gebhart/patrepeval huggingface dataset:
CXC Chemokine Receptor-2 Ligands Are Required for Neutrophil-Mediated Host Defense in Experimental Brain Abscesses (2001)

We have developed a mouse brain abscess model by using Staphylococcus aureus, one of the main etiologic agents of brain abscesses in humans. Direct damage to the blood-brain barrier was observed from 24 h to 7 days after S. aureus exposure as demonstrated by the accumulation of serum IgG in the brain parenchyma. Evaluation of brain abscesses by immunohistochemistry and flow cytometry revealed a prominent neutrophil infiltrate. To address the importance of neutrophils in the early containment of S. aureus infection in the brain, mice were transiently depleted of neutrophils before implantation of bacteria-laden beads. Neutrophil-depleted animals consistently demonstrated more severe brain abscesses and higher CNS bacterial burdens compared with control animals. S. aureus led to the induction of numerous chemokines in the brain, including macrophage-inflammatory protein (MIP)-1alpha/CCL3, MIP-1beta/CCL4, MIP-2/CXCL1, monocyte chemoattractant protein-1/CCL2, and TCA-3/CCL1, within 6 h after bacterial exposure. These chemokines also were expressed by both primary cultures of neonatal mouse microglia and astrocytes exposed to heat-inactivated S. aureus in vitro. Because neutrophils constitute the majority of the cellular infiltrate in early brain abscess development, subsequent analysis focused on MIP-2 and KC/CXCL1, two neutrophil-attracting CXC chemokines. Both MIP-2 and KC protein levels were significantly elevated in the brain after S. aureus exposure. Neutrophil extravasation into the brain parenchyma was impaired in CXCR2 knockout mice and was associated with increased bacterial burdens. These studies demonstrate the importance of the CXCR2 ligands MIP-2 and KC and neutrophils in the acute host response to S. aureus in the brain.
A single cycle VLSI CISC-based workstation: system overview and performance characteristics (2003)

The NexGen workstation is based on a VLSI processor chip set that brings advanced mainframe and workstation technologies to the industry standard desktop market. The processor is based on a complex instruction set architecture to support OS/2 applications. The processor achieves single-cycle execution of most instructions. The processor implementation requires 2.0 million transistors, plus an additional 6.5 million transistors in the cache RAMs (random-access memories).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Involvement of CPP32/Yama(-like) proteases in Fas-mediated apoptosis. (1996)

Fas (Apo-1/CD95) belongs to the tumor necrosis factor/nerve growth factor receptor family and transmits apoptotic signals by binding to its ligand. Interleukin-1beta-converting enzyme (ICE), which shows substantial homology to the product of the cell death gene, ced-3, of Caenorhabditis elegans, is reported to be involved in Fas-mediated apoptosis. Using two human carcinoma-derived cell lines with undetectable levels of ICE, we found that an agonistic antihuman Fas antibody induces the activation of CPP32/Yama(-like) proteases that are ICE(-like) protease family members, and that a tetrapeptide inhibitor of CPP32/Yama protease, DEVD-CHO, inhibits the Fas-mediated activation of the proteases, Fas-mediated apoptosis, and CPP32/Yama(-like) proteolytic activities in vitro. Fas-mediated apoptosis is inhibited by the CPP32/Yama inhibitor DEVD-CHO, but not by the ICE inhibitor YVAD-CHO, suggesting a dominant role for the CPP32/Yama(-like) proteases and not ICE itself in Fas-mediated apoptosis of the human carcinoma cell lines.
Energetics of tetracycline efflux system encoded by Tn10 in Escherichia coli (1985)

