gebhart/patrepeval huggingface dataset:
Pattern of aromatic and hydrophobic amino acids critical for one of two subdomains of the VP16 transcriptional activator. (1993)

Structural features of the transcriptional activation domain of the herpes simplex virion protein VP16 were examined by oligonucleotide-directed mutagenesis. Extensive mutagenesis at position 442 of the truncated VP16 activation domain (delta 456), normally occupied by a phenylalanine residue, demonstrated the importance of an aromatic amino acid at that position. On the basis of an alignment of the VP16 sequence surrounding Phe-442 and the sequences of other transcriptional activation domains, we subjected leucine residues at positions 439 and 444 of VP16 to mutagenesis. Results from these experiments suggest that bulky hydrophobic residues flanking Phe-442 also contribute significantly to the function of the truncated VP16 activation domain. Restoration of amino acids 457-490 to various Phe-442 mutants partially restored activity. Although the pattern of amino acids surrounding Phe-473 resembles that surrounding Phe-442, mutations of Phe-473 did not dramatically affect activity; in fact, Phe-475 appears more sensitive to mutations than does Phe-473. We infer that the two regions of VP16 (amino acids 413-456 and 457-490) possess unique structural features, although neither is likely to be an amphipathic alpha-helix or an "acidic blob." These results, considered with previous in vitro activation and inhibition studies, suggest that the two subdomains of VP16 affect transcription by different mechanisms.
Optical millimeter-wave generation or up-conversion using external modulators (2005)

We have experimentally compared the performances of optical millimeter-wave generation or up-conversion using external modulators based on different modulation schemes. The generated or up-converted optical millimeter wave using the optical carrier suppression (OCS) modulation scheme shows the highest receiver sensitivity, highest spectral efficiency, and smallest power penalty over long-distance delivery. Moreover, the OCS modulation scheme has a simple configuration and low-frequency bandwidth requirement for both electrical and optical components. Employing an OCS modulation scheme, 16-channel dense wavelength-division multiplexing signals at 2.5-Gb/s per channel have been up-converted to a 40-GHz carrier simultaneously.
Calcium, mitochondria and reperfusion injury: a pore way to die (2006)

When mitochondria are exposed to high Ca2+ concentrations, especially when accompanied by oxidative stress and adenine nucleotide depletion, they undergo massive swelling and become uncoupled. This occurs as a result of the opening of a non-specific pore in the inner mitochondrial membrane, known as the MPTP (mitochondrial permeability transition pore). If the pore remains open, cells cannot maintain their ATP levels and this will lead to cell death by necrosis. This article briefly reviews what is known of the molecular mechanism of the MPTP and its role in causing the necrotic cell death of the heart and brain that occurs during reperfusion after a long period of ischaemia. Such reperfusion injury is a major problem during cardiac surgery and in the treatment of coronary thrombosis and stroke. Prevention of MPTP opening either directly, using agents such as cyclosporin A, or indirectly by reducing oxidative stress or Ca2+ overload, provides a protective strategy against reperfusion injury. Furthermore, mice in which a component of the MPTP, CyP-D (cyclophilin D), has been knocked out are protected against heart and brain ischaemia/reperfusion. When cells experience a less severe insult, the MPTP may open transiently. The resulting mitochondrial swelling may be sufficient to cause release of cytochrome c and activation of the apoptotic pathway rather than necrosis. However, the CyP-D-knockout mice develop normally and show no protection against a range of apoptotic stimuli, suggesting that the MPTP does not play a role in most forms of apoptosis.
An inflammation-based prognostic score and its role in the nutrition-based management of patients with cancer (2008)

