gebhart/patrepeval huggingface dataset:
Managing fish, flood plains and food security in the Lower Mekong Basin (2001)

The "Lower Mekong Basin" in this paper refers to the part of the Mekong River Basin which is shared by Cambodia, Laos, Thailand and Viet Nam, all members of the Mekong River Commission, consisting of approx. 2,400 km of mainstream river, numerous tributaries and huge flood plains. Few river basins produce as much fish as the Mekong River Basin, and the fishery in the Lower Mekong Basin is among the biggest and most productive inland fisheries in the world. The flood plains of the Lower Mekong produce some four times as much fish per square kilometre as the North Sea, which is among the most productive marine areas in the world. It is quite clear that the fisheries in the Mekong Basin are very important for the population in respect to their food security and income. Its importance in nutrition is highest in the rural areas, where there are few other low cost sources of protein, and even in highland areas fish is of crucial importance in the diet. Most fish species in the Mekong Basin are migratory, and the economically most important ones are certainly so. However, with economic development gaining speed, the impact on migratory patterns and the competition for the water resources are becoming stronger. The water resources offer a large number of opportunities, and a lot of economic activities need access to the water resources for their development. However, what is seen in one sector as an opportunity may be considered as a threat in another, and a careful balance is necessary in order not to lose opportunities in important sectors. The fate of a large number of river basins in the world is frightening. Most have been left biologically near dead, with some of the big rivers reduced for a time, or forever, to be used as waste water canals for the new industries, and others almost dried out from excessive water extraction before they reach the sea.
THE HEMODYNAMIC EFFECTS OF CREMOPHOR-EL (1991)

A problem associated with parenteral cyclosporine has been the increased incidence of renal toxicity. Cremophor-EL, the vehicle for parenteral cyclosporine has been associated with massive histamine release and anaphylaxis in certain animal models. We investigated the effects of Cremophor-EL on the cardiac output (CO); mean arterial pressure (MAP); and hepatic, renal and pancreatic blood flow in the anesthesized canine model. Doppler flow probes were utilized to calculate individual organ blood flow. Profound adverse affects were noted on the CO, MAP, and hepatic blood flow. There were negative trends noted in the renal and splenic arterial flow that did not reach statistical significance. It was noted that the changes in organ blood flow were partially independent on MAP and the total dose of Cremophor-EL. We therefore conclude that it is prudent to consider the possible adverse hemodynamic role of Cremophor-EL in canine allograft dysfunction.
The AP-1 site and MMP gene regulation: What is all the fuss about? (1997)

Matrix metalloproteinase (MMP) gene expression occurs under tightly regulated mechanisms that lead to cell and tissue-specific expression of the individual genes. Despite this differential expression, there exists a high degree of similarity among the cis-acting elements in the MMP promoters. The Activator Protein-1 (AP-1) site at approximately -70 bp upstream of the transcriptional start site has long been thought to play a dominant role in the transcriptional activation of the MMP promoters, particularly in response to stimulation with phorbol myristate acetate (PMA). However, more recent data indicate that basal transcription, as well as transactivation by PMA, cytokines, and growth factors requires the specific interaction of AP-1 with other cis-acting elements. Particularly important are PEA3 sites, located either adjacent to this AP-1 site or more distally. On the otherhand, the AP-1 site plays a dominant role in repression of MMPs by transforming growth factor beta (TGF-beta), retinoids and glucocorticoids, although some AP-1 independent mechanisms may also contribute. While the AP-1 site is involved in tissue-specific expression of MMPs, the presence of one or more AP-2 elements appears critical. Thus, the AP-1 site, alone, does not regulate transcription of MMPs. Rather, there is an essential interaction with other cis-acting sequences in the promoters and with certain transcription factors that bind to these sequences. Together, these complex interactions control the transcription of the MMPs in response to particular inducers and repressors.
Prevention of Colonization of the Urinary Tract of Mice with Escherichia coli by Blocking of Bacterial Adherence with Methyl -D-Mannopyranoside (1979)

