gebhart/patrepeval huggingface dataset:
Bacterial infections in liver cirrhosis. (1999)

The incidence of bacterial infections in cirrhotic patients admitted to hospital is very high. In several studies, 30% to 50% of cirrhotics presented bacterial infections at admission, or developed this type of complication during hospitalization. Most bacterial infections in cirrhotic patients are hospital-acquired. Between 15% to 35% of cirrhotics admitted to hospital develop nosocomial infections; these figures contrast sharply with the hospital-acquired infection rate in the general hospital population (5% to 7%). Urinary tract infections (12% to 29%), spontaneous bacterial peritonitis (7% to 23%), respiratory tract infections (6% to 10%) and bacteraemia (4% to 9%) are the most frequent bacterial infectious complications seen in cirrhotic patients. However, since spontaneous bacterial peritonitis is the most characteristic bacterial infection in cirrhosis, this report will focus (mainly) on this infectious complication.
Improved Polymerase Chain Reaction Detection of Clonally Rearranged T-Cell Receptor β Chain Genes (1998)

A new method for the detection of all known possible rearrangements at the variable (V), diversity (D), and joining (J) segments of the T-cell receptor beta chain (TcR beta) gene in tissue DNA extracts is described that involves two polymerase chain reactions (PCRs). The first PCR round (screening PCR) allowed the identification of the J beta segment involved in a clonal rearrangement. A J beta-primer was used for the second PCR (J beta-specific PCR), recognizing the J beta segment identified in the screening PCR in combination with a consensus V beta primer. This PCR generated prominent and short amplificates suitable for direct sequence analysis because of their low background. Using this approach, clonal TcR beta gene rearrangements were able to be demonstrated in all T-cell lines (n = 7) and in all peripheral T-cell lymphomas (n = 33) analyzed. No clonal TcR beta gene rearrangements were found in any of the normal tissues studied nor in any B-cell non-Hodgkin lymphomas. This method is applicable to DNA from fresh frozen tissues, and, after the TcR beta rearrangement of a patient's malignant T-cell clone has been identified by the screening PCR, DNA can also be detected in follow-up formalin-fixed paraffin-embedded samples by the J beta-specific PCR with high sensitivity and specificity.
Immunization with a bovine herpesvirus 1 glycoprotein B DNA vaccine induces cytotoxic T-lymphocyte responses in mice and cattle (2005)

Virus-specific cytotoxic T lymphocytes (CTLs) are considered to be important in protection against and recovery from viral infections. In this study, several approaches to induce cytotoxicity against bovine herpesvirus 1 (BHV-1) were evaluated. Vaccination of C57BL/6 mice with BHV-1 induced a strong humoral, but no CTL, response, which may be due to downregulation of major histocompatibility complex class I molecules. In contrast, vaccinia virus expressing glycoprotein B (gB) elicited a weaker antibody response, but strong cytotoxicity, in mice. As an approach to inducing both strong humoral and cellular immune responses, a plasmid vector was then used to express gB. Both antibody and CTL responses were induced by the plasmid encoding gB in C57BL/6 and C3H mice, regardless of the type of vector backbone. This demonstrated that DNA immunization induces a broad-based immune response to BHV-1 gB. Interestingly, removal of the membrane anchor, which resulted in secretion of gB from transfected cells, did not result in reduced cytotoxicity. Here, it is shown that, compared with the cell-associated counterpart, plasmid-encoded secreted protein may induce enhanced immune responses in cattle. Therefore, calves were immunized intradermally with pMASIAtgB, a plasmid encoding the secreted form of gB (tgB), using a needle-free injection system. This demonstrated that pMASIAtgB elicited both humoral responses and activated gamma interferon-secreting CD8+ CTLs, suggesting that a DNA vaccine expressing tgB induces a CTL response in the natural host of BHV-1.
Prostacyclin rather than endogenous nitric oxide is a tissue protective factor in myocardial ischemia (1992)

