gebhart/patrepeval huggingface dataset:
The Heymann nephritis antigenic complex (1995)

Heymann nephritis (HN) has been extensively studied as a model of human membranous nephropathy since it was first described by Heymann in 1959. HN was induced in active form by the immunization of rats with antigens derived from the proximal tubule brush border, resulting in subepithelial glomerular immune deposits. HN was also induced passively by the injection of antibrush border antibodies into normal rats. A breakthrough in the understanding of the pathogenesis of HN was made in the 1970s, when it was established that the disease was due to the binding of circulating antibodies to glomerular components. This in turn led to a search to identify the endogenous antigen(s). In 1982, gp330 (now called megalin), a glycoprotein located in clathrin-coated pits of glomerular and proximal tubular epithelia, was identified as a target antigen. In 1990, a second protein (44 kd), now known as RAP (for receptor associated protein), that binds to megalin was also shown to be a target antigen. Both molecules have been cloned and sequenced, and their role in normal epithelial cells has been explored. It has come to light that megalin (gp330) is a member of the low-density lipoprotein receptor gene family and functions as a multiligand receptor for the uptake of a variety of macromolecules (plasminogen, protease: protease inhibitor complexes, apolipoprotein E-enriched very low-density lipoproteins, lactoferrin, among others). RAP associates with megalin and appears to function as a chaperone assisting in the folding of megalin in the endoplasmic reticulum and its transport to the cell surface. This review considers what is now known about the structure, function, and trafficking of megalin and RAP and the role of these two molecules in the pathogenesis of HN.
Dlk1 expression marks developing endothelium and sites of branching morphogenesis in the mouse embryo and placenta (2006)

The protein product of the Delta-like 1 (Dlk1) gene belongs to the Delta-Notch family of signaling molecules, proteins involved in cell fate determination in many tissues during development. The DLK1 protein is believed to function as a growth factor, maintaining the proliferative state of undifferentiated cells, and is usually down-regulated as immature cells differentiate. The expression pattern of the DLK1 protein has been described in certain human tissues; however, Dlk1 expression is not well understood in the mouse, the most tractable mammalian genetic model system. To better understand the role of Dlk1 in embryonic development, the tissue-specific expression pattern of Dlk1 mRNA during mouse embryogenesis was analyzed by in situ hybridization. In embryonic day 12.5 (e12.5) embryos, high levels of Dlk1 were found in the developing pituitary, pancreas, lung, adrenal, and many mesodermally derived tissues. Strikingly, Dlk1 expression also marks the growing branches of organs that develop through the process of branching morphogenesis. At e16.5, Dlk1 expression is down-regulated in most tissues but remains in the pituitary, the adrenal gland, and in skeletal muscle. In the placenta, expression of Dlk1 is detected in endothelial cells lining the fetal blood vessels of the labyrinth. This pattern is distinct from that seen in the human placenta and suggests a role for Dlk1 in regulating maternal-fetal interactions.
Constructing attack scenarios through correlation of intrusion alerts (2002)

Traditional intrusion detection systems (IDSs) focus on low-level attacks or anomalies, and raise alerts independently, though there may be logical connections between them. In situations where there are intensive intrusions, not only will actual alerts be mixed with false alerts, but the amount of alerts will also become unmanageable. As a result, it is difficult for human users or intrusion response systems to understand the alerts and take appropriate actions. This paper presents a practical technique to address this issue. The proposed approach constructs attack scenarios by correlating alerts on the basis of prerequisites and consequences of intrusions. Intuitively, the prerequisite of an intrusion is the necessary condition for the intrusion to be successful, while the consequence of an intrusion is the possible outcome of the intrusion. Based on the prerequisites and consequences of different types of attacks, the proposed approach correlates alerts by (partially) matching the consequence of some previous alerts and the prerequisite of some later ones. The contribution of this paper includes a formal framework for alert correlation, the implementation of an off-line alert correlator based on the framework, and the evaluation of our method with the 2000 DARPA intrusion detection scenario specific datasets. Our experience and experimental results have demonstrated the potential of the proposed method and its advantage over alternative methods.
Intrinsic direct repeats generate consistent post‐transcriptional gene silencing in tobacco (2002)