Progressive involuntary weight loss, in particular the loss of lean tissue, is common in patients with advanced cancer and has long been recognised to result in a deterioration in performance status and quality of life, increased morbidity and mortality. The aetiology of such weight loss or cachexia is complex and involves both tumour and host responses. Thus, identification of patients who are or are likely to become cachectic has been problematic. In addition to a reduction in appetite and increased satiety leading to poor dietary intake, there is now increasing clinical evidence that the activation of a chronic ongoing systemic inflammatory response is one of the earliest and most important contributory factors to cachexia. Such findings help to explain the failure of simple nutritional programmes to reverse weight loss adequately in patients with cancer. In the present paper the development of an inflammation-based score is described, which is derived from the acute-phase proteins C-reactive protein and albumin and is termed the Glasgow prognostic score (GPS). Its value as a predictor of survival, independent of tumour stage, performance status and treatment (active or palliative), has been shown in a variety of advanced common solid tumours. The nature of the relationship between the GPS, appetite, body composition, performance status and quality of life of the patient with advanced cancer will be described. Recently, it has become evident that the systemic inflammatory response is also present in a smaller proportion of patients with primary operable cancer and is also predictive of disease progression and poor survival. The role of GPS in clinical decision making will be discussed.
Group Interactions in Wireless Cooperative Networks (2011)

This paper introduces a user cooperation technique thought to support content sharing services in wireless environments. WLAN inter-device data exchange is effectively exploited, combined with network coding techniques. Specifically, the content of interest is seeded into the WLAN user group through cellular-enabled devices, while short-range links are used to cooperatively distribute data to all the interested users. The focus is on scenarios where nodes in the same network area are not all interested in the same content, they rather form different cooperative groups. Beneficial effects of intra-group cooperation have already been demonstrated in the past; differently, this research focuses on inter-group cooperation. Objective of this paper is the investigation of any obtainable benefit (either in terms of energy consumption, service latency, or probability of successful service distribution) from such a cooperative attitude of different groups.
Isolation and characterization of the beta-ketoacyl-acyl carrier protein synthase III gene (fabH) from Escherichia coli K-12. (1992)

beta-Ketoacyl-acyl carrier protein (ACP) synthase III catalyzes the condensation of acetyl-CoA with malonyl-ACP in dissociated (Type II) fatty acid synthase systems. A synthase III mutant was used to localize the structural gene to the 24.5-min region of the Escherichia coli chromosome, and the defective synthase III allele was designated fabH1. The fabH gene was identified on a 1.3-kilobase NruI-HindIII chromosomal DNA fragment (plasmid pWO114) that complemented the enzymatic defect in fabH1 strains. The NruI-HindIII fragment was sequenced and contained a single open reading frame predicted to encode a 33,517-dalton protein with an isoelectric point of 4.85. The fabH sequence contained an Ala-Cys-Ala tripeptide characteristic of condensing enzyme active sites. A T7 expression system showed that the NruI-HindIII fragment directed the synthesis of a single 34,800-dalton protein. This protein was purified and the order of the amino-terminal 30 residues of the protein corresponded exactly to the amino acid structure predicted from the DNA sequence. The purified protein possessed both acetoacetyl-ACP synthase and acetyl-CoA:ACP transacylase activities, and cells harboring plasmid pWO114 overproduced the two activities, supporting the conclusion that a single protein carries out both reactions. Overproduction of synthase III resulted in a significant increase in shorter-chain fatty acids in the membrane phospholipids. These catalytic properties are consistent with the proposed role of synthase III in the initiation of fatty acid synthesis.
Evaluating SFI for a CISC architecture (2006)

Executing untrusted code while preserving security requires that the code be prevented from modifying memory or executing instructions except as explicitly allowed. Software-based fault isolation (SFI) or “sandboxing” enforces such a policy by rewriting the untrusted code at the instruction level. However, the original sandboxing technique of Wahbe et al. is applicable only to RISC architectures, and most other previous work is either insecure, or has been not described in enough detail to give confidence in its security properties. We present a new sandboxing technique that can be applied to a CISC architecture like the IA-32, and whose application can be checked at load-time to minimize the TCB. We describe an implementation which provides a robust security guarantee and has low runtime overheads (an average of 21 % on the SPECint2000 benchmarks). We evaluate the utility of the technique by applying it to untrusted decompression modules in an archive tool, and its safety by constructing a machine-checked proof that any program approved by the verification algorithm will respect the desired safety property. 1
In Vivo Detection of Dendritic Cell Antigen Presentation to CD4+ T Cells (1997)