Nitric oxide (NO) and prostacyclin (PGI2) were determined in effluents of Langendorff-perfused rabbit hearts subjected to 2 h of global low-flow ischemia and subsequent reperfusion. PGI2 release [6-oxo-prostaglandin (PG) F1 alpha] was significantly enhanced during early reperfusion and remained elevated. NO formation was reduced during ischemia but did increase substantially during reperfusion. Indomethacin (3 microM) significantly suppressed ischemia-related 6-oxo-PGF1 alpha and NO release. This was accompanied by severely diminished myocardial recovery. NG-nitro-L-arginine (L-NNA) (100 microM) suppressed NO generation without major effects on 6-oxo-PGF1 alpha generation and cardiac dysfunction but with a remarkable increase in coronary perfusion pressure. These effects of L-NNA were antagonized by L-arginine, whereas the effects of indomethacin were not. There was a substantial loss of creatine kinase specific activity from reperfused ischemic hearts, which was further aggravated by indomethacin but not by L-NNA. These data demonstrate a cardioprotective and endothelium-protective role of PGI2 in myocardial ischemia, which also involves preservation of NO generation. Endogenous NO appears to be important for local regulation of coronary flow.
Structure-Switching Signaling Aptamers (2003)

Aptamers are single-stranded nucleic acids with defined tertiary structures for selective binding to target molecules. Aptamers are also able to bind a complementary DNA sequence to form a duplex structure. In this report, we describe a strategy for designing aptamer-based fluorescent reporters that function by switching structures from DNA/DNA duplex to DNA/target complex. The duplex is formed between a fluorophore-labeled DNA aptamer and a small oligonucleotide modified with a quenching moiety (denoted QDNA). When the target is absent, the aptamer binds to QDNA, bringing the fluorophore and the quencher into close proximity for maximum fluorescence quenching. When the target is introduced, the aptamer prefers to form the aptamer-target complex. The switch of the binding partners for the aptamer occurs in conjunction with the generation of a strong fluorescence signal owing to the dissociation of QDNA. Herein, we report on the preparation of several structure-switching reporters from two existing DNA aptamers. Our design strategy is easy to generalize for any aptamer without prior knowledge of its secondary or tertiary structure, and should be suited for the development of aptamer-based reporters for real-time sensing applications.
Oxygen Radicals in Focal Cerebral Ischemia (1994)

Oxygen free radicals have been widely implicated in the pathogenesis of brain injury due to ischemia followed by reperfusion. The success of making transgenic animals overexpressing human CuZn-superoxide dismutase (CuZn-SOD) in brain cells allows researchers to discern the specific role of superoxide radicals in reperfusion injury after focal ischemia. It has been shown that increased brain levels of CuZn-SOD in transgenic mice protect neurons from ischemia/reperfusion injury. However, overexpression of CuZn-SOD does not provide neuronal protection in permanent focal ischemia in mice, when compared with non-transgenic mouse littermates. It is proposed that molecular genetic approaches of modifying antioxidant levels in the brain offer a unique tool for studying oxidative mechanisms in focal cerebral ischemia.
MakeVR: A 3D world-building interface (2013)

MakeVR is an intuitive and accessible digital sandbox for making 3D objects scenes with game-like simplicity for beginners and with advanced tools for experts. It presents a professional CAD engine through a natural immersive two-handed interface. Users reach into space to move themselves through a geometric playground, placing primitive shapes and more complex objects into the scene and then reaching out to modify them via booleans, sweeps, deformation, and other CAD operations. We conducted a preliminary user evaluation of four participant case studies and plan to use this evaluation to improve the system.
Fractal and Multifractal Analysis of Heart Rate Variability (2007)

The paper considers the heart rate variability from the fractal and multifractal standpoints. The short-term inter-beat intervals for arrhythmia patients, recorded before, after and during the amiodarone therapy, have been analyzed.
Estimating the Selectivity of XML Path Expressions for Internet Scale Applications (2001)

Data on the Internet is increasingly presented in XML format. This enables novel applications that pose queries over “all the XML data on the Internet.” Queries over XML data use path expressions to navigate through the structure of the data, and optimizing these queries requires estimating the selectivity of these path expressions. In this paper, we propose two techniques for estimating the selectivity of simple XML path expressions over complex large-scale XML data as would be handled by Internet-scale applications: path trees and Markov tables. Both techniques work by summarizing the structure of the XML data in a small amount of memory and using this summary for selectivity estimation. We experimentally demonstrate the accuracy of our proposed techniques, and explore the different situations that would favor one technique over the other. We also demonstrate that our proposed techniques are more accurate than the best previously known alternative. 1
Carbon Nanotube Thin Film Field Emitting Diode: Understanding the System Response Based on Multiphysics Modeling (2007)

