gebhart/patrepeval huggingface dataset:
Affinity labeling of the allosteric activator site(s) of spinach leaf ADP-glucose pyrophosphorylase. (1988)

Pyridoxal-P has been shown to be an activator of the spinach leaf ADP-glucose pyrophosphorylase. It has a higher apparent affinity than the physiological activator 3-phosphoglycerate but only activates the enzyme activity 6-fold whereas 3-phosphoglycerate gives a 25-fold activation. Reductive phosphopyridoxylation of the spinach leaf enzyme results in enzyme having less dependence on the presence of activator for activity. Labeled pyridoxal-P is incorporated into both the 54- and 51-kilodalton subunits of the spinach leaf enzyme. The incorporation is inhibited by the presence of either 3-phosphoglycerate or the allosteric inhibitor, inorganic phosphate, thus suggesting that pyridoxal phosphate is covalently bound to the allosteric activator site. The pyridoxal phosphate is bound to an epsilon-amino group of a lysine residue. The phosphopyridoxylated enzyme is more resistant to phosphate inhibition than the unmodified form. The modified 51-kDa subunit has been digested with trypsin, and the peptide containing the labeled pyridoxal phosphate has been purified via high performance liquid chromatography and sequenced. Comparison of this sequence with the deduced amino acid sequence of a rice endosperm cDNA clone indicates that the putative allosteric site of the 51-kDa subunit is close to the carboxyl-terminal. This is in contrast to what had been demonstrated for the position of the activator site of the Escherichia coli ADP-glucose pyrophosphorylase which was shown to be close to the amino-terminal of the subunit.
Separation of Nanoparticles by Gel Electrophoresis According to Size and Shape (2007)

We demonstrate the separation of gold and silver nanoparticles according to their size and shape by agarose gel electrophoresis after coating them with a charged polymer layer. The separation is monitored optically using the size- and shape-dependent plasmon resonance of noble metal particles and confirmed by transmission electron microscopy (TEM). Electrophoretic mobilities are quantitatively explained by a model based on the Henry formula, providing a theoretical framework for predicting gel mobilities of polymer coated nanoparticles.
Immunophenotyping of the human bulge region: the quest to define useful in situ markers for human epithelial hair follicle stem cells and their niche (2008)

Since the discovery of epithelial hair follicle stem cells (eHFSCs) in the bulge of human hair follicles (HFs) an important quest has started: to define useful markers. In the current study, we contribute to this by critically evaluating corresponding published immunoreactivity (IR) patterns, and by attempting to identify markers for the in situ identification of human eHFSCs and their niche. For this, human scalp skin cryosections of at least five different individuals were examined, employing standard immunohistology as well as increased sensitivity methods. Defined reference areas were compared by quantitative immunohistochemistry for the relative intensity of their specific IR. According to our experience, the most useful positive markers for human bulge cells turned out to be cytokeratin 15, cytokeratin 19 and CD200, but were not exclusive, while beta1 integrin and Lhx2 IR were not upregulated by human bulge keratinocytes. Absent IR for CD34, connexin43 and nestin on human bulge cells may be exploited as negative markers. alpha6 integrin, fibronectin, nidogen, fibrillin-1 and latent transforming growth factor (TGF)-beta-binding protein-1 were expressed throughout the connective tissue sheath of human HFs. On the other hand, tenascin-C was upregulated in the bulge and may thus constitute a component of the bulge stem cell niche of human HFs. These immunophenotyping results shed further light on the in situ expression patterns of claimed follicular 'stem cell markers' and suggest that not a single marker alone but only the use of a limited corresponding panel of positive and negative markers may offer a reasonable and pragmatic compromise for identifying human bulge stem cells in situ.
Structure and motion in 3D and 2D from hybrid matching constraints (2007)

