gebhart/patrepeval huggingface dataset:
CD114: A New Member of the Neural Crest-Derived Cancer Stem Cell Marker Family (2016)

The neural crest is a population of cells in the vertebrate embryo that gives rise to a wide range of tissues and cell types, including components of the peripheral nervous system and the craniofacial skeleton as well as melanocytes and the adrenal medulla. Aberrations in neural crest development can lead to numerous diseases, including cancers such as melanoma and neuroblastoma. Cancer stem cells (CSCs) have been identified in these neural crest-derived tumors, and these CSCs demonstrate resistance to treatment and are likely key contributors to disease relapse. Patients with neural crest-derived tumors often have poor outcomes due to frequent relapses, likely due to the continued presence of residual treatment-resistant CSCs, and therapies directed against these CSCs are likely to improve patient outcomes. CSCs share many of the same genetic and biologic features of primordial neural crest cells, and therefore a better understanding of neural crest development will likely lead to the development of effective therapies directed against these CSCs. Signaling through STAT3 has been shown to be required for neural crest development, and granulocyte colony stimulating factor (GCSF)-mediated activation of STAT3 has been shown to play a role in the pathogenesis of neural crest-derived tumors. Expression of the cell surface marker CD114 (the receptor for GCSF) has been identified as a potential marker for CSCs in neural crest-derived tumors, suggesting that CD114 expression and function may contribute to disease relapse and poor patient outcomes. Here we review the processes of neural crest development and tumorigenesis and we discuss the previously identified markers for CSC subpopulations identified in neural crest tumors and their role in neural crest tumor biology. We also discuss the potential for CD114 and downstream intracellular signaling pathways as potential targets for CSC-directed therapy. J. Cell. Biochem. 118: 221-231, 2017. © 2016 Wiley Periodicals, Inc.
Dynamics and functional differences between dendroaspin and rhodostomin: Insights into protein scaffolds in integrin recognition (2012)

Dendroaspin (Den) and rhodostomin (Rho) are snake venom proteins containing a PRGDMP motif. Although Den and Rho have different 3D structures, they are highly potent integrin inhibitors. To study their structure, function, and dynamics relationships, we expressed Den and Rho in Pichia pastoris. The recombinant Den and Rho inhibited platelet aggregation with the K(I) values of 149.8 and 83.2 nM. Cell adhesion analysis showed that Den was 3.7 times less active than Rho when inhibiting the integrin αIIbβ3 and 2.5 times less active when inhibiting the integrin αvβ3. In contrast, Den and Rho were similarly active when inhibiting the integrin α5β1 with the IC₅₀ values of 239.8 and 256.8 nM. NMR analysis showed that recombinant Den and Rho have different 3D conformations for their arginyl-glycyl-aspartic acid (RGD) motif. However, the comparison with Rho showed that the docking of Den into integrin αvβ3 resulted in a similar number of contacts. Analysis of the dynamic properties of the RGD loop in Den and Rho showed that they also had different dynamic properties. These results demonstrate that protein scaffolds affect the function, structure, and dynamics of their RGD motif.
A New Polytopic Bis-diazacrown-ether-polypyridine Ligand and Its Complexes with Zn(II) Salts and Mononuclear and Dendritic Ru(II) Precursors. Synthesis, Absorption Spectra, Redox Behavior, and Luminescence Properties (2001)