Tritiated tetracycline was actively accumulated in inverted membrane vesicles prepared from Escherichia coli W3104rif, which has a transposon, Tn10, on the plasmid, R388, by means of a protonmotive force when NADH was added as an energy source. The tetracycline accumulation was reduced to about one-half the full value on the addition of a cation/proton-exchange ionophore, nigericin. In contrast, remarkable stimulation of the tetracycline accumulation was observed with a K+-specific ionophore, valinomycin. The accumulation of [3H]tetracycline could also be driven by an artificially imposed interior-acidic pH gradient (delta pH), but not, however, by an artificially imposed interior-positive membrane potential (delta psi). These results strongly indicate that the plasmid-encoded tetracycline transport was mainly due to an electrically neutral proton/tetracycline antiport system.
Role of the androgen receptor in breast cancer and preclinical analysis of enzalutamide (2014)

AR to ER ratio may influence breast cancer response to traditional endocrine therapy. Enzalutamide elicits different effects on E2-mediated breast cancer cell proliferation than bicalutamide. This preclinical study supports the initiation of clinical studies evaluating enzalutamide for treatment of AR+ tumors regardless of ER status, since it blocks both androgen- and estrogen- mediated tumor growth.
Comparative immunogenicity of conjugates composed of Escherichia coli O111 O-specific polysaccharide, prepared by treatment with acetic acid or hydrazine, bound to tetanus toxoid by two synthetic schemes (1995)

Escherichia coli O111, of various H types and virulence factors, causes enteritis throughout the world, especially in young children. This O type is found rarely in healthy individuals. Serum antibodies to the O-specific polysaccharide of O111 lipopolysaccharide (LPS) protect mice and dogs against infection with this E. coli serotype. The O111 O-specific polysaccharide is composed of a pentasaccharide repeat unit with two colitoses bound to the C-3 and C-6 of glucose in a trisaccharide backbone; this structure is identical to that of Salmonella adelaide (O35), another enteric pathogen. Nonpyrogenic O111 O-specific polysaccharide was prepared by treatment of its LPS with acetic acid (O-SP) or the organic base hydrazine (DeA-LPS). The O-SP had a reduced concentration of colitose. These products were derivatized with adipic acid dihydrazide (ADH) or thiolated with N-succinimidyl-3(2-pyridyldithio) propionate (SPDP). The four derivatives were covalently bound to tetanus toxoid (TT) by carbodiimide-mediated condensation or with SPDP to form conjugates. Immunization of BALB/c and general-purpose mice by a clinically acceptable route showed that DeA-LPS-TTADH, of the four conjugates, elicited the highest level of LPS antibodies. Possible reasons to explain this differential immunogenicity between the four conjugates are discussed.
Current Animal Models of Bronchial Asthma (2006)

Human asthma is on the rise worldwide. The necessity to develop effective treatments against it requires an organized effort which covers every aspect of the disease from the pathological alterations via the genetic background to the use and development of active remedies. In these processes animal experiments have served an indispensable role. As asthma is not a natural disease in the animal kingdom the variety for artificially established animal models is quite wide. The possible selection ranges from the laboratory mouse to the horse, it includes ferret and sheep and even favorite pets such as cats and dogs. The large number of the models indicates that to some extent they might not be appropriate or it means that there is no generally accepted model of human asthma. Whatever the reason for this diversity animal models helped us to understand the detailed pathogenesis of some aspects of the disease, they helped us to develop compounds which are more active then previously used ones, and these models proved to us that human asthma is a unique, possibly species-specific disease the eradication of which requires a huge effort. This enormous task should include the collaboration of the clinical and basic research for the development of improved, advanced animal models, which in turn could strengthen our understanding about human asthma.
A MULTI-OBJECTIVE EVOLUTIONARY ALGORITHM USING NEURAL NETWORKS TO APPROXIMATE FITNESS EVALUATIONS (2005)

