gebhart/patrepeval huggingface dataset:
Distinct Protein Domains of the Yeast Golgi GDP-mannose Transporter Mediate Oligomer Assembly and Export from the Endoplasmic Reticulum (2000)

The substrates for glycan synthesis in the lumen of the Golgi are nucleotide sugars that must be transported from the cytosol by specific membrane-bound transporters. The principal nucleotide sugar used for glycosylation in the Golgi of the yeast Saccharomyces cerevisiae is GDP-mannose, whose lumenal transport is mediated by the VRG4 gene product. As the sole provider of lumenal mannose, the Vrg4 protein functions as a key regulator of glycosylation in the yeast Golgi. We have undertaken a functional analysis of Vrg4p as a model for understanding nucleotide sugar transport in the Golgi. Here, we analyzed epitope-tagged alleles of VRG4. Gel filtration chromatography and co-immunoprecipitation experiments demonstrate that the Vrg4 protein forms homodimers with specificity and high affinity. Deletion analyses identified two regions essential for Vrg4p function. Mutant Vrg4 proteins lacking the predicted C-terminal membrane-spanning domain fail to assemble into oligomers (Abe, M., Hashimoto, H., and Yoda, K. (1999) FEBS Lett. 458, 309-312) and are unstable, while proteins lacking the N-terminal cytosolic tail are stable and multimerize efficiently, but are mislocalized to the endoplasmic reticulum (ER). Fusion of the N terminus of Vrg4p to related ER membrane proteins promote their transport to the Golgi, suggesting that sequences in the N terminus supply information for ER export. The dominant negative phenotype resulting from overexpression of truncated Vrg4-DeltaN proteins provides strong genetic evidence for homodimer formation in vivo. These studies are consistent with a model in which Vrg4p oligomerizes in the ER and is subsequently transported to the Golgi via a mechanism that involves positive sorting rather than passive default.
The endogenous lipid anandamide is a full agonist at the human vanilloid receptor (hVR1) (2000)

The endogenous cannabinoid anandamide was identified as an agonist for the recombinant human VR1 (hVR1) by screening a large array of bioactive substances using a FLIPR-based calcium assay. Further electrophysiological studies showed that anandamide (10 or 100 microM) and capsaicin (1 microM) produced similar inward currents in hVR1 transfected, but not in parental, HEK293 cells. These currents were abolished by capsazepine (1 microM). In the FLIPR anandamide and capsaicin were full agonists at hVR1, with pEC(50) values of 5. 94+/-0.06 (n=5) and 7.13+/-0.11 (n=8) respectively. The response to anandamide was inhibited by capsazepine (pK(B) of 7.40+/-0.02, n=6), but not by the cannabinoid receptor antagonists AM630 or AM281. Furthermore, pretreatment with capsaicin desensitized the anandamide-induced calcium response and vice versa. In conclusion, this study has demonstrated for the first time that anandamide acts as a full agonist at the human VR1.
Polyethylenimine but Not Cationic Lipids Promotes Transgene Delivery to the Nucleus in Mammalian Cells (1998)

The beta-galactosidase reporter gene, either free or complexed with various cationic vectors, was microinjected into mammalian cells. Cationic lipids but not polyethylenimine or polylysine prevent transgene expression when complexes are injected in the nucleus. Polyethylenimine and to a lesser extent polylysine, but not cationic lipids, enhance transgene expression when complexes are injected into the cytoplasm. This latter effect was independent of the polymer vector/cDNA ionic charge ratio, suggesting that nucleic acid compaction rather than surface charge was critical for efficient nuclear trafficking. Cell division was not required for nuclear entry. Finally, comparative transfection and microinjection experiments with various cell lines confirm that barriers to gene transfer vary with cell type. We conclude that polymers but not cationic lipids promote gene delivery from the cytoplasm to the nucleus and that transgene expression in the nucleus is prevented by complexation with cationic lipids but not with cationic polymers.
Redox Imbalance in Cystine/Glutamate Transporter-deficient Mice (2005)

