gebhart/patrepeval huggingface dataset:
Messenger RNA prevalence in sea urchin embryos measured with cloned cDNAs. (1980)

mRNA prevalence during sea urchin development was measured by treating cDNA clone colonies with labeled cDNAs transcribed from unfertilized egg and embryo poly(A)-RNAs. The number of cytoplasmic transcripts per embryo complementary to several clones was determined independently by titration with poly(A)-RNA in solution, and the amount of cDNA bound to these clones in colony hybridizations was shown to be proportional to the concentration of the respective poly(A)-RNAs in the embryo cytoplasm. At the gastrula stage, the most prevalent mRNA species occur in about 10(6) molecules per embryo. If all cells were equivalent, this would be a few hundred molecules per cell. By pluteus stage, the prevalence of some sequences has increased more than 10-fold. Most, though not all, sequences prevalent in later embryos are also present in the maternal RNA of the unfertilized egg. For most poly(A)-RNA sequences, the prevalence levels determined during oogenesis are maintained through the pluteus stage, whereas a minority of sequences display sharp stage-specific changes in representation during development.
Gain/phase imbalance-minimization techniques for LINC transmitters (2001)

Two simple calibration schemes for the correction of the path imbalance in a linear amplification with nonlinear components (LINC) transmitter have been demonstrated. In the foreground algorithm, a baseband digital signal processor (DSP) evaluates the gain and phase imbalance with a set of calibration signals, while in the background algorithm, the imbalance is characterized by exchanging the two LINC vector components. In both cases, the compensation of the path imbalance is accomplished within the DSP by introducing a predistortion term. A prototype LINC system has been tested for CDMA IS-95 baseband input, and -38 and -35-dBc adjacent channel interference were achieved for the foreground and background schemes, respectively. The quadrature errors of the in-phase/quadrature modulators set a limit on the overall performance of both algorithms.
Ethernet Address Resolution Protocol: Or Converting Network Protocol Addresses to 48.bit Ethernet Address for Transmission on Ethernet Hardware (1982)

The implementation of protocol P on a sending host S decides,through protocol P's routing mechanism, that it wants to transmitto a target host T located some place on a connected piece of10Mbit Ethernet cable. To actually transmit the Ethernet packeta 48.bit Ethernet address must be generated. The addresses ofhosts within protocol P are not always compatible with thecorresponding Ethernet address (being different lengths orvalues). Presented here is a protocol that allows dynamicdistribution of the information needed to build tables totranslate an address A in protocol P's address space into a48.bit Ethernet address.
The production of antifungal volatiles by Bacillus subtilis (1993)

A strain of Bacillus subtilis which produces an antibiotic metabolite was also found to produce a volatile compound(s) which was antifungal to Rhizoctonia solani and Pythium ultimum. Growth of the fungi was severely impaired in the presence of the volatiles and physiological abnormalities of the hyphae were observed, including hyphal distortion and vacuolation. A range of media were tested for volatile production and potato dextrose agar (PDA) was found to be the most active. Temperature had a considerable effect on antifungal volatile activity with the greatest inhibition occurring at 30 degrees C. Addition of iron (III) chloride to Sabouraud's glucose agar (SGA) also enhanced the antifungal effect. The volatiles were found to be water soluble and remained active when trapped in SGA.
On the link between error correlation and error reduction in decision tree ensembles (1995)

Recent work has shown that learning an ensemble consisting of multiple models and then making classifications by combining the classifications of the models often leads to more accurate classifications then those based on a single model learned from the same data. However, the amount of error reduction achieved varies from data set to data set. This paper provides empirical evidence that there is a linear relationship between the degree of error reduction and the degree to which patterns of errors made by individual models are uncorrelated. Ensemble error rate is most reduced in ensembles whose constituents make individual errors in a less correlated manner. The second result of the work is that some of the greatest error reductions occur on domains for which many ties in information gain occur during learning. The third result is that ensembles consisting of models that make errors in a dependent but "negatively correlated" manner will have lower ensemble error rates than ensembles whose constituents make errors in an uncorrelated manner. Previous work has aimed at learning models that make errors in a uncorrelated manner rather than those that make errors in an "negatively correlated" manner. Taken together, these results help provide an understanding of why the multiple models approach yields great error reduction in some domains but little in others.
Oct-3/4 and Sox2 Regulate Oct-3/4 Gene in Embryonic Stem Cells (2004)

