gebhart/patrepeval huggingface dataset:
A common export pathway for proteins binding complex redox cofactors? (1996)

The precursor polypeptides of periplasmic proteins binding seven types of redox cofactor have unusually long signal sequences bearing a consensus (S/T)-R-R-x-F-L-K motif immediately before the hydrophobic region. Such "double-arginine' signal sequences are not, in general, found on the precursors of other periplasmic proteins. It is suggested that precursor proteins with double-arginine signal sequences share a common specialization in their export pathway. The nature of this specialization, the structure of the double-arginine signal sequences, and the possible relationship with the double-arginine signal peptide-dependent thylakoid import pathway are discussed.
Fuzzy Identity Based Encryption. (2004)

Abstract. We introduce a new type of Identity-Based Encryption (IBE) scheme that we call Fuzzy Identity-Based Encryption. In Fuzzy IBE we view an identity as set of descriptive attributes. A Fuzzy IBE scheme allows for a private key for an identity, ω, to decrypt a ciphertext en-crypted with an identity, ω′, if and only if the identities ω and ω ′ are close to each other as measured by the “set overlap ” distance metric. A Fuzzy IBE scheme can be applied to enable encryption using biometric inputs as identities; the error-tolerance property of a Fuzzy IBE scheme is precisely what allows for the use of biometric identities, which inher-ently will have some noise each time they are sampled. Additionally, we show that Fuzzy-IBE can be used for a type of application that we term “attribute-based encryption”. In this paper we present two constructions of Fuzzy IBE schemes. Our constructions can be viewed as an Identity-Based Encryption of a message under several attributes that compose a (fuzzy) identity. Our IBE schemes are both error-tolerant and secure against collusion attacks. Additionally, our basic construction does not use random oracles. We prove the security of our schemes under the Selective-ID security model. 1
Water, civil engineers and multipurpose metropolitan government for the old Cape Peninsula municipalities : technical paper (1998)

The paper describes the moves towards unification early this century by the then 11 municipalities in the Cape Peninsula. In 1913, all the municipalities (with the exception of Wynberg)of the then metropolitan area unified, and additional areas were also incorporated. Thus the unified City Council of Cape Town inherited the water problems of each municipality and was forced to take action. The need for adequate water was the single most compelling reason for the unification of the small municipalities and the institution of one local government for the whole metropolitan area - this is the main finding of the paper. The paper highlights the role of civil engineering.
Rates of growth of human solid neoplasms: Part I (1995)

The purpose of this article is to consolidate data collected from a variety of sources that have permitted calculations of the rates of growth of human neoplasms. These sources include Fischel State Cancer Hospital (Columbia, MO); Mallinckrodt Institute of Radiology, (St. Louis, MO); Roentgen Diagnostic Institute, Allmanna Sjukhuset (Malmo, Sweden); University of Louisville (Louisville, Kentucky); University of Heidelberg (Heidelberg, Germany); and St. Luke's Hospital (St. Louis, MO). Included in the data are laboratory measurements of cell replication rates. All gross measurements were made either on imaging studies or with a centimeter scale for surface or palpable neoplasms. Data have been reported for breast and pulmonary cancers and metastases of many types, melanomas, skeletal sarcomas, benign and malignant colonic neoplasms, and isolated cases of less frequent neoplasms. Related cytokinetic measurements by tritriated thymidine labelling, bromodeoxyuridine labelling, S-phase fraction from DNA flow cytometric analysis, and mitotic indices are discussed. The various mathematical formulae applicable to the analysis of the collected data and the determination of rates and patterns of growth are included. Also considered are the clinical implications of these data and the importance of ever better knowledge on the cytokinetics of human cancer. Prior studies on the evolution of insight into this field are cited and discussed. The authors conclude that a more accurate quantification of the growth rates of human cancer is essential for understanding the biological variance of human cancers seen clinically.
Crucial role of TCR gamma chain junctional region in prenyl pyrophosphate antigen recognition by gamma delta T cells. (1998)

