gebhart/patrepeval huggingface dataset:
The Relationships between West Nile and Kunjin Viruses (2001)

Until recently, West Nile (WN) and Kunjin (KUN) viruses were classified as distinct types in the Flavivirus genus. However, genetic and antigenic studies on isolates of these two viruses indicate that the relationship between them is more complex. To better define this relationship, we performed sequence analyses on 32 isolates of KUN virus and 28 isolates of WN virus from different geographic areas, including a WN isolate from the recent outbreak in New York. Sequence comparisons showed that the KUN virus isolates from Australia were tightly grouped but that the WN virus isolates exhibited substantial divergence and could be differentiated into four distinct groups. KUN virus isolates from Australia were antigenically homologous and distinct from the WN isolates and a Malaysian KUN virus. Our results suggest that KUN and WN viruses comprise a group of closely related viruses that can be differentiated into subgroups on the basis of genetic and antigenic analyses.
A multilingual glossary of biotechnological terms : IUPAC recommendations (1995)

English Original (IUPAC-approved) (B. Nagel, et al.) French Version (L. Pinasse) German Version (H. Dellweg & B. Nagel) Japanese Version (Y. Yamada) Portuguese Version (M. Grilo & P. Magalhces) Russian Version (A. Boronin) Spanish Version (E. Mega & L. Pirez) Appendices.
Absolute configuration of allosamizoline, an aminocyclitol derivative of the chitinase inhibitor allosamidin. (1988)

The absolute configuration of allosamizoline (1), a constituent aminocyclitol derivative of allosamidin (2), was elucidated by the exciton chirality method using its 3, 4-bis[p-(dimethylamino)benzoyl]-6-trityl derivative (7).
Treatment Failure of a TLR-7 Agonist Occurs Due to Self-Regulation of Acute Inflammation and Can Be Overcome by IL-10 Blockade (2010)

Multiple TLR agonists have been shown to have antitumor effects in animal models. However, the therapeutic efficacy of TLR agonist monotherapy in cancer treatment has been limited, and the mechanisms of failure remain unknown. We demonstrate that topical treatment with a TLR-7 agonist, imiquimod, can elicit significant regression of spontaneous breast cancers in neu transgenic mice, a model of human HER-2/neu(+) breast cancer. However, tumor growth progressed once imiquimod therapy was ended. Gene expression analysis using tumor-derived RNA demonstrated that imiquimod induced high levels of IL-10 in addition to TNF-alpha and IFN-gamma. Elevated levels of circulating IL-10 were also detected in sera from imiquimod-treated mice. Elevated serum IL-10 appeared to be derived from IL-10 and dual cytokine secreting (IFN-gamma(+) and IL-10(+)) CD4(+) T cells rather than CD4(+)CD25(+)Foxp3(+) T regulatory cells, which were also induced by imiquimod treatment. Blockade of IL-10, but not TGF-beta, enhanced the antitumor effect of imiquimod by significantly prolonging survival in treated mice. These data suggest that the excessive inflammation induced by TLR agonists may result in a self-regulatory immunosuppression via IL-10 induction and that blocking IL-10 could enhance the therapeutic efficacy of these agents.
Efflux pump inhibitors (EPIs) as new antimicrobial agents against Pseudomonas aeruginosa (2011)