Methyl alpha-D-mannopyranoside (alpha MM), a competitor inhibitor of the binding of mannose by Escherichia coli, was tested for its ability to prevent infection of the urinary tract of mice with infective strains of the organisms. Injection of the bacteria in the presence of the drug resulted in a considerable reduction in the number of bacteriuric mice. In this system alpha MM was inactive against Proteus mirabilis in accordance with its inability to inhibit the adherence of this organism to epithelial cells in vitro, and methyl alpha-D-glucopyranoside proved inactive against both E. coli and P. mirabilis.
Control of InAs Nanowire Growth Directions on Si (2008)

We report on control of growth directions of InAs nanowires on Si substrate. We achieved to integrate vertical InAs nanowires on Si by modifying initial Si(111) surface in selective-area metal-organic vapor phase epitaxy with flow-rate modulation mode at low temperature. Cross-sectional transmission electron microscope and Raman scattering showed that misfit dislocation with local strains were accommodated in the interface.
Podridão radicular em feijão no sistema plantio direto (2011)

Podridões radiculares do feijoeiro comum causadas por fungos patogênicos de solo variam de intensidade nas diferentes regiões brasileiras. O objetivo deste trabalho foi avaliar a incidência de podridões radiculares em plantas adultas das cultivares de feijão preto BRS Campeiro, BRS Valente e IPR Uirapuru e sua relação com o rendimento de grãos. Os experimentos foram realizados nas safras agrícolas 2004/05, 2005/06 e 2006/07, no município de Muitos Capões, RS, em área de plantio direto sob rotação de culturas com milho no verão e em sucessão ao trigo no inverno. Na colheita de cada cultivar foram arrancadas todas as plantas de dez metros lineares, em cinco pontos ao acaso da lavoura, determinandose o número total de plantas e o número de plantas doentes. O dano no rendimento de grãos foi obtido pela diferença entre o rendimento real e a estimativa do rendimento potencial. A identificação dos fungos predominantes nas plantas doentes foi feita com base nos sintomas e por meio de isolamento de fragmentos de raiz em meio de cultura Batata-Dextrose-Ágar. As incidências de podridões radiculares foram 24,5%, 40,6% e 22%, com dano médio no rendimento de grãos de 2,8%, 4,1% e 2,4%, respectivamente, para 2004/05, 2005/06 e 2006/07, não diferindo significativamente. Não houve correlação significativa entre incidência de doença e dano comparando as cultivares dentro da safra agrícola e também para médias das cultivares entre safras. O fungo Macrophomina phaseolina apresentou maior frequência em 2004/05 e 2005/06, ao passo que Fusarium spp. mais frequente em 2006/07. A inconsistência da frequência dos fungos identificados nas cultivares e nas três safras agrícolas não permitiu identificar uma relação de suscetibilidade entre genótipo e patógeno.
The sensitivity of real-time PCR amplification targeting invasive Salmonellaserovars in biological specimens (2010)

Our findings corroborate previous clinical findings, whereby the bacterial load of S. Typhi in peripheral blood is low, often below detection by culture and, consequently, below detection by PCR. Whilst the assay may be utilised for environmental sampling or on differing biological samples, our data suggest that PCR performed directly on blood samples may be an unsuitable methodology and a potentially unachievable target for the routine diagnosis of enteric fever.
Porous Metal−Organic Polyhedra:  25 Å Cuboctahedron Constructed from 12 Cu2(CO2)4 Paddle-Wheel Building Blocks (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPorous Metal−Organic Polyhedra: 25 Å Cuboctahedron Constructed from 12 Cu2(CO2)4 Paddle-Wheel Building BlocksM. Eddaoudi, Jaheon Kim, J. B. Wachter, H. K. Chae, M. O'Keeffe, and O. M. YaghiView Author Information Materials Design and Discovery Group Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109-1055 Department of Chemistry Arizona State University, Tempe, Arizona 85287-1604 Cite this: J. Am. Chem. Soc. 2001, 123, 18, 4368–4369Publication Date (Web):April 17, 2001Publication History Received20 February 2001Published online17 April 2001Published inissue 1 May 2001https://pubs.acs.org/doi/10.1021/ja0104352https://doi.org/10.1021/ja0104352rapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views10505Altmetric-Citations616LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Crystal structure,Crystals,Ligands,Molecules,Porosity Get e-Alerts
Zerotree entropy coding of wavelet coefficients for very low bit rate video (2002)