Cystine/glutamate transporter, designated as system x(-)(c), mediates cystine entry in exchange for intracellular glutamate in mammalian cells. This transporter consists of two protein components, xCT and 4F2 heavy chain, and the former is predicted to mediate the transport activity. This transporter plays a pivotal role for maintaining the intracellular GSH levels and extracellular cystine/cysteine redox balance in cultured cells. To clarify the physiological roles of this transporter in vivo, we generated and characterized mice lacking xCT. The xCT(-/-) mice were healthy in appearance and fertile. However, cystine concentration in plasma was significantly higher in these mice, compared with that in the littermate xCT(-/-) mice, while there was no significant difference in plasma cysteine concentration. Plasma GSH level in xCT(-/-) mice was lower than that in the xCT(-/-) mice. The embryonic fibroblasts derived from xCT(-/-) mice failed to survive in routine culture medium, and 2-mercaptoethanol was required for survival and growth. When 2-mercaptoethanol was removed from the culture medium, cysteine and GSH in these cells dramatically decreased, and cells started to die within 24 h. N-Acetyl cysteine also rescued xCT(-/-)-derived cells and permitted growth. These results demonstrate that system x(-)(c) contributes to maintaining the plasma redox balance in vivo but is dispensable in mammalian development, although it is vitally important to cells in vitro.
Incremental test collections (2005)

Corpora and topics are readily available for information retrieval research. Relevance judgments, which are necessary for system evaluation, are expensive; the cost of obtaining them prohibits in-house evaluation of retrieval systems on new corpora or new topics. We present an algorithm for cheaply constructing sets of relevance judgments. Our method intelligently selects documents to be judged and decides when to stop in such a way that with very little work there can be a high degree of confidence in the result of the evaluation. We demonstrate the algorithm's effectiveness by showing that it produces small sets of relevance judgments that reliably discriminate between two systems. The algorithm can be used to incrementally design retrieval systems by simultaneously comparing sets of systems. The number of additional judgments needed after each incremental design change decreases at a rate reciprocal to the number of systems being compared. To demonstrate the effectiveness of our method, we evaluate TREC ad hoc submissions, showing that with 95% fewer relevance judgments we can reach a Kendall's tau rank correlation of at least 0.9.
Overexpression ofNtERF5, a New Member of the Tobacco Ethylene Response Transcription Factor Family Enhances Resistance toTobacco mosaic virus (2004)

A new member of the tobacco (Nicotiana tabacum) AP2/ERF (ethylene response factor) transcription factor family, designated NtERF5, has been isolated by yeast one-hybrid screening. In vitro, recombinant NtERF5 protein weakly binds GCC box cis-elements, which mediate pathogen-regulated transcription of several PR (pathogenesis related) genes. NtERF5 transcription is transiently activated by wounding, by infection with the bacterial pathogen Pseudomonas syringae, as well as by inoculation with Tobacco mosaic virus (TMV). In contrast, NtERF5 transcription is not enhanced after application of salicylic acid, jasmonic acid, or ethylene. Constitutive overexpression of NtERF5 (ERF5-Oex) under control of the 35S promoter results in no visible alterations in plant growth or enhanced resistance to Pseudomonas infection. Furthermore, no constitutive expression of PR genes has been observed. In contrast, ERF5-Oex plants show enhanced resistance to TMV with reference to reduced size of local hypersensitive-response lesions and impaired systemic spread of the virus. Since, in TMV-infected ERF5-Oex plants, the viral RNA accumulates only up to 10 to 30% of the wild-type level, we suggest that NtERF5-regulated gene expression is controlling resistance to viral propagation. Previous research has demonstrated that overexpression of ERF genes enhances resistance to bacterial and fungal pathogens. Here, we provide further evidence that resistance to viral infection can be engineered by overexpression of ERF transcription factors.
Surface IgM-kappa specificity on a Burkitt lymphoma cell in vivo and in derived culture lines. (1968)

Summary An exceptional Burkitt lymphoma patient, a 16-year-old boy, yielded tumor biopsy cells and derived tissue culture lines that displayed a strong surface accumulation of IgM heavy and kappa light chain specificities judged by direct membrane fluorescence and cytotoxicity tests. This property was maintained unchanged in the course of more than 5 months of serial passage in vitro . A fourth biopsy, obtained from the patient after massive necrosis had been induced in the tumor by cytosine arabinoside chemotherapy, did not show this property at either the biopsy stage or in the derived cell line. The possibility that the neoplastic transformation of lymphoid cells may have afflicted a cell specialized to carry immunoglobulin on its surface may be considered. The phenomenon has to be distinguished from immunoglobulin coating in vivo seen with certain biopsy samples from this and other patients. The latter type of coating can be of IgM, IgG, or IgA nature and disappears rapidly on cultivation in vitro .
Automatic characterization and segmentation of human skin using three-dimensional optical coherence tomography (2006)