Abstract. Motion estimation has traditionally been approached either from a pure discrete point of view, using multi-view tensors, or from a pure continuous point of view, using optical-flow-based techniques. This paper builds upon the recent developments of hybrid matching constraints for motion estimation. These hybrid matching constraints are based on both corresponding feature points and the motion of these feature points, thus combining the advantages of both discrete and continuous methods. The main usage of these constraints is as a theoretical basis for filtering approaches to structure and motion recovery, enabling an update of a current motion estimate when a new image becomes available. One important feature is that the update formulas become linear in the motion parameters in the calibrated case, which is a major improvement compared to the standard discrete approach. Another advantage is that fewer points are needed in the update formula than in the traditional discrete case. We will present several hybrid matching constraints and derive their properties as well as show how they can be used for structure and motion estimation. First the hybrid bifocal and trifocal constraints will be treated, extending the traditional discrete epipolar and trifocal constraints. Then we will derive novel hybrid constraints for structure and motion recovery from a rigidly moving calibrated stereo-head. Finally, we will derive novel hybrid matching constraints for the 2D-case, enabling linear update of the motion parameters from a calibrated 2D-camera. 1
Transgenic Tobacco Plants Coexpressing the Agrobacterium tumefaciens iaaM and iaaH Genes Display Altered Growth and Indoleacetic Acid Metabolism (1992)

Transgenic tobacco (Nicotiana tabacum) SR1 plants expressing the Agrobacterium tumefaciens nopaline transferred DNA iaaH gene were transformed with a 35S-iaaM construct. The transformants displayed several morphological aberrations, such as adventitious root formation on stem and leaves, dwarfism, epinastic leaf growth, increased apical dominance, and an overall retardation in development. In addition, xylem lignification was higher than in wild type. Free and conjugated indoleacetic acid (IAA) levels were quantified by gas chromatography-multiple ion monitoring-mass spectrometry in leaves and internodes of wild-type plants and two transformed lines with different phenotypes. Both transformed lines contained elevated levels of free and conjugated IAA, which was associated with increased transcription of the iaaM gene. The line with the highest IAA level also had the most altered pattern of growth and development. These IAA-overproducing plants will provide a model system for studies on IAA metabolism, IAA interactions with other phytohormones, and IAA roles in regulating plant growth and development.
Theoretical Analysis of Reactivity Patterns in Diels–Alder Reactions of Cyclopentadiene, Cyclohexadiene, and Cycloheptadiene with Symmetrical and Unsymmetrical Dienophiles (2015)

The Diels-Alder reactions of cyclopentadiene, cyclohexadiene, and cycloheptadiene with a series of dienophiles were studied with quantum mechanical calculations (M06-2X density functional theory) and analyzed with the distortion/interaction model. The poor reactivities of cyclohexadiene and cycloheptadiene with dienophiles that give relatively synchronous transition states result from the substantial distortion required to achieve a transition state involving the formation of two bonds of the diene simultaneously. However, highly asynchronous or stepwise reactions result in less distortion of the diene and less differences in reactivities of different dienes. The transition state geometry of cyclopentadiene is less distorted in the asynchronous reaction with 1,1-dicyanoethylene compared to that with cis- and trans-1,2-dicyanoethylenes, which react through synchronous transition states.
Disruption of a brain transcription factor, NPAS3, is associated with schizophrenia and learning disability (2005)

A mother and daughter diagnosed with schizophrenia and schizophrenia co-morbid with mild learning disability, respectively, possess a balanced reciprocal translocation t(9,14)(q34.2;q13). Fluorescence in situ hybridization (FISH) with YAC, BAC, and cosmid probes indicate that the chromosome 14q13 breakpoint disrupts a large gene, NPAS3, encoding a CNS expressed transcription factor of the basic helix-loop-helix PAS (bHLH-PAS) gene family. By analogy with other members of the bHLH-PAS family, the putative truncated protein generated from the disrupted gene locus may have a dominant negative effect. The 14q13 region was previously identified by a linkage study of an inherited neurodegenerative condition, idiopathic basal ganglia calcification (IBGC or Fahr syndrome, OMIM:213600/606656), which is often co-morbid with psychosis. Sequencing of the gene in a third patient diagnosed with IBGC, schizophrenia, and mild learning disability did not reveal functional mutations.
Preparation of a Monoclonal Antibody Specific for Human Stanniocalcin. (1998)

