gebhart/patrepeval huggingface dataset:
Magnetoamplification in a Bipolar Magnetic Junction Transistor (2010)

We have demonstrated the first bipolar magnetic junction transistor using a dilute magnetic semiconductor. For an InMnAs p-n-p transistor magnetoamplification is observed at room temperature. The observed magnetoamplification is attributed to the magnetoresistance of the magnetic semiconductor InMnAs heterojunction. The magnetic field dependence of the transistor characteristics confirm that the magnetoamplification results from the junction magnetoresistance. To describe the experimentally observed transistor characteristics, we propose a modified Ebers-Moll model that includes a series magnetoresistance attributed to spin-selective conduction. The capability of magnetic field control of the amplification in an all-semiconductor transistor at room temperature potentially enables the creation of new computer logic architecture where the spin of the carriers is utilized.
Integrated Optics Modules Based Proposal for Quantum Information Processing, Teleportation, QKD, and Quantum Error Correction Employing Photon Angular Momentum (2016)

To address key challenges for both quantum communication and quantum computing applications in a simultaneous manner, we propose to employ the photon angular momentum approach by invoking the well-known fact that photons carry both the spin angular momentum (SAM) and the orbital angular momentum (OAM). SAM is associated with polarization, while OAM is associated with azimuthal phase dependence of the complex electric field. Given that OAM eigenstates are mutually orthogonal, in principle, an arbitrary number of bits per single photon can be transmitted. The ability to generate/analyze states with different photon angular momentum, by using either holographic or interferometric methods, allows the realization of quantum states in multidimensional Hilbert space. Because OAM states provide an infinite basis state, while SAM states are 2-D only, the OAM can also be used to increase the security for quantum key distribution (QKD) applications and improve computational power for quantum computing applications. The goal of this paper is to describe photon angular momentum based deterministic universal quantum qudit gates, namely, {generalized-X, generalized-Z, generalized-CNOT} qudit gates, and different quantum modules of importance for various applications, including (fault-tolerant) quantum computing, teleportation, QKD, and quantum error correction. For instance, the basic quantum modules for quantum teleportation applications include the generalized-Bell-state generation module and the QFT-module. The basic quantum module for quantum error correction and fault-tolerant computing is the nonbinary syndrome calculator module. The basic module for entanglement assisted QKD is either the generalized-Bell-state generation module or the Weyloperator-module. The possibility of implementing all these modules in integrated optics is discussed as well. Finally, we provide security analysis of entanglement assisted multidimensional QKD protocols, employing the proposed qudit modules, by taking into account the imperfect generation of OAM modes.
Botulinum toxin injections for treating neurogenic detrusor overactivity (2015)

Neurogenic detrusor overactivity (NDO) is a disorder that can cause high intravesical pressure, decreased capacity, decreased bladder compliance, and upper urinary system damage. The current treatment options for NDO are established on the basis of agents that block parasympathetic innervation of the detrusor and inhibit involuntary bladder contractions. Several side effects, such as dryness of mouth, constipation, dyspepsia, changes in visual accommodation, somnolence, and being unable to obtain consistently favorable results, caused by anticholinergic agents, which are frequently used for this purpose, decrease the patient's compliance to treatment. Procedures such as neuromodulation, auto-augmentation, and enterocystoplasty are surgical options, and they could be used as the last alternative. Thus, botulinum toxin (BTX) injections to the detrusor have been commonly performed in recent years and lead to satisfactory results. The mechanism of action of BTX in NDO is based on the principal of smooth muscle relaxation in the bladder by the transient inhibition of neuromuscular nerve signals. The aim is to decrease acetylcholine secretion by blocking presynaptic vesicles in the neuromuscular junction. When studies were evaluated, it was observed that BTX injections to the detrusor muscle are a necessary and effective option in patients with incontinence caused by NDO. This treatment option could be indicated in situations where anticholinergic agents are not effective or could not be tolerated, and it could be a valuable alternative to major surgical treatments. In this review, we evaluated the effectiveness and reliability of BTX in patients with NDO.
High-does nitric oxide induces apoptosis in HL-60 human myeloid leukemia cells (1996)

