gebhart/patrepeval huggingface dataset:
Seed odor mediates an obligate ant–plant mutualism in Amazonian rainforests (2008)

Seed dispersal mutualisms are essential for the survival of diverse plant species and communities worldwide. Among invertebrates, only ants have a major role in seed dispersal, and thousands of plant species produce seeds specialized for ant dispersal in "diffuse" multispecies interactions. An outstanding but poorly understood ant-seed mutualism occurs in the Amazonian rainforest, where arboreal ants collect seeds of several epiphyte species and cultivate them in nutrient-rich nests, forming abundant and conspicuous hanging gardens known as ant-gardens (AGs). AG ants and plants are dominant members of lowland Amazonian ecosystems, and their interaction is both specific and obligate, but the means by which ants locate, recognize, and accept their mutualist seeds while rejecting other seeds is unknown. Here we address the chemical and behavioral basis of the AG interaction. We show that workers of the AG ant Camponotus femoratus are attracted to odorants emanating from seeds of the AG plant Peperomia macrostachya, and that chemical cues also elicit seed-carrying behavior. We identify five compounds from P. macrostachya seeds that, as a blend, attract C. femoratus workers. This report of attractive odorants from ant-dispersed seeds illustrates the intimacy and complexity of the AG mutualism and begins to illuminate the chemical basis of this important and enigmatic interaction.
Functional roles for the TATA promoter and enhancers in basal and Tat-induced expression of the human immunodeficiency virus type 1 long terminal repeat (1992)

We have analyzed the contributory role of the human immunodeficiency virus type 1 (HIV-1) promoter and enhancers in basal and Tat-induced transcription. We found that a minimal promoter competent for basal expression is contained within sequences spanning nucleotides -43 to +80. Basal expression from this HIV-1 promoter was boosted more by the additional presence of the NF-kappa B elements than by the Sp1 elements. The minimal long terminal repeat promoter (-43 to +80), while having an intact TAR sequence, was not Tat inducible. However, the simple addition of short synthetic enhancer motifs (AP1, Oct, Sp1, and NF-kappa B) conferred Tat responsiveness. This ability to respond to Tat was in part dependent on the presence of the HIV-1 promoter. Changing the HIV-1 TATA to other eucaryotic TATA or non-TATA initiators minimally affected basal expression but altered Tat inducibility. Our findings suggest a specific context of functional promoter and enhancer elements that is optimal for Tat trans activation of the HIV-1 long terminal repeat. Our results do not allow conclusions about whether Tat acts at the level of initiation or at the level of elongation to be drawn.
Identification and analysis of human erythropoietin receptors on a factor-dependent cell line, TF-1 (1989)

We have recently established a novel cell line, TF-1, from bone marrow cells of a patient with erythroleukemia, that showed an absolute growth dependency on each of three hematopoietic growth factors: erythropoietin (EPO) granulocyte-macrophage colony-stimulating factor (GM-CSF), and interleukin 3 (IL-3). EPO stimulated the proliferation of TF-1 cells even at the physiologic concentration (0.03 U/mL). We performed binding experiments on TF-1 cells using radioiodinated EPO. The binding of radioiodinated EPO to TF-1 was specific, time- and temperature-dependent, and saturable. Scatchard analysis of the saturation binding data suggested the existence of a single class of binding sites (kd = 0.40 nmol/L; number of binding sites = 1,630 per cell). TF-1 cells were usually maintained in RPMI 1640 containing 10% fetal bovine serum and 5 ng/mL GM-CSF. The kd and the number of the EPO receptors were not changed by incubating the cells with IL-3, although culturing the cells in the presence of EPO resulted in down-modulation of EPO receptors. The chemical cross-linking study demonstrated that two molecules with apparent molecular weights of 105 kilodalton (Kd) and 90 Kd were the binding components of EPO. Present data suggest that human EPO receptors are very similar to the previously reported murine EPO receptors.
Inhibition of immunoglobulin gene rearrangement by the expression of a lambda 2 transgene. (1989)