Pseudomonas aeruginosa is an opportunistic human pathogen and one of the leading causes of nosocomial infections worldwide. The difficulty in treatment of pseudomonas infections arises from being multidrug resistant (MDR) and exhibits resistance to most antimicrobial agents due to the expression of different mechanisms overcoming their effects. Of these resistance mechanisms, the active efflux pumps in Pseudomonas aeruginosa that belong to the resistance nodulation division (RND) plays a very important role in extruding the antibiotics outside the bacterial cells providing a protective means against their antibacterial activity. Beside its role against the antimicrobial agents, these pumps can extrude biocides, detergents, and other metabolic inhibitors. It is clear that efflux pumps can be targets for new antimicrobial agents. Peptidomimetic compounds such as phenylalanine arginyl β-naphthylamide (PAβN) have been introduced as efflux pump inhibitors (EPIs); their mechanism of action is through competitive inhibition with antibiotics on the efflux pump resulting in increased intracellular concentration of antibiotic, hence, restoring its antibacterial activity. The advantage of EPIs is the difficulty to develop bacterial resistance against them, but the disadvantage is their toxic property hindering their clinical application. The structure activity relationship of these compounds showed other derivatives from PAβN that are higher in their activity with higher solubility in biological fluids and decreased toxicity level. This raises further questions on how can we compact Pseudomonas infections. Of particular importance, the recent resurgence in the use of older antibiotics such as polymyxins and probably applying stricter control measures in order to prevent their spread in clinical sittings.
Comparative Genomic Hybridization to Dna Microarrays (1997)

Abstract Comparative genomic hybridization (CGH), which involves the simultaneous hybridization of differentially labeled total genomic DNA from test cells and reference normal cells to metaphase chromosomes, has been used extensively to screen tumor genomes for regions of DNA sequence copy number variation. Analysis of these hybridizations requires quantitative analysis of the ratio of intensities of the fluorescent hybridization signals as a function of position along the chromosomes, which basically serve as a convenient genetic map. The ratios need to be measured very accurately since changes of about ± 20% from the average for the genome indicate important genetic events. Widespread use of CGH over the past several years has identified numerous regions of the genome that may contain currently unknown cancer genes. For example, regions of increased copy number may indicate sites of oncogenes, while regions of copy number decrease relative to average for the genome may signify the presence of a tumor suppressor gene.
Molecular Profiling of Heart Endothelial Cells (2005)

These findings provide new markers for the endothelium of heart vessels and reveal a commonality between parenchymal and endothelial gene expression in the heart. The heart-homing peptides provide a means of targeting diagnostic and therapeutic agents to the heart, and their receptors are potential drug discovery targets.
Dynamics of Plant Root Growth under Increased Atmospheric Carbon Dioxide (2013)

Plant growth is influenced by above‐ and belowground environmental conditions and increasing atmospheric carbon dioxide (CO 2 ) concentrations enhances growth and yield of most agricultural crops. This review covers current knowledge on the impact of increasing CO 2 concentration on root dynamics of plants in terms of growth, root/shoot (R/S) ratio, root biomass, root length, root longevity, root mortality, root distribution, root branching, root quality, and the response of these root parameters to management practices including soil water and nutrients. The effects of CO 2 concentration on R/S ratio are contradictory due to complexity in accurate underground biomass estimation under diverse crops and conditions. Roots become more numerous, longer, thicker, and faster growing in crops exposed to high CO 2 with increased root length in many plant species. Branching and extension of roots under elevated CO 2 may lead to altered root architecture and ability of roots to acquire water and nutrients from the soil profile with exploration of the soil volume. Root turnover is important to the global C budget as well as to nutrient cycling in ecosystems and individual plants. Agricultural management practices have a greater impact on root growth than rising atmospheric CO 2 since management practices influence soil physical, chemical, and biological properties of soil, consequently affects root growth dynamics in the belowground. Less understood are the interactive effects of elevated CO 2 and management practices including drought on root dynamics, fine‐root production, and water‐nutrient use efficiency, and the contribution of these processes to plant growth in water and nutrients limited environments.
SPC3, a synthetic peptide derived from the V3 domain of human immunodeficiency virus type 1 (HIV-1) gp120, inhibits HIV-1 entry into CD4+ and CD4- cells by two distinct mechanisms. (1995)

