gebhart/patrepeval huggingface dataset:
Specificity, diversity, and convergence in VEGF and TNF‐α signaling events leading to tissue factor up regulation via EGR‐1 in endothelial cells (2001)

ABSTRACT Tissue factor (TF) has been shown to be up‐regulated in endothelial cells by the inflammatory cytokine tumor necrosis factor a (TNF‐α) as well as by the main angiogenic factor VEGF. Since both stimuli induce the transcription factor EGR‐1, which is critically involved in TF gene regulation, we used EGR‐1‐dependent TF induction as a model to identify potential cross‐talks between the various signal transduction cascades initiated by VEGF and TNF‐α. The data show that at the MAP kinase level, VEGF mainly activates ERK1/2 and p38 MAP kinases in human endothelial cells. TNF‐α is able to activate all three MAP kinase cascades as well as the classical inflammatory IκB/NFκB pathway. Furthermore, the MEK/ERK module of MAP kinases appears to act as the convergence point of VEGF‐ and TNF‐α‐initiated signaling cascades, which lead to the activation of EGR‐1 and subsequent TF expression, whereas the upstream signals are distinct. We found that induction of TF by VEGF via EGR‐1 is strongly PKC dependent. The TNF‐ α‐ initiated MEK/ERK cascade connected to EGR‐1 and TF expression is clearly less sensitive to PKC inhibition. TNF‐ α ‐mediated activation of MEK/ERK and EGR‐1 can be blocked by adenoviral expression of a dominant negative mutant of IKK2, whereas the VEGF signaling pathway is unaffected. Thus, our data demonstrate a new link between the classical inflammatory IKK/IκB and the MEK/ERK cascades triggered by TNF‐ α . The additional finding that EGF induces ERK and EGR‐1 in a PKC independent manner and that this signal is not sufficient to up‐regulate TF emphasizes the importance of a VEGF‐specific signaling pattern for the induction of TF.— Mechtcheriakova, D., Schabbauer, G., Lucerna, M., Clauss, M., de Martin, R., Binder, B. R., Hofer, E. Specificity, diversity, and convergence in VEGF and TNF‐α signaling events leading to tissue factor up‐regulation via EGR‐1 in endothelial cells. FASEB J. 15, 230–242 (2001)
Learning limited dependence Bayesian classifiers (1996)

We present a framework for characterizing Bayesian classification methods. This framework can be thought of as a spectrum of allowable dependence in a given probabilistic model with the Naive Bayes algorithm at the most restrictive end and the learning of full Bayesian networks at the most general extreme. While much work has been carried out along the two ends of this spectrum, there has been surprising little done along the middle. We analyze the assumptions made as one moves along this spectrum and show the tradeoffs between model accuracy and learning speed which become critical to consider in a variety of data mining domains. We then present a general induction algorithm that allows for traversal of this spectrum depending on the available computational power for carrying out induction and show its application in a number of domains with different properties. Introduction Recently, work in Bayesian methods for classification has grown enormously (Cooper &amp;amp; Herskovits 1992) (Buntin...
Adversarial Examples Are Not Easily Detected: Bypassing Ten Detection Methods (2017)

Neural networks are known to be vulnerable to adversarial examples: inputs that are close to natural inputs but classified incorrectly. In order to better understand the space of adversarial examples, we survey ten recent proposals that are designed for detection and compare their efficacy. We show that all can be defeated by constructing new loss functions. We conclude that adversarial examples are significantly harder to detect than previously appreciated, and the properties believed to be intrinsic to adversarial examples are in fact not. Finally, we propose several simple guidelines for evaluating future proposed defenses.
Potent and selective inhibitors of NAD+-dependent 15-hydroxyprostaglandin dehydrogenase (HPGD) (2011)

