gebhart/patrepeval huggingface dataset:
Pseudomonas exotoxin A mutants. Replacement of surface exposed residues in domain II with cysteine residues that can be modified with polyethylene glycol in a site-specific manner. (1994)

Pseudomonas exotoxin A (PE) is a three-domain protein in which domain Ia is involved in recognition of receptors on eukaryotic target cells, domain II promotes translocation of PE into the cytosol, and domain III enzymatically ADP-ribosylates elongation factor 2. Modification of proteins with polyethylene glycol (PEG) has been shown to prolong circulating plasma lifetime and may reduce or eliminate immunogenicity. However, in the case of toxins, PEG may interfere with or block toxin activity. To investigate the effect of polyethylene glycolation on specific residues located on the surface of PE domain II, we substituted cysteine, for each of the five most exposed surface amino acids (H276, E282, N306, R313, and E327) in domain II. These cysteines can serve as unique sites for PEG modification. The PE-Cys proteins retained most of their cytotoxicity even when the free sulfhydryl group was blocked by 5,5'-dithiobis(nitrobenzoic acid) or glutathione. When the PE-Cys proteins were conjugated with ovalbumin using a cleavable disulfide linkage, cytotoxicity was retained, but it was lost with a non-cleavable thioether linkage. In contrast, cytotoxicity was maintained when PE-Cys mutants were coupled to 5- or 20-kDa mPEG, using either a disulfide or a thioether linkage. Unexpectedly in some cases, the thioether conjugate was more active than the disulfide linkage. Pharmacokinetic studies on one of the polyethylene-glycolated molecules (R313C) showed that the mean residence time (t 1/2) was prolonged to 72 min, compared to 20 min for unpolyethylene glycolated PE-Cys(R313C). These studies show it is possible to derivatize PE at specific residues in domain II, maintain significant cytotoxic activity, and alter pharmacokinetics. These studies also suggest that large mPEG molecules can be translocated to the cytosol while still attached to domain II of PE.
Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. (1981)

The model of human Fc fragment was refined at 2.9-A resolution. Two different automated procedures for crystallographic refinement were used [Deisenhofer, J., & Steigemann, W. (1975) Acta Crystallogr., Sec. B B31, 238; Jack, A., & Levitt, M. (1978) Acta Crystallogr., Sect. A A34, 931]. The final R value is 0.22. The dimer of CH3 domains closely resembles the CH1-CL aggregate in Fab fragments. There is no contact between CH2 domains. The contact between CH2 and CH3 domains has about one-third of the size of the CH3-CH3 contact. The carbohydrate, a branched chain of nine hexose units, covers parts of the C-contact face of the CH2 domain, shielding hydrophobic residues on this surface. Six atoms of the carbohydrate are within hydrogen-bonding distance of atoms in the CH2 domain. Crystallographic refinement of the complex between Fc fragment and fragment B of protein A from Staphylococcus aureus reduced the R value of the model is 0.24. A major part of the structure of fragment B consists of two alpha helics; the rest of the polypeptide chain is folded irregularly. In the crystal, fragment B forms two contacts with Fc fragment molecules. Contact 1 involves residues from both helices of fragment B, and residues from the CH2 and CH3 domains of FC, and is predominantly hydrophobic. Contact 2 is smaller than contact 1. Residues from the second helix and adjacent residues of fragment B and residues only from the CH3 domain of Fc contribute to contact 2. The nature of contact 2 is mainly polar and includes a sulfate ion. There are strong arguments that contact 1 is the fragment B-Fc contact formed in solution under physiological conditions, while contact 2 is a crystal contact.
Activation of the p53-MDM4 regulatory axis defines the anti-tumour response to PRMT5 inhibition through its role in regulating cellular splicing (2018)

Evasion of the potent tumour suppressor activity of p53 is one of the hurdles that must be overcome for cancer cells to escape normal regulation of cellular proliferation and survival. In addition to frequent loss of function mutations, p53 wild-type activity can also be suppressed post-translationally through several mechanisms, including the activity of PRMT5. Here we describe broad anti-proliferative activity of potent, selective, reversible inhibitors of protein arginine methyltransferase 5 (PRMT5) including GSK3326595 in human cancer cell lines representing both hematologic and solid malignancies. Interestingly, PRMT5 inhibition activates the p53 pathway via the induction of alternative splicing of MDM4. The MDM4 isoform switch and subsequent p53 activation are critical determinants of the response to PRMT5 inhibition suggesting that the integrity of the p53-MDM4 regulatory axis defines a subset of patients that could benefit from treatment with GSK3326595.
A Novel High-Throughput Screening Method for Microbial Transglutaminases with High Specificity toward Gln141 of Human Growth Hormone (2010)

