gebhart/patrepeval huggingface dataset:
Protein engineering methods applied to membrane protein targets (2012)

Genes encoding membrane proteins have been estimated to comprise as much as 30% of the human genome. Among these membrane, proteins are a large number of signaling receptors, transporters, ion channels and enzymes that are vital to cellular regulation, metabolism and homeostasis. While many membrane proteins are considered high-priority targets for drug design, there is a dearth of structural and biochemical information on them. This lack of information stems from the inherent insolubility and instability of transmembrane domains, which prevents easy obtainment of high-resolution crystals to specifically study structure-function relationships. In part, this lack of structures has greatly impeded our understanding in the field of membrane proteins. One method that can be used to enhance our understanding is directed evolution, a molecular biology method that mimics natural selection to engineer proteins that have specific phenotypes. It is a powerful technique that has considerable success with globular proteins, notably the engineering of protein therapeutics. With respect to transmembrane protein targets, this tool may be underutilized. Another powerful tool to investigate membrane protein structure-function relationships is computational modeling. This review will discuss these protein engineering methods and their tremendous potential in the study of membrane proteins.
Identification of human renal cell carcinoma associated genes by suppression subtractive hybridization (2001)

Renal cell carcinoma (RCC) are frequently chemo- and radiation resistant. Thus, there is a need for identifying biological features of these cells that could serve as alternative therapeutic targets. We performed suppression subtractive hybridization (SSH) on patient-matched normal renal and RCC tissue to identify variably regulated genes. 11 genes were strongly up-regulated or selectively expressed in more than one RCC tissue or cell line. Screening of filters containing cancer-related cDNAs confirmed overexpression of 3 of these genes and 3 additional genes were identified. These 14 differentially expressed genes, only 6 of which have previously been associated with RCC, are related to tumour growth/survival (EGFR, cyclin D1, insulin-like growth factor-binding protein-1 and a MLRQ sub-unit homologue of the NADH:ubiquinone oxidoreductase complex), angiogenesis (vascular endothelial growth factor, endothelial PAS domain protein-1, ceruloplasmin, angiopoietin-related protein 2) and cell adhesion/motility (protocadherin 2, cadherin 6, autotaxin, vimentin, lysyl oxidase and semaphorin G). Since some of these genes were overexpressed in 80-90% of RCC tissues, it is important to evaluate their suitability as therapeutic targets.
Determinants of Thrombin Receptor Cleavage. RECEPTOR DOMAINS INVOLVED, SPECIFICITY, AND ROLE OF THE P3 ASPARTATE (1995)

Thrombin receptor cleavage at the Arg41- decreases -Ser42 peptide bond in the receptor's amino-terminal exodomain is necessary and sufficient for receptor activation. The rate of receptor cleavage at this site is a critical determinant of the magnitude of the cellular response to thrombin. These observations underscore the importance of defining the molecular basis for thrombin-receptor interaction and cleavage. We report that chimeric proteins bearing only thrombin receptor amino-terminal exodomain residues 36-60 are cleaved at rates similar to the wild-type thrombin receptor when expressed on the cell surface. A soluble amino-terminal exodomain protein was also cleaved efficiently by thrombin with a Km of 15-30 microM and k(cat) of approximately 50 s-1, with cleavage occurring only at the Arg41- decreases -Ser42 peptide bond. In the context of previous studies, these data suggest that the receptor's LDPR cleavage recognition sequence and DKYEPF hirudin-like domain account for thrombin-receptor interaction. Because a P3 aspartate in protein C's cleavage site inhibits cleavage by free thrombin, we investigated the role of the P3 aspartate in the receptor's LDPR sequence. Studies with mutant receptors revealed an inhibitory role for this residue only in the absence of the receptor's hirudin-like domain. These and other data suggest that the receptor's hirudin-like domain causes a conformational change in thombin's active center to accommodate the LDPR sequence and promote efficient receptor cleavage. Taken together, these studies imply that the thrombin receptor's amino-terminal exodomain contains all the machinery needed for efficient recognition and cleavage by thrombin. Thrombin appears to bind and cleave this domain independently of the rest of the receptor, with one thrombin molecule probably activating multiple receptors.
Automatic landmarking for building biological shape models (2003)