The new polytopic receptor 1 containing two terpyridine, one phenanthroline, and two diazacrown-ether sites has been prepared using a modular approach. Such a new species contains several pieces of information in its structure which can be processed by different metal ions to give different supramolecular inorganic architectures. Actually, reaction of 1 with Zn(CH(3)COO)(2) in methanol, and subsequent anion exchange, afforded the intramolecular ring-type [Zn(1)](2+) complex, which appears to be formed by a self-assembling reaction. A different synthetic approach, stepwise synthesis, allowed us to synthesize the two multicomponent compounds [(bpy)(2)Ru(mu-1)Ru(bpy)(2)](4+) (Ru2; bpy = 2,2'-bipyridine) and [[(bpy)(2)Ru(mu-2,3-dpp)](2)Ru(mu-1)Ru[(mu-2,3-dpp)Ru(bpy)(2)](2)](12+) (Ru6; 2,3-dpp = 2,3-bis(2-pyridyl)pyrazine). The absorption spectra and luminescence properties of 1 and [Zn(1)](2+) are dominated by pi --> pi transitions and excited states. The absorption spectra of the ruthenium compounds are dominated by ligand-centered (LC) bands in the UV region and metal-to-ligand charge-transfer (MLCT) bands in the visible. The latter compounds undergo several reversible metal-centered oxidations and ligand-centered reductions in the potential window investigated (-2.0/+2.0 V versus SCE) and exhibit MLCT luminescence in both acetonitrile fluid solution at room temperature and in butyronitrile rigid matrix at 77 K. Both the redox and photophysical properties of Ru2 and Ru6 can be assigned to specific subunits of the multicomponent structures. The data indicate that the [Ru(bpy)(2)](2+) and the dendritic [Ru[(mu-2,3-dpp)Ru(bpy)(2)](2)](6+) fragments appended to the polytopic 1ligands behave as independent components of the multicomponent arrays.
Dioxygen Binds End-On to Mononuclear Copper in a Precatalytic Enzyme Complex (2004)

Copper active sites play a major role in enzymatic activation of dioxygen. We trapped the copper-dioxygen complex in the enzyme peptidylglycine-alphahydroxylating monooxygenase (PHM) by freezing protein crystals that had been soaked with a slow substrate and ascorbate in the presence of oxygen. The x-ray crystal structure of this precatalytic complex, determined to 1.85-angstrom resolution, shows that oxygen binds to one of the coppers in the enzyme with an end-on geometry. Given this structure, it is likely that dioxygen is directly involved in the electron transfer and hydrogen abstraction steps of the PHM reaction. These insights may apply to other copper oxygen-activating enzymes, such as dopamine beta-monooxygenase, and to the design of biomimetic complexes.
CCA Security for Self-Updatable Encryption: Protecting Cloud Data When Clients Read/Write Ciphertexts. (2015)

Self-updatable encryption (SUE) is a new kind of public-key encryption, motivated by cloud com-puting, which enables anyone (i.e. cloud server with no access to private keys) to update a past ciphertext to a future ciphertext by using a public key. The main applications of SUE is revocable-storage attribute-based encryption (RS-ABE) that provides an efficient and secure access control to encrypted data stored in cloud storage. In this setting, there is a new threat such that a revoked user still can access past cipher-texts given to him by a storage server. RS-ABE solves this problem by combining user revocation and ciphertext updating functionalities. The mechanism was designed with semantic security (CPA). We have noticed, however, that when anyone can contribute ciphertexts (as this is a public key setting), and when clients have access to some ciphertexts (encrypted data) at storage servers (since we do not exclude this possibility), then, when in order to retrieve plaintexts they employ decryption service (i.e., probe crypto servers in the cloud), this service may be sensitive to Chosen Ciphertext Attacks (CCA) when the adversary plays as a client. Next notice that when considering CCA, the RS-ABE functionality, by definition, allows certain malleability, namely, updating of messages by anyone (e.g., storage servers) over time. This seems, at first, anathema to this security notion, and this has to be
Phacoemulsification and Opaque Intraocular Lens Implantation for the Treatment of Intractable Diplopia (2000)

Intractable diplopia secondary to paralytic strabismus may be treated with the occlusion of the affected eye. Established treatments include occlusion with a patch, opaque spectacles or contact lenses, and performing upper lid lowering procedures or tarsorrhaphies. Two cases are presented in which intractable diplopia was resolved by performing clear lens phacoemulsification and the insertion of an opaque intraocular lens. Both patients reported a resolution of their diplopia having been dissatisfied with other forms of treatment. Although opaque intraocular lens insertion is not recommended as the initial treatment of choice in such cases, it offers a valuable treatment option for those patients in whom other forms of therapy have failed.
Flux maximizing geometric flows (2002)