PEGylation modification has been used to improve the pharmacokinetic properties of protein-based drugs. For example, PEGylated human growth hormone (hGH) has been shown to exhibit better pharmacokinetic profiles than the unmodified hGH. Unlike chemical PEGylation of hGH that is difficult to be controlled to result in homogeneity, microbial transglutaminase (mTGase) only conjugates poly(ethelene glycol) (PEG) on glutamine-40 (Q40) and glutamine-141 (Q141) of hGH, the only glutamine residues exposed. Yet, an mTGase that can selectively conjugate PEG to only 1 glutamine residue is more desirable to control the homogeneity of the product. In this study, the authors have developed a novel high-throughput assay, with which they have identified 5 mTGase mutants that are highly specific for conjugating PEG to Q141 of hGH. In this scintillation proximity assay (SPA)-based method, the authors have (1) achieved a high expression level of active mTGase, which is toxic to the living cell, directly from Escherichia coli (0.2 U/mL/OD600) by in vivo activation; (2) developed a high-throughput affinity purification method to eliminate the strong interference of cellular protein to mTGase reaction; and (3) used therapeutic protein as the substrate. This method is highly sensitive, is easily automated, and could be generally applied to screening mTGases with desired specificity targeting on different therapeutic proteins.
TCP Vegas (1994)

Vegas is a new implementation of TCP that achieves between 40 and 70% better throughput, with one-fifth to one-half the losses, as compared to the implementation of TCP in the Reno distribution of BSD Unix. This paper motivates and describes the three key techniques employed by Vegas, and presents the results of a comprehensive experimental performance study—using both simulations and measurements on the Internet—of the Vegas and Reno implementations of TCP.
Interacting Proteins and Differences in Nuclear Transport Reveal Specific Functions for the NAP1 Family Proteins in Plants (2005)

Nucleosome assembly protein 1 (NAP1) is conserved from yeast to human and facilitates the in vitro assembly of nucleosomes as a histone chaperone. Inconsistent with their proposed function in the nucleus, however, many NAP1 proteins had been reported to localize in the cytoplasm. We investigated the subcellular localization of tobacco (Nicotiana tabacum) and rice (Oryza sativa) NAP1 family proteins first by identification of interacting partners and by direct examination of the localization of green fluorescent protein-tagged proteins. Through treatment of tobacco cells with leptomycin B and mutagenesis of nuclear export signal, we demonstrated that Nicta;NAP1;1 and Orysa;NAP1;1 shuttle between the cytoplasm and the nucleus. Together with the demonstration that tobacco NAP1 proteins bind histone H2A and H2B, our results support the current model and provide additional evidence that function of NAP1 as histone chaperones appears to be conserved in plants. In addition, we show that tobacco NAP1 proteins interact with tubulin and the mitotic cyclin Nicta;CYCB1;1, suggesting a role for NAP1 in microtubule dynamics. Interestingly, in spite of their high homology with the above NAP1 proteins, the other three tobacco proteins and Orysa;NAP1;2 did not show nucleocytoplasmic shuttling and were localized only in the cytoplasm. Moreover, Orysa;NAP1;3 that lacks a typical nuclear localization signal sequence was localized in both the cytoplasm and the nucleus. Finally, we show that only Orysa;NAP1;3 could be phosphorylated by casein kinase 2alpha in vitro. However, this phosphorylation was not responsible for nuclear import of Orysa;NAP1;3 as being demonstrated through mutagenesis studies. Together, our results provide an important step toward elucidating the molecular mechanism of function of the NAP1 family proteins in plants.
Amplified fragment length polymorphism (AFLP) versus randomly amplified polymorphic DNA (RAPD) as new tools for inter- and intra-species differentiation within Bordetella (2005)