15-hydroxyprostaglandin dehydrogenase (15-PGDH; HPGD) is the key enzyme for the inactivation of prostaglandins, and thus regulates processes such as inflammation or proliferation. The anabolic pathways of prostaglandins are well-characterized, especially with respect to regulation of the cyclooxygenase (COX) enzymes. In comparison, little is known about downstream events, including functional interaction of prostaglandin-processing and metabolizing enzymes, as well as the function of prostaglandin receptors. To date, the only known strong inhibitors belong to the family of thiazolinedines that affect other pathways, notably by binding to peroxisome proliferator-activated receptor (PPAR)γ. The present study discloses the discovery and characterization of a potent and competitive HPGD inhibitor that is selective within the dehydrogenase family, ML147 (CID-3245059). It also discloses two high-affinity and uncompetitive HPGD inhibitors that are selective within the dehydrogenase family, ML148 (CID-3243760) and ML149 (CID-2331284). These small molecule probes represent the most potent and selective inhibitors of 15-HPGD reported thus far.
Microtask programming (2014)

Microtask crowdsourcing organizes complex work into workflows, decomposing large tasks into small, relatively independent microtasks. Applied to software development, this model might increase participation in open source software development by lowering the barriers to contribu-tion and dramatically decrease time to market by increasing the parallelism in development work. To explore this idea, we have developed an approach to decomposing programming work into microtasks. Work is coordinated through tracking changes to a graph of artifacts, generating appropriate microtasks and propagating change notifications to artifacts with dependencies. We have implemented our approach in CrowdCode, a cloud IDE for crowd development. To evaluate the feasibility of microtask programming, we performed a small study and found that a small crowd of 12 workers was able to successfully write 480 lines of code and 61 unit tests in 14.25 person-hours of time.
Avoiding traceroute anomalies with Paris traceroute (2006)

Traceroute is widely used, from the diagnosis of network problems to the assemblage of internet maps. However, there are a few serious problems with this tool, in particular due to the presence of load balancing routers in the network. This paper describes a number of anomalies that arise in nearly all traceroute-based measurements. We categorize them as "loops", "cycles", and "diamonds". We provide a new publicly-available traceroute, called Paris traceroute, which controls packet header contents to obtain a more precise picture of the actual routes that packets follow. This new tool allows us to find conclusive explanations for some of the anomalies, and to suggest possible causes for others.
Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model (2020)

Countermeasures to prevent and treat coronavirus disease 2019 (COVID-19) are a global health priority. We enrolled a cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-recovered participants, developed neutralization assays to investigate antibody responses, adapted our high-throughput antibody generation pipeline to rapidly screen more than 1800 antibodies, and established an animal model to test protection. We isolated potent neutralizing antibodies (nAbs) to two epitopes on the receptor binding domain (RBD) and to distinct non-RBD epitopes on the spike (S) protein. As indicated by maintained weight and low lung viral titers in treated animals, the passive transfer of a nAb provides protection against disease in high-dose SARS-CoV-2 challenge in Syrian hamsters. The study suggests a role for nAbs in prophylaxis, and potentially therapy, of COVID-19. The nAbs also define protective epitopes to guide vaccine design.
Primitive hemopoietic stem cells: direct assay of most productive populations by competitive repopulation with simple binomial, correlation and covariance calculations. (1993)

Quantitative analyses of primitive hemopoietic stem cell (PHSC) populations are important both for basic biology and for clinical applications. Unfortunately, many conventional assays fail to measure long-term repopulating ability and maximal differentiating ability, the most important characteristics of the PHSC. The competitive repopulation assay described here focuses on this characteristic, assaying the precursors from which most differentiated cells are descended over large fractions of the life span in laboratory mice. Thus long-term repopulating ability and the ability to differentiate into both myeloid and lymphoid lineages are measured directly from 2.5 to 12.5 months after transplantation. This technique also has found high correlations between granulocytes, macrophages, and T and B lymphocytes as early as 3 weeks after transplantation. All or most differentiated cells of these widely disparate types appear to be descended from a common precursor cell, while myeloid-specific or lymphoid-specific precursors produce few or no descendants. However, large increases in variances between 3 and 6 weeks and 12 weeks after transplantation suggest that most of the initially active multilineage precursors are exhausted. Thus the ability to differentiate into widely disparate lineages does not establish long-term repopulating ability.
Colloidal Jamming at Interfaces: A Route to Fluid-Bicontinuous Gels (2005)

