them attractive candidates for X‐ray crystallography studies aimed at determining the molecular interactions between IFN‐β‐1a and its receptor.
Cloning and nucleic acid sequence of the Salmonella typhimurium pncB gene and structure of nicotinate phosphoribosyltransferase (1991)

The pncB gene of Salmonella typhimurium, encoding nicotinate phosphoribosyltransferase (NAPRTase), was cloned on a 4.7-kb Sau3A fragment. The gene contains a 1,200-bp open reading frame coding for a 400-residue protein. Amino acid sequencing of the amino-terminal and two interior peptides of the purified protein confirmed the deduced sequence and revealed that the amino-terminal methionine residue was removed, giving a 399-residue mature protein of Mr 45,512. No signal sequence was observed in the predicted NAPRTase primary structure, suggesting that the enzyme is not periplasmic. The protein does not demonstrate clear sequence similarity to the other seven phosphoribosyltransferases of known primary structure and frustrates attempts to define a consensus 5-phosphoribosyl-1-pyrophosphate-binding region. The NAPRTase reaction is ATP stimulated, and the protein contains a carboxy-terminal sequence diagnostic of an ATP-binding site. An inverted repeat of the sequence TAAACAA observed in the proposed promoter region of pncB is also present in the promoter of nadA, which, like pncB, is also regulated by the NadR (NadI) repressor. The sequence may thus define an NadR repressor-binding site.
Optimal vaccine allocation to control epidemic outbreaks in arbitrary networks (2013)

We consider the problem of controlling the propagation of an epidemic outbreak in an arbitrary contact network by distributing vaccination resources throughout the network. We analyze a networked version of the Susceptible-Infected-Susceptible (SIS) epidemic model when individuals in the network present different levels of susceptibility to the epidemic. In this context, controlling the spread of an epidemic outbreak can be written as a spectral condition involving the eigenvalues of a matrix that depends on the network structure and the parameters of the model. We study the problem of finding the optimal distribution of vaccines throughout the network to control the spread of an epidemic outbreak. We propose a convex framework to find cost-optimal distribution of vaccination resources when different levels of vaccination are allowed.We illustrate our approaches with numerical simulations in a real social network.
Biomarkers of lipid peroxidation, airway inflammation and asthma (2003)

Oxidative stress, specifically lipid peroxidation, is believed to contribute to the pathophysiology of asthma. This review highlights the pathways through which reactive oxygen species (ROS) may lead to lipid peroxidation. The potential of both the innate and acquired immune systems to activate inflammatory cells and release ROS that may overwhelm the host antioxidant defences and cause lipid peroxidation, accompanied by detrimental pathophysiological effects, are discussed. Despite the evidence demonstrating the importance of lipid peroxidation, systematic characterisation of oxidative stress and antioxidant defences has not been undertaken, largely due to the lack of appropriate biomarkers. This review discusses the emergence of isoprostanes (specifically 8-iso-prostaglandin F2alpha) as reliable, in vivo markers of lipid peroxidation, which provides an appropriate tool for studying oxidative stress. Furthermore, the development of techniques to study induced sputum and breath condensate, derived directly from the airway surface, enables the site of oxidative damage to be closely assessed. Evidence suggests that dietary changes that have occurred over recent years have increased susceptibility to lipid peroxidation, due to reduced antioxidant defences. To date, the limited number of long-term (>1 week) supplementation trials have been promising. However, the development of techniques to study isoprostanes in airway-lining fluid pave the way for further studies investigating the potential for antioxidant supplements to be used as routine therapy in asthma.
Analysis Of 31 Cases Of Delayed Closure Of The Cleft Palate (1992)

Abstract This study includes an analysis of 31 cases treated by delayed closure of hard palate. Emphasis of this study is on speech and maxillary growth. Advantage of delayed closure of the hard palate like better maxillary growth does not seem, compensated for the speech problem associated with the procedure.
Attribute and simile classifiers for face verification (2009)

We present two novel methods for face verification. Our first method - “attribute” classifiers - uses binary classifiers trained to recognize the presence or absence of describable aspects of visual appearance (e.g., gender, race, and age). Our second method - “simile” classifiers - removes the manual labeling required for attribute classification and instead learns the similarity of faces, or regions of faces, to specific reference people. Neither method requires costly, often brittle, alignment between image pairs; yet, both methods produce compact visual descriptions, and work on real-world images. Furthermore, both the attribute and simile classifiers improve on the current state-of-the-art for the LFW data set, reducing the error rates compared to the current best by 23.92% and 26.34%, respectively, and 31.68% when combined. For further testing across pose, illumination, and expression, we introduce a new data set - termed PubFig - of real-world images of public figures (celebrities and politicians) acquired from the internet. This data set is both larger (60,000 images) and deeper (300 images per individual) than existing data sets of its kind. Finally, we present an evaluation of human performance.
Activation of the ppp(A2'p)nA system in interferon-treated, Herpes simplex virus-infected cells and evidence for novel inhibitors of the ppp(A2'p)nA-dependent RNase (1984)