This paper introduces zerotree entropy (ZTE) coding for wavelet transform coefficients of video I-frames and motion-compensated video residuals. ZTE coding is based on but differs significantly from the embedded zerotree wavelet (EZW) algorithm. As in EZW, the new ZTE coding algorithm exploits the self-similarity inherent in the wavelet transform to predict the location of information across wavelet scales. The new ZTE coder does not produce an embedded bitstream as EZW does, but by sacrificing the embedding property, ZTE achieves substantial improvement in coding efficiency and provides greater flexibility and other advantages over EZW.
Effect of film roughness in MgO-based magnetic tunnel junctions (2006)

We have systematically investigated the dependence of tunnel magnetoresistance in MgO-based magnetic tunnel junctions as a function of Ar pressure during sputtering. The MgO surface roughness, and therefore device magnetoresistance, depends strongly on Ar gas pressure. Magnetoresistance of up to 236% was achieved at room temperature after thermal annealing at 425°C and with optimal sputtering conditions. The long mean free path of target atoms at low background pressures increases their kinetic energy at the substrate surface, resulting in smooth surface morphology and correspondingly improved device performance.
In situ detection of basic fibroblast growth factor by highly specific antibodies. (1990)

Basic fibroblast growth factor (bFGF) is thought to be of major importance for fibrosis and angiogenesis. Despite intensive studies dealing with the biochemistry and multiple biologic effects of bFGF, the cellular distribution is virtually unknown. Therefore, using the indirect immunoperoxidase technique, we examined the effect of bFGF on a large pattern of normal, inflammatory, and tumorous human tissues. Staining was performed on cryostat sections with a highly specific affinity-purified antiserum. In normal tissues, especially those of the thymus and placenta, mainly dendritic cells contained the growth factor. High levels of bFGF were also detected in basal cells and gland epithelial cells of skin biopsies. A conspicuous expression was observed in chronic inflammatory tissues corresponding to a generally pronounced proliferation of fibroblasts and endothelial cells in these situations. Tumors revealed a very heterogenous staining pattern. In some lesions, bFGF was predominantly present in infiltrating and endothelial cells. In several, neoplasms tumor cells exhibited an intensive staining. In some, especially vascular tumors, bFGF could not be detected. From the staining results it is concluded that angiogenesis is not simply controlled by the presence of bFGF but is mediated by a balance of several angiogenic inducers and inhibitors.
Structure and biological activity of basement membrane proteins (1989)

Collagen type IV, laminin, heparan sulfate proteoglycans, nidogen (entactin) and BM-40 (osteonectin, SPARC) represent major structural proteins of basement membranes. They are well-characterized in their domain structures, amino acid sequences and potentials for molecular interactions. Such interactions include self-assembly processes and heterotypic binding between individual constituents, as well as binding of calcium (laminin, BM-40) and are likely to be used for basement membrane assembly. Laminin, collagen IV and nidogen also possess several cell-binding sites which interact with distinct cellular receptors. Some evidence exists that those interactions are involved in the control of cell behaviour. These observations have provided a more defined understanding of basement membrane function and the definition of new research goals in the future.
Induction of chronic lymphocytic leukemia (CLL)–specific CD4- and CD8-mediated T-cell responses using RNA-transfected dendritic cells (2003)