Stanniocalcin (STC) is a glycoprotein hormone that was first identified in fish, where it regulates the calcium level in the body fluid. The cDNA which encodes human STC has recently been reported but the function has not been completely elucidated. We have prepared a monoclonal antibody against human STC using an analogous peptide of the putative antigenic domain in human STC; it was conjugated with keyhole limpet hemocyanin (KLH). The monoclonal antibody specifically stained the distal convoluted tubules in human kidney which is a putative target organ of STC. The ELISA was established using the monoclonal antibody and recombinant human STC as a standard antigen. The monoclonal antibody prepared in this study provides a useful tool for clinical studies of STC in human.
Mapping of DNase I-hypersensitive sites in the upstream DNA of human embryonic epsilon-globin gene in K562 leukemia cells. (1984)

We have mapped the DNase I-hypersensitive sites around the epsilon-globin and c-myc genes in two human leukemia cell lines K562 and HL60. In K562 cells in which the epsilon-globin gene is transcribed, six DNase I-hypersensitive sites are found in 6 kilobases (kb) of upstream flanking DNA; in HL60 cells in which the c-myc gene is expressed, two DNase I-hypersensitive sites are observed in 2 kb of upstream DNA. Neither the inactive epsilon-globin gene in HL60 cells nor the inactive c-myc gene in K562 cells displays such upstream DNase I-hypersensitive sites. Our results are consistent with previous studies that have shown DNase I-hypersensitive sites within 1 kb of the 5' end of other expressed genes. In addition, we have found sites displaying even more DNase I sensitivity further upstream of expressed epsilon-globin and c-myc genes. Among the six DNase I-hypersensitive sites of the expressed epsilon-globin gene in K562 cells, the most sensitive site is located about 6 kb upstream of the epsilon-globin gene. When correlated with the DNA sequence upstream of the epsilon-globin gene, this site was found to correspond to a region that contains a stretch of 28 consecutive Ts, three enhancer core-like sequences, and a stretch of consecutive (C-A)15(T-A)6 alternating purine and pyrimidine bases. These findings suggest the possibility that an enhancer element for epsilon-globin gene expression resides within this DNase I-hypersensitive site.
Do Polyamines Have Roles in Plant Development? (1989)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
The role of hepatocyte growth factor and its receptor c‐met in interactions between lymphocytes and stromal cells in secondary human lymphoid organs (2001)

Secondary lymphoid tissue consists of two major populations of cells: lymphoid cells and stromal cells. It is generally accepted that these two cell populations influence each other however, factors mediating these processes are poorly understood. In this paper we characterize one of the possible means of communication between stroma and lymphocytes namely through hepatocyte growth factor/c-met receptor interactions. Hepatocyte growth factor (HGF) is a pleiotropic factor that is mainly produced by mesenchymal cells and acts on cells of epithelial origin which express the HGF receptor c-met. Here we demonstrate that biologically active HGF is constitutively produced by fibroblast-like stromal cells from human lymphoid tissues. HGF secretion from stromal cells was increased by direct contact with activated T cells. This increase was abrogated when activated T cells were separated physically from stromal cells. Using neutralizing antibody or cytokine inhibitors we provide evidence that enhancement of HGF production was due to additive effects of T-cell membrane-associated interleukin-1 (IL-1) and CD40 ligand. Finally, we also show that B lymphocytes activated with CD40L/anti-mu or phorbol 12-myristate 13-acetate (PMA) express c-met receptor. Co-culture of activated B cells with stromal cells from spleen leads to enhanced production of immunoglobulins. This can be partially inhibited by introduction of anti-HGF neutralizing antibodies to the culture system. Substitution of stromal cells with recombinant HGF did not produce enhancement of immunoglobulin secretion. On the other hand stimulation of c-met receptor with HGF leads to enhanced integrin-mediated adhesion of activated B cells to vascular cell adhesion molecule (VCAM-1) and fibronectin. On the basis of the above experiments we conclude that HGF production by fibroblast-like stromal cells can be modulated by activated T cells, thus providing signals for the regulation of adhesion of c-met expressing B cells to extracellular matrix proteins. In this way HGF may indirectly influence immunoglobulin secretion by B cells.
Operating Manual for Ultrashort Pulse Laser System-II (1060 nm Operation) (1997)

