gebhart/patrepeval huggingface dataset:
Strong decrease in lignin content without significant alteration of plant development is induced by simultaneous down‐regulation of cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) in tobacco plants (2001)

Different transgenic tobacco lines down-regulated for either one or two enzymes of the monolignol pathway were compared for their lignin content and composition, and developmental patterns. The comparison concerned CCR and CAD down-regulated lines (homozygous or heterozygous for the transgene) and the hybrids resulting from the crossing of transgenic lines individually altered for CCR or CAD activities. Surprisingly, the crosses containing only one allele of each antisense transgene, exhibit a dramatic reduction of lignin content similar to the CCR down-regulated parent but, in contrast to this transgenic line, display a normal phenotype and only slight alterations of the shape of the vessels. Qualitatively the lignin of the double transformant displays characteristics more like the wild type control than either of the other transgenics. In the transgenics with a low lignin content, the transformations induced other biochemical changes involving polysaccharides, phenolic components of the cell wall and also soluble phenolics. These results show that the ectopic expression of a specific transgene may have a different impact depending on the genetic background and suggest that the two transgenes present in the crosses may operate synergistically to reduce the lignin content. In addition, these data confirm that plants with a severe reduction in lignin content may undergo normal development at least in controlled conditions.
Hydrohalogenation Reaction of Substituted 1,2-Allenic Carboxylic Acids, Esters, Amides, Nitriles, and Diphenyl Phosphine Oxides (2001)

The hydrohalogenation reaction of 1,2-allenic carboxylic acids, esters, amides, nitriles, and diphenyl phosphine oxides with HX or MX (X = I, Br, Cl, M = Na, Li) in different solvents, such as HOAc, CF3CO2H, and CF3CO2H-HOAc (1:1) was studied. The reaction is a nucleophilic conjugate addition in nature and provides efficient entries to 3-halo-3-enoic acids, esters, amides, nitriles, and 2-haloallyl diphenyl phosphine oxides. The β,γ- over α,β-selectivity and stereoselectivity depend on the solvent(s) and the temperature applied. In most cases, the Z- and E-isomers can be easily separated by chromatography on silica gel. The subsequent cross-coupling reaction with organometallic reagents and terminal alkynes showed the synthetic potential of these products.
Expression of MMP-2 and MMP-9, their inhibitors, and the activator MT1-MMP in primary breast carcinomas (1999)

Enhanced expression of the type IV collagenases MMP-2 and MMP-9, or lack of their inhibitors TIMP-1 and TIMP-2, has been associated with tumour invasion and metastatic potential in several experimental models. Regulation of enzyme activity is clearly a key step in tumour invasion, and recently a potent activator of MMP-2, the membrane-associated MT1-MMP, has been described and characterized. Using an immunohistochemical approach, this study has examined the expression and distribution of the type IV collagenases, their inhibitors, and the activator MT1-MMP, in a series of 79 infiltrating ductal carcinomas (IDCs), 8 tubular carcinomas, and 27 infiltrating lobular carcinomas (ILCs). MMP-2 and MT1-MMP were expressed in more than 90 per cent of all carcinomas, with predominantly stromal and tumour cell cytoplasmic staining. However, reactivity localized on tumour cell membranes was recorded for MMP-2 in 34 per cent of cases with a monoclonal antibody and 55 per cent of cases with a polyclonal antibody, and for MT1-MMP in 68 per cent of tumours. In each case, this pattern of staining was significantly associated with the presence of lymph node metastasis (p=0.001, p=0. 008, and p=0.1, respectively). Both tumour cell and stromal staining was observed for TIMP-2, but there was no correlation with metastatic status. The 92 kD gelatinase MMP-9 was expressed by 68 per cent of carcinomas, either in the stromal compartment or by tumour cells. There was a highly significant correlation between the expression pattern of MMP-9 and tumour type, with ILCs displaying greater frequency and more homogeneous cytoplasmic staining than IDCs (p=0.0004). Staining for TIMP-1 was seen in the stroma and also in relation to small blood vessels, with more than 90 per cent of tumours showing this staining pattern using a polyclonal antibody. This study indicates distinct patterns of expression for different MMPs and demonstrates the potential importance of the MMP-2/MT1-MMP system in breast tumour progression. The association of MMP-9 with the infiltrating lobular phenotype may reveal novel mechanisms of control for this metalloproteinase.
Treatment of cow‐waste slurry by a microbial fuel cell and the properties of the treated slurry as a liquid manure (2006)