Oct-3/4 is a key transcriptional factor whose expression level governs the fate of primitive inner cell mass and embryonic stem (ES) cells. Previously, an upstream 3.3-kb distal enhancer (DE) fragment was identified to be responsible for the specific expression of mouse Oct-3/4 in the inner cell mass and ES cells. However, little is known about the cis-elements and trans-factors required for DE activity. In this study, we identified a novel cis-element, called Site 2B here, located approximately 30 bp downstream from Site 2A, which was previously revealed in DE by an in vivo chemical modification experiment. Using the luciferase reporter assay, we demonstrated that both Site 2A and Site 2B are necessary and sufficient for activating DE in the contexts of both the native Oct-3/4 promoter and the heterologous thymidine kinase minimal promoter. In an electrophoretic mobility shift assay we showed that Site 2B specifically binds to Oct-3/4 and Sox2 when ES-derived cell extracts were used, whereas Site 2A binds to a factor(s) present in both ES and NIH 3T3 cells. Furthermore, we showed that the physiological level of Oct-3/4 in ES cells is required for Site 2B-mediated DE activity using the inducible knock-out system of Oct-3/4 in ES cells. These results indicate that Oct-3/4 is a member of the gene family regulated by Oct-3/4 and Sox2, as reported before for the FGF-4, UTF1, Sox2, and Fbx15 genes. Thus, Oct-3/4 and Sox2 comprise a regulatory complex that controls the expression of genes important for the maintenance of the primitive state, including themselves. This autoregulatory circuit of the Sox2.Oct-3/4 complex may contribute to maintaining robustly the precise expression level of Oct-3/4 in primitive cells.
Memory effects in liquid crystal elastomers (1991)

Free-standing monodomain liquid crystal elastomer samples are shown to have a complete memory of the orientational configuration at the time of cross-linking. This memory is demonstrated through samples in which the parent polymer system is first aligned in a magnetic field prior to cross-linking. These films show reversible nematic-isotropic phase transitions and x-ray scattering patterns characteristic of nematic phases. The liquid crystal elastomer films exhibit a remarkable memory effect, in that the sample may be held at temperatures well above the nematic-isotropic transition for extended periods (> 2 weeks), but on cooling into the liquid crystal phase region, both the original director alignment and the degree of preferred orientation are recovered. It is demonstrated that these novel memory effects are equilibrium in nature. The origins of this phenomena in terms of coupling between the mesogenic side-chains and the polymer network are discussed.
Narrowing the semantic gap - improved text-based web document retrieval using visual features (2002)

We present the results of our work that seek to negotiate the gap between low-level features and high-level concepts in the domain of web document retrieval. This work concerns a technique, called the latent semantic indexing (LSI), which has been used for textual information retrieval for many years. In this environment, LSI determines clusters of co-occurring keywords so that a query which uses a particular keyword can then retrieve documents perhaps not containing this keyword, but containing other keywords from the same cluster. In this paper, we examine the use of this technique for content-based web document retrieval, using both keywords and image features to represent the documents. Two different approaches to image feature representation, namely, color histograms and color anglograms, are adopted and evaluated. Experimental results show that LSI, together with both textual and visual features, is able to extract the underlying semantic structure of web documents, thus helping to improve the retrieval performance significantly, even when querying is done using only keywords.
Synthesis of N-(tert-butyloxycarbonyl)-CBI, CBI, CBI-CDPI1, and CBI-CDPI2: enhanced functional analogs of CC-1065 incorporating the 1,2,9,9a-tetrahydrocyclopropa[c]benz[e]indol-4-one (CBI) left-hand subunit (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of N-(tert-butyloxycarbonyl)-CBI, CBI, CBI-CDPI1, and CBI-CDPI2: enhanced functional analogs of CC-1065 incorporating the 1,2,9,9a-tetrahydrocyclopropa[c]benz[e]indol-4-one (CBI) left-hand subunitDale L. Boger, Takayoshi Ishizaki, Paul A. Kitos, and Oranart SuntornwatCite this: J. Org. Chem. 1990, 55, 23, 5823–5832Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://pubs.acs.org/doi/10.1021/jo00310a013https://doi.org/10.1021/jo00310a013research-articleACS PublicationsRequest reuse permissionsArticle Views814Altmetric-Citations111LEARN 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 Get e-Alerts
Antiangiogenic Agents in Cancer Therapy (1999)