The third variable region (V3 loop) of gp120, the HIV-1 surface envelope glycoprotein, plays a key role in HIV-1 infection and pathogenesis. Recently, we reported that a synthetic multibranched peptide (SPC3) containing eight V3-loop consensus motifs (GPGRAF) inhibited HIV-1 infection in both CD4+ and CD4- susceptible cells. In the present study, we investigated the mechanisms of action of SPC3 in these cell types--i.e., CD4+ lymphocytes and CD4- epithelial cells expressing galactosylceramide (GalCer), an alternative receptor for HIV-1 gp120. We found that SPC3 was a potent inhibitor of HIV-1 infection in CD4+ lymphocytes when added 1 h after initial exposure of the cells to HIV-1, whereas it had no inhibitory effect when present only before and/or during the incubation with HIV-1. These data suggested that SPC3 did not inhibit the binding of HIV-1 to CD4+ lymphocytes but interfered with a post-binding step necessary for virus entry. In agreement with this hypothesis, SPC3 treatment after HIV-1 exposure dramatically reduced the number of infected cells without altering gp120-CD4 interaction or viral gene expression. In contrast, SPC3 blocked HIV-1 entry into CD4-/GalCer+ human colon epithelial cells when present in competition with HIV-1 but had no effect when added after infection. Accordingly, SPC3 was found to inhibit the binding of gp120 to the GalCer receptor. Thus, the data suggest that SPC3 affects HIV-1 infection by two distinct mechanisms: (i) prevention of GalCer-mediated HIV-1 attachment to the surface of CD4-/GalCer+ cells and (ii) post-binding inhibition of HIV-1 entry into CD4+ lymphocytes.
Formulas for preparing phantom muscle tissue at various radiofrequencies (1984)

The dielectric properties of various test samples of phantom tissue were measured using an automated and temperature-controlled slotted line. The ingredients for phantom materials were determined for simulating high-water content tissue at 13.56, 27.12, 40.68, 70, 100, 200, 300, 433, 750, 915, and 2,450 MHz. The ingredients consisted of water, TX-150 (a gelling agent), sodium chloride, and polyethylene powder (200-2,450 MHz) or aluminum powder (13.56-100 MHz). The dielectric constant and conductivity of these materials at different temperatures (15, 22, 30 degrees C) were characterized.
Breast Cancer Survival Defined by the ER/PR/HER2 Subtypes and a Surrogate Classification according to Tumor Grade and Immunohistochemical Biomarkers (2014)

Introduction. ER, PR, and HER2 are routinely available in breast cancer specimens. The purpose of this study is to contrast breast cancer-specific survival for the eight ER/PR/HER2 subtypes with survival of an immunohistochemical surrogate for the molecular subtype based on the ER/PR/HER2 subtypes and tumor grade. Methods. We identified 123,780 cases of stages 1-3 primary female invasive breast cancer from California Cancer Registry. The surrogate classification was derived using ER/PR/HER2 and tumor grade. Kaplan-Meier survival analysis and Cox proportional hazards modeling were used to assess differences in survival and risk of mortality for the ER/PR/HER2 subtypes and surrogate classification within each stage. Results. The luminal B/HER2- surrogate classification had a higher risk of mortality than the luminal B/HER2+ for all stages of disease. There was no difference in risk of mortality between the ER+/PR+/HER2- and ER+/PR+/HER2+ in stage 3. With one exception in stage 3, the ER-negative subtypes all had an increased risk of mortality when compared with the ER-positive subtypes. Conclusions. Assessment of survival using ER/PR/HER2 illustrates the heterogeneity of HER2+ subtypes. The surrogate classification provides clear separation in survival and adjusted mortality but underestimates the wide variability within the subtypes that make up the classification.
The Release of Cytochrome c from Mitochondria: A Primary Site for Bcl-2 Regulation of Apoptosis (1997)

In a cell-free apoptosis system, mitochondria spontaneously released cytochrome c, which activated DEVD-specific caspases, leading to fodrin cleavage and apoptotic nuclear morphology. Bcl-2 acted in situ on mitochondria to prevent the release of cytochrome c and thus caspase activation. During apoptosis in intact cells, cytochrome c translocation was similarly blocked by Bcl-2 but not by a caspase inhibitor, zVAD-fmk. In vitro, exogenous cytochrome c bypassed the inhibitory effect of Bcl-2. Cytochrome c release was unaccompanied by changes in mitochondrial membrane potential. Thus, Bcl-2 acts to inhibit cytochrome c translocation, thereby blocking caspase activation and the apoptotic process.
Porphyromonas gingivalis Gingipains and Adhesion to Epithelial Cells (2001)

