gebhart/patrepeval huggingface dataset:
A Novel Cytochrome b5-like Domain Is Linked to the Carboxyl Terminus of the Saccharomyces cerevisiae Δ-9 Fatty Acid Desaturase (1995)

Cytochrome b5 is an amphipathic mobile membrane protein that is predominantly located at the endoplasmic reticulum surface. It is an essential component of a number of membrane-bound redox systems. In animal and fungal cells cytochrome b5 is thought to be an electron donor for sterol modifying enzymes and fatty acid desaturases. Disruption of the Saccharomyces cytochrome b5 gene, however, yielded cells that had no nutritional requirement for either sterols or unsaturated fatty acids. Expression of sterol and fatty acid-modifying genes was increased in the cytochrome b5-disrupted cells, however, suggesting that cytochrome b5 may play some nonessential role in these functions. Unsaturated fatty acids in yeast are formed by Ole1p, an oxygen-dependent delta-9 fatty acid desaturase that is an intrinsic endoplasmic reticulum membrane protein. Although the yeast delta-9 fatty acid desaturase does not appear to require cytochrome b5, introduction of the rat liver stearoyl-CoA desaturase gene into an ole1-disrupted, cytochrome b5-disrupted yeast strain revealed that this enzyme specifically requires cytochrome b5 to function. Comparison of the coding sequences of the yeast and rat desaturase genes showed that the yeast protein contains a 113-amino acid carboxyl-terminal extension not found in the rat enzyme. That extension has regions of strong homology to cytochrome b5, particularly in the heme binding and electron transfer motifs. Truncation or disruption of the desaturase cytochrome b5-like domain in cells that contain the wild type diffusible b5 produced unsaturated fatty acid auxotrophy, suggesting that the cytochrome b5-like domain of Ole1p plays an essential role in the desaturase reaction.
Multiple View Camera Calibration for Localization (2007)

The recent development of distributed smart camera networks allows for automated multiple view processing. Quick and easy calibration of uncalibrated multiple camera setups is important for practical uses of such systems by non-experts and in temporary setups. In this paper we discuss options for calibration, illustrated with a basic two-camera setup where each camera is a smart camera mote with a highly parallel SIMD processor and an 8051 microcontroller. In order to accommodate arbitrary (lens) distortion, perspective mapping and transforms for which no analytic inverse is known, we propose the use of neural networks to map projective grid space back to Euclidean space for use in 3D localization and 3D view interpretation.
Alternative splicing of TGF-betas and their high-affinity receptors TβRI, TβRII and TβRIII (betaglycan) reveal new variants in human prostatic cells (2007)

In general, expression of the splice variants was more heterogeneous in contrast to the well-known isoforms. The identification of the splice variants T beta RIB and the novel isoform T beta RIIC in man clearly contributes to the growing complexity of the TGF-beta family.
AAL881, a Novel Small Molecule Inhibitor of RAF and Vascular Endothelial Growth Factor Receptor Activities, Blocks the Growth of Malignant Glioma (2006)

Malignant gliomas are highly proliferative and angiogenic cancers resistant to conventional therapies. Although RAS and RAF mutations are uncommon in gliomas, RAS activity is increased in gliomas. Additionally, vascular endothelial growth factor and its cognate receptors are highly expressed in gliomas. We now report that AAL881, a novel low-molecular weight inhibitor of the kinase activities associated with B-RAF, C-RAF (RAF-1), and VEGF receptor-2 (VEGFR2), showed activity against glioma cell lines and xenografts. In culture, AAL881 inhibited the downstream effectors of RAF in a concentration-dependent manner, with inhibition of proliferation associated with a G(1) cell cycle arrest, induction of apoptosis, and decreased colony formation. AAL881 decreased the proliferation of bovine aortic endothelial cells as well as the tumor cell secretion of vascular endothelial growth factor and inhibited the invasion of glioma cells through an artificial extracellular matrix. Orally administered AAL881 was well tolerated with minimal weight loss in non-tumor-bearing mice. Established s.c. human malignant glioma xenografts grown in immunocompromised mice treated with a 10-day course of oral AAL881 exhibited growth delays relative to control tumors, frequently resulting in long-term complete regressions. AAL881 treatment extended the survival of immunocompromised mice bearing orthotopic glioma xenografts compared with placebo controls. The intraparenchymal portions of orthotopic AAL881-treated tumors underwent widespread necrosis consistent with vascular disruption compared with the subarachnoid elements. These effects are distinct from our prior experience with VEGFR2 inhibitors, suggesting that targeting RAF itself or in combination with VEGFR2 induces profound tumor responses in gliomas and may serve as a novel therapeutic approach in patients with malignant gliomas.
Quorum sensing controls expression of the type III secretion gene transcription and protein secretion in enterohemorrhagic and enteropathogenic Escherichia coli (1999)