The treatment of human promyeloid leukemia cell line HL-60 cells with nitric oxide (NO) is associated with loss of proliferative apacity and induction of monocytic differentiation. The present results demonstrate that treatment of asynchronous human HL-60 leukemia cells with sodium nitroprusside (SNP), a NO generating agent, is also associated with oligonucleosomal DNA cleavage, including morphological changes, condensation of nuclear chromatin, nuclear fragmentation, and the apoptotic peak of propidium iodide-stained nuclei in flow cytometric analysis. SNP-induced apoptosis was associated with a steep inhibition of the proliferation of the cells in a time- and concentration- dependent manner. Endonucleolytic cleavage was prevented by addition of ZnSO4 or -acetylcysteine, a free radical-scavenging thiol compound. In addition, potassium ferricyanide, which is structurally similar to SNP except for the absence of a nitroso group, did not induce growth inhibition and apoptosis in HL-60 cells. However, the cells which did not undergo apoptosis displayed characteristics of monocytic differentiation, including spreading, vacuolization, expression of monocyte marker CD14, and increased capacity to produce hydrogen peroxide. Since it was of interest to examine whether NO also induce apoptosis in the cells which was undergone differentiation, DNA fragmentation was studied in the cells pretreated with phorbol ester, a monocytic differentiation agent, for 48 h and then monitored for 18 h in the presence of SNP. Flow cytometric analysis revealed no characteristic apoptotic pattern in phorbol 12-myristate 13 acetate-pretreated cells, implying that a more efficient defense mechanism may exist in the differentiating cells. Collectively, these data suggest that NO elaborated in the bone marrow microenvironment might have biphasic regulatory roles in normal and malignant hematopoietic programmed cell death in addition to its already known role as a cell differentiating molecule in HL-60 cells.
Principles and Design of a Novel Magnetic Force Mechanical Conditioning Bioreactor for Tissue Engineering, Stem Cell Conditioning, and Dynamic In Vitro Screening (2006)

Mechanical conditioning of cells and tissue constructs in bioreactors is an important factor in determining the properties of tissue being produced. Mechanical conditioning within a bioreactor environment, however, has proven difficult. This paper presents the theoretical basis, design, and initial results of a mechanical conditioning system for cell and tissue culture which is based on biocompatible magnetic micro- and nanoparticles acting as a remote stress mechanism without invasion of the sterile bioreactor environment.
Effect of rhPDGF-BB Delivery on Mediators of Periodontal Wound Repair (2006)

Growth factors such as platelet-derived growth factor (PDGF) exert potent effects on wound healing including the regeneration of tooth-supporting structures. This investigation examined the effect of the local delivery of PDGF-BB when combined with reconstructive periodontal surgery on local wound fluid (WF) levels of PDGF-AB, vascular endothelial growth factor (VEGF), and bone collagen telopeptide (ICTP) in humans with advanced periodontitis. Sixteen patients exhibiting localized periodontal osseous defects were randomized to one of three groups (beta-TCP carrier alone, beta-TCP + 0.3 mg/mL of recombinant human PDGF-BB [rhPDGF-BB], or beta-TCP + 1.0 mg/mL of rhPDGF-BB) and monitored for 6 months. WF was harvested and analyzed for PDGF-AB, VEGF, and ICTP WF levels. Teeth contralateral to the target lesions served as controls. Increased levels of VEGF in the WF was observed for all surgical treatment groups with the 1.0 mg/mL rhPDGF-BB group showing the most pronounced difference at 3 weeks in the AUC analysis versus control (p < 0.0001). PDGF-AB WF levels were increased for the carrier alone group compared to both rhPDGFBB groups. Low-dose rhPDGF-BB application elicited increases in ICTP at days 3-5 in the wound healing process, suggesting a promotion of bone turnover at early stages of the repair process (p < 0.02). These results demonstrate contrasting inducible expression patterns of PDGF-AB, VEGF, and ICTP during periodontal wound healing in humans.
Exogenous BH4/Bcl-2 Peptide Reverts Coronary Endothelial Cell Apoptosis Induced by Oxidative Stress (2004)