ABSTRACT Resource recycling and the proper treatment of animal waste to reduce its environmental impact are currently important issues for the livestock industry. A microbial fuel cell (MFC), a new type of bioreactor, is expected to play roles in both waste‐water purification and energy recovery. However, the generation of electricity from cow waste has not yet been examined. In this study, using an MFC, we examined the possibility of generating electricity from dairy‐cow waste slurry, and analyzed the properties of the treated slurry as liquid manure for resource recycling. The MFC treatment of the slurry generated electricity in a dose‐dependent manner, and the maximum power output by the MFC from a 1 g of chemical oxygen demand/L slurry was 0.34 mW/m 2 . After the MFC treatment, 84% of the biological oxygen demand in the slurry was removed and three essential fertilizer elements (nitrogen, phosphorus, and potassium) were retained at 84, 70, and 91% levels, respectively. The amount of ammonia nitrogen in the slurry, as an element of fast‐release fertilizer, was increased by 1.9‐fold. Although the treated slurry displayed properties that made it preferable as liquid manure, further studies to improve the electrical power output by the MFC are required for practical use.
Infrared microscopy of epithelial cancer cells in whole tissues and in tissue culture, using synchrotron radiation (2003)

Oral epithelial tumour tissue, and cultured cervical epithelial carcinoma cells have been studied using synchrotron infrared microspectroscopy. Mid infrared absorption spectra collected at cellular spatial resolution from within oral tumours were found to be sufficiently distinct, when analysed by principal component analysis, to distinguish between three different cell types within the tumour. The resulting data were sufficiently robust to allow correct classification of spectra from cells within subsequent tissue samples. These results go some way to demonstrate the potential of infrared spectroscopy as a tool in the post-operative screening of oral cancer patients by the examination of exfoliated epithelial cells. To gain a better understanding of the inherent variability in the infrared spectra of such epithelial cells, we have studied A431 carcinoma cells under the stimulus of the growth-stimulating hormone EGF. We have detected key changes in the infrared spectrum that relate to the activation of the growth factor signalling mechanism.
Molecular Basis for the Interaction of [Nle4,d-Phe7]Melanocyte Stimulating Hormone with the Human Melanocortin-1 Receptor (Melanocyte α-MSH Receptor) (1997)

The melanocortin-1 receptor (MC1R) is a seven-transmembrane (TM) G-protein-coupled receptor whose natural ligands are the melanocortin peptides, adrenocorticotropic hormone, and alpha-, beta-, and gamma- melanocyte stimulating hormone (MSH). To test a previously constructed three-dimensional model of the molecular interaction between the long-acting, superpotent alpha-MSH analog [Nle4,D-Phe7]MSH (NDP-MSH) and the human MC1R we examined the effects of site-directed receptor mutagenesis on the binding affinity and potency of NDP-MSH. In addition, we also examined the effects of these same mutations on the binding affinity and potency of the structurally related agonists alpha-MSH, gamma-MSH, and Ac-Nle4-cyclic-[Asp5,His6,D-Phe7,Arg8,Trp9,Lys10]NH2 (MT-II). Mutagenesis of acidic receptor residues Glu94 in TM2 and Asp117 or Asp121 in TM3 significantly altered the binding affinity and potency of all four agonists suggesting that these receptor residues are important to the ligand-receptor interactions of all. A disproportionate change in agonist potency versus affinity observed with simultaneous mutation of these acidic residues (mutant constructs D117A/D121A or E94A/D117A/D121A) or introduction of a single positive charge (mutant construct D121K) also implicates these residues in receptor activation. In addition, results from the individual mutation of aromatic receptor residues Phe175, Phe196, and Phe257, and simultaneous mutation of multiple TM4, -5, and -6 tyrosine and phenylalanine residues suggests that aromatic-aromatic ligand-receptor interactions also participate in binding these melanocortins to the MC1R. These experiments appear to have identified some of the critical receptor residues involved in the ligand-receptor interactions between these melanocortins and the hMC1R.
Dps Protects Cells against Multiple Stresses during Stationary Phase (2004)