Colloidal particles or nanoparticles, with equal affinity for two fluids, are known to adsorb irreversibly to the fluid-fluid interface. We present large-scale computer simulations of the demixing of a binary solvent containing such particles. The newly formed interface sequesters the colloidal particles; as the interface coarsens, the particles are forced into close contact by interfacial tension. Coarsening is markedly curtailed, and the jammed colloidal layer seemingly enters a glassy state, creating a multiply connected, solidlike film in three dimensions. The resulting gel contains percolating domains of both fluids, with possible uses as, for example, a microreaction medium.
Modeling of Biomimetic Robotic Fish Propelled by An Ionic Polymer–Metal Composite Caudal Fin (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, a physics-based model is proposed for a biomimetic robotic fish propelled by an ionic polymer–metal composite (IPMC) actuator. Inspired by the biological fin structure, a passive plastic fin is further attached to the IPMC beam. The model incorporates both IPMC actuation dynamics and the hydrodynamics, and predicts the steady-state cruising speed of the robot under a given periodic actuation voltage. The interactions between the plastic fin and the IPMC actuator are also captured in the model. Experimental results have shown that the proposed model is able to predict the motion of robotic fish for different tail dimensions. Since most of the model parameters are expressed in terms of fundamental physical properties and geometric dimensions, the model is expected to be instrumental in optimal design of the robotic fish. </para>
Mining roles with noisy data (2010)

There has been increasing interest in automatic techniques for generating roles for role based access control, a process known as role mining. Most role mining approaches assume the input data is clean, and attempt to optimize the RBAC state. We examine role mining with noisy input data and suggest dividing the problem into two steps: noise removal and candidate role generation. We introduce an approach to use (non-binary) rank reduced matrix factorization to identify noise and experimentally show that it is effective at identifying noise in access control data. User- and permission-attributes can further be used to improve accuracy. Next, we show that our two-step approach is able to find candidate roles that are close to the roles mined from noise-less data. This method performs better than the approach of mining noisy data directly and offering the administrator increased control in the noise removal and candidate role generation phases. We note that our approach is applicable outside role engineering and may be used to identify errors or predict missing values in any access control matrix.
Construction of high‐density bacterial colony arrays and patterns by the ink‐jet method (2003)

We have developed a method for fabricating bacterial colony arrays and complex patterns using commercially available ink-jet printers. Bacterial colony arrays with a density of 100 colonies/cm(2) were obtained by directly ejecting Escherichia coli (E. coli) onto agar-coated substrates at a rapid arraying speed of 880 spots per second. Adjusting the concentration of bacterial suspensions allowed single colonies of viable bacteria to be obtained. In addition, complex patterns of viable bacteria as well as bacteria density gradients were constructed using desktop printers controlled by a simple software program.
PD‐L1 (B7‐H1) expression by urothelial carcinoma of the bladder and BCG‐induced granulomata (2007)

Collectively, these data indicate that tumor PD-L1 may facilitate localized stage-advancement of UC and attenuate responses to BCG immunotherapy by neutralizing T cells that normally guard against cancer invasion from the epithelium into the bladder musculature.
Endovascular Coil Occlusion of Intracranial Aneurysms Assisted by a Novel Self-Expandable Nitinol Microstent (Neuroform) (2002)