Although lymphoid dendritic cells (DC) are thought to play an essential role in T cell activation, the initial physical interaction between antigen-bearing DC and antigen-specific T cells has never been directly observed in vivo under conditions where the specificity of the responding T cells for the relevant antigen could be unambiguously assessed. We used confocal microscopy to track the in vivo location of fluorescent dye-labeled DC and naive TCR transgenic CD4(+) T cells specific for an OVA peptide-I-Ad complex after adoptive transfer into syngeneic recipients. DC that were not exposed to the OVA peptide, homed to the paracortical regions of the lymph nodes but did not interact with the OVA peptide-specific T cells. In contrast, the OVA peptide-specific T cells formed large clusters around paracortical DC that were pulsed in vitro with the OVA peptide before injection. Interactions were also observed between paracortical DC of the recipient and OVA peptide-specific T cells after administration of intact OVA. Injection of OVA peptide-pulsed DC caused the specific T cells to produce IL-2 in vivo, proliferate, and differentiate into effector cells capable of causing a delayed-type hypersensitivity reaction. Surprisingly, by 48 h after injection, OVA peptide-pulsed, but not unpulsed DC disappeared from the lymph nodes of mice that contained the transferred TCR transgenic population. These results demonstrate that antigen-bearing DC directly interact with naive antigen-specific T cells within the T cell-rich regions of lymph nodes. This interaction results in T cell activation and disappearance of the DC.
Quantitative structure–activity relationship study on BTK inhibitors by modified multivariate adaptive regression spline and CoMSIA methods (2015)

Bruton's tyrosine kinase (BTK) plays a crucial role in B-cell activation and development, and has emerged as a new molecular target for the treatment of autoimmune diseases and B-cell malignancies. In this study, two- and three-dimensional quantitative structure-activity relationship (2D and 3D-QSAR) analyses were performed on a series of pyridine and pyrimidine-based BTK inhibitors by means of genetic algorithm optimized multivariate adaptive regression spline (GA-MARS) and comparative molecular similarity index analysis (CoMSIA) methods. Here, we propose a modified MARS algorithm to develop 2D-QSAR models. The top ranked models showed satisfactory statistical results (2D-QSAR: Q(2) = 0.884, r(2) = 0.929, r(2)pred = 0.878; 3D-QSAR: q(2) = 0.616, r(2) = 0.987, r(2)pred = 0.905). Key descriptors selected by 2D-QSAR were in good agreement with the conclusions of 3D-QSAR, and the 3D-CoMSIA contour maps facilitated interpretation of the structure-activity relationship. A new molecular database was generated by molecular fragment replacement (MFR) and further evaluated with GA-MARS and CoMSIA prediction. Twenty-five pyridine and pyrimidine derivatives as novel potential BTK inhibitors were finally selected for further study. These results also demonstrated that our method can be a very efficient tool for the discovery of novel potent BTK inhibitors.
A self-coherence anti-jamming GPS receiver (2005)

In this correspondence, we present a self-coherence anti-jamming Global Positioning System (GPS) receiver that relies on the unique structure of the coarse/acquisition (C/A) code of the GPS signals. Since the C/A-code is repeated 20 times within each navigation symbol, the GPS signal exhibits strong self-coherence between chip-rate samples separated by integer multiples of the spreading gain. The proposed receiver utilizes this inherent self-coherence property to excise interferers whose temporal structures are different from those of the GPS signals. It is shown that the proposed receiver is a blind receiver that does not require the knowledge of the satellite positions.
Quantitative analyses of cadmium: quality assured? (1992)