Human gamma delta T cells recognize prenyl pyrophosphate Ags and their analogues in a V gamma 2V delta 2 TCR-dependent manner. Few data are available regarding the TCR structural requirements for recognition of such prenyl pyrophosphate Ags by gamma delta T cells. Presently, we made chain pair switch, chimeric, and site mutant gamma delta TCRs and transfected them into TCR- mutant Jurkat T cells to examine the effects of changing the TCR gamma junctional region sequences on reactivity to prenyl pyrophosphate Ags. Substitution of the TCR gamma junctional region (N and J) sequences from an Ag-reactive TCR with TCR gamma junctional region sequences from an Ag-nonreactive TCR abrogated reactivity to the prenyl pyrophosphate Ag isopentenyl pyrophosphate and to its synthetic analogue ethyl pyrophosphate but not to a mycobacterial supernatant containing a mixture of prenyl pyrophosphate Ags. Substitution of only the TCR gamma N nucleotide region with that from this Ag-nonreactive TCR destroyed reactivity to isopentenyl pyrophosphate and to the mycobacterial supernatant. Substitution of the entire V delta 2 chain from the Ag-reactive TCR with a V delta 1 chain from an Ag-nonreactive TCR yielded a prenyl pyrophosphate Ag-nonreactive TCR. Thus, using TCR mutagenesis and TCR transfectants, we show that gamma delta TCR reactivity to prenyl pyrophosphate Ags is dependent upon the junctional region of the TCR gamma chain and upon pairing of V gamma 2 and V delta 2 TCR chains. These structural requirements of TCR gamma delta recognition of prenyl pyrophosphates distinguish this reactivity from that of protein superantigens and emphasize the importance of the TCR gamma CDR3 loop and adjacent residues.
Proteomic exploitation on prothymosin α‐induced mononuclear cell activation (2007)

Prothymosin alpha (ProTalpha) is an acidic polypeptide associated both with cell proliferation and immune regulation. Although ProTalpha's immunomodulating activity is well established at cellular level, limited information is available regarding the signaling pathways triggered by ProTalpha. Using 2-DE proteomic technology, we investigated changes in protein expression of ProTalpha-stimulated peripheral blood mononuclear cells (PBMC) in the course of a 3-day incubation. Using healthy donor- and cancer patient-derived PBMC, 12 gels were studied, identifying 53 differing protein spots via PMF comparison analysis. Among others, we identified interleukin-1 receptor-associated kinase 4, heat-shock protein 90, lipocalin 2, ribophorin 1, eukaryotic elongation factor 2, 14-3-3 protein, L-plastin, and MX2 protein, all of which were found to be overexpressed upon ProTalpha activation. Based on the physiological role of upregulated proteins, we propose the following model for ProTalpha's immunological mode of action: on day 1, ProTalpha triggers monocyte activation, possibly via toll-like receptor signaling, and enhances antigen presentation, consequently promoting and stabilizing monocyte-T-cell immune synapse; on day 2, activated monocytes produce interleukin (IL)-1, while T-cell receptor triggering promotes T-cell proliferation and IL-2 production; finally, on day 3, ProTalpha-activated PBMC express proteins related to adhesion and cytotoxic effector functions, both contributing to the increase of their lytic activity.
Mapping Symptoms to Brain Networks with the Human Connectome (2018)

Complex neurologic and psychiatric syndromes cannot be understood on the basis of focal brain lesions. Functional neuroimaging, maps of interrelated regions called the connectome, and the combination of lesion analysis with networks of the connectome offer a new way to understand neurologic function and disease.
Unión bancaria: ¿de hormigón o de paja? (2013)