The rearrangement of Ig genes is known to be regulated by the production of H and kappa L chains. To determine whether lambda L chains have a similar effect, transgenic mice were produced with a lambda 2 gene. It was necessary to include the H chain enhancer, since a lambda gene without the added enhancer did not result in transgene expression. The lambda 2 transgene with the H enhancer was expressed in lymphoid cells only. The majority of the B cells of newborn transgenic mice produced lambda, whereas kappa + cells were reduced. Concomitantly, serum levels of kappa and kappa mRNA were diminished. By 2 wk after birth the proportion of kappa-expressing cells was dramatically increased. Adults had reduced proportions of B cells that produced lambda only, but the levels of lambda were still higher than in normal littermates. Also, kappa + cells were still lower than in normal mice. Analysis of hybridomas revealed that reduction of kappa gene rearrangement was the basis for the decreased frequency of kappa + cells. Furthermore, many cells also contained an unrearranged H chain allele. It was concluded that feedback inhibition by the lambda 2 together with endogenous H protein may have inhibited recombinase activity in early pre-B cells, leading to inhibition of both H chain and kappa gene rearrangement. Thus, lambda 2 can replace kappa in a feedback complex. The levels of serum lambda 1 and, to a lesser degree, of spleen lambda 1 mRNA were reduced in the lambda 2 transgenic mice. However, the proportion of hybridomas with endogenous lambda gene rearrangement was at least as high as in normal mice. It was therefore concluded that the suppression of functional lambda 1 may be a consequence of decreased selection of endogenous lambda-producing cells because of the excess of transgenic lambda. The escape of kappa-producing cells from feedback inhibition may be the result of several mechanisms that operate to varying degrees, among them: (a) kappa rearrangement during a period in which the recombinase is still active after appearance of a lambda 2/mu stop signal; (b) a B cell lineage that is not feedback inhibited at the pre-B cell stage; (c) subthreshold levels of transgenic lambda 2 in some pre-B cells; and (d) loss of the lambda 2 transgenes in rare pre-B cells.
Polarimetric Assay for the Medium-Throughput Determination of α-Amino Acid Racemase Activity (2004)

A polarimetric assay has been developed for the identification of alpha-amino acid racemase activity. The setup consists of a microcuvette polarimeter (40 microL volume) connected to a pipetting robot for microtiter plates, a pump, and data processing. It could be demonstrated for a glutamate racemase from Lactobacillus fermentii, expressed in Escherichia coli, serving as model enzyme, that its activity can be determined from the time-dependent change of the optical rotation using l-glutamate as substrate. Thus, the specific activity was determined to 111.4 mdeg/min which corresponds to 45.7 micromol/min per mg purified enzyme. Moreover, a protocol was developed that allows the measurement of racemase activity from 96-well microtiter plates using purified enzymes. Thus, the method described can be used to determine racemase activity in an automatic manner. It should be also applicable for the screening of enzyme libraries created by directed evolution.
Vertical ridge augmentation using a membrane technique associated with osseointegrated implants. (1994)

The purpose of this study was to evaluate: (1) the surgical protocol, effectiveness, and reliability for vertical ridge augmentation using a new titanium-reinforced membrane and osseointegrated implants; and (2) the histologic characteristics of the interface between a pure titanium implant and newly regenerated human bone. Five patients received 15 conical Brånemark-type implants in six different surgical sites requiring vertical augmentation. The implants protruded 4 to 7 mm from the bone crest. Pure titanium miniscrews (1.3 x 10 mm) were positioned distally to the implants, protruding 3 to 4 mm from the bone level. The implants and the miniscrews were covered with a titanium-reinforced membrane, and the flaps were sutured. Membranes were removed at the stage 2 surgery after 9 months of healing. Measurements of biopsy specimens showed a gain in bone height from 3 to 4 mm. Histologic examination showed that all retrieved miniscrews were in direct contact with bone. Histomorphometric analysis of bone contact gave a mean value of 42.5 +/- 3.6% for five of the six examined miniscrews. The results suggest that the placement of implants protruding 3 to 4 mm from the top of resorbed bone surfaces may result in vertical bone regeneration to the top of the implant cylinder and that the regenerated bone is able to osseointegrate pure titanium implants.
Frequency and prognostic evaluation of 3p21‐22 allelic losses in non‐small‐cell lung cancer (1995)