Dps, the nonspecific DNA-binding protein from starved cells, is the most abundant protein in stationary-phase Escherichia coli. Dps homologs are found throughout the bacteria and in at least one archaeal species. Dps has been shown to protect cells from oxidative stress during exponential-phase growth. During stationary phase, Dps organizes the chromosome into a highly ordered, stable nucleoprotein complex called the biocrystal. We show here that Dps is required for long-term stationary-phase viability under competitive conditions and that dps mutants have altered lag phases compared to wild-type cells. We also show that during stationary phase Dps protects the cell not only from oxidative stress but also from UV and gamma irradiation, iron and copper toxicity, thermal stress, and acid and base shock. The protective roles of Dps are most likely achieved through a combination of functions associated with the protein-DNA binding and chromosome compaction, metal chelation, ferroxidase activity, and regulation of gene expression.
Coordinated, Differential Expression of Two Genes through Directed mRNA Cleavage and Stabilization by Secondary Structures (2000)

Metabolic engineering and multisubunit protein production necessitate the expression of multiple genes at coordinated levels. In bacteria, genes for multisubunit proteins or metabolic pathways are often expressed in operons under the control of a single promoter; expression of the genes is coordinated by varying transcript stability and the rate of translation initiation. We have developed a system to place multiple genes under the control of a single promoter and produce proteins encoded in that novel operon in different ratios over a range of inducer concentrations. RNase E sites identified in the Rhodobacter capsulatus puf operon and Escherichia coli pap operon were separately placed between the coding regions of two reporter genes, and novel secondary structures were engineered into the 5' and 3' ends of the coding regions. The introduced RNase E site directed cleavage between the coding regions to produce two secondary transcripts, each containing a single coding region. The secondary transcripts were protected from exonuclease cleavage by engineered 3' secondary structures, and one of the secondary transcripts was protected from RNase E cleavage by secondary structures at the 5' end. The relative expression levels of two reporter genes could be varied up to fourfold, depending on inducer concentration, by controlling RNase cleavage of the primary and secondary transcripts. Coupled with the ability to vary translation initiation by changing the ribosome binding site, this technology should allow one to create new operons and coordinate, yet separately control, the expression levels of genes expressed in that operon.
Cutting Edge: Dominance by an MHC-Independent Inhibitory Receptor Compromises NK Killing of Complex Targets (2006)

Inhibitory receptors that recognize MHC class I molecules regulate NK cell responses and self-tolerance. Recent evidence indicates that self-ligands not present in the MHC locus also can modulate NK function. In this study, we show that an inhibitory receptor that recognizes an MHC-independent ligand is over expressed in SHIP(-/-) mice at all stages of NK development and differentiation. Overexpression of this receptor compromises key cytolytic NK functions, including killing of allogeneic, tumor, and viral targets. These results further demonstrate the critical role that SHIP plays in regulation of the NK receptor repertoire and show that regulation of MHC-independent inhibitory receptors is crucial for NK recognition and cytolysis of complex targets.
Cell Separation Methods and Applications (1997)

Background: historical and useful methods of preselection and preparative scale sorting. Physical methods of separation: new approaches in density gradient separation using colloidal silica gradients in the processing of human haematopoietic progenitor cells centrifugal elutriation - a powerful separation technique in cell biology immunology, and haematology. Antibody-based methods: isolation, activation, expansion, and gene transduction of cell-based therapeutics using polystyrene immunoaffinity devices the CEPRATER SC system - technology, clinical development, and future directions high density particles - a novel, highly efficient cell separation technology antibody and complement mediated cell separation. Magnetic methods: magnetic cell sorting with colloidal superparamagnetic particles immunomagnetic cell separation using antibodies and superparamagnetic microspheres free flow magnetophoresis - continuous immunomagnetic sorting of cells and organelles by magnetic deviation and focusing. Flow cytometry: cell separation using flow cytometric cell sorting. Special applications: employing surface markers for the selection of transfected cells CD34 cell sorting and enrichment - applications in blood banking and transplantation. Appendices: cellular properties for cell separation CD antigen designations. Glossary.
Evaluation of electronic, digital blood glucose monitors. (1991)