In this paper, we model the evolution and self-assembly of randomly oriented carbon nanotubes (CNTs), grown on a metallic substrate in the form of a thin film for field emission under diode configuration.Despite high output, the current in such a thin film device often decays drastically.
A self-correcting neighbor protocol for mobile ad-hoc wireless networks (2003)

Mobile wireless ad-hoc networks lack some basic abilities taken for granted in wired networks, such as the ability to know adjacent nodes. We present a neighbor discovery protocol, with particular application to broadcast flooding. The neighbor exchange protocol (NXP) has two main improvements over simple periodic broadcast schemes: (1) it only sends Hello packets when necessary to maintain topology and (2) uses sequence numbers in redistributed information to aid in convergence. In simulation, we compare NXP to a periodic protocol and simple flooding for all-node packet broadcasts and two dissemination techniques. We show that we maintain similar delivery rates while using fewer control packets in most configurations.
ARIES/IM: an efficient and high concurrency index management method using write-ahead logging (1992)

This paper provides a comprehensive treatment of index management in transaction systems. We present a method, called ARIESIIM (Algorithm for Recovery and Isolation Exploiting Semantics for Index Management) , for concurrency control and recovery of B + -trees. ARIES/IM guarantees serializability and uses write-ahead logging for recovery. It supports very high concurrency and good performance by (1) treating as the lock of a key the same lock as the one on the corresponding record data in a data page (e.g., at the record level), (2) not acquiring, in the interest of permitting very high concurrency, commit duration locks on index pages even during index structure modification operations (SMOs) like page splits and page deletions, and (3) allowing retrievals, inserts, and deletes to go on concurrently with SMOs. During restart recovery, any necessary redos of index changes are always performed in a page-oriented fashion (i.e., without traversing the index tree) and, during normal processing and restart recovery, whenever possible undos are performed in a page-oriented fashion. ARIES/IM permits different granularities of locking to be supported in a flexible manner. A subset of ARIES/IM has been implemented in the OS/2 Extended Edition Database Manager. Since the locking ideas of ARIES/IM have general applicability, some of them have also been implemented in SQL/DS and the VM Shared File System, even though those systems use the shadow-page technique for recovery.
Key multiplicity issues in clinical drug development (2012)

Much progress has been made over the past decade with the development of novel methods for addressing increasingly more complex multiplicity problems arising in confirmatory Phase III clinical trials. This includes traditional problems with a single source of multiplicity, for example, analysis of multiple endpoints or dose-placebo contrasts. In addition, more advanced problems with several sources of multiplicity have attracted attention in clinical drug development. These problems include two or more families of objectives such as multiple endpoints evaluated at multiple dose levels or in multiple patient populations. This paper provides a review of concepts that play a central role in defining and solving multiplicity problems (error rate definitions) and introduces main classes of multiple testing procedures widely used in clinical trials (nonparametric, semiparametric, and parametric procedures). The paper also presents recent advances in multiplicity research, including gatekeeping procedures for clinical trials with multiple sets of objectives. The concepts and methods introduced in the paper are illustrated using several case studies on the basis of real clinical trials. Software implementation of commonly used multiple testing and gatekeeping procedures is discussed.
Progestins, Progesterone Receptors, and Breast Cancer (1996)

Endocrine therapy used either prophylactically or therapeutically for the treatment of locally advanced or metastatic breast cancers offers many advantages to patients whose tumors contain functional estrogen (ER) and progesterone (PR) receptors (Horwitz et al., 1975). The range of treatments defined as endocrine include surgical ablation of endocrine glands, adminis¬tration of pharmacologic doses of steroid hormones, chemical blockade of steroid hormone biosynthesis, and inhibition of endogenous steroid hormone action at the tumor with synthetic antagonists. The last of these approaches is the most widely used, making the antiestrogen tamoxifen the preferred first- line therapeutic agent for treatment of hormone-dependent metastatic breast cancer. The widespread use of tamoxifen reflects its efficacy and low toxicity, and the fact that it makes good physiological sense to block the local proliferative effects of estrogens directly at the breast. But are estrogens the only hormones with a proliferative impact on the breast and on breast cancers? This chapter focuses on evidence that progesterone also has proliferative actions in the breast; on preliminary data showing that progesterone antagonists may be new tools for the management of metastatic breast cancer; and on recent data suggesting that antiprogestin-occupied PRs have novel mechanisms of action that bear on tissue specificity and development of hormone resistance.
How microorganisms use hydrophobicity and what does this mean for human needs? (2014)