Enterohemorrhagic Escherichia coli O157:H7 and enteropathogenic E. coli cause a characteristic histopathology in intestinal cells known as attaching and effacing. The attaching and effacing lesion is encoded by the Locus of Enterocyte Effacement (LEE) pathogenicity island, which encodes a type III secretion system, the intimin intestinal colonization factor, and the translocated intimin receptor protein that is translocated from the bacterium to the host epithelial cells. Using lacZ reporter gene fusions, we show that expression of the LEE operons encoding the type III secretion system, translocated intimin receptor, and intimin is regulated by quorum sensing in both enterohemorrhagic E. coli and enteropathogenic E. coli. The luxS gene recently shown to be responsible for production of autoinducer in the Vibrio harveyi and E. coli quorum-sensing systems is responsible for regulation of the LEE operons, as shown by the mutation and complementation of the luxS gene. Regulation of intestinal colonization factors by quorum sensing could play an important role in the pathogenesis of disease caused by these organisms. These results suggest that intestinal colonization by E. coli O157:H7, which has an unusually low infectious dose, could be induced by quorum sensing of signals produced by nonpathogenic E. coli of the normal intestinal flora.
Inverse scattering for rotationally scanned optical coherence tomography (2006)

Optical coherence tomography of luminal structures, such as for intravascular or gastrointestinal imaging, is performed by using a fiber-optic catheter as a beam-delivery probe. The interrogating beam is scanned angularly by rotating the fiber around a fixed central axis. Because the beam is focused only at a fixed distance from the center of the fiber, only scatterers near this distance are resolved. We present a solution of the inverse scattering problem that provides an estimate of the susceptibility of the sample for an angularly scanned Gaussian beam focused at a fixed distance from the origin. This solution provides quantitatively meaningful reconstructions while also extending the volume of the sample that is resolvable by the instrument.
Involvement of extracellular signal-regulated kinase 2 and stress-activated protein kinase/Jun N-terminal kinase activation by transforming growth factor beta in the negative growth control of breast cancer cells. (1997)

Although transforming growth factor beta (TGF-beta) is known to be a potent growth inhibitor of breast cancer cells (BCCs), the signaling mechanisms mediating TGF-beta responses have not been defined. We have demonstrated previously that TGF-beta can activate Ras and extracellular signal-regulated kinase (ERK) 1 in untransformed epithelial cells (K. M. Mulder and S. L. Morris, J. Biol. Chem., 267: 5029-5031, 1992; M. T. Hartsough and K. M. Mulder, J. Biol. Chem., 270: 7117-7124, 1995). We have also shown that TGF-beta signaling is altered in epithelial cells when Ras activation is blocked (Hartsough et at., J. Biol. Chem., 271: 22368-22375). Here we demonstrate the ability of the TGF-beta3 isoform to activate the signaling component ERK2 in TGF-beta-sensitive BCCs but not in TGF-beta-resistant cells. The ERK2 isoform was activated by 6-fold within 10 min of TGF-beta3 addition to the TGF-beta-sensitive BCC line Hs578T. Moreover, the IC50 for inhibition of DNA synthesis by TGF-beta3 in this cell line correlated with the EC50 for TGF-beta3 activation of ERK2. In contrast, TGF-beta3 had little effect on either DNA synthesis or ERK2 activation in ZR-75 BCCs lacking the type-II TGF-beta receptors (R(II)), or in ZR-75 BCCs stably transfected with R(II) yet still TGF-beta resistant. In addition, our data demonstrate that TGF-beta3 affected a sustained activation of the stress-activated protein kinase/Jun N-terminal kinase (SAPK/JNK) type of mitogen-activated protein kinase (MAPK); maximal induction levels were 2.5-fold above basal values and were attained at 30 min after TGF-beta3 treatment. In contrast, TGF-beta3 did not increase SAPK/JNK activity in the TGF-beta-resistant ZR-75 R(II) BCCs. Our data provide the first evidence that TGF-beta activation of ERK2 and SAPK/JNK is associated with negative growth control of BCCs. This is also the first demonstration that TGF-beta can activate the SAPK/JNK type of MAPK and that the TGF-beta3 isoform can regulate MAPK activity.
Proximodistal axis formation in the Drosophila leg: subdivision into proximal and distal domains by Homothorax and Distal-less (1999)

