gebhart/patrepeval huggingface dataset:
Phosphoenolpyruvate Carboxykinase Assayed at Physiological Concentrations of Metal Ions Has a High Affinity for CO2 (2002)

The effect of Mn2+/Mg2+ concentration on the activity of intact, homogeneous phosphoenolpyruvate carboxykinase (PEPCK) from leaves of the C4 grass, Guinea grass (Panicum maximum), have been investigated. Assay conditions were optimized so that PEPCK activity could be measured at concentrations of Mn2+/Mg2+ similar to those found in the cytosol (low micromolar Mn2+ and millimolar Mg2+). PEPCK activity was totally dependent on Mn2+ and was activated at low micromolar concentrations of Mn2+ by millimolar concentrations of Mg2+. Therefore, at physiological concentrations of Mn2+, PEPCK has a requirement for Mg2+. Assay at physiological concentrations of Mn2+/Mg2+ led to a marked decrease in its affinity for ATP and a 13-fold increase in its affinity for CO2. The Km (CO2) was further decreased by assay at physiological ATP to ADP ratios, reaching values as low as 20 microM CO2, comparable with the Km (CO2) of ribulose 1,5-bisphosphate carboxylase-oxygenase. This means that PEPCK will catalyze a reversible reaction and that it could operate as a carboxylase in vivo, a feature that could be particularly important in algal CO2-concentrating systems.
Molecular ion fragmentation and its effects on mass isotopomer abundances of fatty acid methyl esters ionized by electron impact (1999)

We have analyzed the isotopomer abundance ratios of an equimolar mixture of nine fatty acid methyl esters (decanoate, undecanoate, laurate, tridecanoate, myristate, pentadecanoate, palmitate, heptadecanoate, and stearate) by selected-ion monitoring gas chromatography/electron impact/mass spectrometry (GC/EI/MS). The abundance of the second lowest m/z isotopomer (IM1) increased disproportionately compared with the abundance of the lowest m/z isotopomer (IM0) as a function of: (1) increasing sample size; (2) decreasing repeller voltage; and (3) decreasing alkyl chain length. We also compared the abundance of the third lowest m/z isotopomer (IM2) and the abundance of the second lowest m/z isotopomer (IM1) of methyl palmitate and [4,4-2H2]methyl palmitate. We observed that the IM2/IM1 for methyl palmitate was significantly lower than IM2/IM1 for [4,4-2H2]methyl palmitate. From these results, as well as a consideration of basic principles of ion chemistry and ion physics, we conclude that gas-phase chemistry, specifically proton (or deuteron) transfer from fragment ions to molecules, is a major contributor to the sample size dependence observed in mass isotopomer abundance measurements of fatty acid methyl esters ionized by EI. Our results and analysis do not support hydrogen abstraction as the reaction mechanism. In addition, we calculate that rearranged molecular ions are unlikely to contribute significantly to intermolecular proton transfer because of their relatively brief lifetime. We also discuss alternative analytical techniques which might improve the precision and accuracy of isotopomer measurements by reducing molecular ion fragmentation.
The mRNA Expression of Serotonin 2C Subtype Receptors Uncoupled With Inositol Hydrolysis in NG108-15 Cells (2002)

Cell culture systems seem to be useful for clarifying the cellular physiological mechanisms of serotonin 2C subtype receptors (5-HT2CR) and related drug action mechanisms. However, there are still few reports about cells that contain intrinsic 5-HT2CR. This report demonstrates by using RT/PCR that 5-HT2CR mRNA exists in splicing variant forms in NGI08-15 cells. The PCR results using a pair of primers that recognized sequences near the third intracellular loop site showed two neighboring bands at about 500 bp upon electrophoresis in acrylamide gels. The sequence analysis demonstrated that one band was the rat 5-HT2CR sequence and the other one was that of the mouse. Serotonin, however, did not enhance the inositol phosphates formation in NG108-15 cells. It has been reported that post-translational modifications of RNA, splicing and editing, occur at the site of the second intracellular loop domain in 5-HT2CR mRNA. Accordingly, a pair of primers that recognized this site were designed. The molecular size of the PCR product was shorter than that expected based on the sequence of the native 5-HT2CR. The fragment lacked the 95 nucleotides of native 5-HT2CR mRNA. This seems to be the reason why serotonin did not enhance inositol phosphates formation in NG108-15 cells.
Proviruses are adjacent to c-myc in some murine leukemia virus-induced lymphomas. (1984)