Recently, it was demonstrated that transfection of dendritic cells (DCs) with tumor-derived RNA can elicit effective T-cell responses. This technique does not require the definition of the tumor antigen or HLA haplotype of the patients. We applied this approach to induce HLA class I- and class II-restricted T-cell responses directed against malignant cells from patients with chronic lymphocytic leukemia (B-CLL). Here, we show that DCs generated from monocytes of patients with B-CLL induce leukemia-specific cytotoxic and proliferative T-cell responses on transfection with total RNA isolated from autologous leukemic B lymphocytes. Standard 51Cr-release assays showed specific major histocompatibility complex (MHC) class I-restricted cytotoxic activity against the autologous leukemic B cells and DCs transfected with CLL-RNA, whereas nonmalignant B cells were spared. The specificity of the cytotoxic T-lymphocyte (CTL) response was confirmed using cold target inhibition assays and by blocking HLA class I molecules. Furthermore, we established a protocol for the amplification of whole B-CLL mRNA. The use of DCs transfected with in vitro amplified B-CLL mRNA elicited specific T-cell responses similar to the results obtained with native mRNA. These data suggest that vaccinations using DCs transfected with RNA might be a potent new strategy in the treatment of CLL.
Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array (2002)

We report a microarray of cantilevers to detect multiple unlabeled biomolecules simultaneously at nanomolar concentrations within minutes. Ligand-receptor binding interactions such as DNA hybridization or protein recognition occurring on microfabricated silicon cantilevers generate nanomechanical bending, which is detected optically in situ. Differential measurements including reference cantilevers on an array of eight sensors can sequence-specifically detect unlabeled DNA targets in 80-fold excess of nonmatching DNA as a background and discriminate 3' and 5' overhangs. Our experiments suggest that the nanomechanical motion originates from predominantly steric hindrance effects and depends on the concentration of DNA molecules in solution. We show that cantilever arrays can be used to investigate the thermodynamics of biomolecular interactions mechanically, and we have found that the specificity of the reaction on a cantilever is consistent with solution data. Hence cantilever arrays permit multiple binding assays in parallel and can detect femtomoles of DNA on the cantilever at a DNA concentration in solution of 75 nM.
Some proline substituent effects in the tandem mass spectrum of protonated pentaalanine (1992)

Tandem mass spectral effects of the replacement of alanine by proline in pentaalanine were studied. The principal difference when residue 3 or 4 is proline is the great enhancement of the y3 or y2 ion, respectively. This is precisely the principal difference which thermochemical arguments predict, since a y-type ion with N-terminal proline is estimated to be 32 kJ mol-1 more stable than with N-terminal alanine. When this proline effect and the effect of neutral diketopiperazine loss occur simultaneously, the y-type ion is not observed, as predicted from the additivity of substituent effects by the kinetic approach. No interpretation is offered for observations of b-type ion intensities, since the pattern is not obvious to us.
Titelbild: Angew. Chem. 11/2002 (2002)

Das Titelbild zeigt die berechnete energieminimierte 3D-Struktur eines in einer mehrstufigen Synthese hergestellten Polyphenylendendrimers. Das Nanoteilchen enthält drei unterschiedliche Chromophortypen, die sich im Zentrum (Terrylen), innerhalb des Gerüstes (Perylen) und an der Peripherie (Naphthalin) befinden. Diese Multichromophortriade absorbiert über den gesamten sichtbaren Bereich und ermöglicht einen schrittweisen vektoriellen Energietransfer über eine Entfernung von 30 Å von der Oberfläche zum Kern. Mehr über Polyphenylenchromophore erfahren Sie in der Zuschrift von Müllen et al. auf S. 1980 ff.
In vivo retroviral gene transfer into human bronchial epithelia of xenografts. (1992)

Cystic fibrosis (CF) is the most common lethal inherited disease in the Caucasian population with an incidence of approximately 1 in 2,500 live births. Pulmonary complications of CF, which are the most morbid aspects of the disease, are caused by primary abnormalities in epithelial cells that lead to impaired mucociliary clearance. One potential therapeutic strategy is to reconstitute expression of the CF gene in airway epithelia by somatic gene transfer. To this end, we have developed an animal model of the human airway using bronchial xenografts and have tested the efficiency of in vivo retroviral gene transfer. Using the LacZ reporter gene, we find the efficiency of in vivo retroviral gene transfer to be dramatically dependent on the regenerative and mitotic state of the epithelium. Within an undifferentiated regenerating epithelium in which 40% of nuclei labeled with BrdU, 5-10% retroviral gene transfer was obtained. In contrast, no gene transfer was noted in a fully differentiated epithelium in which 1% of nuclei labeled with BrdU. These findings suggest that retroviral mediated gene transfer to the airway in vivo may be feasible if the proper regenerative state can be induced.
Nucleotide Sequences and Novel Structural Features of Human and Chinese Hamster hsp60 (Chaperonin) Gene Families (1990)