It is well documented that transgenes with inverted repeats can efficiently trigger post-transcriptional gene silencing (PTGS), presumably via a double stranded RNA induced by complementary sequences in their transcripts. We show here that transgenes with intrinsic direct repeats can also induce PTGS at a very high frequency (80-100%). A transgene with three or four repeats induced PTGS in almost 100% of the primary transformants, regardless of whether a strong (enhanced 35S promoter) or a relatively weak (chlorophyll a/b binding protein promoter) promoter was used. The PTGS induced by three or four repeats is consistently inherited in subsequent generations, and can inactivate homologous genes in trans. Based on the high frequency and consistent heritability, we propose that the intrinsic direct repeat within a transgene may act as a primary determinant of PTGS referred to as direct repeat-induced PTGS (driPTGS). Silencing occurred in all five genes, in this and two previous reports, suggesting that driPTGS might be a universal gene silencing mechanism both in dicotyledonous tobacco plants and monocotyledonous rice cells. In addition, driPTGS may help dissect the gene silencing mechanism and generate silenced phenotypes useful for research and plant biotechnology products.
Internalin A can mediate phagocytosis of Listeria monocytogenes by mouse macrophage cell lines (1996)

Listeria monocytogenes internalin A (InlA) is a surface protein that mediates the attachment of Listeria to, and invasion of, hepatocytes, epithelial, and endothelial cells. In this study, we tested whether InlA could also mediate phagocytosis of L. monocytogenes by the non-listericidal mouse macrophage cell lines J774A.1 and H36.12j. Recombinant InlA (rInlA) was used to derive mouse monoclonal anti-InlA antibodies (mAb) and rabbit anti-InlA antibodies. Fluorescence microscopy demonstrated that these anti-InlA antibodies reacted with wild-type L. monocytogenes, L. ivanovii, and L. innocua+, a mutant transformed with the inlAB operon that expresses surface InlA but failed to react with Bug 8, an InlA/InlB-negative transposon mutant of L. monocytogenes or with noninvasive Listeria sp. Fluorescence microscopy, radiolabeling, and flow cytometry showed that rInlA bound specifically to both macrophage cell lines. Incubation of macrophages and wild-type L. monocytogenes in the presence of rInlA or pretreatment of Listeria with anti-InlA antibodies specifically inhibited, by at least 50%, the phagocytosis of Listeria by both of these cells. By comparison, treatment with these reagents failed to affect the phagocytosis of Streptococcus pyogenes by either macrophage cell line nor did these reagents alter the ability of macrophages to internalize wild-type L. monocytogenes. We found that Bug 8, but not wild-type L. monocytogenes, failed to grow within both of these non-listericidal macrophage cell lines. In contrast to infection by wild-type L. monocytogenes, Bug 8 was rapidly eliminated from the spleens of both C57Bl/6 and DBA/2 mice. Data presented here show that only invasive Listeria sp. have surface InlA and that L. monocytogenes can enter non-listericidal macrophage cell lines by binding of bacterial InlA to the macrophage cell surface.
Spectroscopic Identification of Tremor Phenomena over Hydrocarbon Reservoirs (2002)

H-46 SPECTROSCOPIC IDENTIFICATION OF TREMOR PHENOMENA OVER HYDROCARBON RESERVOIRS J. M. SINGER 1 O. BARZANDJI 1 W. LEU 1 E. D. RODE 1 K. AKRAWI 2 Abstract 1 S. LINTHORST 2 and S. DANGEL 3 1 ADNR Technology Services Sagl Via San Gottardo 56 CH-6648 Minusio Switzerland 2 ADCO Abu Dhabi Company for Onshore Oil Operations 3 University of Zurich Dept. of Geography We report on the observation of seismic tremor phenomena over hydrocarbon reservoirs. The seismic signal of the earth in the frequency range [0.1-20]Hz is recorded continuously using ultra sensitive velocity sensors. Hydrocarbon reservoirs are characterized by a
Bactericidal effect of iron oxide nanoparticles on Staphylococcus aureus (2010)

In order to study the effects of iron oxide (IO) nanoparticles on Staphylococcus aureus, IO nanoparticles were synthesized via a novel matrix-mediated method using polyvinyl alcohol (PVA). The IO nanoparticles were characterized by transmission electron microscopy and dynamic light scattering. Further, S. aureus were grown in the presence of three different IO nanoparticle concentrations for four, 12, and 24 hours. Live/dead assays were performed and the results provide evidence that IO/PVA nanoparticles inhibited S. aureus growth at the highest concentration (3 mg/mL) at all time points.
Multi-functionalized graphene oxide based anticancer drug-carrier with dual-targeting function and pH-sensitivity (2010)