A set of fully automated algorithms that is specialized for analyzing a three-dimensional optical coherence tomography (OCT) volume of human skin is reported. The algorithm set first determines the skin surface of the OCT volume, and a depth-oriented algorithm provides the mean epidermal thickness, distribution map of the epidermis, and a segmented volume of the epidermis. Subsequently, an en face shadowgram is produced by an algorithm to visualize the infundibula in the skin with high contrast. The population and occupation ratio of the infundibula are provided by a histogram-based thresholding algorithm and a distance mapping algorithm. En face OCT slices at constant depths from the sample surface are extracted, and the histogram-based thresholding algorithm is again applied to these slices, yielding a three-dimensional segmented volume of the infundibula. The dermal attenuation coefficient is also calculated from the OCT volume in order to evaluate the skin texture. The algorithm set examines swept-source OCT volumes of the skins of several volunteers, and the results show the high stability, portability and reproducibility of the algorithm.
Agent-based conferencing using mobile IP-telephony (1999)

This paper presents a new approach to provide computer telephony integration for mobile users and distribute services over the hybrid network domain. A new multimedia processing paradigm is presented in the form of a distributed, agent-based architecture, called 'Distributed Agent Network', DAN, together with example services. The proposed architecture is designed to support user and data mobility, media integration, and universal multimedia messaging. We provide a consistent distributed service platform and dedicated media processing algorithms for mobile multimedia conferencing, mobile messaging and related services. New agent-based techniques are introduced to deal with the abstraction of roles, embedding of media and to overcome the current obstacles in one-to-one and multiparty conferences. Techniques for novel software mobility are presented. The main benefits include scalability of services over different media types, and the ability to use agent intelligence in distributed communications for carrying out dedicated missions. The proposed architecture is demonstrated with a case study of an Internet video call center.
Inhibitory effect of Capsella bursa-pastoris extract on growth of Ehrlich solid tumor in mice. (1976)

The treatment of ICR mice with i.p. injections (0.14 g/kg/day) of the extract of Capsella bursa-pastoris herb (Cruciferae) caused 50 to 80% inhibition of the solid growth of Ehrlich tumor cells that had been inoculated into the s.c. tissue of the animals. The tumor lumps in the treated mice showed multifocal necroses and the infiltartion of host fibrous tissue cells. Experiments were also performed to isolate and identify the active component for the antitumor action, and an acidic substance was isolated in crystalline form from the herb extract. This acidic substance was identified as fumaric acid and was effective in inhibiting the growth of Ehrlich solid tumor at a dose of 10 mg/kg/day. The 50% lethal dose (i.p.) of this acid was 266 mg/kg.
Selectively targeting Mcl-1 for the treatment of acute myelogenous leukemia and solid tumors: Figure 1. (2012)

Bcl-2, Bcl-x(L), Mcl-1, and A1 are the predominant anti-apoptotic members of the Bcl-2 family in somatic cells. Malignant B lymphocytes are critically dependent on Bcl-2 or Bcl-x(L) for survival. In contrast, a new study by Glaser and colleagues in the January 15, 2012, issue of Genes & Development (pp. 120-125) demonstrates that Mcl-1 is essential for development and survival of acute myelogenous leukemia cells. These results provide new impetus for the generation of selective Mcl-1 inhibitors.
Localization of residues that confer antibody binding specificity using human chorionic gonadotropin/luteinizing hormone beta subunit chimeras and mutants. (1990)