The developing legs of Drosophila are subdivided into proximal and distal domains by the activity of the homeodomain proteins Homothorax (Hth) and Distal-less (Dll). The expression domains of Dll and Hth are initially reciprocal. Wingless and Dpp define both domains by activating Dll and by repressing Hth in the distal region of the disc. Wg and Dpp do not act through Dll to repress Hth. Hth functions to reduce the sensitivity of proximal cells to Wg and Dpp. This serves to limit the effective range of these signals in regulating later-acting genes such as Dac. We present evidence that proximal and distal cells tend to sort-out from one another. Cells forced to express Hth are unable to mix with distal cells. Likewise, cells forced to express Dll are unable to mix with proximal cells. Clones of cells unable to express Dll in the distal region sort-out from the disc. Clones of cells unable to express Hth lose the specialized population of cells at the interface between proximal and distal territories and cause fusion between body wall and leg segments. These observations suggest that sorting-out behavior of Hth- and Dll-expressing cells contributes to subdivision of the leg into proximal and distal domains.
Loss of melanogenic properties in tyrosinases induced by glucosylation inhibitors within malignant melanoma cells. (1982)

Glycosylation inhibitors, glucosamine or tunicamycin, have been found to be specific inhibitory modulators for melanogenesis, which is accentuated generally in malignant melanoma cells. Exposure to glucosamine (1 mg/ml) or tunicamycin (0.2 to 0.4 micrograms/ml) induces a marked pigment loss within melanoma cells in vitro with a decrease in their grown curves. This melanogenic inhibition occurs without a substantial decrease in the synthesis of DNA, RNA, and protein in comparison with a specific, marked suppression of carbohydrate synthesis as revealed by suppressed mannose incorporation into these cells. Assay of tyrosinase of glucosamine- or tunicamycin-induced unpigmented melanoma cells has revealed a selective and marked decrease in the melanosome-rich large-granule fraction, but no substantial decrease in the total activity of remaining subcellular fractions. Electrophoresis of tyrosinase in the 30,000 X g supernatant fraction demonstrates an increase in the T1 form of soluble tyrosinase, while a disappearance of or marked decrease in membrane-bound tyrosinase, T3, is seen in the small- and large-granule fractions. Glycoprotein synthesis in the melanogenic subcellular compartments of pigment cells seems to play an integral role in melanogenesis which is principally enhanced in their carcinogenic status.
Stretching the rubber sheet (1993)

Article Free Access Share on Stretching the rubber sheet: a metaphor for viewing large layouts on small screens Authors: Manojit Sarkar Department of Computer Science, Brown University, Providence, RI Department of Computer Science, Brown University, Providence, RIView Profile , Scott S. Snibbe Department of Computer Science, Brown University, Providence, RI Department of Computer Science, Brown University, Providence, RIView Profile , Oren J. Tversky Department of Computer Science, Brown University, Providence, RI Department of Computer Science, Brown University, Providence, RIView Profile , Steven P. Reiss Department of Computer Science, Brown University, Providence, RI Department of Computer Science, Brown University, Providence, RIView Profile Authors Info & Claims UIST '93: Proceedings of the 6th annual ACM symposium on User interface software and technologyDecember 1993 Pages 81–91https://doi.org/10.1145/168642.168650Published:01 December 1993Publication History 160citation1,270DownloadsMetricsTotal Citations160Total Downloads1,270Last 12 Months59Last 6 weeks11 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Development of a Plant Transformation Selection System Based on Expression of Genes Encoding Gentamicin Acetyltransferases (1988)