Sixty-one murine leukemia virus-induced lymphomas were examined for evidence of proviral insertions adjacent to known oncogenes. Five of these lymphomas were found to have alterations adjacent to c-myc. Two of the lymphomas with altered c-myc sequences were examined in detail. Evidence was obtained showing that the alterations in the c-myc sequences in these two lymphomas were the result of proviral integrations. This result suggests that lymphomagenesis by murine leukemia viruses can result from insertional mutagenesis of cellular oncogenes.
Antiangiogenic Therapy: A Universal Chemosensitization Strategy for Cancer? (2006)

For more than 50 years, a major goal of research in cancer therapeutics has been to develop universally effective agents that render cancer cells more sensitive to cytotoxic chemotherapy without substantially increasing toxicity to normal cells. The results of recent clinical trials indicate that certain antiangiogenic drugs may produce this long-sought effect. Here, I describe three distinct mechanisms that may help to explain the chemosensitizing activity of these drugs: normalizing tumor vasculature, preventing rapid tumor cell repopulation, and augmenting the antivascular effects of chemotherapy. I then discuss how these potential mechanisms might be exploited to maximize therapeutic efficacy.
Detection of DNA and Protein Molecules Using an FET‐Type Biosensor with Gold as a Gate Metal (2004)

Abstract In this study, a field effect transistor (FET)‐type biosensor based on 0.5 μm standard complementary metal oxide semiconductor (CMOS) technology is proposed and its feasibility for detecting deoxyribonucleic acid (DNA) and protein molecules is investigated. Au, which has a chemical affinity with thiol by forming a self‐assembled monolayer (SAM), was used as the gate metal in order to immobilize DNA and protein molecules. A Pt pseudo‐reference electrode was employed for the detection of biomolecules. The sensor was fabricated as a p‐channel (P)MOSFET‐type because PMOSFET with positive surface potential is useful for detecting negatively charged biomolecules from the view point of its high sensitivity and fast response time. DNA and protein molecules were detected by measuring the variation of the drain current due to the variation of biomolecular charge and capacitance. DNA and protein molecules used in the experiment were 15mer–oligonucleotide probe and streptavidin‐biotin protein complexes, respectively. DNA was detected by both in situ and ex situ measurements. Additionally, to verify the interactions among SAM, streptavidin, and biotin, surface plasmon resonance (SPR) measurement was performed.
Mutations of CpG dinucleotides located in the triiodothyronine (T3)-binding domain of the thyroid hormone receptor (TR) beta gene that appears to be devoid of natural mutations may not be detected because they are unlikely to produce the clinical phenotype of resistance to thyroid hormone. (1994)

Thyroid hormone receptor (TR) beta gene mutations identified in patients with resistance to thyroid hormone (RTH) revealed two clusters ("hot" areas) of mutations (RTHmut) in the triiodothyronine (T3)-binding domain. Furthermore, 45% of RTHmuts and 90% of recurring mutations are located in CpG dinucleotides ("hot spots"). To investigate why the region between the two hot areas lacks RTHmuts, we produced 10 artificial mutant TR beta s (ARTmut) in this "cold" region according to the hot spot rule (C-->T or G-->A substitutions in CpGs). The properties of ARTmuts were compared with those of six RTHmuts. Among all RTHmuts, R320H manifesting a mild form of RTH showed the least impairment of T3-binding affinity (Ka). In contrast, Ka was normal in six ARTmuts (group A), reduced to a lesser extent than R320H in three (group B), and one that was truncated (R410X) did not bind T3. All RTHmuts had impaired ability to transactivate T3-responsive elements and exhibited a strong dominant negative effect on cotransfected wild-type TR beta. Group B and A ARTmuts had minimally impaired or normal transactivation and weak or no dominant negative effect, respectively. R410X showed neither transactivation nor dominant negative effect. Natural mutations expected to occur in the cold region of TR beta should fail to manifest as RTH (group A) or should escape detection (group B) since the serum thyroid hormone levels required to compensate for the reduced binding affinity should be inferior to those found in subjects with R320H. R410X would manifest RTH only in the homozygote state. The cold region of the putative T3-binding domain is relatively insensitive to amino acid changes and, thus, may not be involved in a direct interaction with T3.
Mechanisms involved in protection provided by immunization against core lipopolysaccharides of Escherichia coli J5 from lethal Haemophilus pleuropneumoniae infections in swine (1986)