The glycoprotein hormones are a family of conserved heterodimeric proteins which share a common alpha subunit but differ in their hormone-specific beta subunits. We used chimeras of human chorionic gonadotropin (hCG) and luteinizing hormone (hLH) beta subunits to identify residues which enable monoclonal antibodies (mAb) to distinguish the two hormones. The LH beta-CG beta chimeras appeared to fold similar to hCG beta, since they combined with hCG alpha and, depending on their sequences, were recognized by hCG-selective mAbs. Amino acid residues Arg8-Arg10,Gly47-Ala51, and Gln89-Leu92 form a major epitope region and appear to be adjacent to each other on the surface of hCG beta. Gly47-Ala51 and Gln89-Leu92 are recognized by dimer-specific mAbs while Arg8-Arg10 is recognized by mAbs which have highest affinity for the free beta subunit. These observations suggest that the conformation of this region of the beta subunit changes when the alpha and beta subunits combine. Residues which are C-terminal of Asp112 form a second epitope domain. mAbs to the third domain distinguish hCG beta and hLH beta by the presence of Asn77 in hCG beta and can be detected after hCG binds to receptors. These findings were used to develop a model of hCG beta which predicts the locations of these residues and their positions relative to the alpha subunit and receptor interfaces.
Pharmacokinetics and pharmacodynamics of ( + )-threo-methylphenidate enantiomer in patients with hypersomnia (1994)

The pharmacokinetics of (+)-methylphenidate after oral administration of 20 mg racemic methylphenidate hydrochloride and the relationship between clinical effects of plasma (+)-methylphenidate concentration were investigated in 15 patients with hypersomnia and four healthy volunteers. The elimination half-life of (+)-methylphenidate in patients was within the range of 2.6 to 3 hours, and the time to reach the peak concentration ranged from 1 to 3 hours. The values of half-life and time to reach the peak concentration in the patients were almost the same as the values in healthy subjects. The plasma (+)-methylphenidate concentration profiles after repeated administration of racemic methylphenidate were similar to those after single administration. No correlation was observed between the plasma (+)-methylphenidate concentration and the subjective sleepiness as measured by Stanford Sleepiness Scale. On the other hand, a significant correlation was found between the sleep latency as measured by the multiple sleep latency test and the plasma concentrations of (+)-methylphenidate (r = 0.850). The time course of the sleep latency after repeated administration was similar to that after single administration. The sleep latency of more than 10 minutes was achieved by maintaining the plasma (+)-methylphenidate concentrations above 3 ng/ml.
Reducing Plenoptic Camera Artifacts (2010)

Abstract The focused plenoptic camera differs from the traditional plenoptic camera in that its microlenses are focused on the photographed object rather than at infinity. The spatio‐angular tradeoffs available with this approach enable rendering of final images that have significantly higher resolution than those from traditional plenoptic cameras. Unfortunately, this approach can result in visible artifacts when basic rendering is used. In this paper, we present two new methods that work together to minimize these artifacts. The first method is based on careful design of the optical system. The second method is computational and based on a new lightfield rendering algorithm that extracts the depth information of a scene directly from the lightfield and then uses that depth information in the final rendering. Experimental results demonstrate the effectiveness of these approaches.
Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. (1996)

A long-term goal in the field of restriction-modification enzymes has been to generate restriction endonucleases with novel sequence specificities by mutating or engineering existing enzymes. This will avoid the increasingly arduous task of extensive screening of bacteria and other microorganisms for new enzymes. Here, we report the deliberate creation of novel site-specific endonucleases by linking two different zinc finger proteins to the cleavage domain of Fok I endonuclease. Both fusion proteins are active and under optimal conditions cleave DNA in a sequence-specific manner. Thus, the modular structure of Fok I endonuclease and the zinc finger motifs makes it possible to create "artificial" nucleases that will cut DNA near a predetermined site. This opens the way to generate many new enzymes with tailor-made sequence specificities desirable for various applications.
Thermal conductivity of phase-change material Ge2Sb2Te5 (2006)

The thermal conductivity of thin films of the phase-change material Ge2Sb2Te5 is measured in the temperature range of 27°C&amp;lt;T&amp;lt;400°C using time-domain thermoreflectance. From the low thermal conductivity of amorphous phase, the conductivity increases irreversibly with increasing temperature and undergoes large changes with phase transformations. Thermal transport in the amorphous and early cubic phases can be described by a random walk of vibrational energy, i.e., the minimum thermal conductivity. In the hexagonal phase, the electronic contribution to the thermal conductivity is larger than the lattice contribution. Crystallization by laser processing produces a cubic phase with a lower thermal conductivity than cubic phases produced by thermal annealing; the authors attribute this difference in conductivity to a larger degree of atomic-scale disorder in films that are crystallized on short time scales.
Similarities and differences in the Fc-binding glycoprotein (gE) of herpes simplex virus types 1 and 2 and tentative mapping of the viral gene for this glycoprotein (1982)