Our results indicate that TAT-BH4 peptide can protect endothelial cells from ROS-induced apoptosis.
HLA matching in allogeneic stem cell transplantation (2004)

HLA alleles are functionally relevant. Unrelated HCT can be optimized by comprehensive and precise donor-recipient allele matching. For patients with high-risk diseases who lack matched donors, use of donors with a single HLA mismatch may permit early treatment before disease progression.
High-performance liquid chromatography study of the pharmacokinetics of various spin traps for application to in vivo spin trapping (1999)

In vivo spin trapping is potentially a very useful tool to investigate the role of free radicals in physiologic processes and disease development. Unfortunately, knowledge on the stability and distribution of spin traps in living systems is limited. Therefore, in our study, we selected 11 acyclic and cyclic nitrone spin traps with diverse properties to determine their pharmacokinetics in mice. At varying times after intraperitoneal administration, we measured the concentration of the spin traps in the liver, heart, and blood. Our results showed that most spin traps were rapidly absorbed and were approximately evenly distributed throughout the mouse body. It was also found that most of the traps were relatively stable in vivo with more than half of the injected amount still available for spin trapping free radicals after an hour. Two of the 11 tested spin traps, however, decomposed after injection. These results indicate that for a successful in vivo spin trapping experiment, the stability of the spin trap is not of major concern, but the time course of distribution may be important.
Metabolic network design and engineering in Escherichia coli (2005)

This thesis is a study of metabolic engineering to design and engineer novel metabolic networks with improved metabolic processes that can increase product yield and enhance cellular properties. The succinate synthesis pathways in E. coli were chosen as the model system for network design and optimization. The ultimate goal is to create succinate production systems in E. coli that not only achieve the maximum theoretical yield of succinate, but also are highly efficient and robust.\nDifferent carbon sources with different oxidation states and transport systems, such as sorbitol and xylose, were used to address the requirements of cofactor NADH and precursor PEP in order to improve succinate synthesis.\nPhosphoenolpyruvate carboxylase and pyruvate carboxylase were coexpressed to drive the carbon flux toward succinate. Competing pathways of succinate synthesis, the lactate and acetate pathways, were also inactivated to increase more carbon flux toward succinate. The intracellular acetyl-CoA pool was increased by overexpressing pantothenate kinase to enhance the activity of PEPC and PYC in order to improve succinate production.\nNovel metabolic networks were designed and constructed to enable E. coli to produce succinate as a product under complete aerobic conditions. Since this is naturally not possible, extensive pathway manipulations had to be carried out.\nThe potential to produce succinate aerobically in E. coli would offer great advantages over anaerobic fermentation in terms of higher biomass generation, faster carbon throughput and product formation. After a series of pathway reconstructions, several aerobic succinate production systems were finally developed that could achieve the maximum theoretical succinate yield predicted by pathway modeling and simulation.\nFed batch reactor experiments were carried out for the most efficient succinate production system under aerobic conditions and the results demonstrated that it has a tremendously high capacity for succinate production. This system not only sustained fast productivity and maximal yield, it also produced succinate at a level never imagined feasible under aerobic conditions. Examination of the metabolite profiles, enzyme activities, and gene expression profiles showed that the metabolic processes of the most efficient aerobic succinate production system were more robust than the other systems.
Spectral and temporal characterization of a fused-quartz-microresonator optical frequency comb (2011)

We report on the fabrication of high-$Q$, fused-quartz microresonators and the parametric generation of a frequency comb with 36-GHz line spacing using them. We have characterized the intrinsic stability of the comb in both the time and frequency domains to assess its suitability for future precision metrology applications. Intensity autocorrelation measurements and line-by-line comb control reveal near-transform-limited picosecond pulse trains that are associated with good relative phase and amplitude stability of the comb lines. The comb's 36-GHz line spacing can be readily photodetected, which enables measurements of its intrinsic and absolute phase fluctuations.
Les programmes routiers a haute intensite de main-d'oeuvre : problemes et solutions - l'experience du Ghana (1996)