The vicious loop between sovereign and bank debt threatens the integrity of the euro zone. This article examines why the banking union is a prerequisite to break this loop and concludes that the current design is clearly insuffi cient to achieve this goal. In particular, the transitional phase poses serious risks for the euro zone as financial markets remain fragmented and the crisis is far from being resolved.
The article discusses the components of a solid banking union, what we call a banking union made of concrete. Current plans by the euro area envisage a union that seeks to limit the use of taxpayer funds by extending the principle of bail-in. It is a banking union that runs the risk of being insuffi cient to face a systemic crisis.
This banking union, albeit limited, is diffi cult to implement in the short term given the current legal framework of the economic and monetary union. As a result, the union designed for the transitional period, which can be lengthy, will lack key elements such as a pan-European backstop that operates as a lender of last resort for sovereigns. Therefore, it is far from being a banking union made of concrete. This can be a flimsy construction, not even made of wood but of straw. The risk is that it may be unable to withstand the challenges of the current crisis.
Receptor choice determinants in the envelope glycoproteins of amphotropic, xenotropic, and polytropic murine leukemia viruses (1992)

The envelope glycoproteins (SU) of mammalian type C retroviruses possess an amino-terminal domain of about 200 residues, which is involved in binding a cell surface receptor. In this domain, highly conserved amino acid sequences are interrupted by two segments of variable length and sequence, VRA and VRB. We have studied the role of these variable regions in receptor recognition and binding by constructing chimeric molecules in which portions of the amino-terminal domains from amphotropic (4070A), xenotropic (NZB), and polytropic (MCF 247) murine leukemia virus SU proteins were permuted. These chimeras, which exchanged either one or two variable regions, were expressed at the surface of replication-defective viral particles by a pseudotyping assay. Wild-type or recombinant env genes were transfected into a cell line producing Moloney murine leukemia virus particles devoid of envelope glycoproteins in which a retrovirus vector genome carrying an Escherichia coli lacZ gene was packaged. The host range and sensitivity to interference of pseudotyped virions were assayed, and we observed which permutations resulted in receptor switch or loss of function. Our results indicate that the determinants of receptor choice are found within the just 120 amino acids of SU proteins. Downstream sequences contribute to the stabilization of the receptor-specific structure.
Similarities and differences among 105 members of the Int family of site-specific recombinases (1998)

Alignments of 105 site-specific recombinases belonging to the Int family of proteins identified extended areas of similarity and three types of structural differences. In addition to the previously recognized conservation of the tetrad R-H-R-Y, located in boxes I and II, several newly identified sequence patches include charged amino acids that are highly conserved and a specific pattern of buried residues contributing to the overall protein fold. With some notable exceptions, unconserved regions correspond to loops in the crystal structures of the catalytic domains of lambda Int (Int c170) and HP1 Int (HPC) and of the recombinases XerD and Cre. Two structured regions also harbor some pronounced differences. The first comprises beta-sheets 4 and 5, alpha-helix D and the adjacent loop connecting it to alpha-helix E: two Ints of phages infecting thermophilic bacteria are missing this region altogether; the crystal structures of HPC, XerD and Cre reveal a lack of beta-sheets 4 and 5; Cre displays two additional beta-sheets following alpha-helix D; five recombinases carry large insertions. The second involves the catalytic tyrosine and is seen in a comparison of the four crystal structures. The yeast recombinases can theoretically be fitted to the Int fold, but the overall differences, involving changes in spacing as well as in motif structure, are more substantial than seen in most other proteins. The phenotypes of mutations compiled from several proteins are correlated with the available structural information and structure-function relationships are discussed. In addition, a few prokaryotic and eukaryotic enzymes with partial homology with the Int family of recombinases may be distantly related, either through divergent or convergent evolution. These include a restriction enzyme and a subgroup of eukaryotic RNA helicases (D-E-A-D proteins).
Nonlinear Noise Theory for Synchronized Oscillators (1979)

A nonlinear theory of noise in synchronized oscillators is outlined, thus extending Kurokawa's work from small to arbitrary injection levels. The description is of phenomenological nature: it uses the describing function method of control theory for calculating the carrier waves, and the circuit theory of periodically driven nonlinear systems for an analysis of the noise sidebands. Simple expressions are derived for the various output noise and noise conversion factors in the case when the nonlinear characteristic of the active device can be described by a third-order (van-der-Pol) polynomial.
Cloning and expression of a mammalian Na+/amino acid cotransporter with sequence similarity to Na+/glucose cotransporters. (1993)