A dual-targeting drug delivery and pH-sensitive controlled release system based on multi-functionalized graphene oxide (GO) was established in order to enhance the effect of targeted drug delivery and realize intelligently controlled release. A superparamagnetic GO–Fe3O4 nanohybrid was firstly prepared via a simple and effective chemical precipitation method. Then folic acid, a targeting agent toward some tumor cells, was conjugated onto Fe3O4 nanoparticlesvia the chemical linkage with amino groups of the 3-aminopropyl triethoxysilane (APS) modified superparamagnetic GO–Fe3O4 nanohybrid, to give the multi-functionalized GO. Doxorubicin hydrochloride (Dox) as an anti-tumor drug model was loaded onto the surface of this multi-functionalized GO via π–π stacking. The drug loading capacity of this multi-functionalized GO is as high as 0.387 mg mg−1 and the drug release depends strongly on pH values. Cell uptake studies were carried out using fluorescein isothiocyanate labeled or Dox loaded multi-functionalized GO to evaluate their targeted delivery property and toxicity to tumor cells. The results show that this multi-functionalized GO has potential applications for targeted delivery and the controlled release of anticancer drugs.
Quantum transport in metallic nanowires fabricated by electrochemical deposition/dissolution (1998)

A nonmechanical method for fabricating a metallic narrow constriction between two electrodes using electrochemical deposition is described. The width of the constriction can be adjusted by slowly dissolving metal atoms away or redepositing atoms onto the constriction which can be controlled flexibly by the electrodes’ potentials. Well-defined plateaus near the integer numbers of the conductance quantum have been observed in these constrictions at room temperature. Since no mechanical movements are involved, this method has the potential of fabricating nanoconstrictions with long term stability.
Insertional Mutagenesis at Positions 520 and 584 of Adeno-Associated Virus Type 2 (AAV2) Capsid Gene and Generation of AAV2 Vectors with Eliminated Heparin- Binding Ability and Introduced Novel Tropism (2006)

Recombinant adeno-associated virus (AAV) vectors are promising in the context of gene therapy because of their ability to mediate efficient gene transfer and stable gene expression. AAV2 uses heparin sulfate as its primary receptor, which is widely expressed on the various tissues and organs. This limits the application of AAV2 in targeting specific tissues. To make an AAV2 vector with modified tropism, we constructed various AAV2 capsid mutants by inserting RGD-4C peptide at position 520 and/or at position 584. Eight mutants were generated, identified, and characterized. Heparin-binding ability was completely abrogated in five mutants, and partially reduced in three mutants. Solid-phase ELISA and gene transduction assays confirmed that the novel tropism is determined by the introduced RGD epitope, which binds to cellular integrin receptor. Our observations suggest that simultaneous modification at both sites, tentatively involved in heparin binding, results in altered tropism and improved transduction efficiency in vitro.
Aluminium carboxylates in aqueous solutions. Part 3. Synthesis and solution state of [Al2(cit)2(H2O)6], [Al2(tart)3(H2O)4] and [Al(gluc)(OH)2](H3cit = citric acid, H2tart = tartaric acid, Hgluc = gluconic acid) (1993)

The complexes [Al2(cit)2(H2O)6] and [Al2(tart)3(H2O)4](H3cit = citric acid, H2tart = tartaric acid) have been prepared by controlled addition of the relevant α-hydroxycarboxylic acids to Al(OH)3 while [Al(gluc)(OH)2](Hgluc = gluconic acid) was obtained by stoichiometric addition of potassium gluconate to a solution of [Al(H2O)6]3+. The solution state of these complexes was investigated by means of combined IR and 1H NMR spectroscopies in D2O, at room temperature. In all cases, solutions were analysed at autogeneous (2.5–4.0) and at physiological pH values, with the aim of checking the agreement between the solution state as predicted from available thermodynamic data and the real, toxicologically relevant, state stemming from spectroscopic observations. The AlIII-citrate system is found to behave according to the thermodynamic expectations down to millimolar metal concentrations. On the contrary, the tartrate and gluconate systems do not agree with thermodynamic predictions, albeit differently, at 0.1 and 0.3 mol dm–3 analytical concentrations.
Interleukin-13 Receptor α2, EphA2, and Fos-Related Antigen 1 as Molecular Denominators of High-Grade Astrocytomas and Specific Targets for Combinatorial Therapy (2008)