Maintenance of a normoglycemic blood glucose concentration is commonly suggested as a major goal for the control of the pathogenesis associated with diabetes mellitus. This maintenance requires accurate, reliable self-blood glucose monitoring (SBGM). Six SBGM instruments intended for home use were evaluated in this study for accuracy, precision, and human factor characteristics. Each monitor was tested on samples of blood that had glucose concentrations of 74 mg/dL, 185 mg/dL, and 294 mg/dL. Accuracy was defined as blood glucose concentration measurements within 15% of the reference value of a control blood glucose sample. Individual measurements within this range averaged 83% to 16%. The inter- and intraobserver reliabilities/precisions varied greatly among monitors. The interobserver variations, in general, were greater than the intraobserver variations. A critical factor in SBGM accuracy and reliability was the highly variable user-device interaction. So long as the user-sensitive design found in these SBGM systems is used, the accuracy and reliability of SBGM will be variable.
Molecular phenotype of simian virus 40 large T antigen-induced primitive neuroectodermal tumors in four different lines of transgenic mice. (1994)

We conclude that Simian virus 40 T antigen-induced PNETs in TGM exhibit the molecular phenotype of developing neurons or neuronal progenitor cells. Although many factors could influence the phenotype of these experimental PNETs (e.g., promoter, site of integration of the transgene) these PNETs appear to be suitable TGM models of human PNETs of the central nervous system.
Loss of material from chromosome arm 1p during malignant progression of meningioma revealed by fluorescent in Situ hybridization (1998)

The results of the current study support the existence of tumor suppressor gene(s) on 1p associated with malignant progression of meningioma, and suggest that detection of the allelic status of chromosome 1p by FISH may assist physicians in predicting the clinical prognosis of patients affected by this type of brain tumor.
Unified Loop Closing and Recovery for Real Time Monocular SLAM (2008)

We present a unified method for recovering from tracking fail ure and closing loops in real time monocular simultaneous localisation and mapping. Within a graph-based map representation, we show that recovery and loop closing both reduce to the creation of a graph edge. We describe and implement a bag-of-words appearance model for ranking potential loop closures, and a robust method for using both structure and image appearance to confirm likely matches. The resulting system closes loops and recovers from failures while mapping thousands of landmarks, all in real time.
CAMP: a context-aware mobile portal (2002)

Context-awareness-enhanced mobile computing is expected to be one of the major ingredients of the future wireless services based on IT technologies. This article proposes the concept of such a modular mobile Internet portal enhanced with context awareness features. Some services built into the portal are explained and the benefit for mobile users analyzed. A functional prototype is presented that has been successfully used as a concept proof.
Polymerase chain reaction cloning of a developmentally regulated member of the sialyltransferase gene family (1993)

We have cloned a new member of the sialyltransferase gene family from newborn rat brain cDNA using the polymerase chain reaction and degenerate primers based on sequences found in a continuous region of homology present in three previously cloned sialyltransferases. The predicted amino acid sequence of the new gene contains 24 of the 31 amino acids that are invariantly conserved in the previously cloned sialyltransferases and encodes a type II transmembrane protein characteristic of glycosyltransferases. In contrast to previously cloned sialyltransferase genes, the expression of the new gene is highly restricted, being abundantly expressed in newborn brain but not in adult brain or any other adult or newborn tissues.
Multipole storage assisted dissociation, a novel in-source dissociation technique for electrospray ionization generated ions (1998)