In Antiangiogenic Agents in Cancer Therapy, Beverly Teicher and a panel of distinguished investigators survey the state-of-the-art of antiangiogenesis research from the lab bench to clinical trials. Timely and authoritative, the contributors summarize our current understanding of tumor growth and its dependence on vascular development, as well as the present status of antiangiogenic agents in preclinical and clinical development. In addition, the book also examines what is known about the mechanisms by which these therapeutic agents interfere with tumor vasculature and grapples with the problem of establishing criteria by which to assess their clinical efficacy. Antiangiogenic Agents in Cancer Therapy offers a unique cutting-edge compendium of antiangiogenic research, taking stock of what has been accomplished, where the experimental therapeutics of antiangiogenic agents are going, and the continuing evolution of their role in cancer treatment and novel drug development. Comprehensive and up-to-date, this book constitutes a key resource-rich in novel means and methods-for the clinical development of this important, highly promising new class of anticancer drugs
Functional Analysis of Cathepsin B-like Cysteine Proteases fromLeishmania donovani Complex (2002)

Cathepsin B-like genes from Leishmania donovani and Leishmania chagasi have been isolated and characterized. It is a single gene, which is constitutively expressed in all the life cycle stages of the parasite. Studies using cathepsin B-specific inhibitor treatment suggested that cathepsin B does not seem to play a role in the promastigote stages of the parasite, however it aids in the parasite survival within the host macrophages. Antisense mRNA inhibition of cathepsin B gene also revealed that it plays an important role in the parasite survival within the host macrophages. Furthermore, for the first time, we have shown that Leishmania whole cell lysates as well as the recombinant cathepsin B protein cleaved human recombinant latent transforming growth factor (TGF)-beta1 into a mature peptide releasing the latency associated protein, in a cell-free incubation system. Mink lung epithelial cell growth inhibition assay revealed that the cleaved TGF-beta1 was biologically active, suggesting that Leishmania cathepsin B can cleave latent TGF-beta1 into mature and active form. These results suggest that cathepsin B plays an important role in Leishmania survival within the host macrophages by activating latent TGF-beta1.
Inducible formation of liver tumors in transgenic mice. (1993)

Transgenic mice have been generated with an inducible SV40 t/T antigen construct with the aim of analysing the early changes that take place in the course of liver tumorigenesis. The strictly liver-specific human C-reactive protein (CRP) gene promoter was chosen for the control of the transgene expression because this promoter can be turned on transiently by injection of bacterial lipopolysaccharide. Among 10 independently derived CRP-Tag mouse lines five showed inducible expression of the CRP-Tag transgene in liver. However, only one had a tight control of the transgene with virtually no expression under physiological conditions and high levels of Tag expression after stimulation. Females of this line were used to analyse the progression of liver alterations upon repeated induction of the t/T antigen for different lengths of time. The first signs of transgene-induced liver alterations could be monitored by the activation of the marker enzyme gamma-glutamyltranspeptidase 30 days after the start of the induction program. After 90 days hepatocellular carcinomas were already detectable. Thus, CRP-Tag mice constitute an excellent system to analyse the sequential events that take place during liver carcinogenesis.
Recombinant interleukin 6 stimulates immature murine megakaryocytes. (1990)