Legislation has been a powerful stimulus for measuring the concentrations of cadmium in many different matrices. Unfortunately, much of the quantitative data in the literature is flawed because of a paucity of information on the reliability of sampling and measurement. Non-specific analytical methods, inaccurate calibration, lack of matrix reference materials, poor laboratory technique in general, lack of statistical control, and ignorance of contamination all militate against gathering truly valid data. The implications for bioavailability of chemical and physical speciation also need to be considered, especially in the analysis of airborne particulates and foodstuffs. Effective quality assurance serves several distinct purposes: (1) to allay analysts' concern for the quality of their work; (2) to discharge management's responsibility for the cost and quality of the laboratory's output; (3) to inform users of the quality of the data sets; and (4) to provide archival data and documentation.
Serum Amyloid A Induces Monocyte Tissue Factor (2007)

C-reactive protein (CRP) and serum amyloid A (SAA) increase in the blood of patients with inflammatory conditions and CRP-induced monocyte tissue factor (TF) may contribute to inflammation-associated thrombosis. This study demonstrates that SAA is a potent and rapid inducer of human monocyte TF. SAA induced TF mRNA in PBMC within 30 min and optimal procoagulant activity within 4 h, whereas CRP (25 mug/ml)-induced activity was minimal at this time. Unlike CRP, SAA did not synergize with LPS. Procoagulant activity was inhibited by anti-TF and was dependent on factors VII and X, and TF Ag levels were elevated on CD14(+) monocytes. Responses were optimal with lymphocytes, although these were not obligatory. Inhibitor studies indicate activation of NF-kappaB through the ERK1/2 and p38 MAPK pathways; the cyclo-oxygenase pathway was not involved. SAA-induced TF was partially inhibited by high-density lipoprotein, but not by low-density lipoprotein or by apolipoprotein A-I. SAA is a ligand for the receptor for advanced glycation end products (RAGE), and TF generation was suppressed by approximately 50% by a RAGE competitor, soluble RAGE, and by approximately 85% by anti-RAGE IgG. However, another RAGE ligand, high mobility group box-1 protein, capable of inducing monocyte chemotactic protein-1 mRNA in 2 h, did not induce TF within 24 h. Cross-linking studies confirmed SAA binding to soluble RAGE. Elevated SAA is a marker of disease activity in patients with rheumatoid arthritis, and PBMC from patients with rheumatoid arthritis were more sensitive to SAA than normals, suggesting a new link between inflammation and thrombosis.
Heterocyclization of Orthoaminoester and Orthoamino‐nitrile‐thieno[2,3‐c]pyridine: The Facile Synthesis of Fused Pyridothienopyrimidines. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Controlling molecular ground-state dissociation by optimizing vibrational ladder climbing (2003)

To achieve large population transfer to high vibrational levels in a selected ground-state mode of a polyatomic molecule [Cr(CO)6], we apply chirped femtosecond mid-infrared laser pulses at 2000 cm−1 to optimize vibrational ladder climbing as an energy deposition mechanism, which in turn controls the outcome of a unimolecular dissociation process. Its dependence on excitation parameters (frequency, intensity, chirp) is investigated and found to be in excellent agreement with a theoretical calculation. In particular, it is shown that optimizing vibrational ladder climbing allows for coherently controlled excitation even in a polyatomic molecule.
Soulful Voices: Birds, Language and Prophecy in Amazonia (2010)

This paper explores the significance of human-bird interactions among Peruvian Urarina, focusing on bird speech and its relation to concepts of voice, power and prophecy. It suggests that while the potential status of birds as subjects remains complex and uncertain, this very ambiguity has stimulated the development and refinement of more abstract ideas of meaning, language, and what it means to be human. The ways in which bird sounds signify is not simply arbitrary, but rather indexical or analogic, leading to the impression of a privileged access to reality and a powerful claim to truth. Together with their vocal transparency - their capacity to give voice to messages or insights that purportedly originate with powerful divinities – this largely accounts for birds’ prophetic qualities, and their role as a model of the authoritative and efficacious speech striven for by ritual specialists, in which meaning cannot be reduced to the intentions of a single speech actor. This particular language ideology, inspired by birds, is further inscribed in local models of the person and grounds a vision of the heart-soul as the voice of conscience. Este artículo explora la importancia de las interacciones humano-aviar entre los Urarina de Perú, centrándose en el habla de pájaros y su relación con conceptos de la voz, el poder y la profecía. Se sugiere que, si bien la situación potencial de las aves como sujetos resulta compleja e incierta, esta misma ambigüedad ha estimulado el desarrollo de ideas más abstractas sobre el significado, el lenguaje, y lo que significa ser humano. Los sonidos de pájaros llegan a significar algo de manera no simplemente arbitraria, sino indicial o analógica, dando lugar a la impresión de un acceso privilegiado a la realidad y la verdad. Junto con la transparencia vocal - la capacidad de dar voz a los mensajes o ideas que supuestamente vienen de las divinidades - esto explica las cualidades proféticas de los pájaros y el papel de su habla como modelo del discurso eficaz y autoritativo replicado por los chamanes, en el cual el significado no se puede reducir a las intenciones de un solo hablante. Esta ideología del lenguaje, inspirada por los pájaros, también se encuentra en modelos de la persona, y en el corazón-alma como la voz de la conciencia.
A four-step camera calibration procedure with implicit image correction (2002)