Automated amplified fragment length polymorphism (AFLP) and randomly amplified polymorphic DNA (RAPD) techniques with fluorescently labelled primers were used to track differences among isolates of the eight known species of the Bordetella genus. Eighty-one representative strains of these species from international and Polish bacterial collections were genotyped according to RAPD protocols using primer 1254 or 1247, and AFLP involving EcoRI/MseI or newly designed SpeI/ApaI restriction/ligation/amplification procedures. By comparing AFLP and RAPD data, it was concluded that the discriminatory power of AFLP is higher in comparison with RAPD for both intra- and inter-species differentiation of isolates of the Bordetella genus. The most precise level of inter-species discrimination and the highest level of intra-species discrimination of the Bordetella isolates of the eight species were observed in the AFLP EcoRI/MseI and SpeI/ApaI sets, respectively. Both techniques might provide alternative tools for the identification of Bordetella at the genomic species and strain levels, and thus may be valuable in human and veterinary diagnostics as well as in epidemiology. By applying the AFLP technique presented in this article, more precise data on the emergence of newly acquired and/or on expanded clones and transmission routes of isolates of the Bordetella genus in the human and animal environments might be obtained.
Retinal angiomatous proliferation associated with risk alleles of ARMS2/HTRA1 gene polymorphisms in Japanese patients (2013)

Our results suggest that the risk alleles of the ARMS2/HTRA1 SNPs may be associated with development of RAP and play a major role in the pathogenesis of intraretinal angiogenesis.
Exendin-4–Based Radiopharmaceuticals for Glucagonlike Peptide-1 Receptor PET/CT and SPECT/CT (2010)

These promising pharmacokinetic and imaging data show that [Lys(40)(Ahx-DOTA-(68)Ga)NH(2)]-exendin-4 and [Lys(40)(Ahx-HYNIC-(99m)Tc/EDDA)NH(2)]-exendin-4 are suitable candidates for clinical GLP-1 receptor imaging studies.
High Charge Carrier Mobilities and Lifetimes in Organolead Trihalide Perovskites (2013)

Organolead trihalide perovskites are shown to exhibit the best of both worlds: charge-carrier mobilities around 10 cm2 V−1 s−1 and low bi-molecular charge-recombination constants. The ratio of the two is found to defy the Langevin limit of kinetic charge capture by over four orders of magnitude. This mechanism causes long (micrometer) charge-pair diffusion lengths crucial for flat-heterojunction photovoltaics.
Expression of the candidate Wilm's tumor gene, WT1, in human leukemia cells. (1993)

Wilms' tumor (WT) is a pediatric malignancy that occurs in embryonic kidney. Recently, a putative Wilms' tumor gene (WT1), located on chromosome 11p13, was isolated and characterized. We found constitutive expression of WT1 mRNA in eight out of 22 hematopoietic cell lines and seven out of 26 clinical samples which were derived from patients with various types of hematologic malignancies. WT1 mRNA was detected in four out of six myeloid cell lines, four out of 10 cases of acute myelocytic leukemia, three out of 15 lymphoid cell lines, one out of nine cases of lymphoid malignancies, and one out of six cases of chronic myelocytic leukemia in accelerated phase and blast crisis. One unclassified hematopoietic cell line and a case of myelodysplastic syndrome also expressed WT1 mRNA. No mutations were detectable in the cell lines by Southern blot analysis and a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis in the four zinc finger domains of the WT1 gene. These results suggest that WT1 gene is expressed in several types of immature lymphoid or myeloid leukemia cells possibly without alterations of the WT1 gene.
Serf and Turf: Crowdturfing for Fun and Profit (2011)

Popular Internet services in recent years have shown that remarkable things can be achieved by harnessing the power of the masses using crowd-sourcing systems. However, crowd-sourcing systems can also pose a real challenge to existing security mechanisms deployed to protect Internet services. Many of these techniques make the assumption that malicious activity is generated automatically by machines, and perform poorly or fail if users can be organized to perform malicious tasks using crowd-sourcing systems. Through measurements, we have found surprising evidence showing that not only do malicious crowd-sourcing systems exist, but they are rapidly growing in both user base and total revenue. In this paper, we describe a significant effort to study and understand these "crowdturfing" systems in today's Internet. We use detailed crawls to extract data about the size and operational structure of these crowdturfing systems. We analyze details of campaigns offered and performed in these sites, and evaluate their end-to-end effectiveness by running active, non-malicious campaigns of our own. Finally, we study and compare the source of workers on crowdturfing sites in different countries. Our results suggest that campaigns on these systems are highly effective at reaching users, and their continuing growth poses a concrete threat to online communities such as social networks, both in the US and elsewhere.
α4β1 Integrin Mediates the Recruitment of Immature Dendritic Cells across the Blood-Brain Barrier during Experimental Autoimmune Encephalomyelitis (2010)