High doses (100-1000 reference units/ml) of alpha or beta interferons are required to inhibit the growth of herpes simplex virus types I and II (HSV-I and HSV-II) in human Chang cells. In contrast, much lower doses (10-100 reference units/ml) of interferon inhibit replication of encephalomyocarditis virus (EMCV) in these cells. In the HSV-infected cells these high doses did not prevent the virus-induced shut off of host protein synthesis. The interferons were more effective in reducing the virus yield of HSV-I than of HSV-II. At the above concentrations they inhibited HSV-I protein synthesis but had little apparent effect on that of HSV-II. Similar amounts of (2'-5')oligo(adenylate)s were synthesised in response to HSV-I, HSV-II and EMCV infection of Chang cells after treatment with alpha or beta interferons. No (i.e. less than 1 nM) (2'-5')oligo(adenylate)s were found in control cells or on virus infection alone. Only low levels of ppp(A2'p)nA-specific rRNA cleavage were observed in the interferon-treated HSV-infected cells. In contrast, high levels were found in response to EMCV, despite the fact that ppp(A2'p)nA accumulated to similar levels with each of the three viruses in these cells. High-performance liquid chromatographic analysis of material from interferon-treated Chang cells 18 h after infection with HSV-I or HSV-II, combined with radiobinding, radioimmune and rRNA cleavage assays, confirmed the presence of ppp(A2'p)2A and ppp(A2'p)3A at greater than nanomolar concentration. In addition, apparently equivalent amounts of two other putative (2'-5')oligo(adenylate) derivatives which compete in the radiobinding and radioimmune assays, were present. These compounds were only weak activators of the ppp(A2'p)nA-dependent RNase and under appropriate conditions were capable of inhibiting the activation of this RNase by authentic ppp(A2'p)nA. The presence of these potentially inhibitory compounds provides a possible explanation for the relatively low levels of activation of the ppp(A2'p)nA-dependent RNase in interferon-treated, HSV-infected Chang cells.
Subacute reconstruction of lower leg and foot defects due to high velocity-high energy injuries caused by gunshots, missiles, and land mines (2005)

The present study reviews 215 male patients suffering high velocity-high energy injuries of the lower leg or foot caused by war weapons such as missiles, gunshots, and land mines. They were treated in the Department of Plastic and Reconstructive Surgery at Gulhane Military Medical Academy (Ankara, Turkey) between November 1993-January 2001. Severe soft-tissue defects requiring flap coverage and associated open bone fractures that were treated 7-21 days (mean, 9.6 days) after the injury were included in the study. Twenty-three of 226 extremities (10.2%) underwent primary below-knee amputation. The number of debridements prior to definitive treatment was between 1-3 (mean, 1.9). Gustilo type III open tibia fractures accompanied 104 of 126 soft-tissue defects of the lower leg. Sixty-four bone defects accompanied 83 soft-tissue defects of the feet. Eighteen local pedicled muscle flaps and 208 free muscle flaps (latissimus dorsi, rectus abdominis, and gracilis) were used in soft-tissue coverage of 209 defects. Overall, the free muscle flap success rate was 91.3%. Bone defects were restored with 106 bone grafts, 25 free fibula flaps, and 14 distraction osteogenesis procedures. Osseous and soft-tissue defects were reconstructed simultaneously at the first definitive treatment in 94% of cases. The mean follow-up after definitive treatment was 25 (range, 9-47) months. The average full weight-bearing times for lower leg and feet injuries were 8.4 months and 4 months, respectively. Early, aggressive, and serial debridement of osseous and soft tissue, early restoration of bone and soft-tissue defects at the same stage, intensive rehabilitation, and patient education were the key points in the management of high velocity-high energy injuries of the lower leg and foot.
Financing higher education in Africa : Makerere, the quiet revolution (1999)

This report is one of a series that examines the state of higher education in a variety of countries in Africa at the end of the twentieth century. This one tells the dramatic story oh how Makerere University in Uganda has addressed the pervasive problem of how to provide quality education at the tertiary level without undue financial dependence upon the state. It describes the main reform measures adopted, assesses their impact, considers some of the reasons for the success of chosen measures, identifies remaining issues for attention and looks at the question of sustainability.
Isolation, nucleotide sequence analysis, and disruption of the MDH2 gene from Saccharomyces cerevisiae: evidence for three isozymes of yeast malate dehydrogenase. (1991)