In geometrical camera calibration the objective is to determine a set of camera parameters that describe the mapping between 3-D reference coordinates and 2-D image coordinates. Various methods for camera calibration can be found from the literature. However surprisingly little attention has been paid to the whole calibration procedure, i.e., control point extraction from images, model fitting, image correction, and errors originating in these stages. The main interest has been in model fitting, although the other stages are also important. In this paper we present a four-step calibration procedure that is an extension to the two-step method. There is an additional step to compensate for distortion caused by circular features, and a step for correcting the distorted image coordinates. The image correction is performed with an empirical inverse model that accurately compensates for radial and tangential distortions. Finally, a linear method for solving the parameters of the inverse model is presented.
Identification of a nucleotide exchange-promoting activity for p21ras. (1990)

The biological activity of proteins encoded by the ras family of oncogenes is dependent on whether they are bound to GTP or GDP: the type of nucleotide bound is dependent on the rate of GTP hydrolysis (promoted by the GTPase-activating protein, GAP) and the rate of nucleotide exchange with cytosolic pools. A protein that stimulates the rate of exchange of guanine nucleotide on p21ras has been identified and characterized in cytoplasmic extracts of human placenta. The exchange-promoting protein runs on a gel filtration column with an apparent relative molecular weight of about 60,000. It is sensitive to heat and to trypsin. The exchange-promoting protein acts reversibly and does not cause degradation of p21ras. It is inactive towards the alpha subunit of a heterotrimeric GTP-binding protein (Go alpha) but acts on a large number of different mutant ras proteins, including transforming and effector mutants that are insensitive to the action of GAP. This protein, which we have termed REP (ras exchange-promoting), has the characteristics expected of a physiological activator of p21ras in cellular growth-signal-transduction pathways.
Prospective Randomized Trial of High-Dose Interleukin-2 Alone or in Conjunction With Lymphokine-Activated Killer Cells for the Treatment of Patients With Advanced Cancer (1993)

As these studies continue, efforts are underway to develop improved immunotherapies using tumor-infiltrating lymphocytes (TIL) and gene-modified TIL.
Antineoplastic Agents II: Four Furostanol Glycosides from Rhizomes ofDioscorea collettiivar.hypoglauca (1997)

During activity-guided fractionations to screen for antineoplastic agents, further studies by means of preparative HPLC led to the isolation of four known furostanol saponins: protoneodioscin, protodioscin, protoneogracillin, protogracillin, along with their corresponding artifacts: methyl protoneodioscin, methyl protodioscin, methyl protoneogracillin, and methyl protogracillin, from the rhizomes of Dioscorea collettii var. hypoglauca. Among them, protoneodioscin, protodioscin, and protoneogracillin are first reported from the title plant. The structures of the compounds were established on the basis of chemical evidence and spectral analysis (1H-NMR, 13C-IMMR, 1H-1H COSY, HMQC, HMBC, and FAB-MS). These eight compounds all caused morphological abnormality of Pyricularia oryzae mycelia. They also showed cytotoxic activities against the cancer cell line of K562 in vitro as antineoplastic agents.