Abstract : This report describes the ultrashort pulse laser system, USP-II, installed in the research laboratory and which is comprised of components manufactured by both Spectra-Physics and Coherent Laser Group. This laser system uses state of the art laser technology to provide very high energy single pulses in the visible and near IR spectra for pulsewidths near 100 femtoseconds This report describes in detail the turn-on and operating procedures so that the system operator can bring it up to specificationc and fine-tune the subsystems to give optimum pulsewidth and energy pulse outputs. The basic system has been configured to operate on a single 4 by 12 ft optical bench with some diagnostic instruments permanently mounted to the table. The major subsystems which comprise the USP-II are described briefly as to their operating characteristics and how the output characteristics of each unit affects the output of the following unit. This report is not designed to replace the operating procedures of each subsystem but rather to describe how the complete system works in unison. Each subsystem is described ir the same order as required to turn on the system and reach specified outputs. The theory of operation is incorporated into this turn-On procedure along with optimizing procedures. If any subsystem output does not meet its specifications, the operator is referred to the manufacturer's operating and maintenance procedures for that particular laser. Correct output signals for each laser are described and optimizing procedures for obtaining these optimum levels are also described. This report should be adequate for the daily operation of the system if no problems occur within any subsystem.
A genetic linkage map of human chromosome 21: analysis of recombination as a function of sex and age. (1992)

A genetic linkage map of human chromosome 21 has been constructed using 22 anonymous DNA markers and five complementary DNAs (cDNAs) encoding the amyloid beta protein precursor (APP), superoxide dismutase 1 (SOD1), the ets-2 proto-oncogene (ETS2), the estrogen inducible breast cancer locus (BCEI), and the leukocyte antigen, CD18 (CD18). Segregation of RFLPs detected by these DNA markers was traced in the Venezuelan Reference Pedigree (VRP). A comprehensive genetic linkage map consisting of the 27 DNA markers spans 102 cM on the long arm of chromosome 21. We have confirmed our initial findings of a dramatically increased rate of recombination at the telomere in both females and males and of significantly higher recombination in females in the pericentromeric region. By comparing patterns of recombination in specific regions of chromosome 21 with regard to both parental sex and age, we have now identified a statistically significant downward trend in the frequency of crossovers in the most telomeric portion of chromosome 21 with increasing maternal age. A less significant decrease in recombination with increasing maternal age was observed in the pericentromeric region of the chromosome. These results may help in ultimately understanding the physical relationship between recombination and nondisjunction in the occurrence of trisomy 21.
Electrical stimulation promotes the angiogenic potential of adipose-derived stem cells (2019)

Autologous fat transfer (AFT) is limited by post-operative volume loss due to ischemia-induced cell death in the fat graft. Previous studies have demonstrated that electrical stimulation (ES) promotes angiogenesis in a variety of tissues and cell types. In this study we investigated the effects of ES on the angiogenic potential of adipose-derived stem cells (ASC), important progenitor cells in fat grafts with proven angiogenic potential. Cultured human ASC were electrically stimulated for 72 hours after which the medium of stimulated (ES) and non-stimulated (control) ASC was analysed for angiogenesis-related proteins by protein array and ELISA. The functional effect of ES on angiogenesis was then assessed in vitro and in vivo. Nine angiogenesis-related proteins were detected in the medium of electrically (non-)stimulated ASC and were quantified by ELISA. The pro-angiogenic proteins VEGF and MCP-1 were significantly increased following ES compared to controls, while the anti-angiogenic factor Serpin E1/PAI-1 was significantly decreased. Despite increased levels of anti-angiogenic TSP-1 and TIMP-1, medium of ES-treated ASC significantly increased vessel density, total vessel network length and branching points in chorio-allantoic membrane assays. In conclusion, our proof-of-concept study showed that ES increased the angiogenic potential of ASC both in vitro and in vivo.
Exact closed form formula for partial mutual inductances of on-chip interconnects (2003)

In this paper we propose a new exact closed form mutual inductance equation for on-chip interconnects. We express the mutual inductance between two parallel rectangular conductors as a weighted sum of self-inductances. We do not place any restrictions on the alignment of the two parallel rectangular conductors. Moreover they could be co-planar or reside on different layers. Most important, experimental results show that our formula is numerically more stable than that derived by Hoer and Love (1965) for long parallel onchip interconnects.
Moving Beyond Adsorption Capacity in Design of Adsorbents for CO2 Capture from Ultradilute Feeds: Kinetics of CO2 Adsorption in Materials with Stepped Isotherms (2018)