Previous loss of heterozygosity (LOH) studies of chromosome 3p loci have displayed a 60% deletion frequency in non-small-cell lung cancers (NSCLC), as opposed to small-cell lung cancers, in which the 3p deletion is consistently found. However, the high stromal-cell admixture found in NSCLC and the use of the Southern-blot method lead to under-evaluation of this frequency. In this study, we used a very precise microdissection technique followed by PCR amplification of 6 3p21-22 polymorphic genomic sequences to analyze LOH in 86 NSCLC and in normal adjacent tissue. We found the sensitivity of the microdissection-PCR-based LOH technique higher than the sensitivity of the Southern-blot technique: 87% of the squamous-cell carcinomas and 84% of the large-cell undifferentiated carcinomas showed a clear LOH for a 3p21-22 locus. All doubly informative cases but 4 showed concordant deletion at all 3p21-22 loci. The analysis of 3p microsatellite sequences displayed only 2 cases of genomic instability, one of them also displaying features of tumoral heterogeneity as regards the instability genotype. Four carcinomas in situ adjacent to these NSCLC showed the same allelic profile as the invasive tumors. The only prognostic factors in this study were the disease stage and histology. The 3p21-22 deletion was not related to the stage of the disease and did not appear to be a significant prognostic factor of survival. 3p21 loss appears, so far, to be the most frequent and the earliest genetic alteration described in NSCLC, but does not seem to carry significant prognostic information in invasive tumors.
The effect of niacinamide on reducing cutaneous pigmentation and suppression of melanosome transfer (2002)

The data suggest niacinamide is an effective skin lightening compound that works by inhibiting melanosome transfer from melanocytes to keratinocytes.
Identification of a site in the alpha chain of platelet glycoprotein Ib that participates in von Willebrand factor binding. (1990)

The binding of von Willebrand factor (vWF) to the platelet receptor glycoprotein (GP) Ib-IX complex is a key event in hemostasis and may participate in the development of thrombotic vascular occlusion. We present here evidence that residues Ser251-Tyr279 in the GP Ib alpha-chain participate in this function. Initial studies suggested that the modality of vWF interaction with GP Ib depended on the conditions used for induction of binding, either in the presence of ristocetin, or botrocetin, or with asialo-vWF. In fact, only the 45-kDa amino-terminal fragment of GP Ib alpha inhibited the vWF-GP Ib interaction under all conditions tested, while the 84-kDa macroglycopeptide was significantly effective only in the presence of ristocetin. Moreover, the 45-kDa fragment with reduced disulfide bonds still inhibited ristocetin-induced binding but had no effect, at the concentrations tested, on botrocetin-mediated or direct asialo-vWF binding. In order to localize in more detail the functional site, the entire sequence of the 45-kDa fragment was reproduced in 27 overlapping synthetic peptides that were then used in inhibition of binding assays. This led to the identification of a linear GP Ib alpha sequence (residues Ser251-Tyr279) that effectively inhibited platelet interaction with vWF mediated by ristocetin and, at higher concentration, also by botrocetin. A shorter peptide overlapping with the longer one (residues Gly271-Glu285) was the second most active inhibitory species. This region of the molecule contains several residues with a high surface probability index, as expected for a site involved in ligand binding. Thus, while native conformation of GP Ib alpha appears to be important for optimal interaction with vWF, the results obtained with short synthetic peptides may help in defining the amino acid residues participating in this essential function.
Construction and preliminary characterization of the rat casein and alpha-lactalbumin cDNA clones. (1981)