We describe the full-length sequence and functional expression of a cDNA cloned from LLC-PK1 cells, which appears to encode a mammalian Na(+)-dependent neutral amino acid transporter with properties characteristic of system A. This sequence, designated SAAT1, is 76% identical and 89% similar in amino acid sequence to the Na(+)-dependent glucose transporter SGLT1 of the same species. A leucine zipper region was detected in both SAAT1 and SGLT1. The message for SAAT1 was a single 2.4-kilobase species in kidney, but mRNA species of 2.4 and 3.7 kilobases were observed in LLC-PK1 cells as well as in intestine. Transcripts were also found in spleen, liver, and muscle. Expression of SAAT1 in COS-7 cells resulted in increased levels of Na(+)-dependent uptake of 2-(methylamino)isobutyric acid, a specific substrate for the system A amino acid transporter. Uptake due to cDNA expression was inhibited by a range of amino acids that are transported by system A and exhibited a km of 0.8 +/- 0.2 mM. These results suggest that the system A amino acid transporter is closely related to the Na+/glucose transporter SGLT1.
Direct T helper-B cell interactions induce an early B cell activation antigen. (1986)

We have explored the consequences for the B cell of cognate interaction with T cells. Early expression of the B cell-restricted cell surface activation antigen, BLAST-2, has been used as an assay system to measure direct T-B cell collaboration. BLAST-2 is preferentially expressed by allogenic B cells cultured with MHC class II antigen-restricted Th clone cells matched to the DR specificity of the target B cells. B cells cultured with DR-mismatched allospecific Th cells express minimal BLAST-2. Th cell-induced BLAST-2 expression appears to be accessory cell independent and occurs as early as 8 h after initiation of culture, with peak expression at 18 h. Direct T-B cell contact, rather than Th-derived lymphokines, provides the most efficient stimulus for BLAST-2 expression. Crosslinking of sIg on B cells is a poor stimulus for BLAST-2 expression. The BLAST-2 assay permits the evaluation of early events associated with B cell activation through cognate interactions, and may facilitate subsequent studies of the mechanism of B cell differentiation.
The invariant chain forms complexes with class II major histocompatibility complex molecules and antigenic peptides "in vivo". (1990)

The binding of a chicken ovalbumin peptide (residues 323-339), Ova-(323-339), to I-Ad molecules was investigated in vitro and in vivo. By using antigenic peptides labeled either with a hapten or with fluorescein, complexes formed in vitro between I-Ad and antigenic peptides were detected by Western blot analysis with an antibody recognizing the hapten 7-nitrobenzo-2-oxa-1,3-diazole and by scanning gels for fluorescence emitted by fluoresceinated peptide. Both techniques reveal that Ova-(323-339) binds not only to I-Ad alpha/beta heterodimers and separated alpha and beta chains but also to complexes of higher molecular mass. Additional analysis shows that one of these additional complexes contains I-Ad heterodimers, antigenic peptides, and also invariant chain. To explore the physiological role of these complexes, cells were incubated with haptenated peptide and the I-Ad-peptide complexes formed in vivo were purified by affinity chromatography using hapten-specific antibody. The complexes formed migrate with a significantly higher apparent molecular mass than the alpha/beta heterodimers. A band at 180 kDa contained the alpha/beta heterodimer, the antigenic peptide, and the invariant chain. These results show that in vivo high molecular mass complexes formed by the I-Ad heterodimer and the invariant chain bind antigenic peptides.
Genetic, Individual, and Group Facilitation of Disease Resistance in Insect Societies (2008)

In this review, we provide a current reference on disease resistance in insect societies. We start with the genetics of immunity in the context of behavioral and physiological processes and scale up levels of biological organization until we reach populations. A significant component of this review focuses on Apis mellifera and its role as a model system for studies on social immunity. We additionally review the models that have been applied to disease transmission in social insects and elucidate areas for future study in the field of social immunity.
Fabrication of complex multilevel microchannels in PDMS by using three-dimensional photoresist masters (2007)