We present a new method for automatic landmark extraction from the contours of biological specimens. Our ultimate goal is to enable automatic identification of biological specimens in photographs and drawings held in a database. We propose to use active appearance models for visual indexing of both photographs and drawings. Automatic landmark extraction will assist us in building the models. We describe the results of using our method on drawings and photographs of examples of diatoms, and present an active shape model built using automatically extracted data.
PET imaging in breast cancer. (2001)

The basis of tumour imaging with PET is a specific uptake mechanism of positron emitting radiopharmaceuticals. Among the potential tracers for breast cancer (fluorodeoxyglucose, methionine, tyrosine, fluoro-estradiol, nor-progesterone), 2-deoxy-2-fluoro-D-glucose labelled with fluorine (FDG) is the most widely used radiopharmaceutical because breast cancer is particularly avid of FDG and 18F has the advantages of a relatively long physical half-life. Mammography is the first choice examination in studying breast masses, due to its very good performances, an excellent compliance and the best value regarding the cost/effectiveness aspects. However FDG-PET revealed to be effective in the study of patients with ambiguous mammographies. The FDG uptake in tissue correlates with the histological grade and potential aggressiveness of breast cancer and this may have prognostic consequences. Besides the evaluation of breast lesions, FDG-PET shows a great efficacy in staging lymph node involvement prior surgery and this could have a great value in loco-regional staging. Whole body PET provides also information with regard to metastasis localizations both in soft tissue and bone, and plays an important clinical role mainly in detecting recurrent metastatic disease. In fact for its metabolic characteristics PET visualizes regions of enhanced metabolic activity and can complements other imaging modalities based on structural anatomic changes. Even though CT and MRI show superior resolution characteristics, it has been demonstrated that PET provides more accurate information in discriminating between viable tumour, fibrotic scar or necrosis. Several clinical evidences demonstrated that FDG-PET is also able to predict wether cancer will respond to the therapy, or, when applied at the end of the treatment, it can assess the response to the therapy. These statements are coming from the examination of more than 2000 breast cancer patients included in 88 articles or abstracts on studies in which FDG-PET was used for breast cancer detection.
The extracellular adherence protein (Eap) of Staphylococcus aureus inhibits wound healing by interfering with host defense and repair mechanisms (2005)

Staphylococcus aureus is a major human pathogen interfering with host-cell functions. Impaired wound healing is often observed in S aureus-infected wounds, yet, the underlying mechanisms are poorly defined. Here, we identify the extracellular adherence protein (Eap) of S aureus to be responsible for impaired wound healing. In a mouse wound-healing model wound closure was inhibited in the presence of wild-type S aureus and this effect was reversible when the wounds were incubated with an isogenic Eap-deficient strain. Isolated Eap also delayed wound closure. In the presence of Eap, recruitment of inflammatory cells to the wound site as well as neovascularization of the wound were prevented. In vitro, Eap significantly reduced intercellular adhesion molecule 1 (ICAM-1)-dependent leukocyte-endothelial interactions and diminished the consequent activation of the proinflammatory transcription factor nuclear factor kappaB (NFkappaB) in leukocytes associated with a decrease in expression of tissue factor. Moreover, Eap blocked alphav-integrin-mediated endothelial-cell migration and capillary tube formation, and neovascularization in matrigels in vivo. Collectively, the potent anti-inflammatory and antiangiogenic properties of Eap provide an underlying mechanism that may explain the impaired wound healing in S aureus-infected wounds. Eap may also serve as a lead compound for new anti-inflammatory and antiangiogenic therapies in several pathologies.
Sophisticated strategies for information encounter in the lymph node: the reticular network as a conduit of soluble information and a highway for cell traffic (1996)