Porphyromonas gingivalis is one of the principal organisms associated with adult periodontitis. Bacterial surface proteins such as fimbriae and gingipain hemagglutinin domains have been implicated as adhesins that actuate colonization of epithelium lining the gingival sulcus. We investigated the genetics of P. gingivalis adhesion to monolayers of epithelial cells using wild-type and gingipain mutant strains. These experiments suggested that arginine-specific gingipain (Rgp) catalytic activity modulated adhesion. From the data obtained with rgp mutants, we constructed a working hypothesis predicting that attachment and detachment of P. gingivalis to epithelial cells were mediated by gingipain adhesin and Rgp catalytic domains, respectively. A membrane-based epithelial cell binding assay, used to locate adhesins in extracellular fractions of wild-type and mutant strains, recognized gingipain peptides as adhesins rather than fimbriae. We developed a capture assay that demonstrated the binding of gingipain adhesin peptides to oral epithelial cells. The adherence of fimbrillin to epithelial cells was detected after heat denaturation of cell fractions. The prediction that Rgp catalytic activities mediated detachment was substantiated when the high level of attachment of an rgp mutant was reduced in the presence of wild-type cell fractions that contained gingipain catalytic activities.
Interference Mitigation in Wireless Communications (2005)

The primary objective of this thesis is to design advanced interference resilient schemes for asynchronous slow frequency hopping wireless personal area networks (FH-WPAN) and time division multiple access (TDMA) cellular systems in interference dominant environments. We also propose an interference-resilient power allocation method for multiple-input-multiple-output (MIMO) systems.\n\nFor asynchronous FH-WPANs in the presence of frequent packet collisions, we propose a single antenna interference canceling dual decision feedback (IC-DDF) receiver based on joint maximum likelihood (ML) detection and recursive least squares (RLS) channel estimation. For the system level performance evaluation, we propose a novel geometric method that combines bit error rate (BER) and the spatial distribution of the traffic load of CCI for the computation of packet error rate (PER). We also derived the probabilities of packet collision in multiple asynchronous FH-WPANs with uniform and nonuniform traffic patterns. \n\nFor the design of TDMA receivers resilient to CCI in frequency selective channels, we propose a soft output joint detection interference rejection combining delayed decision feedback sequence estimation (JD IRC-DDFSE) scheme. In the proposed scheme, IRC suppresses the CCI, while DDFSE equalizes ISI with reduced complexity. Also, the soft outputs are generated from IRC-DDFSE decision metric to improve the performance of iterative or non-iterative type soft-input outer code decoders.\n\nFor the design of interference resilient power allocation scheme in MIMO systems, we investigate an adaptive power allocation method using subset antenna transmission (SAT) techniques. Motivated by the observation of capacity imbalance among the multiple parallel sub-channels, the SAT method achieves high spectral efficiency by allocating power on a selected transmit antenna subset. For 4 x 4 V-BLAST MIMO systems, the proposed scheme with SAT showed analogous results. Adaptive modulation schemes combined with the proposed method increase the capacity gains. From a feasibility viewpoint, the proposed method is a practical solution to CCI-limited MIMO systems since it does not require the channel state information (CSI) of CCI.
Neural transplantation: restoring complex circuitry in the striatum. (2001)