Cell surface hydrophobicity (CSH) plays a crucial role in the attachment to, or detachment from the surfaces. The influence of CSH on adhesion of microorganisms to biotic and abiotic surfaces in medicine as well as in bioremediation and fermentation industry has both negative and positive aspects. Hydrophobic microorganisms cause the damage of surfaces by biofilm formation; on the other hand, they can readily accumulate on organic pollutants and decompose them. Hydrophilic microorganisms also play a considerable role in removing organic wastes from the environment because of their high resistance to hydrophobic chemicals. Despite the many studies on the environmental and metabolic factors affecting CSH, the knowledge of this subject is still scanty and is in most cases limited to observing the impact of hydrophobicity on adhesion, aggregation or flocculation. The future of research seems to lie in finding a way to managing the microbial adhesion process, perhaps by steering cell hydrophobicity.
Acquisition of Polyfunctionality by Epstein-Barr Virus-Specific CD8 + T Cells Correlates with Increased Resistance to Galectin-1-Mediated Suppression (2009)

Latent membrane antigen 1 and -2 (LMP-1/2)-specific CD8(+) T cells from newly diagnosed and relapsed Hodgkin's lymphoma (HL) patients display a selective functional impairment. In contrast, CD8(+) T cells specific for Epstein-Barr virus (EBV) nuclear proteins and lytic antigens retain normal T-cell function. Reversion to a dysfunctional phenotype of LMP-1/2-specific T cells is coincident with the regression of HL. To delineate the potential basis for this differential susceptibility for the loss of function, we have carried out a comprehensive functional analysis of EBV-specific T cells using ex vivo multiparametric flow cytometry in combination with assessment of antigen-driven proliferative potential. This analysis revealed that LMP-1/2-specific T cells from healthy virus carriers display a deficient polyfunctional profile compared to that of T cells specific for epitopes derived from EBV nuclear proteins and lytic antigens. Furthermore, LMP-specific T-cells are highly susceptible to galectin-1-mediated immunosuppression and are less likely to degranulate following exposure to cognate peptide epitopes and poorly recognized endogenously processed epitopes from virus-infected B cells. More importantly, ex vivo stimulation of these T cells with an adenoviral vector encoding multiple minimal CD8(+) T-cell epitopes as a polyepitope, in combination with a gammaC cytokine, interleukin-2, restored polyfunctionality and shielded these cells from the inhibitory effects of galectin-1.
Unique ERα Cistromes Control Cell Type-Specific Gene Regulation (2008)

Estrogens play an important role in normal physiology and in a variety of pathological states involving diverse tissues including breast and bone. The mechanism by which estrogens exert cell type- and disease-specific effects, however, remains to be explained. We have compared the gene expression profile of the MCF7 breast cancer cell line with that of the osteoblast-like cell line U2OS-ERalpha by expression microarrays. We find that fewer than 10% of the 17beta-estradiol (E2)-regulated genes are common to both cell types. We have validated this in primary calvarial osteoblasts. To dissect the mechanism underlying the cell type-specific E2 regulation of gene expression in MCF7 and U2OS-ERalpha cells, we compared the ERalpha binding sites on DNA in the two cell types by performing chromatin immunoprecipitation (ChIP) on genomic tiling arrays (ChIP-on-chip). Consistent with the distinct patterns of E2-regulated gene expression in these two cell lines, we find that the vast majority of ERalpha binding sites are also cell type specific and correlate both in position and number with cell type-specific gene regulation. Interestingly, although the forkhead factor FoxA1 plays a critical role in defining the ERalpha cistrome in MCF7 cells, it is not expressed in U2OS-ERalpha cells, and forkhead motifs are not enriched in the ERalpha cistrome in these cells. Finally, the ERalpha cistromes are correlated with cell type-specific epigenetic histone modifications. These results support a model for the cell type-specific action of E2 being driven primarily through specific ERalpha occupancy of epigenetically marked cis-regulatory regions of target genes.
A low-power low-voltage NMOS bulk-mixer with 20 GHz bandwidth in 90 nm CMOS (2004)