Two different methods to accelerate the search of a Multi-Objective Evolutionary Algorithm (MOEA) using Artificial Neural Networks are presented. Two different methods are proposed. One using ANN to approximate the fitness of the solutions alternated with the real fitness evaluation, being the ANN approximation used only when the estimated error of the neural network was lower than a pre-defined value. In the second method, the ANN is used as a local search strategy by defining new better solutions from the precedent generation. These methods can substantially reduce the number of fitness evaluations on computational expensive problems while not compromise the good search capabilities of MOEA. The efficiency of the methods proposed is tested on several benchmark functions as well on a real multi-optimization problem of polymer extrusion.
Building Networking Applications from a NoC-Enhanced FPGA (2015)

An embedded Network-on-Chip (NoC) has been proposed to augment the traditional, fine-grained FPGA interconnect with a fast and efficient system-level interconnect. This thesis aims to build the case for its inclusion by presenting complete applications that can benefit from a NoC-enhanced FPGA, and tools to facilitate their design. The applications chosen – network switches and packet processors – target Software-Defined Networking (SDN), a rapidly growing field in computer networks. The presented network switch architecture uses the NoC as a crossbar and a new buffering scheme, achieving 819 Gb/s 16×16 switching, while being 1.8× and 1.6× more hardware- and power-efficient, respectively, compared to the most efficient previous FPGA-based design. A new packet processor design style is also presented, using the embedded NoC to provide high degrees of efficiency (1.7×-3.2× less area compared to previous work), performance (400G and 800G), and flexibility suitable for programmable computer networks.
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)

The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
HIV-1 entry inhibitors: an overview (2009)

A CCR5 antagonist and a fusion inhibitor are approved for use as HIV-1 entry inhibitors. Development of drugs targeting other steps in HIV-1 entry is ongoing.
Highly Flexible WDM PON System with a Single TDM Time Lens Source Enabling Record 150 km Downstream Reach (2018)

We propose a new OLT transmitter for WDM-PON based on optical Fourier transformation of a single-source TDM-PON signal to WDM-PON signals. We demonstrate flexible bit rates (10×1-to-64×2Gb/s) and 40×1Gb/s WDM-PON record unamplified downstream transmission reach of 150 km.
3D spatial self-organization of a modular artificial skin (2014)

In this paper, we present a new approach to spatially self-organize a modular artificial skin in 3D space. We were motivated by the demand to efficiently and automatically acquire the position and orientation of a steadily growing number of artificial skin sensor elements. Here, we combine our 3D surface reconstruction algorithm for individual patches of artificial skin, with a common active visual marker approach. Light emitting diodes, built into every element of our modular artificial skin, enable us to turn each reconstructed patch of skin into an active 6 DoF visual marker. With the help of a calibrated monocular camera, we can then estimate the homogeneous transformations between multiple, at least partially visible skin patches e.g. when distributed on the body of a robot. Our approach allows to quickly combine distributed tactile and visual coordinate systems into one homogeneous rigid body representation. We demonstrate the robustness of our approach by calibrating several patches mounted on a robot arm using only a standard web-cam.
Expanded spectrum of viral therapy in the treatment of nervous system tumors (1992)

Despite aggressive therapy, many nervous system neoplasms, including malignant gliomas, medulloblastomas, malignant meningiomas, and neurofibrosarcomas, maintain high mortality rates. The authors recently utilized a thymidine kinase-negative herpes simplex-1 mutant virus, dlsptk, with reduced neurovirulence, for the effective treatment of malignant human gliomas in cell culture and in nude mouse in vivo models. The range of human nervous system tumors that might be responsive to viral therapy is now expanded. Three medulloblastoma, four malignant or atypical meningioma, and five neurofibrosarcoma cell lines or early-passage tumors were treated with the dlsptk virus in cell culture. A cell death rate of at least 99% was evident in every tumor tested for at least one multiplicity of infection within 14 days after treatment. Control tumor cell cultures remained viable. To test dlsptk therapy in vivo, the authors treated human medulloblastoma subcutaneous xenografts with two doses of dlsptk. Mean growth ratios were significantly inhibited in the treated group when compared to control tumors, and there was a significant number of tumor regressions in the treated animals. Similar results were seen with human malignant meningioma xenografts in a subrenal capsule study. These results encourage the further investigation of viral therapy in the treatment of a broad spectrum of nervous system tumors refractory to conventional treatment methods.
A Molecular Imaging Primer: Modalities, Imaging Agents, and Applications (2012)