Several geometric active contour models have been proposed for segmentation in computer vision and image analysis. The essential idea is to evolve a curve (in 2D) or a surface (in 3D) under constraints from image forces so that it clings to features of interest in an intensity image. Recent variations on this theme take into account properties of enclosed regions and allow for multiple curves or surfaces to be simultaneously represented. However, it is still unclear how to apply these techniques to images of narrow elongated structures, such as blood vessels, where intensity contrast may be low and reliable region statistics cannot be computed. To address this problem, we derive the gradient flows which maximize the rate of increase of flux of an appropriate vector field through a curve (in 2D) or a surface (in 3D). The key idea is to exploit the direction of the vector field along with its magnitude. The calculations lead to a simple and elegant interpretation which is essentially parameter free and has the same form in both dimensions. We illustrate its advantages with several level-set-based segmentations of 2D and 3D angiography images of blood vessels.
<title>Evaluation and comparison of the pattern-transfer-induced image placement distortions on e-beam projection lithography masks</title> (2001)

Masks for electron projection lithography require the use of thin membrane structures due tot he short scattering range of electrons in solid materials. The two leading mask formats for electron projection lithography are the continuous membrane scatterer mask and the stencil mask. The reduced mechanical stability of the membranes used for electron projection masks relative to conventional optical masks leads to increased levels of process induced image placement distortions. This paper evaluates the image placement distortions due to the pattern transfer processes on the continuous membrane mask format. Image placement was measured from both a cross-mask and intramembrane perspective to evaluate the effects of different patterns, pattern densities and density gradients on the observed image placement and the experimental results obtained were then compared to those predicted by finite element modeling.
Carbon Nanotubes in the Liquid Phase: Addressing the Issue of Dispersion (2012)

The inherent size and hollow geometry with extraordinary electronic and optical properties make carbon nanotubes (CNTs) promising building blocks for molecular or nanoscale devices. Unfortunately, their hydrophobic nature and their existence in the form of agglomerated and parallel bundles make this interesting material inadequately soluble or dispersible in most of the common solvents, which is crucial to their processing. Therefore, various ingenious techniques have been reported to disperse the CNTs in various solvents with different experimental conditions. However, by analyzing the published scientific research articles, it is evident that there is an important issue or misunderstanding between the term "dispersion" and "solubilization". As a result many researchers use the terms interchangeably, particularly when stating the interaction of CNTs with liquids, which causes confusion among the readers, students, and researchers. In this article, this fundamental issue is addressed in order to give basic insight to the researchers who are working with CNTs, as well as to the scientists who deal with nano-related research domains.
Elastic properties of diffusion-limited aggregates (1985)

A transfer matrix method has been used to investigate the power law dependence of the effective elastic moduli of a two-dimensional diffusion-limited aggregate on the size l of the aggregate. Scaling exponents have been found to depend on the type of applied deformation. For stretching along the direction of growth the elastic modulus scales as l-2.2+or-0.2, while for deformations in the direction perpendicular to the direction of growth it is proportional to l-2.8+or-0.2.
Disinfection of Needleless Catheter Connectors and Access Ports With Alcohol May Not Prevent Microbial Entry: The Promise of a Novel Antiseptic-Barrier Cap (2006)

The findings of this study show that, if the membranous septum of a needleless luer-activated connector is heavily contaminated, conventional disinfection with 70% alcohol does not reliably prevent entry of microorganisms. In contrast, the antiseptic-barrier cap provided a high level of protection, even in the presence of very heavy contamination. This novel technology deserves to be studied in a clinical trial.
Examination of the Traumatized Patient, Wound Healing and Treatment Principles (2000)

This chapter contains section titled: Examination of the Traumatized Patient Wound Healing and Treatment Principles
Synthesis of organic nitriles from esters over zeolites and modified SiO 2 -Al 2 O 3 catalysts (1996)

Benzonitrile and acetonitrile are synthesized from ethylbenzoate and ethylacetate over HZSM-5 (Si/Al=30, 150 and 280), HY, H-mordenite, SAPO (TPA-40 type) and modified SiO 2 -Al 2 O 3 catalysts. The typical maximum yields of benzonitrile obtained were 85.4 and 97.1% over HZSM-5 (30) and ThO 2 -SiO 2 -Al 2 O 3 catalysts; respectively. The yields of acetonitrile were 80.6 and 79.4% over HZSM-5 (30) and HY catalysts, respectively.
Characterization of Spherical Oxide Filler Synthsized by Spray Pyrolysis (2006)

