gebhart/patrepeval huggingface dataset:
Determination of surface concentrations of individual molecule-layers used in nanoscale biosensors by in situ ATR-FTIR spectroscopy (2012)

For the development of nanowire sensors for chemical and medical detection purposes, the optimal functionalization of the surface is a mandatory component. Quantitative ATR-FTIR spectroscopy was used in situ to investigate the step-by-step layer formation of typical functionalization protocols and to determine the respective molecule surface concentrations. BSA, anti-TNF-α and anti-PSA antibodies were bound via 3-(trimethoxy)butylsilyl aldehyde linkers to silicon-oxide surfaces in order to investigate surface functionalization of nanowires. Maximum determined surface concentrations were 7.17 × 10(-13) mol cm(-2) for BSA, 1.7 × 10(-13) mol cm(-2) for anti-TNF-α antibody, 6.1 × 10(-13) mol cm(-2) for anti-PSA antibody, 3.88 × 10(-13) mol cm(-2) for TNF-α and 7.0 × 10(-13) mol cm(-2) for PSA. Furthermore we performed antibody-antigen binding experiments and determined the specific binding ratios. The maximum possible ratio of 2 was obtained at bulk concentrations of the antigen in the μg ml(-1) range for TNF-α and PSA.
The Canonical Helix of Urea Oligomers at Atomic Resolution: Insights Into Folding‐Induced Axial Organization (2009)

Helical by nature: Urea-based peptidomimetics with proteinogenic side chains are fully helical in the crystalline state (see picture). Four acyclic residues are sufficient to drive complete helix formation with all complementary H-bonding sites being satisfied (up to 14 for a 8-mer). Helices pack head-to-tail to create infinite H-bonded networks with different topologies.
Understanding the Biology of CRLF2-Overexpressing Acute Lymphoblastic Leukemia (2011)

Recent genomic analyses of childhood and adult B-precursor acute lymphoblastic leukemia (ALL) samples have identified novel genetic alterations in essential lymphoid development and signal transduction pathways, providing insight into the pathogenesis of high-risk ALL associated with treatment failure. Particular advances have been made in unraveling the genetics of ALL associated with overexpression of the cytokine receptor-like factor 2 gene (CRLF2), which is frequently accompanied by simultaneous activating mutations in genes encoding Ikaros (IKZF1), Janus kinase 1 (JAK1) and Janus kinase 2 (JAK2), and/or the IL-7 receptor alpha chain (IL7RA). Children and adults with high-risk CRLF2-overexpressing ALL have high rates of relapse and dismal overall survival. Various groups have thus attempted to characterize the biochemical consequences of these genetic lesions via preclinical models with the goal of identifying targets for new therapies. These studies provide early data suggesting the promise of signal transduction inhibitors (STIs) of the JAK/STAT and PI3K pathways for CRLF2-overexpressing ALL. Additional research efforts continue to elucidate these aberrant signaling networks to provide rationale for bringing STIs into the clinic for these high-risk patients. This review highlights the current knowledge of the incidence, prognostic significance, and biology of CRLF2-overexpressing ALL and future directions for development of targeted therapies.
A Remote Memory Swapping System for Cluster Computers (2007)

This paper describes the use of remote memory for virtual memory swapping in a cluster computer. Our design uses a lightweight kernel-to-kernel communications channel for fast, efficient data transfer. Performance tests are made to compare our system to normal hard disk swapping. The tests show significantly improved performance when data access is random.
Apoptosis Induced by Drosophila Reaper and Grim in a Human System (1998)