A number of clones that specifically hybridize to the human hsp60 cDNA (chaperonin protein; GroEL homolog) were isolated from human and Chinese hamster ovary cell genomic libraries. DNA sequence analysis shows that one of these clones, pGem-10, is completely homologous to the human hsp60 cDNA (in both coding and noncoding regions) with no intervening sequences. The other human clones analyzed were all nonfunctional pseudogenes containing numerous small additions, deletions, and base substitutions, but no introns. On the basis of sequence data, six different hsp60 pseudogenes were identified in human cells. In addition, we also cloned and completely sequenced a genomic clone from CHO cells. This clone, which was also a pseudogene, contained a small 87-nucleotide intron near the 3' end. Southern blot analysis of human, mouse, and Chinese hamster DNA, digested with unique restriction enzymes (no sites in cDNA), indicates the presence of about 8-12 genes for hsp60 in the vertebrate genomes. The sequence data, however, suggest that most of these genes, except one (per haploid genome), are likely to be nonfunctional pseudogenes.
The Hyaluronan Receptors CD44 and Rhamm (CD168) Form Complexes with ERK1,2 That Sustain High Basal Motility in Breast Cancer Cells (2007)

CD44 is an integral hyaluronan receptor that can promote or inhibit motogenic signaling in tumor cells. Rhamm is a nonintegral cell surface hyaluronan receptor (CD168) and intracellular protein that promotes cell motility in culture. Here we describe an autocrine mechanism utilizing cell surface Rhamm-CD44 interactions to sustain rapid basal motility in invasive breast cancer cell lines that requires endogenous hyaluronan synthesis and the formation of Rhamm-CD44-ERK1,2 complexes. Motile/invasive MDA-MB-231 and Ras-MCF10A cells produce more endogenous hyaluronan, cell surface CD44 and Rhamm, an oncogenic Rhamm isoform, and exhibit more elevated basal activation of ERK1,2 than less invasive MCF7 and MCF10A breast cancer cells. Furthermore, CD44, Rhamm, and ERK1,2 uniquely co-immunoprecipitate and co-localize in MDA-MB-231 and Ras-MCF10A cells. Combinations of anti-CD44, anti-Rhamm antibodies, and a MEK1 inhibitor (PD098059) had less-than-additive blocking effects, suggesting the action of all three proteins on a common motogenic signaling pathway. Collectively, these results show that cell surface Rhamm and CD44 act together in a hyaluronan-dependent autocrine mechanism to coordinate sustained signaling through ERK1,2, leading to high basal motility of invasive breast cancer cells. Therefore, an effect of CD44 on tumor cell motility may depend in part on its ability to partner with additional proteins, such as cell surface Rhamm.
Identification of novel spinal cholinergic genetic subtypes disclose Chodl and Pitx2 as markers for fast motor neurons and partition cells (2010)

Spinal cholinergic neurons are critical for motor function in both the autonomic and somatic nervous systems and are affected in spinal cord injury and in diseases such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy. Using two screening approaches and in situ hybridization, we identified 159 genes expressed in typical cholinergic patterns in the spinal cord. These include two general cholinergic neuron markers, one gene exclusively expressed in motor neurons, and nine genes expressed in unknown subtypes of somatic motor neurons. Further, we present evidence that chondrolectin (Chodl) is expressed by fast motor neurons and that estrogen-related receptor beta (ERRbeta) is a candidate marker for slow motor neurons. In addition, we suggest paired-like homeodomain transcription factor 2 (Pitx2) as a marker for cholinergic partition cells.