Amine-functionalized metal organic frameworks (MOFs) such as Mg2(dobpdc) have shown some of the highest capacities for CO2 capture under simulated direct air capture (DAC) conditions, i.e., at a CO2 partial pressure at 0.4 mbar. The most widely studied materials of this kind have adsorption isotherms whose shape is controlled by the material's underlying cooperative adsorption mechanism for CO2. Previous analyses of these materials, however, have focused primarily on equilibrium adsorption. Here, we study adsorption of CO2 in amine-functionalized MOFs under ultradilute conditions relevant to DAC using a packed bed breakthrough system to understand the challenges of using these materials in practical separations. By examining the effects of flow rate, temperature, and CO2 concentration on the observed breakthrough profiles, we show how the isotherm shape, mass transfer resistances and adsorption/desorption kinetics impact the system's performance. An empirical model for the packed bed that accounts for the cooperative reaction mechanism for adsorption of CO2 in N,N′-dimethyl ethylene diamine (MMEN)–Mg2(dobpdc) is developed. The kinetics of CO2 adsorption at CO2 concentrations of 400 ppm are characterized through an Avrami model, while at higher CO2 concentrations, a kinetic model based on a Michaelis–Menten expression is more successful. It is also suggested that, at low concentrations, mass transfer rate is limited by cooperative insertion of CO2. Overall, this work has identified the system performance (i.e., rate of CO2 extraction, CO2 capture fraction, and breakthrough curve types) for different feed concentrations of CO2. Critically, this work shows that the use of materials with stepped isotherm for applications such as DAC has some fundamental challenges that cannot be addressed by efforts that focus solely on modifying the overall equilibrium adsorption capacity or swing capacity.
The Functional Association of Polymyxin B with Bacterial Lipopolysaccharide Is Stereospecific:  Studies on Polymyxin B Nonapeptide (2000)

The Gram-negative bacterial endotoxin lipopolysaccharide (LPS) is a major inducer of sepsis. The natural cyclic peptide polymyxin B (PMB) is a potent antimicrobial agent, albeit highly toxic, by virtue of its capacity to neutralize the devastating effects of LPS. However, the exact mode of association between PMB and LPS is not clear. In this study, we have synthesized polymyxin B nonapeptide, the LPS-binding cyclic domain of PMB, and its enantiomeric analogue and studied several parameters related to their interaction with LPS and their capacity to sensitize Gram-negative bacteria toward hydrophobic antibiotics. The results suggest that whereas the binding of the two enantiomeric peptides to E. coli and to E. coli LPS is rather similar, functional association with the bacterial cell is stereospecific. Thus, the L-enantiomer is capable of synergism with the hydrophobic antimicrobial drugs novobiocin and erythromycin, whereas the D-enantiomer is devoid of such activity. The potential of understanding and consequently utilizing the PMB-LPS association for novel, nontoxic PMB-derived drugs is discussed.
The tumor suppressor gene DAPK2 is induced by the myeloid transcription factors PU.1 and C/EBPα during granulocytic differentiation but repressed by PML-RARα in APL (2013)

DAPK2 is a proapoptotic protein that is mostly expressed in the hematopoietic tissue. A detailed DAPK2 expression analysis in two large AML patient cohorts revealed particularly low DAPK2 mRNA levels in APL. DAPK2 levels were restored in APL patients undergoing ATRA therapy. PML-RARA is the predominant lesion in APL causing transcriptional repression of genes important for neutrophil differentiation. We found binding of PML-RARA and PU.1, a myeloid master regulator, to RARA and PU.1 binding sites in the DAPK2 promoter. Ectopic expression of PML-RARA in non-APL, as well as knocking down PU.1 in APL cells, resulted in a significant reduction of DAPK2 expression. Restoring DAPK2 expression in PU.1 knockdown APL cells partially rescued neutrophil differentiation, thereby identifying DAPK2 as a relevant PU.1 downstream effector. Moreover, low DAPK2 expression is also associated with C/EBPα-mutated AML patients, and we found C/EBPα-dependent regulation of DAPK2 during APL differentiation. In conclusion, we identified first inhibitory mechanisms responsible for the low DAPK2 expression in particular AML subtypes, and the regulation of DAPK2 by two myeloid transcription factors underlines its importance in neutrophil development.