Molecular imaging is revolutionizing the way we study the inner workings of the human body, diagnose diseases, approach drug design, and assess therapies. The field as a whole is making possible the visualization of complex biochemical processes involved in normal physiology and disease states, in real time, in living cells, tissues, and intact subjects. In this review, we focus specifically on molecular imaging of intact living subjects. We provide a basic primer for those who are new to molecular imaging, and a resource for those involved in the field. We begin by describing classical molecular imaging techniques together with their key strengths and limitations, after which we introduce some of the latest emerging imaging modalities. We provide an overview of the main classes of molecular imaging agents (i.e., small molecules, peptides, aptamers, engineered proteins, and nanoparticles) and cite examples of how molecular imaging is being applied in oncology, neuroscience, cardiology, gene therapy, cell tracking, and theranostics (therapy combined with diagnostics). A step-by-step guide to answering biological and/or clinical questions using the tools of molecular imaging is also provided. We conclude by discussing the grand challenges of the field, its future directions, and enormous potential for further impacting how we approach research and medicine.
The glycoprotein products of varicella-zoster virus gene 14 and their defective accumulation in a vaccine strain (Oka) (1990)

Many characteristics of the putative protein encoded by varicella-zoster virus (VZV) open reading fram (ORF) 14 indicate that it is a glycoprotein, which has been designated gpV. To identify the protein products of the gene, the coding sequences were placed under the control of the vaccinia virus p7.5 promoter and recombinant vaccinia viruses were constructed. Heterogeneous polypeptides with molecular weights of 95,000 to 105,000 (95K to 105K polypeptides) were expressed in cells infected by a vaccinia virus recombinant (vKIP5) containing ORF 14 from VZV Scott but were not expressed by control vaccinia viruses. These polypeptides were recognized by antibodies present in human sera that contained high levels of anti-VZV antibodies. Conversely, antisera raised in rabbits inoculated with vKIP5 reacted specifically with heterogeneous 95K to 105K polypeptides present in VZV Scott-infected but not uninfected cells; these polypeptides show a patchy plasma membrane fluorescence pattern in VZV Scott-infected cells. These same antisera neutralized VZV strain Scott infectivity in the absence of complement. Endoglycosidase F treatment of isolated gpV polypeptides and tunicamycin treatment of cells infected with the vKIP5 recombinant indicated that the polypeptides were glycosylated. Three sets of data imply that the VZV strain Oka, which has been used to produce a live attenuated virus vaccine, accumulates low levels of gpV polypeptides relative to wild-type strains: (i) blocking of antibodies in human sera with excess VZV Oka-infected cell antigen yielded residual antibodies which were reactive with the 95K to 105K gpV polypeptides expressed in cells infected by VZV strain Scott and by the vKIP5 vaccinia virus recombinant, but not with Oka-infected cell polypeptides; (ii) antisera raised to vKIP5 detected very low levels of reactive polypeptides made in VZV Oka-infected cells and neutralized VZV Oka virus much less efficiently than VZV Scott; and (iii) comparisons of the reactivity of sera from live attenuated virus vaccine vaccinees with sera derived from patients recovering from wild-type infections indicated greatly reduced levels of gpV-specific antibodies in some vaccinees.
Cleavage of NIK by the API2-MALT1 Fusion Oncoprotein Leads to Noncanonical NF-κB Activation (2011)