Spherical SiO2 and Al2O3 fillers were synthesized by ultrasonic spray pyrolysis. The particles characteristics of these fillers were studied by SEM, TEM, XRD and a pycnometer. Crysalline state of both as-prepared fillers was amorphous. The morphology of SiO2 fillers was maintained at up to 900°C . The morphology of SiO2 fillers was changed to irregular shape after crystallization of cristobalite at 1100°C. On the other hand, the morphology of Al2O3 was retained after crystallization of α-alumina at 1100°C. By the surface modification of these fillers with a silane coupling agent, the composite materials of epoxy resin and fillers was successfully prepared. The Vickers hardness and thermal conductivity of composite materials were investigated. The use of fillers with a broad particle size distribution and spherical morphology led to an improvement in the packing fraction of fillers, Vickers hardness and thermal conductivity.
GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis (2020)

Our work not only demonstrates that complex genomics analyses can be performed on lightweight computing systems, but also benefits High-Performance Computing (HPC). The associated source code for f5c along with GPU optimised ABEA is available at https://github.com/hasindu2008/f5c .
An In Vitro Perfusion System to Enhance Outflow Studies in Mouse Eyes (2016)

We engineered a unique perfusion system that can accurately measure changes in C. We then used the system to show that NOS3 and CAV1 are key components of mechanism(s) controlling outflow.
Corrosion Performance of Hybrid Epoxy Resin Coatings withElectrochemical impedance Spectroscopy (2012)

A hybrid epoxy resin one pack emulsion was synthesized with conventional emulsion polymerization technique. Electrochemical impedance tests were applied to steel specimens coated with hybrid epoxy and tested after immersion in 3.5% Nacl solution for different periods at room temperature. Results taken from Nyquist and Bode plots and as were analyzed by means of software provided with the instrument. Specimens were examined under scanning electron microscope shows a clear rupture and degradation in hybrid epoxy coatings
Multiple sclerosis: some epidemiological clues to etiology. (1975)

The diagnosis of multiple sclerosis is frequently made with undue haste and without a firm basis. A false positive diagnosis is made in about 20 to 30% of the cases originally labeled as multiple sclerosis. The proportion of false positive diagnosis is probably still higher in countries where this disease is less frequent. An exhaustive investigation (neurological, clinical, neurorradiological, isotopic, etc.) is necessary before accepting such a diagnosis. This is particularly important because many of the lesions which can masquerade as multiple sclerosis are amenable to medical or surgical treatment. The prevalence of multiple sclerosis varies widely throughout the world, with a very definite preference for the white race. This difference seems to be caused, at least in part, by dietary habits. Lack of breastfeeding and excessive consumption of cow's milk during infancy is postulated as an important factor in the appearance of multiple sclerosis later in life. A lack of essential fatty acids (and may be of certain minerals and vitamins) in such a diet during pregnancy and childhood may result in the synthesis of abnormally unstable myelin. This underlying deficiency in myelin composition may be the substrate on which immunological factors act to produce the disease. The breakdown of this unstable myelin may be initiated by a variety of factors; natural decay of abnormally weak bonds in proteolipids, viral infection, immune reactions or even trauma. Immune reactions can explain, at least in part, the onset and the course of the disease, and probably immunodeficiency is the most important factor. Demyelination, once it starts, may continue until all abnormally formed myelin is destroyed, or until the building up of immunological defenses can stop the process. It follows from this that prevention of multiple sclerosis should be based mainly on dietic measures which ensure a sufficient supply of essential fatty acids, minerals and vitamins, during pregnancy and childhood. Breast feeding is probably the most important preventive factor. Skin pigmentation, either natural or from exposition to sunshine also seems to act as a preventive factor, and its mode of action deserves further investigation. Treatment of multiple sclerosis should be based on the improvement of immunological defenses, the elimination of possible allergens and saturated fats from the diet, and on the administration of sufficient amounts of essential fatty acids and of other various elements.
The M2 autoantigen of central nervous system myelin, a glycoprotein present in oligodendrocyte membrane. (1986)