Human recombinant interleukin 6 (IL-6) was found to stimulate the growth of immature mouse megakaryocytes maximally at 2 ng/ml, leading to significant increases in the number of large megakaryocytes readily detectable by light microscopy. IL-6 did not stimulate megakaryocyte progenitor cells to form colonies of megakaryocytes, but potentiated megakaryocyte colony formation when added in the presence of interleukin 3. The stimulation could be neutralized by an anti-IL-6 serum. The data indicate that IL-6 is a potent differentiation stimulus of megakaryocyte development in cell culture.
Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes (1998)

Proteolytic enzymes are synthesized as inactive precursors, or "zymogens," to prevent unwanted protein degradation, and to enable spatial and temporal regulation of proteolytic activity. Upon sorting or appropriate compartmentalization, zymogen conversion to the active enzyme typically involves limited proteolysis and removal of an "activation segment." The sizes of activation segments range from dipeptide units to independently folding domains comprising more than 100 residues. A common form of the activation segment is an N-terminal extension of the mature enzyme, or "prosegment," that sterically blocks the active site, and thereby prevents binding of substrates. In addition to their inhibitory role, prosegments are frequently important for the folding, stability, and/or intracellular sorting of the zymogen. The mechanisms of conversion to active enzymes are diverse in nature, ranging from enzymatic or nonenzymatic cofactors that trigger activation, to a simple change in pH that results in conversion by an autocatalytic mechanism. Recent X-ray crystallographic studies of zymogens and comparisons with their active counterparts have identified the structural changes that accompany conversion. This review will focus upon the structural basis for inhibition by activation segments, as well as the molecular events that lead to the conversion of zymogens to active enzymes.
Precursors to two nuclear-encoded chloroplast proteins bind to the outer envelope membrane before being imported into chloroplasts. (1985)

Precursor forms of chloroplast proteins synthesized in cell-free translation systems can be imported posttranslationally into isolated, intact chloroplasts. Radiochemically pure precursors to the small subunit of ribulose-1,5-bisphosphate carboxylase and to the light-harvesting chlorophyll a/b protein have been prepared by in vitro translation of hybrid-selected mRNA and used to study this import process. If chloroplasts are pretreated with the uncoupler nigericin, import does not occur, but the precursors bind to the chloroplast surface. Reincubation of the precursor-chloroplast complex in the presence of ATP results in import of bound precursors. The binding appears to be mediated by proteins of the outer chloroplast envelope membrane because pretreatment of chloroplasts with protease inhibits their ability to bind as well as to import precursors. These results indicate that at least a portion of the observed binding is to functional receptor proteins involved in the import process.
Synthesis and Structure-Activity Relationships of Phenylenebis(methylene)-Linked Bis-Tetraazamacrocycles That Inhibit HIV Replication. Effects of Macrocyclic Ring Size and Substituents on the Aromatic Linker (1995)