Previous genetic studies have established Reaper and Grim as central regulators of apoptosis in Drosophila melanogaster. Reaper and Grim induce extensive apoptosis in Drosophila, yet share no homology to known vertebrate proteins. In this study, we show for the first time that ectopic expression of Reaper or Grim induced substantial apoptosis in mammalian cells. Reaper- or Grim-induced apoptosis was inhibited by a broad range of caspase inhibitors and by human inhibitor of apoptosis proteins cIAP1 and cIAP2. Additionally, in vivo binding studies demonstrated that both Reaper and Grim physically interacted with human IAPs through a homologous 15-amino acid N-terminal segment. Deletion of this segment from either Reaper or Grim abolished binding to cIAPs. In vitro binding experiments indicated that Reaper and Grim bound specifically to the BIR domain-containing region of cIAPs as deletion of this region resulted in loss of binding. The physical interaction was further confirmed by immunolocalization. When co-expressed, Reaper or Grim co-localized with cIAP1. However, deletion of the N-terminal 15 amino acids of Reaper or Grim abolished co-localization with cIAP1, suggesting that this homologous region can serve as a protein-protein interacting domain in regulating cell death. Moreover, by virtue of this interaction, we demonstrate that cIAPs can regulate Reaper and Grim by abrogating their ability to activate caspases and thereby inhibit apoptosis. This is the first function attributed to this 15-amino acid N-terminal domain that is the only region having significant homology between these Drosophila death inducers.
EXIT chart analysis of non-regular signal constellation sets for BICM-ID (2004)

A key design element of bit-interleaved coded modulation with iterative decoding (BICM-ID) is the mapping of the bit patterns to the elements of the signal constellation set (SCS). Recently, we proposed mappings and new non-regular SCSs with superior asymptotic performance, i.e., lower error o ors. These proposed mappings use signal constellation sets with less elements than the number of bit patterns to be transmitted and an appropriate assignment of the bit patterns to them. The puncturing introduced by the not one-to-one relation between assigned bit patterns and the elements of the SCS is compensated by the usage of extrinsic information obtained in the iterations. We further show the theoretical limits for the improvement of BICM-ID by this technique. Based on the mutual information concept of EXIT charts, a method is presented allowing easy determination of the achievable gains by dieren t mappings for dieren t kinds of channels. The results are conrmed by simulations.
Conformational analysis. 42. Monosubstituted tetrahydropyrans (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformational analysis. 42. Monosubstituted tetrahydropyransErnest L. Eliel, Karl D. Hargrave, K. Michal Pietrusiewicz, and Muthiah ManoharanCite this: J. Am. Chem. Soc. 1982, 104, 13, 3635–3643Publication Date (Print):June 1, 1982Publication History Published online1 May 2002Published inissue 1 June 1982https://pubs.acs.org/doi/10.1021/ja00377a015https://doi.org/10.1021/ja00377a015research-articleACS PublicationsRequest reuse permissionsArticle Views550Altmetric-Citations97LEARN 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-Alertsclose Get e-Alerts
Akt suppresses androgen-induced apoptosis by phosphorylating and inhibiting androgen receptor (2001)

Whereas several apoptosis-related proteins have been linked to the antiapoptotic effects of Akt serine-threonine kinase, the search continues to explain the Akt signaling role in promoting cell survival via antiapoptotic effects. Here, we demonstrate that Akt phosphorylates the androgen receptor (AR) at Ser-210 and Ser-790. A mutation at AR Ser-210 results in the reversal of Akt-mediated suppression of AR transactivation. Activation of the phosphatidylinositol-3-OH kinase/Akt pathway results in the suppression of AR target genes, such as p21, and the decrease of androgen/AR-mediated apoptosis, which may involve the inhibition of interaction between AR and AR coregulators. Together, these findings provide a molecular basis for cross-talk between two signaling pathways at the level of Akt and AR-AR coregulators that may help us to better understand the roles of Akt in the androgen/AR-mediated apoptosis.
Error propagation analysis for file systems (2009)

Unchecked errors are especially pernicious in operating system file management code. Transient or permanent hardware failures are inevitable, and error-management bugs at the file system layer can cause silent, unrecoverable data corruption. We propose an interprocedural static analysis that tracks errors as they propagate through file system code. Our implementation detects overwritten, out-of-scope, and unsaved unchecked errors. Analysis of four widely-used Linux file system implementations (CIFS, ext3, IBM JFS and ReiserFS), a relatively new file system implementation (ext4), and shared virtual file system (VFS) code uncovers 312 error propagation bugs. Our flow- and context-sensitive approach produces more precise results than related techniques while providing better diagnostic information, including possible execution paths that demonstrate each bug found.
Dipeptidyl Peptidase IV (DP IV, CD26) in Patients with Inflammatory Bowel Disease (2001)