We performed affinity chromatography and immunoprecipitation experiments to determine whether cells infected with herpes simplex virus type 2 (HSV-2) expressed a glycoprotein that was functionally and antigenically related to the HSV-1 Fc-binding glycoprotein designated gE. We found that a protein from extracts of HSV-2-infected HEp-2 cells bound specifically to an Fc affinity column and that the electrophoretic mobility of this protein in sodium dodecyl sulfate-acrylamide gels was slightly less than the mobility of HSV-1 gE. Immunoprecipitation experiments performed with an antiserum prepared against HSV-1 gE revealed that (i) extracts from HSV-2-infected cells contained a glycoprotein that was antigenically related to HSV-1 gE; (ii) the electrophoretic mobility of the HSV-2 gE was indistinguishable from the mobility of the HSV-2 Fc-binding protein; (iii) the antiserum reacted with both newly synthesized transient forms and stable fully processed forms of both HSV-1 gE and HSV-2 gE; and (iv) the transient and stable forms of HSV-2 gE all had lower electrophoretic mobilities than their HSV-1 counterparts. Electrophoretic analyses of gE precipitated from extracts of HEp-2 cells infected with two sets of HSV-1 x HSV-2 intertypic recombinant viruses suggested that the gene for gE is located at the right end of the HSV genome (0.85 to 0.97 map units) in the unique portion of the S component.
An Alternatively Spliced Variant of CXCR3 Mediates the Inhibition of Endothelial Cell Growth Induced by IP-10, Mig, and I-TAC, and Acts as Functional Receptor for Platelet Factor 4 (2003)

The chemokines CXCL9/Mig, CXCL10/IP-10, and CXCL11/I-TAC regulate lymphocyte chemotaxis, mediate vascular pericyte proliferation, and act as angiostatic agents, thus inhibiting tumor growth. These multiple activities are apparently mediated by a unique G protein-coupled receptor, termed CXCR3. The chemokine CXCL4/PF4 shares several activities with CXCL9, CXCL10, and CXCL11, including a powerful angiostatic effect, but its specific receptor is still unknown. Here, we describe a distinct, previously unrecognized receptor named CXCR3-B, derived from an alternative splicing of the CXCR3 gene that mediates the angiostatic activity of CXCR3 ligands and also acts as functional receptor for CXCL4. Human microvascular endothelial cell line-1 (HMEC-1), transfected with either the known CXCR3 (renamed CXCR3-A) or CXCR3-B, bound CXCL9, CXCL10, and CXCL11, whereas CXCL4 showed high affinity only for CXCR3-B. Overexpression of CXCR3-A induced an increase of survival, whereas overexpression of CXCR3-B dramatically reduced DNA synthesis and up-regulated apoptotic HMEC-1 death through activation of distinct signal transduction pathways. Remarkably, primary cultures of human microvascular endothelial cells, whose growth is inhibited by CXCL9, CXCL10, CXCL11, and CXCL4, expressed CXCR3-B, but not CXCR3-A. Finally, monoclonal antibodies raised to selectively recognize CXCR3-B reacted with endothelial cells from neoplastic tissues, providing evidence that CXCR3-B is also expressed in vivo and may account for the angiostatic effects of CXC chemokines.
Expression of nitric oxide synthase in inflammatory bowel disease is not affected by corticosteroid treatment. (1998)

Expression of nitric oxide synthase is increased in both ulcerative colitis and Crohn's disease and appears to be unaffected by treatment with corticosteroids. Disease severity necessitated surgery in all the cases included in this study, regardless of whether or not the patients had received long term corticosteroid treatment. It seems therefore that a high level of iNOS expression and, presumably, production of nitric oxide characterise cases which are refractory to clinical treatment; this suggests that specific inhibition of the enzyme may be a useful therapeutic adjunct.