We have previously described the potent and selective inhibition of several strains of human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) by JM2763, an n-propyl-linked dimer of the 1,4,8,11-tetraazamacrocyclic (cyclam) ring system. Upon further investigation, we have also found that incorporating an aromatic rather than aliphatic linker leads to analogs with higher antiviral potency. The prototype, JM3100 (19a, isolated as the octahydrochloride salt), which contains a p-phenylenebis(methylene) moiety linking the cyclam rings, inhibited the replication of HIV-1 (IIIB) and HIV-2 (ROD) at EC50's of 4.2 and 5.9 nM, respectively, while remaining nontoxic to MT-4 cells at concentrations exceeding 421 microM. In order to identify the structural features of bis-tetraazamacrocycles required for potent activity, we have prepared a novel series of phenylenebis(methylene)-linked analogs, in which the macrocyclic ring size was varied from 12 to 16 ring members. Depending upon the substitution of the phenylenebis(methylene) linker (para or meta), sub-micromolar anti-HIV activity was exhibited by analogs bearing macrocycles of 12-14 ring members but with varying cytotoxicity to MT-4 cells. Furthermore, while we found that identical macrocyclic rings are not required for activity, substituting an acyclic polyamine equivalent for one of the cyclam rings in 19a resulted in a substantial reduction in anti-HIV potency, clearly establishing the importance of the constrained macrocyclic structure. A short series of transition metal complexes of 19a were also prepared and evaluated. Complexes of low kinetic stability such as the bis-zinc complex retained activity comparable to that of the parent compound. Finally, the activity of bicyclam analogs appears to be insensitive to the electron-withdrawing or -donating properties of substituents introduced onto the linker, but sterically hindering groups such as phenyl markedly reduced activity. As a result, several analogs with anti-HIV potency comparable to that of 19a have been identified.
Metabolomics in Systems Biology (2003)

The primary aim of "omic" technologies is the nontargeted identification of all gene products (transcripts, proteins, and metabolites) present in a specific biological sample. By their nature, these technologies reveal unexpected properties of biological systems. A second and more challenging aspect of omic technologies is the refined analysis of quantitative dynamics in biological systems. For metabolomics, gas and liquid chromatography coupled to mass spectrometry are well suited for coping with high sample numbers in reliable measurement times with respect to both technical accuracy and the identification and quantitation of small-molecular-weight metabolites. This potential is a prerequisite for the analysis of dynamic systems. Thus, metabolomics is a key technology for systems biology. The aim of this review is to (a) provide an in-depth overview about metabolomic technology, (b) explore how metabolomic networks can be connected to the underlying reaction pathway structure, and (c) discuss the need to investigate integrative biochemical networks.
Multilevel nanoimprint lithography with submicron alignment over 4 in. Si wafers (2001)

We demonstrate that multilevel nanoimprint lithography (NIL) with submicron alignment over an entire 4 in. Si wafer can be achieved. Average alignment accuracy of 1 μm with a standard deviation 0.4 μm in both X and Y directions was obtained in ten consecutive tests of multilevel NIL. The multilevel alignment was achieved by aligning the wafer and the mask with an aligner, fixing them with a holder, and imprinting in an imprint machine. The issues that are critical to the alignment accuracy, such as relative movement during the press, relative thermal expansion, wafer bending, and resist, are discussed. The alignment accuracy currently achieved on the system is limited by the aligning accuracy of the aligner, instead of the process of multilevel NIL.
Protective Relay Synchrophasor Measurements During Fault Conditions (2006)

This paper describes details of the signal processing techniques that a protective relay uses to provide both synchronized phasor measurements and line distance protection. The paper also presents a comprehensive system model of normal and faulted power system operating conditions. Finally, the paper provides power system model test results that demonstrate the ability of the described protective relay to provide synchrophasor measurements during both normal and faulted conditions
Spatio-Temporal Modeling and Prediction of Visual Attention in Graphical User Interfaces (2016)

We present a computational model to predict users' spatio-temporal visual attention on WIMP-style (windows, icons, menus, pointer) graphical user interfaces. Like existing models of bottom-up visual attention in computer vision, our model does not require any eye tracking equipment. Instead, it predicts attention solely using information available to the interface, specifically users' mouse and keyboard input as well as the UI components they interact with. To study our model in a principled way, we further introduce a method to synthesize user interface layouts that are functionally equivalent to real-world interfaces, such as from Gmail, Facebook, or GitHub. We first quantitatively analyze attention allocation and its correlation with user input and UI components using ground-truth gaze, mouse, and keyboard data of 18 participants performing a text editing task. We then show that our model predicts attention maps more accurately than state-of-the-art methods. Our results underline the significant potential of spatio-temporal attention modeling for user interface evaluation, optimization, or even simulation.