Endovascular treatment of wide neck intracranial aneurysms is technically difficult and leads to less favorable treatment results and long term outcome. We participated in a multicenter prospective study to evaluate the safety and performance of a new self-expandable nitinol micro stent (Neuroform) in stent assisted coil occlusion of wide neck intracranial aneurysms. Eighteen patients were enrolled in the study in a single center. The anatomy of the target aneurysm and the parent vessel, technical details of the procedure, device functionality, anatomic and clinical results were evaluated. All enrolled aneurysms were either wide necked or showed an unfavorable neck-to-fundus ratio. In 16 out of 18 patients the Neuroform device allowed stent assisted coil occlusion of the aneurysm. The occlusion rate was 95% in eight patients and 100% in eight patients. The two failures were both due to anatomic reasons. Flexibility of the stent, behavior during deployment and subsequent ability to retain coils within the aneurysmal sac were considered as good as or better than the properties of previous balloon expandable stents. No device-related adverse events were encountered. Procedure-related clinical complications occurred in seven patients but caused no severe permanent neurological deficit. The Neuroform neurovascular stenting system is a safe and effective adjunct for the stent-assisted coil occlusion of wide necked intracranial aneurysms. The major advantages of this device are its self-expanding property and very high flexibility which allows safe navigation, easy sizing, as well as accurate positioning of the stent while providing sufficient bridging of the aneurysm neck for subsequent coil placement.
Section Review: Anti-infectives: Recent developments in the treatment of hepatitis D infection (1996)

Chronic hepatitis D is an often severe form of liver disease, due to infection with the hepatitis delta virus (HDV), a unique RNA virus that requires the hepatitis B virus (HBV) helper function to exert its pathogenic potential. Alpha IFN is at present the only choice of treatment for chronic HBV/HDV infection, but the results obtained are far from satisfactory. Available data show that IFN is more effective if administered to patients with a recent infection (lasting < 1 year) at high doses (9 - 10 MU thrice weekly) and for a prolonged period of time (12 months). Long-term response is associated with the clearance of hepatitis B surface antigen (HBsAg) from serum, an event which can occur at the end of treatment or even months after treatment discontinuation. On treatment, clearance of HDV-RNA and reduction of alanine aminotransferase (ALT) levels to normal values do not predict long-term response. Prolonged administration of high IFN doses can induce severe psychiatric side-effects, sometimes leading to suicide. IFN should therefore be given for no longer than 12 months and under careful medical supervision. Better therapeutic options are clearly needed. The association of HBV with HDV infection suggests that treatment with the new deoxynucleotide analogues should be considered. Antisense oligonucleotides directed against the self-cleavage domain of HDV-RNA, which can disrupt HDV replication in vitro, may represent the new frontier of HDV therapy.
p38α mitogen-activated protein kinase inhibitors, a patent review (2005 – 2011) (2011)

In the last few years, compounds have become more potent and more selective, for example, by induction of the so-called glycine flip. Furthermore, some companies are striving for selectivity with respect to isoforms. The increasing availability of rapid screening services, which include more than 400 kinases, has encouraged companies to reconsider traditional approaches. The most promising approach appears to be the development of linear binding molecules that feature a carbonyl oxygen that can enforce the glycine flip. Furthermore, recent projects increasingly target new fields of application, for example, pulmonary diseases. This might be the most important trend of the past few years.
Reliability Impact of Chalcogenide-Structure Relaxation in Phase-Change Memory (PCM) Cells—Part I: Experimental Study (2009)

The phase-change memory (PCM) relies on the electrical properties of the chalcogenide materials to represent the stored bit of information. As a result, data stability depends on structural relaxation (SR) in the amorphous chalcogenide phase, which results in a temperature-accelerated time evolution of the electrical properties of the active material. Here, we address the time, temperature, and bias dependence of SR effects on the amorphous Ge <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Sb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Te <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> (GST) material used in PCM cells. Electrical measurements for increasing annealing time and temperature indicate that SR can be described by a defect annihilation process in the amorphous chalcogenide material. Finally, the stability of chalcogenide resistance as a function of the read conditions is discussed, for the purpose of reducing the impact of SR on the reliability of PCM devices.
Disección supraomohioidea: Análisis de 53 casos (1999)