In this work we present a novel in-source dissociation scheme referred to as multipole storage assisted dissociation (MSAD) for electrospray ionization (ESI) generated ions in which dissociation is effected by employing extended ion accumulation intervals in a high pressure rf-only hexapole assembly prior to mass analysis. Following an extended ion accumulation interval in which ions are confined in the rf-only hexapole, ions are gated out of the hexapole, trapped, and mass analyzed in the trapped ion cell of a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. The accumulation region is comprised of an rf-only hexapole ion guide which separates two electrodes, a biased skimmer cone, and an auxiliary 'gate' electrode at the low pressure end of the hexapole. This technique should be applicable to other mass spectrometry platforms compatible with pulsed ionization sources including quadrupole ion traps, and time-of-flight mass analyzers. This concept is demonstrated with the dissociation of a small protein in which selective fragmentation is observed at labile amino acid linkages producing primarily y-type fragment ions.
Characterization of interleukin-10 receptors on human and mouse cells. (1993)

Human interleukin (IL)-10 is a pleiotropic cytokine acting on a variety of immune cells. Here we show that the protein can be enzymatically iodinated to high specific radioactivity with retention of biological activity. The radiolabeled ligand binds specifically to its receptor in several mouse and human cell lines, notably human B-lymphoma line JY and mouse mast cell line MC/9. Human IL-10 apparently binds as a dimer to a single class of receptor in both the JY and MC/9 cell lines with a Kd in the 50-200 pM range. Interestingly, mouse IL-10 was capable of blocking binding of human IL-10 to mouse but not human cells. There appears to be at most only a few hundred IL-10 receptors/cell for both mouse and human cell lines examined. Chemical cross-linking of the radioiodinated hIL-10 to JY and MC/9 cells revealed a common protein complex with an apparent molecular mass of about 97 kDa. Additional high molecular weight complexes were detected with JY but not MC/9 cells.
D-dimer Testing for Suspected Pulmonary Embolism in Outpatients (1997)

The plasma level of D-dimer, a fibrin degradation product (FDP), is nearly always increased in the presence of acute pulmonary embolism (PE). Hence, a normal D-dimer level (below a cutoff value of 500 micrograms/L by enzyme-linked immunosorbent assay [ELISA]) may allow the exclusion of PE. To assess the negative predictive value of a D-dimer concentration below 500 micrograms/L in outpatients with suspected PE, and the safety of withholding anticoagulant treatment from such patients, we performed D-dimer assays, lower limb venous compression ultrasonography, and lung scans in 671 consecutive outpatients presenting in the Emergency Center of the Geneva University Hospital with suspected PE. Pulmonary angiography was reserved for patients with an inconclusive noninvasive workup. Patients with a normal D-dimer concentration were discharged without anticoagulant treatment and followed for 3 mo. The prevalence of PE was 29%, and D-dimer (using a cutoff of 500 micrograms/L) had a diagnostic sensitivity for PE of 99.5%. Overall diagnostic specificity of D-dimer was 41%, but it was lower among older patients. Of the 198 patients with a D-dimer concentration below the cutoff value, 196 were free of PE, one had a PE, and one had incomplete information because of loss to follow-up. Thus, the negative predictive value of D-dimer concentration fell between 197 of 198 and 196 of 198 cases of PE (99% [95% CI: 96.4 to 99.9]). Using a cutoff value of 4,000 micrograms/L, the overall specificity of D-dimer concentration for PE was 93.1%. In conclusion, a plasma D-dimer concentration below 500 micrograms/L allows the exclusion of PE in 29% of outpatients suspected of having PE. Withholding anticoagulation from such patients is associated with a conservative 1% risk of thromboembolic events during follow-up.
BRCA1 regulates p53-dependent gene expression (1998)

Mutations in BRCA1 are present in 45% of families that segregate with susceptibility for breast cancer and in 80-90% of families with both breast and ovarian cancer. Here we report that BRCA1 stimulates artificial and genomic promoter constructs containing p53-responsive elements. This activity of BRCA1 depends on the presence of wild-type p53, which was shown by using mouse fibroblasts expressing temperature-sensitive forms of p53, or p53(+/+) and p53(-/-) fibroblasts obtained from p53 knockout mice. Furthermore, mutant forms of BRCA1 lacking the C-terminal second BRCA1 C-terminal (BRCT) domain showed reduced p53-mediated transcriptional activation. Finally, we found that BRCA1 coimmunoprecipitates with p53, in vitro and in vivo. These findings suggest a function of BRCA1 as a p53 coactivator.