In an investigation of the potential protective effects of immunity against common lipopolysaccharide core antigens of gram-negative bacteria during a severe gram-negative infection in the natural host, we induced Haemophilus pleuropneumoniae infections in weanling pigs immunized with a vaccine of an Rc mutant of Escherichia coli (strain J5). To help define the mechanism involved in J5-mediated protection, we compared the clinical, hematologic, bacteriologic, and serologic responses following an H. pleuropneumoniae infection in J5-immunized pigs with those following an H. pleuropneumoniae infection in nonimmunized control animals. As a result of an intranasal inoculation, all of the control animals and the J5-immunized animals were infected with H. pleuropneumoniae. However, while 80% (4 of 5) of the nonimmunized pigs died within 24 h as a result of the infection, no deaths occurred in the J5-immunized animals. In the immunized group, J5 titers dropped during the acute stages of the infection and rebounded to well above the prechallenge levels during convalescence. The J5 titer also increased in the single surviving control animal. These findings suggest that antibodies against common subsurface components of gram-negative bacterial cell walls correlate with protection from an otherwise lethal challenge of H. pleuropneumoniae but do not prevent infection. Important growth-phase-dependent antigenic changes have been recognized to occur during the growth of H. pleuropneumoniae in cultures (R. Nielson, Nord. Veterinaermed. 28:337-348, 1976). In a study of these changes and during an inquiry into the mechanism of J5 antibody-mediated protection, measured quantities of H. pleuropneumoniae were removed from a broth culture at hourly intervals and used to absorb hyperimmune equine J5 antiserum. Significantly greater amounts of J5-specific antibodies were absorbed during the log phase of bacterial growth than during the early or late phase. The availability of epitopes recognized by J5 antibodies appears to be closely related to the rate of bacterial multiplication. The results of these experiments suggest a mechanism of protection provided by increased immunity to E. coli J5 during gram-negative infections.
Role of Propeptide Glycan in Post-Translational Processing and Transport of Barley Lectin to Vacuoles in Transgenic Tobacco (1990)

Thea A. Wilkins, Sebastian Y. Bednarek, Natasha V. Raikhel, Role of Propeptide Glycan in Post-Translational Processing and Transport of Barley Lectin to Vacuoles in Transgenic Tobacco, The Plant Cell, Vol. 2, No. 4 (Apr., 1990), pp. 301-313
Catalyst-free water mediated reduction of nitroarenes using glucose as a hydrogen source (2013)

The highly chemo- and regioselctive reduction of nitroarenes to their corresponding amines has been carried out using D-glucose as a hydrogen source in H2O : DMSO (1 : 1). The method is simple, inexpensive, easily scaled-up and applicable to the preparation of different substituted anilines. Advantageously, the present method does not require any catalyst, elaborated experimental setup or the use of high-pressure equipment compared with conventional hydrogenation methods.
Bcr/Abl expression stimulates integrin function in hematopoietic cell lines. (1996)