espanolEl tratamiento de la region cervical en los tumores de cabeza y cuello ha evolucionado con el conocimiento de los patrones de expansion tumoral y las exigencias cada vez mayores de lograr un mejor resultado estetico y funcional, sin disminuir el control de la enfermedad. La diseccion supraomohioidea es un procedimiento ampliamente aceptado en el tratamiento de tumores de cavidad oral sin afectacion cervical, mientras continua la discusion en cuanto a su papel en cuellos clinicamente afectados. El proposito de este estudio es analizar 53 pacientes tratados en nuestro servicio mediante diseccion supraomohioidea entre 1993 y 1997, analizando parametros anatomopatologicos, asi como la evolucion posterior, tras un seguimiento medio de 18,3m. En nuestra serie no se ha producido ningun caso de recidiva ganglionar clinica en areas IV o V (no incluidas en la diseccion supraomohioidea), dentro de un bajo porcentaje de recidivas cervicales. Como conclusion, consideramos la diseccion supraomohioidea como el procedimiento de eleccion en pacientes con carcinoma escamoso de cavidad oral sin afectacion cervical (NO), y en metastasis aisladas, menores de 3 cm (N1) en areas I o II. EnglishThe treatment of the cervical region in head and neck tumors has evolutioned with the knowledge of the tumoral extension patterns and the increasing demands of a better aesthetic and functional result, without decreasing the disease control. Supraomohyoid neck dissection is a widely accepted procedure in the treatment of oral cavity tumors with negative cervical lymph nodes, meanwhile controversy continues on its role on clinically positive necks. The purpose of this paper is to analize 53 patients who underwent supraomohyoid neck dissection in our department between 1993 and 1997, analizing histologic features and post operative courses, aftera mediumfollowing of 18.3 months. We haven\'t had any case of Iymph node recurrence in areas IV or V(not included in the supraomohyoid dissection), from the total percentage of cervical recurrences. As a conclusion, we consider supraomohyoid neck dissection as an adequate procedure for patients with squamous cell carcinoma of the oral cavity with negative cervical lymph nodes (NO) and patients with limited metastasis under 3cm. (N1) in areas I or II.
Application of Improved Methods To Assess Pathways for Biosynthesis of Long- and Very-Long-Chain Fatty Acids (1997)

Improved microscale methods for analyzing individual carbon atoms of long- and very-long-chain fatty acids are described. These methods allow quantitation of radiolabel in at least 50% of individual carbon atoms from the carboxyl terminal of such fatty acids. These methods have been used to study metabolic pathways leading to long- and very-long-chain fatty acids of seeds. The approach begins with HPLC separation of free fatty acids from saponified, total lipid extracts. Subsequently, individual free acids are analyzed by Schmidt degradation to reveal the extent of carboxyl labeling or are subjected to α-oxidation followed by HPLC separation of free acid homologues. An improvement in the procedure for α-oxidation results in 0.2−2 times higher recovery of longer homologues. Carboxy-labeling of homologues is then determined using Schmidt degradation. For unsaturated acids, microscale hydrogenation and HPLC purification are done prior to α-oxidation. Results detail existing evidence that long- and very-long-chain fatty acids of seeds from various oilseed plants are solely formed by fatty-acid-synthase-mediated reactions. In addition, observations are consistent with the utilization of more than one pool of precursor oleic acid for synthesis of 20:1 and 22:1 in Brassica seeds. Keywords: α-Oxidation; Schmidt degradation; HPLC; hydrogenation; fatty acids
DNS Extensions to support IP version 6 (1995)

This document defines the changes that need to be made to the Domain Name System (DNS) to support hosts running IP version 6 (IPv6). The changes include a resource record type to store an IPv6 address, a domain to support lookups based on an IPv6 address, and updated definitions of existing query types that return Internet addresses as part of additional section processing. The extensions are designed to be compatible with existing applications and, in particular, DNS implementations themselves.
Defective Natural Killer Cell Cytotoxic Activity in Feline Immunodeficiency Virus-Infected Cats (1995)

Flow cytometry has been employed to study NK cell cytotoxic activity in cats infected with feline immunodeficiency virus. The results show that animals infected for 12 months or more have decreased levels of NK cell cytotoxic activity in their blood. The impairment could not be overcome by in vitro treatment of effector cells with interleukin 2. Additional results suggest that the NK cells of infected cats are defective, in that they are still able to bind to target cells but have a reduced ability to kill them.