The lymph node is the crossroad in which soluble signals and cells carried by lymph meet lymphocytes emigrating from blood. Efficient interactions among these elements depend on the reticular network, which comprises reticular fibers, related extracellular matrix components, and associated fibroblastic reticular cells. This network provides a three-dimensional scaffold for attachment of APCs and pathways for the migration of T cells to these APCs. In addition, the network constitutes a miniature conduit system for bulk flow delivery of soluble molecules to distinct sites in the paracortex, particularly the high endothelial venule. The delivered mediators, such as chemokines, regulate the phenotype of the high endothelial venule, the recruitment of lymphocytes, and the behavior of the recruited lymphocytes. Thus, the reticular network is a multifunctional infrastructure that facilitates encounters of cells with other cells and factors necessary for effective and efficient immune surveillance.
Development of the Non‐Palindromic Adaptor Polymerase Chain Reaction (NPA‐PCR) for the Amplification of Alpha‐and Beta‐Chain T‐Cell Receptor cDNAs (1992)

We have developed a highly efficient new method for the amplification of alpha- and beta-chain human T-cell receptor (TCR) cDNAs. This method is designated non-palindromic adaptor polymerase chain reaction (NPA-PCR). cDNA was synthesized from total RNA isolated from mononuclear leucocytes, using either an oligo (dT)15-NotI or a C alpha-NotI or a C beta-NotI primer and RNase H-negative reverse transcriptase. The double-stranded cDNA was ligated with the non-palindromic adaptors EcoRI-XmnI [d(ATTCGAACCCCTTCG)] and XmnI G strand [d(pCGAAGGGGTTCG)] (phosphorylated), which resulted in the addition of the EcoRI-XmnI site in both 5' and 3' ends. These two non-palindromic adaptors, EcoRI-XmnI and XmnI G strand, are complementary to each other and both are required for ligation. The EcoRI-XmnI adaptor was removed from the 3' end by treatment with NotI restriction nuclease, whereas it was retained at the 5' end. The non-palindromic adaptor EcoRI-XmnI was used as the 5' amplification primer. C alpha or C beta constant region primers were used as 3' amplification primers. The amplified cDNAs were cloned and the plasmids were used to transform DH5 alpha competent cells. Over 1000 white colonies per 0.1-0.25 micrograms of total RNA or per 10,000 to 50,000 human peripheral blood mononuclear cells were obtained after amplification of either the alpha- or the beta-chain TCR cDNAs. Between 40 and 62% of the colonies (range from five donors) were positive after screening with either a C alpha or a C beta probe, located 5' to the C alpha and C beta amplification primers. A total of 50 amplified alpha- or beta-chain cDNA positive clones from two normal donors were randomly chosen and sequenced, and the sequences obtained were typical of alpha beta TCR. Two new J alpha gene segments were identified. Approximately 30% of the alpha-chain positive clones have 5' untranslated region, and most of the remaining alpha- or beta-chain TCR clones started from the initiation codon or near the 5' end. NPA-PCR has several advantages over existing PCR methods for the amplification of cDNAs with unknown or variable 5' end, such as the T-cell antigen receptors and the immunoglobulins. Among these advantages is that only one 5' end extension primer is required. Because of the large number of TCR V alpha and V beta families, a large number of different 5' end primers are required for amplification of alpha beta TCR cDNAs by conventional PCR.
Fabrication of silicon nitride waveguides for visible-light using PECVD: a study of the effect of plasma frequency on optical properties (2008)

This paper presents work aimed at optimizing the fabrication of silicon nitride Si(x)N(y) thin-film visible-light planar waveguides using plasma-enhanced chemical vapour deposition (PECVD). The effects of plasma frequency, precursor gas ratio, and thermal annealing in relation to waveguide optical properties (refractive index, propagation losses) are studied. Experimental results over a wide range of precursor gas ratios show convincingly that waveguides fabricated using low-frequency PECVD have lower propagation losses in the visible range compared to waveguides of equal refractive index fabricated with high-frequency PECVD.
Electrolyte Formulations Based on Dinitrile Solvents for High Voltage Li-Ion Batteries (2013)