We have constructed a double-stranded cDNA library using total poly(A)-containing RNA extracted from 8-day lactating rat mammary gland and have utilized this library to isolate clones for each of the four major milk proteins. These four cDNA clones, representing the three major rat caseins and alpha-lactalbumin, were initially identified by colony hybridization with labeled cDNA probes synthesized from individual mRNA fractions purified by preparative gel electrophoresis. Additional characterization was accomplished by hybridizing individual clones labeled with 32P by nick translation to a Northern gel blot of an enriched fraction of the four major milk protein mRNAs. The individual mRNAs were clearly resolved by electrophoresis on fully denaturing methylmercury hydroxide agarose gels. The identity of each milk protein clone was further established by the location of unique restriction enzyme sites within each clone. Final identification of each clone was performed by hybrid-arrested cell-free translation. The sizes of the milk protein cDNA clones ranged frm 70% for the alpha-lactalbumin gene to essentially full length for the gamma-casein gene, in comparison to their respective mRNAs. This represents the first isolation of a family of peptide hormone-responsive genes.
Analysis of Human C1q by Combined Bottom-up and Top-down Mass Spectrometry (2009)

C1q is a subunit of the C1 complex, a key player in innate immunity that triggers activation of the classical complement pathway. Featuring a unique structural organization and comprising a collagen-like domain with a high level of post-translational modifications, C1q represents a challenging protein assembly for structural biology. We report for the first time a comprehensive proteomics study of C1q combining bottom-up and top-down analyses. C1q was submitted to proteolytic digestion by a combination of collagenase and trypsin for bottom-up analyses. In addition to classical LC-MS/MS analyses, which provided reliable identification of hydroxylated proline and lysine residues, sugar loss-triggered MS(3) scans were acquired on an LTQ-Orbitrap (Linear Quadrupole Ion Trap-Orbitrap) instrument to strengthen the localization of glucosyl-galactosyl disaccharide moieties on hydroxylysine residues. Top-down analyses performed on the same instrument allowed high accuracy and high resolution mass measurements of the intact full-length C1q polypeptide chains and the iterative fragmentation of the proteins in the MS(n) mode. This study illustrates the usefulness of combining the two complementary analytical approaches to obtain a detailed characterization of the post-translational modification pattern of the collagen-like domain of C1q and highlights the structural heterogeneity of individual molecules. Most importantly, three lysine residues of the collagen-like domain, namely Lys(59) (A chain), Lys(61) (B chain), and Lys(58) (C chain), were unambiguously shown to be completely unmodified. These lysine residues are located about halfway along the collagen-like fibers. They are thus fully available and in an appropriate position to interact with the C1r and C1s protease partners of C1q and are therefore likely to play an essential role in C1 assembly.
Performance analysis of DRX mechanism considering analogue beamforming in millimeter-wave mobile broadband system (2014)

To meet the explosive growth of mobile traffic, it is necessary to guarantee high data rate in today's communication system. One of the methods to support high data rate is to use wide bandwidth (spectrum). Due to the limitation of frequency spectrum for the commercial usage, we choose millimeter-Wave (mmW) band of 30GHz and exploit analogue beamforming technique, focusing electro-magnetic wave energy at a certain direction, not an omni-direction. In the analogue beamforming technique, beam selection is required so that base station (BS) and mobile station (MS) communicate with the best beam each other and this procedure is performed periodically for the selected beams not to be mis-aligned. To extend battery lifetime of user equipment, current broadband system such as 3GPP LTE/LTE Advanced adopts discontinuous reception (DRX) which the new mmW system needs too. Therefore, we propose the DRX mechanism considering analogue beamforming technique and analyze the performance of the system varying parameters of beam selection and DRX according to the given beam pattern, traffic model and movement of MS.
Ring-Opening Polymerization of Cyclic Monomers by Biocompatible Metal Complexes. Production of Poly(lactide), Polycarbonates, and Their Copolymers (2007)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTRing-Opening Polymerization of Cyclic Monomers by Biocompatible Metal Complexes. Production of Poly(lactide), Polycarbonates, and Their CopolymersDonald J. Darensbourg, Wonsook Choi, and Casseday P. RichersView Author Information Department of Chemistry, Texas A&M University, College Station, Texas 77843 Cite this: Macromolecules 2007, 40, 10, 3521–3523Publication Date (Web):April 18, 2007Publication History Received4 December 2006Revised28 March 2007Published online18 April 2007Published inissue 1 May 2007https://pubs.acs.org/doi/10.1021/ma062780nhttps://doi.org/10.1021/ma062780nrapid-communicationACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views2093Altmetric-Citations142LEARN 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:Calcium,Catalysts,Inorganic carbon compounds,Polymers,Ring-opening polymerization Get e-Alerts
Ultrastructural and light microscopic evidence of apoptosis after middle cerebral artery occlusion in the rat. (1995)