The development of selectable markers for transformation has been a major factor in the successful genetic manipulation of plants. A new selectable marker system has been developed based on bacterial gentamicin-3-N-acetyltransferases [AAC(3)]. These enzymes inactivate aminoglycoside antibiotics by acetylation. Two examples of AAC(3) enzymes have been manipulated to be expressed in plants. Chimeric AAC(3)-III and AAC(3)-IV genes were assembled using the constitutively expressed cauliflower mosaic virus 35S promoter and the nopaline synthase 3' nontranslated region. These chimeric genes were engineered into vectors for Agrobacterium-mediated plant transformation. Petunia hybrida and Arabidopsis thaliana tissue transformed with these vectors grew in the presence of normally lethal levels of gentamicin. The transformed nature of regenerated Arabidopsis plants was confirmed by DNA hybridization analysis and inheritance of the selectable phenotype in progeny. The chimeric AAC(3)-IV gene has also been used to select transformants in several additional plant species. These results show that the bacterial AAC(3) genes will serve as useful selectable markers in plant tissue culture.
Human immune responses to influenza virus vaccines administered by systemic or mucosal routes (1995)

Healthy adult volunteers were immunized by parenteral or oral routes with trivalent inactivated influenza vaccine (A/Chile/1/83 (H1N1), A/Mississippi/1/85 (H3N2), and B/Ann Arbor/1/86), or intranasally with live attenuated, cold-adapted influenza type A/Texas/1/85 (H1N1) reassortant virus. In all volunteers, cells spontaneously secreting IgA, IgG or IgM antibodies specific to influenza virus were detected in peripheral blood on days 6-13 after immunization, and specific IgA, IgG and IgM antibodies to influenza vaccine were measured in sera and external secretions (saliva and nasal lavage). Following systemic immunization, a raise in specific antibodies of all isotypes was observed in sera beginning on day 13. Although small variations in IgA and IgM antibodies in saliva and nasal lavages were detected, antigen-specific IgG significantly increased between days 13 and 27. Intranasal administration of attenuated virus induced IgA and IgG antibodies in serum as well as in secretions. Serum antibodies were not substantially influenced by oral immunization, only a small increase in all isotypes was observed in volunteers' sera 21 days after ingestion of vaccine. However, in secretions, antigen-specific IgA and IgG responses were detected one week after immunization and reached a peak response on day 20. These studies show that different routes of immunization can be effective for the induction of specific antibodies, and support the concept of the common mucosal immune system in humans by demonstrating that the oral or intranasal administration of antigen-induced specific antibodies of IgA isotype in external secretions, preceded by the transient appearance in peripheral blood of specific antibody-producing cells.
Differentiation-dependent expression of sialyl stage-specific embryonic antigen-1 and I-antigens on human lymphoid cells and its implications for carbohydrate-mediated adhesion to vascular endothelium (1993)

Expression of two developmentally regulated carbohydrate antigens, the sialyl stage-specific embryonic antigen-1 (SSEA-1) and I-antigens, in human lymphocytes and lymphocytic leukemia cells was investigated using specific monoclonal antibodies. Sialyl SSEA-1 was expressed only on natural killer (NK) cells, and was essentially absent on resting mature T and B cells among normal peripheral lymphocytes. On the other hand, the I-antigen was strongly expressed on virtually all mature B cells, moderately expressed on most mature T cells, but not expressed on NK cells in normal donors. Expression of the two antigens on normal T and B cells was reversible; in vitro stimulation of normal lymphocytes with concanavalin A (Con A) resulted in the loss of I-antigen and appearance of sialyl SSEA-1 on CD3+ T blasts, whereas stimulation with pokeweed mitogen led to loss of I-antigen expression and appearance of sialyl SSEA-1 antigen on CD19+ B blasts. Among lymphocytic leukemia cells, sialyl SSEA-1 was detected primarily on leukemia cells having immature properties such as most common acute lymphocytic leukemia (cALL) blasts, while the I-antigen was frequently expressed on malignant cells having relatively mature properties, such as those found in adult T- cell leukemia or chronic lymphocytic leukemia, and only occasionally on cALL blasts. Among normal peripheral lymphocytes, the sialyl SSEA-1+I- antigen- NK cells selectively underwent E-selectin (ELAM-1, endothelial- leukocyte adhesion molecule-1)-dependent adhesion to endothelial cells, while the I-antigen+sialyl SSEA-1- mature T and B cells did not, in line with the recent finding that sialyl SSEA-1 serves as a specific ligand for E-selectin. Con A blasts, which are sialyl SSEA-1+I-antigen- , also exhibited significant E-selectin-dependent adhesion to endothelial cells. These results indicate that expression of the sialyl SSEA-1 and I-antigens varies alternately depending on the differentiation/activation status of the lymphocytes, and that this at least partly regulates the behavior of lymphocytes at the vessel wall.
webmedcentral (2013)