Dendritic cells (DCs) within the CNS are recognized to play an important role in the effector phase and propagation of the immune response in experimental autoimmune encephalomyelitis (EAE), a mouse model for multiple sclerosis. However, the mechanisms regulating DC trafficking into the CNS still need to be characterized. In this study, we show by performing intravital fluorescence videomicroscopy of the inflamed spinal cord white-matter microvasculature in SJL mice with EAE that immature, and to a lesser extent, LPS-matured, bone marrow-derived DCs efficiently interact with the CNS endothelium by rolling, capturing, and firm adhesion. Immature but not LPS-matured DCs efficiently migrated across the wall of inflamed parenchymal microvessels into the CNS. Blocking alpha4 integrins interfered with the adhesion but not the rolling or capturing of immature and LPS-matured DCs to the CNS microvascular endothelium, inhibiting their migration across the vascular wall. Functional absence of beta1 integrins but not of beta7 integrins or alpha4beta7 integrin similarly reduced the adhesion of immature DCs to the CNS microvascular endothelium, demonstrating that alpha4beta1 but not alpha4beta7 integrin mediates this step of immature DCs interaction with the inflamed blood-brain barrier during EAE. Our study shows that during EAE, especially immature DCs migrate into the CNS, where they may be crucial for the perpetuation of the CNS-targeted autoimmune response. Thus therapeutic targeting of alpha4 integrins affects DC trafficking into the CNS and may therefore lead to the resolution of the CNS autoimmune inflammation by reducing the number of CNS professional APCs.
The World Health Organization Health and Work Performance Questionnaire (HPQ) (2003)

This report describes the World Health Organization Health and Work Performance Questionnaire (HPQ), a self-report instrument designed to estimate the workplace costs of health problems in terms of reduced job performance, sickness absence, and work-related accidents-injuries. Calibration data are presented on the relationship between individual-level HPQ reports and archival measures of work performance and absenteeism obtained from employer archives in four groups: airline reservation agents (n = 441), customer service representatives (n = 505), automobile company executives (n = 554), and railroad engineers (n = 850). Good concordance is found between the HPQ and the archival measures in all four occupations. The paper closes with a brief discussion of the calibration methodology used to monetize HPQ reports and of future directions in substantive research based on the HPQ.
On the Difference Between Air-cleaning and Self-cleaning (2016)

Abstract There is a common notion in the field of photocatalysis that the same requirements for air purification hold also for self-cleaning surfaces, and that the same product may be adequate for the two purposes. This notion was tested on cementitious objects by comparing the activity of a series of commercially available TiO
Association between the risk of coronary artery disease in South Asians and a deletion polymorphism in glutathioneS-transferase M1 (2003)