A fully differential low-voltage mixer topology is presented. The problem of stacking input-, cascode- and switching-transistors within 1.2 V supply voltage is solved by the use of a bulk driven mixer core. In order to demonstrate the feasibility a test chip was manufactured in INFINEON triple well 90 nm standard CMOS process. The differential mixer includes an on-chip resistive 50 /spl Omega/ termination and an operational amplifier for measurements. The chip features a gain of 3.2 dB, a DSB noise figure of 17.4 dB, an input IP3 of -2.1 dBm, an input 1dB compression point of -13.3 dBm and consumes 1.8 mW at a power supply voltage of 1.2 V. The mixer has a 3 dB low-pass bandwidth of 20 GHz.
A Conserved GXXXG Motif in APH-1 Is Critical for Assembly and Activity of the γ-Secretase Complex (2004)

The multipass membrane protein APH-1, found in the gamma-secretase complex together with presenilin, nicastrin, and PEN-2, is essential for Notch signaling in Caenorhabditis elegans embryos and is required for intramembrane proteolysis of Notch and beta-amyloid precursor protein in mammalian and Drosophila cells. In C. elegans, a mutation of the conserved transmembrane Gly123 in APH-1 (mutant or28) leads to a notch/glp-1 loss-of-function phenotype. In this study, we show that the corresponding mutation in mammalian APH-1aL (G122D) disrupts the physical interaction of APH-1aL with hypoglycosylated immature nicastrin and the presenilin holoprotein as well as with mature nicastrin, presenilin, and PEN-2. The G122D mutation also reduced gamma-secretase activity in intramembrane proteolysis of membrane-tethered Notch. Moreover, we found that the conserved transmembrane Gly122, Gly126, and Gly130 in the fourth transmembrane region of mammalian APH-1aL are part of the membrane helix-helix interaction GXXXG motif and are essential for the stable association of APH-1aL with presenilin, nicastrin, and PEN-2. These findings suggest that APH-1 plays a GXXXG-dependent scaffolding role in both the initial assembly and subsequent maturation and maintenance of the active gamma-secretase complex.
Hybrid III-V Silicon Photonic Integrated Circuits for Optical Communication Applications (2016)

This paper summarizes recent advances of integrated hybrid InP/silicon-on-insulator lasers and transmitters based on a wafer bonding technique. First, directly modulated hybrid III-V/Si tunable lasers integrated with an external ring resonator filter are demonstrated, enabling the improvement of the dynamic extinction ratio. An efficient tunable filter is then reported mainly for access applications. Finally, results on integrated distributed feedback laser and electro-absorption modulator at 1.3 μm are presented, showing the capability of operation up to <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\text{32}\,\text{Gb}/\text{s}$</tex-math></inline-formula> . Meanwhile, an integrated tunable laser with an electro-absorption modulator is demonstrated at 1.5 μm, exhibiting excellent bit-error-rate performance at <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\text{10}\,\text{Gb}\text{/s}$</tex-math> </inline-formula> .
Operational Evaluation of ASON/GMPLS Interdomain Capability over a JGN II Network Testbed (2008)

Traffic engineering in backbone networks is an important issue in supporting an appropriate QoS level to accommodate various types of traffic flows efficiently. Automatically switched optical networks and generalized multiprotocol label switching control planes are promising functionalities to achieve the sophisticated mechanism of interdomain traffic engineering. In this article we address dynamic operational scenarios to control IP traffic flows using the ASON/GMPLS control plane. This includes cut-through IP/MPLS routers and the rerouting of failed links through the tunnel of optical label-switched paths. This article presents an operational evaluation of traffic engineering. More specifically, we present QoS recovery for protecting high priority traffic using policy controllers and fault recovery of inter-domain LSPs over the JGN II network testbed. This article evaluates and discusses the feasibility of these operational scenarios using state-of-the-art optical switching and control- plane technologies.