Cell adhesion to the extracellular matrix is largely mediated by adhesion molecules of the integrin family and is often diminished upon oncogenic transformation. However, we show here that the chronic myelogenous leukemia oncogene Bcr/Abl has positive effects on VLA-4 and VLA-5 integrin function. The presence of Bcr/Abl in the GM-CSF- or IL-3-dependent hematopoietic cell lines MO7e, 32D, and BaF/3 enhanced cell binding to both soluble and immobilized fibronectin. The effect was due to enhanced function of the VLA-5 integrin fibronectin receptor and not to increased surface expression. In parallel, Bcr/Abl stimulated cell adhesion to the VLA-4 integrin ligand VCAM-1. Stimulation of VLA-5 function directly correlated with induction of Bcr/Abl tyrosine kinase activity in a temperature-sensitive kinase mutant. Thus, Bcr/Abl stimulates integrin-dependent cell adhesion, by a mechanism involving increased ligand binding, with the tyrosine kinase activity of Bcr/Abl likely playing a key role. Consistent with these results, hematopoietic precursor cells from chronic myelogenous leukemia patients also showed increased adhesion to fibronectin.
Co-repressor complexes and remodelling chromatin for repression (2000)

Recent progress identifies targeted chromatin remodelling by co-repressor complexes as being an integral component of transcriptional silencing. Here we discuss how chromatin structure and the basal transcriptional machinery are manipulated by the co-repressor complex containing the Mi-2 nucleosomal ATPase, the histone-binding protein RbAp48 and histone deacetylase and by the co-repressor complex containing SIN3, RbAp48 and histone deacetylase. Remarkably, both of these complexes also contain methyl-CpG-binding proteins. This observation provides a molecular mechanism to integrate DNA methylation fully into gene control in vertebrates.
Structure Guided Design and Kinetic Analysis of Highly Potent Benzimidazole Inhibitors Targeting the PDEδ Prenyl Binding Site (2014)

K-Ras is one of the most frequently mutated signal transducing human oncogenes. Ras signaling activity requires correct cellular localization of the GTPase. The spatial organization of K-Ras is controlled by the prenyl binding protein PDEδ, which enhances Ras diffusion in the cytosol. Inhibition of the Ras-PDEδ interaction by small molecules impairs Ras localization and signaling. Here we describe in detail the identification and structure guided development of Ras-PDEδ inhibitors targeting the farnesyl binding pocket of PDEδ with nanomolar affinity. We report kinetic data that characterize the binding of the most potent small molecule ligands to PDEδ and prove their binding to endogenous PDEδ in cell lysates. The PDEδ inhibitors provide promising starting points for the establishment of new drug discovery programs aimed at cancers harboring oncogenic K-Ras.
β43′: An Enhancer Displaying Neural-Restricted Activity Is Located in the 3′-Untranslated Exon of the Rat Nicotinic Acetylcholine Receptor β4 Gene (1997)

Members of a neuronal nicotinic acetylcholine receptor subunit gene cluster ordered beta4, alpha3, alpha5 in the vertebrate genome are expressed in highly restricted patterns in the PNS and CNS. Nothing is known, however, about the regulatory elements that control transcription of these genes in selected neuronal cell populations. We report here a novel enhancer, designated beta43', that is positioned in the beta4 3'-untranslated exon. It is composed of two nearly identical 37 bp direct repeats that are separated by 6 bp. Multimerization of the enhancer upstream of the alpha3 minimal promoter results in synergistic activation. Analysis in different cell types, including three neural lines and primary keratinocytes, shows that beta43' is preferentially active in the neural line PC12, which expresses all members of the cluster. Mobility shift assays reveal a cell-type-specific complex, which forms with the first repeat of the enhancer and PC12 extracts. Complexes co-migrating with the PC12 cell complex are not detected with extracts from other lines, which suggests that PC12 cells contain a differentially expressed factor that may be important for the restricted activity of beta43'. The cell-type-specific activity of the beta43' enhancer suggests that it is important for regulating restricted expression patterns of one or more clustered neuronal acetylcholine receptor genes. Its location within the beta4 gene may be a selective pressure for maintaining tight linkage of clustered neuronal nAchR genes.
A Step, Stride and Heading Determination for the Pedestrian Navigation System (2004)