South Asians living in Western societies show a greater risk of coronary artery disease (CAD) than the indigenous Caucasian population, probably related to the change to a Westernised lifestyle and an associated genetic susceptibility. Modulation of DNA damage and mutation caused by polymorphisms in detoxification enzymes, including the glutathione S-transferases (GSTs), is a well-established risk factor for tobacco-related carcinogenesis, and a similar change in cellular damage may be involved in the risk of vascular disease associated with tobacco smoking. In this study we examined whether polymorphisms in GST genes influence the risk of CAD in a case-control group of South Asians, following our recent observation of such an association in Caucasians from the same region of the UK. Blood was obtained from 170 patients of South Asian origin admitted for angiographic investigation of chest pain and from 203 controls. Patients were subdivided into those with and without previous acute myocardial infarction (AMI), and DNA was analysed for deletions in the GSTM1 and GSTT1 genes. An association was found between the prevalence of the GSTM1 null genotype and the risk of developing CAD in this study population. The frequency of the null genotype was 52.7% in healthy controls and 41.2% in patients (odds ratio [OR] 0.63, 95% confidence interval [95% CI] 0.42-0.95, p = 0.029). The effect was similar in subjects with or without a prior history of AMI. The association was also independent of smoking history, with both non-smokers and smokers showing a similar pattern of genotype distribution, the frequency of the null genotype being 51.2% in controls versus 37.0% in patients in 'never' smokers (OR 0.56, 95% CI 0.33-0.94, p = 0.037) and 60.0% in controls versus 46.2% in patients in 'ever' smokers (OR 0.57, 95% CI 0.25-1.28, p = 0.223). The association remained after adjusting for age, sex, body mass index and the presence or absence of stenosis. No significant associations were observed between the GSTT1 genotype and cardiovascular disease (chi(2) test, p > 0.1). The results of this study indicate that the GSTM1 null genotype is protective against both CAD and AMI. However, further study is required in order to elucidate the, as yet unexplained, mechanisms underlying this association.
Prolonged hypotensive effect of human tissue kallikrein gene delivery and recombinant enzyme administration in spontaneous hypertension rats (2004)

To evaluate the feasibility of treating hypertension by human tissue kallikrein gene (KLK1) delivery and by enzyme (rK1) administration, two recombinant vectors expressing KLK1 cDNA were constructed for gene delivery (pcDNA-KLK1) and recombinant enzyme preparation (pOV-KLK1). Expression of the pcDNA-KLK1 vector in COS-1 cells was confirmed by immunofluorescence and in spontaneous hypertension rats (SHR) by enzymatic detection. Following intramuscular or intravenous injection with the pcDNA-KLK1 vector, systolic pressure of SHR was significantly decreased, which lasted for 20 d to two months depending on dose, route and/or time of injection. Egg white containing recombinant hK1 was prepared by injection of egg-laying hens with the oviduct-specific expression vector pOV-KLK1 and administered into SHR via oral gavage. Following administration, systolic pressure of the SHR was decreased to that of normal rats, which lasted for 3-5 d depending on the dosage used. These data suggest that both hKLK1 gene delivery and recombinant enzyme administration can be used as alternative strategies for treating human hypertension.
Routing Bridges (RBridges): Appointed Forwarders (2011)

The IETF TRILL (TRansparent Interconnection of Lots of Links) protocol provides least cost pair-wise data forwarding without configuration in multi-hop networks with arbitrary topology, safe forwarding even during periods of temporary loops, and support for multipathing of both unicast and multicast traffic.TRILL accomplishes this by using IS-IS (Intermediate System to Intermediate System) link state routing and by encapsulating traffic using a header that includes a hop count.Devices that implement TRILL are called "RBridges" (Routing Bridges).TRILL supports multi-access LAN (Local Area Network) links that can have multiple end stations and RBridges attached.Where multiple RBridges are attached to a link, native traffic to and from end stations on that link is handled by a subset of those RBridges called "Appointed Forwarders", with the intent that native traffic in each VLAN (Virtual LAN) be handled by at most one RBridge.The purpose of this document is to improve the documentation of the Appointed Forwarder mechanism; thus, it updates RFC 6325.
Selective dysregulation of the FcγIIB receptor on memory B cells in SLE (2006)

The inappropriate expansion and activation of autoreactive memory B cells and plasmablasts contributes to loss of self-tolerance in systemic lupus erythematosus (SLE). Defects in the inhibitory Fc receptor, FcgammaRIIB, have been shown to contribute to B cell activation and autoimmunity in several mouse models of SLE. In this paper, we demonstrate that expression of FcgammaRIIB is routinely up-regulated on memory B cells in the peripheral blood of healthy controls, whereas up-regulation of FcgammaRIIB is considerably decreased in memory B cells of SLE patients. This directly correlates with decreased FcgammaRIIB-mediated suppression of B cell receptor-induced calcium (Ca2+) response in those B cells. We also found substantial overrepresentation of African-American patients among those who failed to up-regulate FcgammaRIIB. These results suggest that the inhibitory receptor, FcgammaRIIB, may be impaired at a critical checkpoint in SLE in the regulation of memory B cells; thus, FcgammaRIIB represents a novel target for therapeutic interventions in this disease.