The literature gives two explanations for contractors' reluctance to adopt labor-based methods. First, contractors believe the cost of learning this new technology is high. Programs designed to promote labor-based methods have always included subsidized training to address this problem. This study argues that focusing on training often diverts attention away from more substantive problems inherent in adopting labor-based methods. Second, the more fundamental, some have argued that the cost of managing large labor forces, which is difficult to quantify in unit-cost comparisons, makes labor-based methods less competitive than equipment-based methods. This study shows that although labor-based methods can be financially more attractive to Ghanaian contractors, market-structure conditions thwart their use. Unit-rate cost comparisons of labor-based and equipment-based methods, therefore, cannot predict firm behavior. In particular, there is a very important distinction between small and large contractors. Labor-based methods are more attractive to small firms than to large firms. Small firms, because they are small, can supervise their sites themselves and thus find it easier to develop strategies to increase worker productivity and control truancy. Moreover, unlike large firms, small firms who wish to use equipment-based methods face high variable costs: they either own older, less-efficient equipment-with high maintenance costs-or must rent equipment at a high cost. Large firms, in contrast, find labor-based methods much less attractive. Large firms have high monitoring costs because of their size and because they often undertake many projects simultaneously.
Molecular epitope identification by limited proteolysis of an immobilized antigen-antibody complex and mass spectrometric peptide mapping. (1990)

Sequences of antigenic determinants were identified by limited proteolysis of peptide antigens bound to an immobilized monoclonal antibody and direct molecular weight determination of the monoclonal antibody-bound peptide fragments by 252Cf plasma desorption mass spectrometry. The epitope peptides to the monoclonal antibody h453 [Burger, R., Zilow, G., Bader, A., Friedlein, A. & Naser, W. (1988) J. Immunol. 141, 553-558] were isolated from immobilized antigen-antibody complexes by partial trypsin digestion. A synthetic eicosapeptide comprised of the C-terminal sequence of the human complement component polypeptide des-Arg77-C3a as well as guinea pig des-Arg78-C3a was used as an antigen. Conditions were developed under which trypsin specifically degraded the antigens without inactivation of the immobilized antibody. After proteolysis, epitope peptides were dissociated from the antibody with 4 M MgCl2. The antigenic peptides were purified by HPLC and identified by 252Cf plasma desorption mass spectrometry. The epitope recognized by h453 resides on the C-terminal tryptic peptides of human (residues 70-76) and guinea pig (residues 70-77) C3a. As an estimation of accuracy this method is able to provide, trypsin digestion of immune complexes caused cleavage of the antigen within a distance of two amino acid residues upstream from the epitope.
Molecular mechanisms and implications for infection of lipopolysaccharide variation in Neisseria (1995)

The lipopolysaccharides of the pathogenic Neisseria species are subject to structural variation owing to a combination of intrinsic changes in lipopolysaccharide (LPS) biosynthesis and external modification of the LPS molecule with sialic acid. This variation appears to control bacterial behaviour by altering their ability to interact with human cells and to evade host immune defences. This interconversion of LPS phenotypes, which is also observed during the natural infection, is probably due to environmental regulation of LPS biosynthesis superimposed on spontaneous changes in the DNA of distinct LPS loci. LPS variation may be a common strategy of mucosal pathogens to colonize and persist within the human host.
Removing pedestrians from Google street view images (2010)