The major nonmitochondrial isozyme of malate dehydrogenase (MDH2) in Saccharomyces cerevisiae cells grown with acetate as a carbon source was purified and shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to have a subunit molecular weight of approximately 42,000. Enzyme assays and an antiserum prepared against the purified protein were used to screen a collection of acetate-nonutilizing (acetate-) yeast mutants, resulting in identification of mutants in one complementation group that lack active or immunoreactive MDH2. Transformation and complementation of the acetate- growth phenotype was used to isolate a plasmid carrying the MDH2 gene from a yeast genomic DNA library. The amino acid sequence derived from complete nucleotide sequence analysis of the isolated gene was found to be extremely similar (49% residue identity) to that of yeast mitochondrial malate dehydrogenase (molecular weight, 33,500) despite the difference in sizes of the two proteins. Disruption of the MDH2 gene in a haploid yeast strain produced a mutant unable to grow on minimal medium with acetate or ethanol as a carbon source. Disruption of the MDH2 gene in a haploid strain also containing a disruption in the chromosomal MDH1 gene encoding the mitochondrial isozyme produced a strain unable to grow with acetate but capable of growth on rich medium with glycerol as a carbon source. The detection of residual malate dehydrogenase activity in the latter strain confirmed the existence of at least three isozymes in yeast cells.
Modelling of active forms of protein kinases: p38--a case study. (1997)

An active form of p38 protein kinase, belonging to the mitogen-activated protein kinases subfamily, has been designed based on crystallographically known structures of two other kinases, an active form of protein kinase A (PKA) and an inactive form of extracellular signal-regulated kinase 2 (ERK2). The modelling procedure is described. Its general scheme can also be applied to other kinases. The structure of the active forms of p38 and PKA is very similar in the region which binds the substrate. The ATP-binding mode is very similar in the active forms of all the three studied kinases. Models of the active forms allow for further studies on transphosphorylation processes at the molecular level, and modelling of inhibitors competitive with ATP and/or substrates.
A Prospective Study of Free Bilirubin and Other Risk Factors in the Development of Kernicterus in Premature Infants (1982)

To assess the value of free bilirubin (FB) measurements in predicting kernicterus (KI) in sick premature infants, 91 newborns weighing less than 1,500 gm at birth were observed during the first week of life with twice daily FB and total bilirubin determinations. Autopsies were performed on 30 of the 53 infants who died. Seven had KI and 23 did not. There were no differences between infants with and without KI in the maximum FB level (KI 18.2 ± 4.5 [SEM] nm/liter, no KI 11.1 ± 0.9 nm/liter, P not significant) or the total bilirubin level (KI 7.3 ± 1.3 mg/100 ml, no KI 6.1 ± 0.5 mg/100 ml, P not significant). In fact, three kernicteric infants had very low maximum FB levels (&amp;lt;10 nm/liter). These three infants had prolonged episodes of acidosis, hypoxemia, or hypothermia during the 24 hours preceding their maximum level of FB. Although elevated levels of FB may be predictive of KI in some infants, other factors may make the blood-brain barrier more permeable to low levels of FB. This may limit the clinical applicability of FB measurements.
Cabazitaxel or mitoxantrone with prednisone in patients with metastatic castration-resistant prostate cancer (mCRPC) previously treated with docetaxel: Estimating mean overall survival (OS) for health economic analyses from a phase III trial (TROPIC). (2011)

128^ Background: TROPIC evaluated the efficacy and safety of the novel taxane cabazitaxel in men with mCRPC previously treated with docetaxel. Median OS was significantly improved, as previously reported (12.7 months in mitoxantrone arm vs 15.1 months in cabazitaxel arm, HR=0.72 [0.61 – 0.84], p&lt;0.0001- updated OS results). Median OS is the most useful descriptive statistic for physicians and patients as it reflects a point estimate in time by which 50% patients may survive regardless of disease status or progression. It avoids assumptions on long-term survival beyond the follow-up period of the clinical trial. Payers however are interested in making a coverage and reimbursement decisions based on the overall therapeutic benefit relative to its risk, and the expected impact on healthcare expenditures. Analyses such as cost-effectiveness analysis therefore require the estimation of mean OS. Methods: Mean OS is only observable when the last patient has died. Its estimation can be derived via an extrapolation of the trial Kaplan-Meier curve using a survival function. Several parametric distributions (exponential, weibull, lognormal, loglogistic and Gompertz) were tested. The parametric distribution that best fitted the trial Kaplan-Meier curves was selected using the Akaike's Information criteria (AIC), the Bayesian Information Criteria (BIC) and graphical method to evaluate the goodness of fit of the distributions. Mean OS from the best fitted model was generated to support payer decision making. Results: Using AIC/BIC and graphical method, the Weibull survival function, S(t)=exp(-l t s ) where l is a scale parameter and s a shape parameter, was selected as the distribution that best fitted the TROPIC data. Results of the estimated mean survival assuming a Weibull function are described in the table. Conclusions: Assuming a Weibull distribution, mean OS is estimated at 14.5 months in mitoxantrone arm vs 18.5 months in cabazitaxel arm, leading to 4 months OS difference in favour of cabazitaxel. [Table: see text] [Table: see text]