This paper demonstrates a new method of implementing complex microchannels in PDMS, which is simply constructed using three-dimensional photoresist structures as a master mold for the PDMS replica process. The process utilizes UV-insensitive LOR resist as a sacrificial layer to levitate the structural photoresist. In addition, the thickness of photoresist structures can be controlled by multi-step UV exposure. By using these techniques, various three-dimensional photoresist structures were successfully implemented, including the recessed cantilevers, suspended bridges, and the complex plates with micro-pits or micro-villi. We demonstrate that the three-dimensional photoresist structures are applicable to implementing complex multiple microchannels in PDMS by using the PDMS replica method.
Protein Loop Grafting to Construct a Variant of Tissue-type Plasminogen Activator That Binds Platelet Integrin αIIbβ3 (1995)

Protein-protein interactions can be guided by contacts between surface loops within proteins. We therefore investigated the hypothesis that novel protein-protein interactions could be created using a strategy of "loop grafting" in which the amino acid sequence of a biologically active, flexible loop on one protein is used to replace a surface loop present on an unrelated protein. To test this hypothesis we replaced a surface loop within an epidermal growth factor module with the complementarity-determining region of a monoclonal antibody. Specifically, the HCDR3 from Fab-9, an antibody selected to bind the beta 3-integrins with nanomolar affinity (Smith, J. W., Hu, D., Satterthwait, A., Pinz-Sweeney, S., and Barbas, C. F., III (1994) J. Biol. Chem. 269, 32788-32795), was grafted into the epidermal growth factor-like module of human tissue-type plasminogen activator (t-PA). The resulting variant of t-PA bound to the platelet integrin alpha IIb beta 3 with nanomolar affinity, retained full enzymatic activity, and was stimulated normally by the physiological co-factor fibrin. Binding of the novel variant of t-PA to integrin alpha IIb beta 3 was dependent on the presence of divalent cations and was inhibited by an RGD-containing peptide, demonstrating that, like the donor antibody, the novel t-PA binds specifically to the ligand-binding site of the integrin. These findings suggest that surface loops within protein modules can, at least in some cases, be interchangeable and that phage display can be combined with loop grafting to direct proteins, at high affinity, to selected targets. In principle, these targets could include not only other proteins but also peptides, nucleic acids, carbohydrates, lipids, or even uncharacterized markers of specific cell types, tissues, or viruses.
Generation of Bovine Respiratory Syncytial Virus (BRSV) from cDNA: BRSV NS2 Is Not Essential for Virus Replication in Tissue Culture, and the Human RSV Leader Region Acts as a Functional BRSV Genome Promoter (1999)

In order to generate recombinant bovine respiratory syncytial virus (BRSV), the genome of BRSV strain A51908, variant ATue51908, was cloned as cDNA. We provide here the sequence of the BRSV genome ends and of the entire L gene. This completes the sequence of the BRSV genome, which comprises a total of 15,140 nucleotides. To establish a vaccinia virus-free recovery system, a BHK-derived cell line stably expressing T7 RNA polymerase was generated (BSR T7/5). Recombinant BRSV was reproducibly recovered from cDNA constructs after T7 RNA polymerase-driven expression of antigenome sense RNA and of BRSV N, P, M2, and L proteins from transfected plasmids. Chimeric viruses in which the BRSV leader region was replaced by the human respiratory syncytial virus (HRSV) leader region replicated in cell culture as efficiently as their nonchimeric counterparts, demonstrating that all cis-acting sequences of the HRSV promoter are faithfully recognized by the BRSV polymerase complex. In addition, we report the successful recovery of a BRSV mutant lacking the complete NS2 gene, which encodes a nonstructural protein of unknown function. The NS2-deficient BRSV replicated autonomously and could be passaged, demonstrating that NS2 is not essential for virus replication in cell culture. However, growth of the mutant was considerably slower than and final infectious titers were reduced by a factor of at least 10 compared to wild-type BRSV, indicating that NS2 provides a supporting factor required for full replication capacity.
David M. Kovenock (1996)

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