IL-13R alpha 2, EphA2, and Fra-1 are attractive therapeutic targets representing molecular denominators of high-grade astrocytomas. One hundred percent of GBM tumors overexpress at least one of these proteins, providing the basis for rational combinatorial targeted therapies/diagnostics suitable for all patients with this disease.
Error-Prone Repair DNA Polymerases in Prokaryotes and Eukaryotes (2002)

DNA repair is crucial to the well-being of all organisms from unicellular life forms to humans. A rich tapestry of mechanistic studies on DNA repair has emerged thanks to the recent discovery of Y-family DNA polymerases. Many Y-family members carry out aberrant DNA synthesis-poor replication accuracy, the favored formation of non-Watson-Crick base pairs, efficient mismatch extension, and most importantly, an ability to replicate through DNA damage. This review is devoted primarily to a discussion of Y-family polymerase members that exhibit error-prone behavior. Roles for these remarkable enzymes occur in widely disparate DNA repair pathways, such as UV-induced mutagenesis, adaptive mutation, avoidance of skin cancer, and induction of somatic cell hypermutation of immunoglobulin genes. Individual polymerases engaged in multiple repair pathways pose challenging questions about their roles in targeting and trafficking. Macromolecular assemblies of replication-repair "factories" could enable a cell to handle the complex logistics governing the rapid migration and exchange of polymerases.
Molecular basis for the specific recognition of the metazoan cyclic GMP-AMP by the innate immune adaptor protein STING (2015)

Cyclic GMP-AMP containing a unique combination of mixed phosphodiester linkages (2'3'-cGAMP) is an endogenous second messenger molecule that activates the type-I IFN pathway upon binding to the homodimer of the adaptor protein STING on the surface of endoplasmic reticulum membrane. However, the preferential binding of the asymmetric ligand 2'3'-cGAMP to the symmetric dimer of STING represents a physicochemical enigma. Here we show that 2'3'-cGAMP, but not its linkage isomers, adopts an organized free-ligand conformation that resembles the STING-bound conformation and pays low entropy and enthalpy costs in converting into the active conformation. Our results demonstrate that analyses of free-ligand conformations can be as important as analyses of protein conformations in understanding protein-ligand interactions.
Smart Streaming: A High-Throughput Fault-tolerant Online Processing System (2020)

In recent years, there has been considerable interest in developing frameworks for processing streaming data. Like the precursor commercial systems for data-intensive processing, these systems have largely not used methods popular within the HPC community (for example, MPI for communication). In this paper, we demonstrate a system for stream processing that offers a high-level API to the users (similar to MapReduce), is fault-tolerant, and is also more efficient and scalable than current solutions. Particularly, a cost-efficient MPI/OpenMP based fault-tolerant scheme is incorporated so that the system can survive node failures with only a modest degradation of performance. We evaluate both the functionality and efficiency of Smart Streaming using four common applications in machine learning and data analytics. A comparison against state-of-the-art streaming frameworks shows our system boosts the throughput of test cases by up to 10X and achieve desirable parallelism when scaled out. Additionally, the performance loss upon failures is only proportional to the share of failed resources.
Evaluating adsorbent filter performance for enteric virus concentrations in tap water (1981)

Under varying operating conditions, the performance limits of an electropositive adsorbent filter were equivalent to those of a conventional electronegative adsorbent filter. Performance limits were determined with respect to adsorption flow rate (hydraulic flux), tap water process volume (hydraulic load), stability of adsorbed virus during storage, and ability to concentrate several different enteric viruses.
Charge-induced phase separation in lipid membranes (2014)