The data emphasize two practical methods of increasing the robustness of mass spectrometry data analysis. The data show that 1) using multiple search engines can expand the number of identified proteins (union) and validate protein identifications (intersection), and 2) analysis of 2 or 3 technical replicates can substantially expand protein identifications. Moreover, information can be extracted from a dataset by performing database searching with different engines and performing technical repeats, which requires no additional sample preparation and effectively utilizes research time and effort.
Hydrogenation of Esters to Alcohols with a Well‐Defined Iron Complex (2014)

We present the first base-free Fe-catalyzed ester reduction applying molecular hydrogen. Without any additives, a variety of carboxylic acid esters and lactones were hydrogenated with high efficiency. Computations reveal an outer-sphere mechanism involving simultaneous hydrogen transfer from the iron center and the ligand. This assumption is supported by NMR experiments.
Designing Zinc-Finger ADR1 Mutants with Altered Specificity of DNA Binding to T in UAS1 Sequences (1995)

Yeast ADR1 contains two Cys2,His2 zinc fingers needed for DNA binding to the upstream activation sequence UAS1, with bases T5T6G7-G8A9G10 in the ADH2 promoter. Potential DNA-contacting amino acid residues at -1, +3, and +6 in the alpha-helical domains of ADR1's fingers one and two include RHR-RLR; however, the latter finger two residues Leu146 and Arg149 had not proved to be crucial for ADR1 binding, even though Leu146-T6 and Arg149-T5 interactions with UAS1 DNA were predicted. We altered Leu146 or Arg149 by PCR cassette mutagenesis, to study ADR1 mutant binding to 16 UAS1 variants of thymine bases T5 and T6. Mutation of Leu146 to His, making finger two (RLR) like finger one (RHR), decreased binding to wild type UAS1 having T6, but enhanced its binding strength to sequences having purines G6 or A6, similar to binding seen between finger one's His118 and base A9 of UAS1. Mutating Leu146 to Lys caused this finger two RKR mutant to bind strongly to both G6 and T6, possibly by lysine's amine H-bonding to the carbonyl of guanine or thymine. Specificity of ADR1 for UAS1 with T6 may thus be due to hydrophobic interaction between Leu146 and the T6 methyl group. ADR1 mutants with either His or Lys in the central +3 residue (146) of zinc finger two, which have Arg149 in the +6 alpha-helical position, bind with UAS1 mutant sequences having G5 very strongly, T5 strongly, A5 intermediately, and C5 weakly.(ABSTRACT TRUNCATED AT 250 WORDS)
Identification of novel small molecule activators of nuclear factor‐κb with neuroprotective action via high‐throughput screening (2010)

Neuronal noncytokine-dependent p50/p65 nuclear factor-κB (the primary NF-κB complex in the brain) activation has been shown to exert neuroprotective actions. Thus neuronal activation of NF-κB could represent a viable neuroprotective target. We have developed a cell-based assay able to detect NF-κB expression enhancement, and through its use we have identified small molecules able to up-regulate NF-κB expression and hence trigger its activation in neurons. We have successfully screened approximately 300,000 compounds and identified 1,647 active compounds. Cluster analysis of the structures within the hit population yielded 14 enriched chemical scaffolds. One high-potency and chemically attractive representative of each of these 14 scaffolds and four singleton structures were selected for follow-up. The experiments described here highlighted that seven compounds caused noncanonical long-lasting NF-κB activation in primary astrocytes. Molecular NF-κB docking experiments indicate that compounds could be modulating NF-κB-induced NF-κB expression via enhancement of NF-κB binding to its own promoter. Prototype compounds increased p65 expression in neurons and caused its nuclear translocation without affecting the inhibitor of NF-κB (I-κB). One of the prototypical compounds caused a large reduction of glutamate-induced neuronal death. In conclusion, we have provided evidence that we can use small molecules to activate p65 NF-κB expression in neurons in a cytokine receptor-independent manner, which results in both long-lasting p65 NF-κB translocation/activation and decreased glutamate neurotoxicity.