Brains from eight rats subjected to transient focal ischemia (2 hours) and reperfusion (22 hours) revealed an ultrastructural appearance of apoptosis and light microscopic features of cells exhibiting DNA fragmentation. The number of cells exhibiting DNA fragmentation was significantly higher (P < 0.01) in the ipsilateral hemisphere (216 +/- 43 per section) than in the contralateral hemisphere and in normal (n = 4) and sham operated (n = 4) rats (0 to 3 positive cells per section in controls). Cells exhibiting DNA fragmentation were primarily located in the inner boundary zone to the infarct. Cells exhibiting DNA fragmentation provided morphological information of apoptosis. Apoptosis may contribute to the development of infarct after transient focal cerebral ischemia.
Preliminary evidence that different domains are involved in cytolytic activity and receptor (cholesterol) binding in listeriolysin O, the Listeria monocytogenes thiol-activated toxin (1989)

The inactive truncated 52 Kilodaltons (kDa) Listeriolysin O (LLO) produced by a transposon Tn 1545-induced Listeria monocytogenes non-hemolytic/avirulent mutant previously described (Gaillard et al. (1986) Infect. Immun. 52, 55–55), that lacks a 48 aminoacid fragment at the C-terminal end including the single cysteine residue essential for activity (Mengaud et al. (1988) Infect. Immun. 56, 766–772), bound to the SH-cytolysin membrane receptor cholesterol, as did the active 60 kDa toxin. These results indicate that the missing fragment is a functionally important region needed in the 60 kDa LLo to cause membrane-disruption but not to bind to cholesterol, which strongly suggests that in LLO (and presumably in the other SH-cytolysins, in accordance with their structural and functional homologies) different domains are involved in cytolytic activity and cholesterol binding. The cysteine residue contained in the missing fragment, therefore, would not be essential for cholesterol binding, as in currently thought, rather it seems to be essential specifically for cell lysis.
Resilient Modulus Behavior of Rubberized Asphalt Concrete Mixtures Containing Reclaimed Asphalt Pavement (2008)

ABSTRACT The resilient modulus is the modulus to be used with the elastic theory during any analysis of a flexible pavement. It is well known that most paving materials (e.g., asphalt pavements) are not elastic but experience some permanent deformation after each load application. With respect to the complexity of the Rubberized Asphalt Concrete (RAC) containing Reclaimed Asphalt Pavement (RAP), the Indirect Tensile Strength (ITS) and resilient modulus evaluation of modified mixtures are important to understand. The aging of binder containing crumb rubber obviously alters the visco-elastic and plastic characteristics of the modified mixtures. The deformation of the mixture under repeated loading, nearly completely recoverable, should also be considered. The experimental design included the use of two aggregate sources, one rubber type (ambient), four rubber contents (0%, 5%, 10%, and 15%), one crumb rubber size (-40 mesh [-0.425 mm]), and four RAP contents (0%, 15%, 25%, and 30%). The findings indicated that an increase in the rubber content in the modified mixture leads to a decrease in ITS and resilient modulus values regardless of rubber content, and this increase also improves the aging resistance and increases the viscous characteristics of the modified binder. However, as RAP content increased, not only the viscosity and G*sinδ values of the modified binder increased, the ITS and resilient modulus values of the modified mixtures also increased.
Antitumor Effects of Interferon (1989)

Both natural and recombinant interferons have shown definite antitumor activity in some patients with some malignancies. The history of the development of interferon as an antitumor agent is reviewed, with special attention to its use in mice bearing 'spontaneously' appearing tumors and in mice injected with tumorigenic viruses or transplantable tumor cells. Interferon can inhibit the growth of primary tumors as well as the development of metastases. These experimental results have provided some indications as to the probable optimal regimens of interferon administration in man. Although the mechanisms of interferon's antitumor activity are unknown, it seems likely that interferon can act directly on the tumor cells as well as on the tumor bearing host.