During the last 30 years, the promise of neural transplantation as a therapeutic strategy for neurodegenerative disease has been slowly recognised. Across the world, clinical transplants of embryonic primary dopamine neurones have been shown to ameliorate some of the motor deficits in Parkinson s disease (PD) patients, and more recently, systematic clinical trials have been initiated for the replacement of striatal projection neurones lost in Huntington's disease (HD). Clinical transplantation as a prospective therapy for HD poses a particular set of difficulties. The hallmarks of this neurodegenerative disease include extensive loss of medium spiny long-distance projection neurones of the caudate and putamen, affecting downstream target nuclei, the globus pallidus and substantia nigra, leading to dysregulation of motor control. In addition, extensive loss of cortical neurones that form the afferent systems to the basal ganglia leads to widespread cognitive decline. If transplantation therapy is to succeed in replacing degenerating neurones in HD and reinstating controlled function of complex basal gan-glia circuitry, the new neurones must be able to develop specific long-distance projections that can form accurate and functional connections with neurones in precise target regions. Our ongoing studies are aimed at addressing how we can improve the function of striatal transplants, in particular to optimise the reformation of precise long-distance connections and to re-establish normal motor and cognitive function. In particular, we have investigated optimal requirements for embryonic primary tissue to achieve these aims, and also the potential of other cell sources to provide long-distance projection neurones and reconnect complex circuitry. This review describes current progress of experiments to optimise the reconstruction of neuronal circuitry using primary embryonic tissue transplants, as well as our current initiatives to use neural stem cells or precursors to replace long distance projection neurones in the degenerating basal ganglia.
The Theory and Practice of Discourse Parsing and Summarization (2000)

This book documents the first serious attempt to construct automatically and use nonsemantic computational structures for text summarization. Until now, most discourse researchers have assumed that full semantic understanding is necessary to derive the discourse structure of texts. This book documents the first serious attempt to construct automatically and use nonsemantic computational structures for text summarization. Daniel Marcu develops a semantics-free theoretical framework that is both general enough to be applicable to naturally occurring texts and concise enough to facilitate an algorithmic approach to discourse analysis. He presents and evaluates two discourse parsing methods: one uses manually written rules that reflect common patterns of usage of cue phrases such as "however" and "in addition to"; the other uses rules that are learned automatically from a corpus of discourse structures. By means of a psycholinguistic experiment, Marcu demonstrates how a discourse-based summarizer identifies the most important parts of texts at levels of performance that are close to those of humans. Marcu also discusses how the automatic derivation of discourse structures may be used to improve the performance of current natural language generation, machine translation, summarization, question answering, and information retrieval systems. Bradford Books imprint
The genomic structure of the human glucocorticoid receptor. (1991)

We have determined the structure of the human glucocorticoid receptor (hGR) gene after the isolation and characterization of cosmid clones mapping to discrete regions of the cDNA. The gene contains a total of 10 exons and has a minimum size of 80 kilobases. Exon 1 consists solely of 5'-untranslated sequence, and exon 2 encodes the amino-terminal portion of the receptor. The two putative zinc fingers are separately encoded by two exons, and a total of five exons combine to form the cortisol-binding domain. By restriction mapping and sequence analysis of cosmids located on the 3'-end of the gene, we have established that the two receptor isoforms, hGR alpha and hGR beta, originate from the same gene by alternative splicing. Each hGR isoform is encoded by nine exons, of which the first eight are identical, whereas the ninth exons are heterologous. Multiple GC boxes and no obvious TATA or CAAT elements have been found in the 5'-flanking region. S1 nuclease analysis yielded one major band, and the transcription start site is localized to the *C residue within TAC*CCTC. Alignment of sequences around the splice junctions of hGR with those of other members of the steroid receptor superfamily revealed three different splice positions within the DNA-binding domain. This comparison also permitted the prediction of the positions of the splice sites and the sizes of the putative exons in the human mineralocorticoid receptor.
Automated protein crystallization and a new crystal form of a subtilisin:eglin complex (1987)

A procedure is described for automating labour-intensive steps of the 'hanging drop' protein crystallization method. An automatic sample changer is employed to fill the wells in a multi-well plate so that concentration gradients in various components are obtained. The sample changer is also used for preparing droplets on a second multi-well plate. Subsequently, this second plate is manually turned around and placed on top of the first multi-well plate such that a large number of chambers with different conditions is obtained simultaneously. During initial trials a new crystal form of a subtilisin:eglin complex was obtained. The crystals have space group P2(1), contain two enzyme inhibitor complexes per asymmetric unit and diffract beyond 2.2 A.