Recently, several simple and cost-effective pedestrian navigation systems (PNS) have been introduced. These systems utilized accelerometers and gyros in order to determine step, stride and heading. The performance of the PNS depends on not only the accuracy of the sensors but also the measurement processing methods. In most PNS, a vertical impact is measured to detect a step. A step is counted when the measured vertical impact is larger than the given threshold. The numbers of steps are miscounted sometimes since the vertical impacts are not correctly measured due to inclination of the foot. Because the stride is not constant and changes with speed, the step length parameter must be determined continuously during the walk in order to get the accurate travelled distance. Also, to get the accurate heading, it is required to overcome drawbacks of low grade gyro and magnetic compass. This paper proposes new step, stride and heading determination methods for the pedestrian navigation system: A new reliable step determination method based on pattern recognition is proposed from the analysis of the vertical and horizontal acceleration of the foot during one step of the walking. A simple and robust stride determination method is also obtained by analyzing the relationship between stride, step period and acceleration. Furthermore, a new integration method of gyroscope and magnetic compass gives a reliable heading. The walking test is preformed using the implemented system consists of a 1-axis accelerometer, a 1-axis gyroscope, a magnetic compass and 16-bit microprocessor. The results of walking test confirmed the proposed method.
Kinetics and Reaction Engineering of Levulinic Acid Production from Aqueous Glucose Solutions (2012)

We have developed a kinetic model for aqueous-phase production of levulinic acid from glucose using a homogeneous acid catalyst. The proposed model shows a good fit with experimental data collected in this study in a batch reactor. The model was also fitted to steady-state data obtained in a plug flow reactor (PFR) and a continuously stirred tank reactor (CSTR). The kinetic model consists of four key steps: (1) glucose dehydration to form 5-hydroxymethylfurfural (HMF); (2) glucose reversion/degradation reactions to produce humins (highly polymerized insoluble carbonaceous species); (3) HMF rehydration to form levulinic acid and formic acid; and (4) HMF degradation to form humins. We use our model to predict the optimal reactor design and operating conditions for HMF and levulinic acid production in a continuous reactor system. Higher temperatures (180-200 °C) and shorter reaction times (less than 1 min) are essential to maximize the HMF content. In contrast, relatively low temperatures (140-160 °C) and longer residence times (above 100 min) are essential for maximum levulinic acid yield. We estimate that a maximum HMF carbon yield of 14% can be obtained in a PFR at 200 °C and a reaction time of 10 s. Levulinic acid can be produced at 57% carbon yield (68% of the theoretical yield) in a PFR at 149 °C and a residence time of 500 min. A system of two consecutive PFR reactors shows a higher performance than a PFR and CSTR combination. However, compared to a single PFR, there is no distinct advantage to implement a system of two consecutive reactors.
The role of folate receptor α in cancer development, progression and treatment: Cause, consequence or innocent bystander? (2006)

Folate receptor alpha (FRalpha) is a membrane-bound protein with high affinity for binding and transporting physiologic levels of folate into cells. Folate is a basic component of cell metabolism and DNA synthesis and repair, and rapidly dividing cancer cells have an increased requirement for folate to maintain DNA synthesis, an observation supported by the widespread use of antifolates in cancer chemotherapy. FRalpha levels are high in specific malignant tumors of epithelial origin compared to normal cells, and are positively associated with tumor stage and grade, raising questions of its role in tumor etiology and progression. It has been suggested that FRalpha might confer a growth advantage to the tumor by modulating folate uptake from serum or by generating regulatory signals. Indeed, cell culture studies show that expression of the FRalpha gene, FOLR1, is regulated by extracellular folate depletion, increased homocysteine accumulation, steroid hormone concentrations, interaction with specific transcription factors and cytosolic proteins, and possibly genetic mutations. Whether FRalpha in tumors decreases in vivo among individuals who are folate sufficient, or whether the tumor's machinery sustains FRalpha levels to meet the increased folate demands of the tumor, has not been studied. Consequently, the significance of carrying a FRalpha-positive tumor in the era of folic acid fortification and widespread vitamin supplement use in countries such as Canada and the United States is unknown. Epidemiologic and clinical studies using human tumor specimens are lacking and increasingly needed to understand the role of environmental and genetic influences on FOLR1 expression in tumor etiology and progression. This review summarizes the literature on the complex nature of FOLR1 gene regulation and expression, and suggests future research directions.