In this work, we have investigated the suitability of aliphatic dinitrile solvents with the chemical formula NC-(CH 2 ) n -CNwhere n varies from 3 to 8 in single, binary (mixed with ethylene carbonate, EC) or ternary (mixed with EC and dimethyl carbonate, DMC) electrolyte solutions for the high voltage (4.7 V) LiMn 1.5 Ni 0.5 O 4 cathode material in lithium batteries. We report that the conductivity of all the electrolyte solutions (with LiTFSI or LiBF 4 as salt) decreases as a function of "n", i.e. as the alkane chain become longer while the viscosity increases. The electrochemical stability window is about 7 V for the single electrolyte solutions and drops to 6-6.5 V for the binary and ternary ones. ATR IR spectra of all the electrolyte solutions indicate the presence of a strong interaction between Li ions and the different solvents. Li/LiMn 1.5 Ni 0.5 O 4 half cell batteries assembled using dinitriles as the main solvent (50% by volume), LiBF 4 salt and LiBOB co-salt show good performance only in the ternary solutions. Those with shorter alkane dinitriles with n = 4 and 5 retain the capacity better after 50 cycles than the longer ones with n = 6 and 8. Investigation of the surface of the cycled electrode by XPS reveals that DMC plays a great role in surface passivation at high voltages by preventing salt decomposition in ternary solutions.
Human T-cell lymphotropic virus IIIB glycoprotein (gp120) bound to CD4 determinants on normal lymphocytes and expressed by infected cells serves as target for immune attack. (1987)

The lymphocyte differentiation antigen CD4 serves as a receptor for human retroviruses associated with acquired immunodeficiency syndrome (AIDS) through its interaction with the major envelope virion glycoprotein, gp120, which is also expressed on the surface of infected cells. In these experiments, purified gp120 was shown to bind to normal human T-lymphocyte populations. The gp120-CD4 complex served as a target antigen for antibody-dependent complement-mediated cytolysis by a goat serum raised against native gp120. However, patient sera that bound to gp120-adsorbed cells failed to direct their destruction in the presence of complement. In contrast, these sera were potent mediators of antibody-dependent cellular cytotoxicity. These studies demonstrate that gp120 situated on the cell surface can serve as an effective target for immune destruction by patient antibodies and effector lymphocytes. The possible contribution of this type of immunity to control of disease progression, on the one hand, and to lymphocyte destruction and immunopathology observed in AIDS, on the other, is discussed.
Effect of the Addition of Oligosaccharides on the Biological Activities and Antigenicity of Influenza A/H3N2 Virus Hemagglutinin (2004)

Influenza A/H3N2 viruses have developed an increased number of glycosylation sites on the globular head of the hemagglutinin (HA) protein since their appearance in 1968. Here, the effect of addition of oligosaccharide chains to the HA of A/H3N2 viruses on its biological activities was investigated. We constructed seven mutant HAs of A/Aichi/2/68 virus with one to six glycosylation sites on the globular head, as found in natural isolates, by site-directed mutagenesis and analyzed their intracellular transport, receptor binding, and cell fusion activities. The glycosylation sites of mutant HAs correspond to representative A/H3N2 isolates (A/Victoria/3/75, A/Memphis/6/86, or A/Sydney/5/97). The results showed that all the mutant HAs were transported to the cell surface as efficiently as wild-type HA. Although mutant HAs containing three to six glycosylation sites decreased receptor binding activity, their cell fusion activity was not affected. The reactivity of mutant HAs having four to six glycosylation sites with human sera collected in 1976 was much lower than that of wild-type HA. Thus, the addition of new oligosaccharides to the globular head of the HA of A/H3N2 viruses may have provided the virus with an ability to evade antibody pressures by changing antigenicity without an unacceptable defect in biological activity.
Expression and co-expression of the members of the epidermal growth factor receptor (EGFR) family in invasive breast carcinoma (2004)