Phase separation in lipid bilayers that include negatively charged lipids is examined experimentally. We observed phase-separated structures and determined the membrane miscibility temperatures in several binary and ternary lipid mixtures of unsaturated neutral lipid, dioleoylphosphatidylcholine (DOPC), saturated neutral lipid, dipalmitoylphosphatidylcholine (DPPC), unsaturated charged lipid, dioleoylphosphatidylglycerol (DOPG((-))), saturated charged lipid, dipalmitoylphosphatidylglycerol (DPPG((-))), and cholesterol. In binary mixtures of saturated and unsaturated charged lipids, the combination of the charged head with the saturation of the hydrocarbon tail is a dominant factor in the stability of membrane phase separation. DPPG((-)) enhances phase separation, while DOPG((-)) suppresses it. Furthermore, the addition of DPPG((-)) to a binary mixture of DPPC/cholesterol induces phase separation between DPPG((-))-rich and cholesterol-rich phases. This indicates that cholesterol localization depends strongly on the electric charge on the hydrophilic head group rather than on the ordering of the hydrocarbon tails. Finally, when DPPG((-)) was added to a neutral ternary system of DOPC/DPPC/cholesterol (a conventional model of membrane rafts), a three-phase coexistence was produced. We conclude by discussing some qualitative features of the phase behaviour in charged membranes using a free energy approach.
Confronting Security and Privacy Threats in Modern RFID Systems (2006)

The modern form of RFID technology that is set to dominate is that enabled by low cost RFID technology. This paper presents an overview of the technological aspects vital to illuminating associated security and privacy threats The paper also describes a simple security model and briefly considers some of the vulnerabilities faced by such low cost RFID systems. Finally the authors would like to extend preliminary work published on a minimalist encryption method first published in [26] and [27].
Electrophysiological Studies in Migraine: A Comprehensive Review of Their Interest and Limitations (2003)

Electrophysiological methods may help to unravel some of the pathophysiological mechanisms of migraine. Lack of habituation is the principal and most reproducible interictal abnormality in sensory processing in migraineurs. It is found in evoked potential (EP) studies for every stimulation modality including nociceptive stimuli, and it is likely to be responsible for the increased intensity dependence of EP. We have hypothesized that deficient EP habituation in migraine could be due to a reduced preactivation level of sensory cortices because of hypofunctioning subcortico-cortical aminergic pathways. This is not in keeping with simple hyperexcitability of the cortex, which has been suggested by some, but not all, studies of transcranial magnetic stimulation (TMS). A recent study of the effects of repetitive TMS on visual EP strongly supports the hypothesis that migraine is characterized by interictal cortical hypoexcitability. With regard to pain mechanisms in migraine, electrophysiological studies of trigeminal pathways using nociceptive blink and corneal reflexes have confirmed that sensitization of central trigeminal nociceptors occurs during migraine attacks.
A 32-channel tunable receiver module for wavelength-division multiple-access networks (1997)

We report the realization of a 32-channel tunable optical receiver module for packet-switched multiwavelength computer networks. The tunable receiver consists of a planar array waveguide grating demultiplexer, photodetector array and followed by selectable receivers. The channel selection is based on sequential switching of the received optical signals in stages at the analogue level. Typical receiver sensitivity is -24 dBm at 10/sup -9/, using a 700-Mb/s nonreturn-to-zero (NRZ) pseudorandom binary sequence (PRBS). The channel switching time is /spl sim/40 ns.
Identification of novel DNA methylation markers in colorectal cancer using MIRA-based microarrays (2012)

To identify novel hypermethylated genes in colorectal cancer (CRC) and to test their potential application in CRC early diagnosis, a genome-wide screening of 57,723 CpG dinucleotides covering 4,010 genes was performed using MIRA-based microarrays in paired DNA samples extracted from 3 fresh frozen CRC tissues and their matching non-cancer tissues from 3 CRC patients undergoing curative surgery. Candidate hypermethylated genes screened by MIRA-based microarrays were further validated in independent CRC samples. A total of 297 CpG dinucleotides covering 211 genes were found to be hypermethylated in CRC tissues. From these 211 candidate methylated genes, three novel hypermethylated genes with more than four probes positive were picked up for validation. Direct bisulfite sequencing revealed that methylations occurred at multiple CpG sites of these three genes in cancer tissues, especially for PHOX2B and FGF12. Combined bisulfite restriction analysis showed that these three genes were methylated in cancer samples but not in non-cancer samples. We also compared the methylation levels of these three novel hypermethylated genes with those of vimentin and SEPT9, well-known hypermethylated genes in CRC, and found that methylated PHOX2B, FGF12 and GAD2 were better than methylated vimentin and SEPT9 in differentiating CRC cancer tissue from non-cancer tissue. Significant enrichment analysis of GO terms of the hypermethylated genes showed that a high proportion of hypermethylated genes in cancer tissues are involved in the regulation of transcription. In conclusion, we found a set of novel hypermethylated genes in CRC, which may have potential to be used as biomarkers for the early diagnosis of CRC.