Proper regulation of nuclear factor κB (NF-κB) transcriptional activity is required for normal lymphocyte function, and deregulated NF-κB signaling can facilitate lymphomagenesis. We demonstrate that the API2-MALT1 fusion oncoprotein created by the recurrent t(11;18)(q21;q21) in mucosa-associated lymphoid tissue (MALT) lymphoma induces proteolytic cleavage of NF-κB-inducing kinase (NIK) at arginine 325. NIK cleavage requires the concerted actions of both fusion partners and generates a C-terminal NIK fragment that retains kinase activity and is resistant to proteasomal degradation. The resulting deregulated NIK activity is associated with constitutive noncanonical NF-κB signaling, enhanced B cell adhesion, and apoptosis resistance. Our study reveals the gain-of-function proteolytic activity of a fusion oncoprotein and highlights the importance of the noncanonical NF-κB pathway in B lymphoproliferative disease.
Development and Evaluation of a Novel Loop-Mediated Isothermal Amplification Method for Rapid Detection of Severe Acute Respiratory Syndrome Coronavirus (2004)

ABSTRACT The development and evaluation of a one-step single-tube accelerated real-time quantitative reverse transcription (RT) loop-mediated isothermal amplification (LAMP) assay is reported for rapid detection of the severe acute respiratory syndrome coronavirus (SARS-CoV) replicase gene. A total of 49 samples (15 throat washes, 13 throat swabs, and 21 combined throat and nasal swabs) collected from patients admitted to the Hanoi-French and Ninhbinh hospitals in Vietnam during the SARS epidemic were evaluated and compared to conventional RT-PCR. The RT-LAMP assay demonstrated 100-fold-greater sensitivity, with a detection limit of 0.01 PFU. The sensitivity and specificity of RT-LAMP assay for detecting viral RNA in clinical specimens with regard to RT-PCR were 100 and 87%, respectively. The specificity of the RT-LAMP assay was further validated by restriction analysis as well as nucleotide sequencing of the amplified product. The concentration of virus in most of the clinical samples was 0.1 PFU (0.1 to 10 2 PFU), as determined from the standard curve of SARS RT-LAMP and based on the time of positivity. The assay procedure is quite simple, wherein the amplification is carried out in a single tube under isothermal conditions at 63°C, and the result can be obtained in less than 1 h (as early as 11 min). Thus, the RT-LAMP assay reported here has the advantages of rapid amplification, simple operation, and easy detection and will be useful for rapid and reliable clinical diagnosis of SARS-CoV in developing countries.
Cyclophane Chemistry: Synthesis, Structures and Reactions (1993)

[n ]Phanes [2.2]Phanes [3.3]Phanes [m.n]Phanes (m, n 2) Multiply Bridged Phanes Multi-layered Cyclophanes [m n] [m,n]Phanes Porphyrinophanes Protophanes' and Aliphanes' Exotic Phanes Naturally Occurring Phanes Molecular Recognition with Phanes as Host Molecules Concluding Remarks and Future Outlook Indexes.
The Sortase SrtA of Listeria monocytogenes Is Involved in Processing of Internalin and in Virulence (2002)

Listeria monocytogenes is an intracellular gram-positive human pathogen that invades eucaryotic cells. Among the surface-exposed proteins playing a role in this invasive process, internalin belongs to the family of LPXTG proteins, which are known to be covalently linked to the bacterial cell wall in gram-positive bacteria. Recently, it has been shown in Staphylococcus aureus that the covalent anchoring of protein A, a typical LPXTG protein, is due to a cysteine protease, named sortase, required for bacterial virulence. Here, we identified in silico from the genome of L. monocytogenes a gene, designated srtA, encoding a sortase homologue. The role of this previously unknown sortase was studied by constructing a sortase knockout mutant. Internalin was used as a reporter protein to study the effects of the srtA mutation on cell wall anchoring of this LPXTG protein in L. monocytogenes. We show that the srtA mutant (i) is affected in the display of internalin at the bacterial surface, (ii) is significantly less invasive in vitro, and (iii) is attenuated in its virulence in the mouse. These results demonstrate that srtA of L. monocytogenes acts as a sortase and plays a role in the pathogenicity.