The epidermal growth factor receptor (EGFR) family plays an important role in breast carcinogenesis. Much interest has been focused recently on its members because of their potential role as prognostic indicators in breast cancer and their involvement in cancer therapy. We have evaluated more than 1500 cases of invasive breast carcinoma immunohistochemically using tissue microarray technology to examine the expression of EGFR family receptor proteins. We have found that 20.1 and 31.8% of cases were positive for EGFR and c-erbB-2, respectively, and 45 and 45.1% of tumours overexpressed for c-erbB-3 and c-erbB-4, respectively. The expression of either EGFR or c-erbB-2 was associated with other bad prognostic features and with poor outcome. Neither c-erbB-3 nor c-erbB-4 had any association with survival. c-erbB-2 had an independent prognostic effect on overall and disease-free survival (DFS) in all cases, as well as in the subset of breast carcinoma patients with nodal metastases. Several hetero- and homodimeric combinations have been reported between the EGFR members. Those dimers can evoke diverse signal transduction pathways with variable cellular responses. We stratified cases according to their co-expression of receptors into distinct groups with different receptor-positive combinations. Patients whose tumours co-expressed c-erbB-2 and c-erbB-3, as well as those whose tumours co-expressed EGFR, c-erbB-2 and c-erbB-4 showed an unfavourable outcome compared with other groups, while combined c-erbB-3 and c-erbB-4 expression was associated with a better outcome. In cases showing expression of one family member only (homodimers), we found a significant association between c-erbB-4 homodimer-expressing tumours and better DFS. In contrast, patients with c-erbB-2 homodimer-expressing tumours had a significant poorer DFS compared with other cases. These data imply that the combined profile expression patterns of the four receptor family members together provide more accurate information on the tumour behaviour than studying the expression of each receptor individually.
The cellular transcription factor E2f requires viral E1A and E4 gene products for increased DNA-binding activity and functions to stimulate adenovirus E2A gene expression (1989)

Whereas a wide variety of cellular proteins interact with the cis-regulatory elements of the adenovirus E1A and E2A genes, only the DNA-binding activity of the cellular E2f factor is modulated by viral early-gene expression. An analysis of cellular E2f protein levels and adenovirus early-gene expression in a panel of independently cloned virus-transformed rodent cell lines and in virus-infected rodent cells has established that both the E1A 289-amino-acid (289R) protein and a yet-to-be-defined E4 gene product are required for maximal E2f DNA-binding activity. To distinguish between the multiple roles the E1A protein could serve in this process, the E2f DNA-binding activity was determined in a virus-transformed cell line which contains a conditional-lethal mutation affecting the 289R protein. Since E4 gene expression was not altered by the incubation conditions, the observation of reduced cellular E2f activity at the nonpermissive temperature suggests a direct role for the E1A 289R protein in E2f activation. When a virus containing a deletion in the E4 gene was introduced into cell lines which can complement the E4 gene defect, a correlation between high cellular E2f levels and increased rates of E2A gene transcription was observed. A time course analysis of the viral infection revealed that E2f functions catalytically to stimulate viral E2A gene transcription. These observations have led to several hypotheses concerning possible mechanisms by which elevated E2A gene expression, which leads to cytotoxicity, might be avoided in the transformed cell.
Effect of general anesthetics on IOP in rats with experimental aqueous outflow obstruction. (2000)

All anesthetics resulted in rapid and substantial decreases in IOP in all eyes and increased the interanimal variability in IOPs. Measurement of IOP in awake animals provides the most accurate documentation of pressure histories for rat glaucoma model studies.
Filtering Offensive Language in Online Communities using Grammatical Relations (2010)

Offensive language has arisen to be a big issue to the health of both online communities and their users. To the online community, the spread of offensive language undermines its reputation, drives users away, and even directly affects its growth. To users, viewing offensive language brings negative influence to their mental health, especially for children and youth. When offensive language is detected in a user message, a problem arises about how the offensive language should be removed, i.e. the offensive language filtering problem. To solve this problem, manual filtering approach is known to produce the best filtering result. However, manual filtering is costly in time and labor thus can not be widely applied. In this paper, we analyze the offensive language in text messages posted in online communities, and propose a new automatic sentence-level filtering approach that is able to semantically remove the offensive language by utilizing the grammatical relations among words. Comparing with existing automatic filtering approaches, the proposed filtering approach provides filtering results much closer to manual filtering. To demonstrate our work, we created a dataset by manually filtering over 11,000 text comments from the YouTube website. Experiments on this dataset show over 90% agreement in filtered results between the proposed approach and manual filtering approach. Moreover, we show the overhead of applying proposed approach to user comments filtering is reasonable, making it practical to be adopted in real life applications.