Autoantibodies with in-vitro demyelinating capacity induced in Hartley and strain 13 guinea pigs with homologous central nervous system (CNS) tissue were used to characterize the target autoantigen M2. Using the Dot Immunobinding technique, M2 was found to be a component of CNS myelin different from basic protein (BP) and from cerebroside. The expression of M2 on oligodendrocytes, cells known to produce CNS myelin, also confirmed that M2 was a component of CNS myelin. Furthermore, the autoradiography of immunoprecipitates formed with radiolabelled guinea pig myelin and analysed in sodium dodecyl sulphate gels showed that M2 was specific to CNS myelin and absent in peripheral nervous system (PNS) myelin. On electrophoresis M2 appeared as two CNS myelin protein bands at the 27 and 54 KD molecular weight levels, distinct from the major protein bands of proteolipid and BP. M2 bands were of glycoprotein nature, as was demonstrated by affinity chromatography of CNS myelin on wheat germ agglutinin (WGA)-Sepharose. A monoclonal antibody induced by BP-free CNS glycoproteins recognized the same bands as anti-M2 serum in guinea pig CNS myelin. This would imply that both M2 bands share common determinants. M2 bands similar to the above in guinea pig were also shown in rat, rabbit and bovine CNS myelin with guinea pig antibodies. The same type of anti-M2 antibodies were induced in rabbit immunized with homologous CNS tissue. Although only a minor component of myelin, M2 is strongly immunogenic compared to BP. M2 antigen could thus be the target of chronic demyelinating processes such as experimental allergic encephalomyelitis.
Statistical Analysis on High Strain Rate Tensile Strength of T700 Carbon Fiber (2007)

Tensile mechanical behavior of T700 fiber bundles have been studied in the strain rate range from 0.001 l/s to 1000 l/s and complete stress strain curves were obtained. Results show that both ultimate strength and failure strain are strain rate insensitive, and T700 carbon fiber can be regarded as strain rate insensitive materials. On basis of the fiber bundles model and the statistic theory of fiber strength, a statistical constitutive model based on Weibull distribution function has been developed to describe mechanical behavior of T700 fiber. And a method for determine the statistic parameters of fibers by tensile tests of fiber bundles is established, too. The simulated stress strain curves from the model are in good agreement with the test data. Simulated results show that the strength of T700 fiber can be described by single Weibull distribution function.
Fibrin Glue and Polyglycolic Acid Nonwoven Fabric as a Biocompatible Dural Substitute (2006)

Dural substitute created using fibrin glue and polyglycolic acid fabric is advantageous in that it exerts excellent closing ability without requiring suture and can replace biological tissue without causing incompatibility.
Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin (2007)

Abstract The rapid evolution of the H5N1 serotype of avian influenza has been explained by a mechanism involving the selection of single nucleotide polymorphisms generated by copy errors. The recent emergence of H5N1 Clade 2.2 in fifty countries, offered a unique opportunity to view the acquisition of new polymorphism in these evolving genomes. We analyzed the H5N1 hemagglutinin gene from a fatal human case from Nigeria in 2007. The newly emerged polymorphisms were present in diverse H5N1 isolates from the previous year. The aggregation of these polymorphisms from clade 2.2 sub-clades was not supported by recent random mutations, and was most easily explained by recombination between closely related sequences.
Arterial stiffness and endothelial dysfunction in stable COPD patients (2012)

Cardiovascular disease is common in COPD patients and is associated with poorer prognosis. Arterial stiffness (AS) is a validated measure of cardiovascular risk. Aim: To assess AS and endothelial dysfunction (ED) in COPD patients, to determine thier association with other clinical and cardiopulmonary functional parameters. Methods: We enrolled 41 COPD patients (64.5±7.6 yrs, FEV1 37.7±14.1%) and 34 normal control subjects (CS). Lung function, blood gases, six-minute walking distance (6MWD), nocturnal pulseoximetry, serum C-reactive protein (CRP) were measured. Assessment of AS was performed by use of digital photoplethysmography (Pulse Trace PCA 2 Micro Medical). Change in reflection index (RI) of the digital volume pulse in response to salbutamol (RISALB) and serum endotelin-1 (ET-1) were used to assess ED. Results: In COPD patients stiffness index (SI) was higher than in CS: 11.3±3.3 vs 6.9±0.9 m/s, p 0,05. The ET-1 levels were elevated in COPD patients and correlated with RISALB (r=-0.46, p=0.03). RISALB was significantly associated with mean nocturnal SpO2 (r=0.38), DLCO (r=0.45). Conclusion: AS and ED are significantly impaired in COPD patients. Decreased FEV1, 6MWD and systemic inflammation were associated with ED. Hypoxemia, elevated ET-1 level and decreased DLCO have an association with both AS and ED.