Since the introduction of Google Street View, a part of Google Maps, vehicles equipped with roof-mounted mobile cameras have methodically captured street-level images of entire cities. The worldwide Street View coverage spans over 10 countries in four different continents. This service is freely available to anyone with an internet connection. While this is seen as a valuable service, the images are taken in public spaces, so they also contain license plates, faces, and other information information deemed sensitive from a privacy standpoint. Privacy concerns have been expressed by many, in particular in European countries. As a result, Google has introduced a system that automatically blurs faces in Street View images. However, many identifiable features still remain on the un-blurred person. In this paper, we propose an automatic method to remove entire pedestrians from Street View images in urban scenes. The resulting holes are filled in with data from neighboring views. A compositing method for creating “ghost-free” mosaics is used to minimize the introduction of artifacts. This yields Street View images as if the pedestrians had never been there. We present promising results on a set of images from cities around the world.
Structure of the full-length HPr kinase/phosphatase from Staphylococcus xylosus at 1.95 Å resolution: Mimicking the product/substrate of the phospho transfer reactions (2002)

The histidine containing phospho carrier protein (HPr) kinase/phosphatase is involved in carbon catabolite repression, mainly in Gram-positive bacteria. It is a bifunctional enzyme that phosphorylates Ser-46-HPr in an ATP-dependent reaction and dephosphorylates P-Ser-46-HPr. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The N-terminal domain has a betaalphabeta fold similar to a segment from enzyme I of the sugar phosphotransferase system and to the uridyl-binding portion of MurF; it is structurally organized in three dimeric modules exposed to form the propeller blades. Two unexpected phosphate ions associated with highly conserved residues were found in the N-terminal dimeric interface. The C-terminal kinase domain is similar to that of the Lactobacillus casei enzyme and is assembled in six copies to form the compact central hub of the propeller. Beyond previously reported similarity with adenylate kinase, we suggest evolutionary relationship with phosphoenolpyruvate carboxykinase. In addition to a phosphate ion in the phosphate-binding loop of the kinase domain, we have identified a second phosphate-binding site that, by comparison with adenylate kinases, we believe accommodates a product/substrate phosphate, normally covalently linked to Ser-46 of HPr. Thus, we propose that our structure represents a product/substrate mimic of the kinase/phosphatase reaction.
Heat shock protein 90 promotes epithelial to mesenchymal transition, invasion, and migration in colorectal cancer (2014)

Epithelial to mesenchymal transition (EMT), invasion, and motility are essential steps in colorectal cancer (CRC) metastasis regulated by HIF-1α and NF-κB. Since HSP90 activates HIF-1α and NF-κB, we hypothesized that inhibition of HSP90 leads to inhibition of HIF-1α and NF-κB resulting in inhibition of EMT, invasion, and motility. Treatment of colorectal cancer cell lines HT-29 and HCT-116 with ganetespib at 50 nM for 24 h inhibited EMT (downregulated vimentin and upregulated E-cadherin), matrigel invasion, and spheroid migration. Ganetespib treatment or HSP90 knockdown downregulated molecular pathways associated with EMT, invasion, and motility. The overexpression of HIF-1α or NF-κB resulted in increased EMT, invasion, and motility in both cell lines and these effects were inhibited by ganetespib. Similar effects were observed in animal xenografts treated with ganetespib. Taken together, our data demonstrate for the first time that inhibition of HSP90 downregulates both HIF-1α and NF-κB leading to inhibition of EMT, motility, and invasiveness in colorectal cancer.
Disappearance of certain acidic organelles (endosomes and Langerhans cell granules) accompanies loss of antigen processing capacity upon culture of epidermal Langerhans cells. (1990)

Freshly isolated epidermal Langerhans cells (LC) can actively process native protein antigens, but are weak in sensitizing helper T cells. During culture, when LC mature into potent immunostimulatory dendritic cells, T cell sensitizing capacity develops but antigen processing capacity is downregulated. Processing of exogenous antigens for class II-restricted antigen presentation involves acidic organelles. We used the DAMP-technique to monitor acidic organelles at the ultrastructural level in fresh, as well as cultured, mouse and human LC. We observed that the loss of antigen processing capacity with culture of LC was reflected by the disappearance of certain acidic organelles, namely endosomes (particularly early ones), and the hitherto enigmatic LC granules ("Birbeck Granules"). Our findings support the notion that endosomes are critical for antigen processing and suggest that LC granules might be involved as well.