The changes of DP IV in patients with IBD highlight alterations at an interface between immune function and metabolism of peptide hormones, with potential importance for the pathophysiology of IBD. Furthermore, these changes may help to refine the assessment of IBD activity.
The pan-Pituitary Activator of Transcription, Ptx1 (Pituitary Homeobox 1), Acts in Synergy with SF-1 and Pit1 and Is an Upstream Regulator of the Lim-Homeodomain Gene Lim3/Lhx3 (1998)

The Ptx1 (pituitary homeobox 1) homeobox transcription factor was isolated as a transcription factor of the pituitary POMC gene. In corticotrope cells that express POMC, cell-specific transcription is conferred in part by the synergistic action of Ptx1 with the basic helix-loop-helix factor NeuroD1. Since Ptx1 expression precedes pituitary development and differentiation, we investigated its expression and function in other pituitary lineages. Ptx1 is expressed in most pituitary-derived cell lines and as is the related Ptx2 (Rieger) gene. However, Ptx1 appears to be the only Ptx protein in corticotropes and the predominant one in gonadotrope cells. Most pituitary hormone-coding gene promoters are activated by Ptx1. Thus, Ptx1 appears to be a general regulator of pituitary-specific transcription. In addition, Ptx1 action is synergized by cell-restricted transcription factors to confer promoter-specific expression. Indeed, in the somatolactotrope lineage, synergism between Ptx1 and Pit1 is observed on the PRL promoter, and strong synergism between Ptx1 and SF-1 is observed in gonadotrope cells on the betaLH promoter but not on the alphaGSU (glycoprotein hormone alpha-subunit gene) and betaFSH promoters. Synergism between these two classes of factors is reminiscent of the interaction between the products of the Drosophila genes Ftz (fushi tarazu) and Ftz-F1. Antisense RNA experiments performed in alphaT3-1 cells that express the alphaGSU gene showed that expression of endogenous alphaGSU is highly dependent on Ptx1 whereas many other genes are not affected. Interestingly, the only other gene found to be highly dependent on Ptx1 for expression was the gene for the Lim3/Lhx3 transcription factor. Thus, these experiments place Ptx1 upstream of Lim3/Lhx3 in a cascade of regulators that appear to work in a combinatorial code to direct pituitary-, lineage-, and promoter-specific transcription.
Atom Transfer Radical Polymerization in Microemulsion (2005)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTAtom Transfer Radical Polymerization in MicroemulsionKe Min and Krzysztof MatyjaszewskiView Author Information Center for Macromolecular Engineering, Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213 Cite this: Macromolecules 2005, 38, 20, 8131–8134Publication Date (Web):September 8, 2005Publication History Received28 July 2005Revised20 August 2005Published online8 September 2005Published inissue 1 October 2005https://pubs.acs.org/doi/10.1021/ma051675vhttps://doi.org/10.1021/ma051675vrapid-communicationACS PublicationsCopyright © 2005 American Chemical SocietyRequest reuse permissionsArticle Views2142Altmetric-Citations130LEARN 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:Emulsions,Micelles,Particle size,Polymerization,Radical polymerization Get e-Alerts
Auditory thalamocortical projections in the cat: Laminar and areal patterns of input (2000)

Thalamocortical projections were studied in adult cats using biotinylated dextran amines, wheat germ agglutinin conjugated to horseradish peroxidase, and autoradiography with tritiated leucine and/or proline. The input from 7 architectonically defined nuclei to 14 auditory cortical fields was characterized qualitatively and quantitatively. The principal results were that 1) every thalamic nucleus projected to more than 1 field (range, 4-14 fields; mean, 7 fields); 2) only the projection from the ventral division to some primary fields (primary auditory cortex and posterior auditory cortex) had a periodic, clustered distribution, whereas the input from other divisions to nonprimary areas was continuous; 3) layers III-V received >85% of the total axonal profiles; 4) in most experiments, five or more layers were labeled; 5) the projections to nonprimary auditory areas had many laterally oriented axons; 6) the heaviest input to layer I in all experiments was usually in its upper half, suggesting a sublaminar arrangement; 7) the largest axonal trunks (up to 6 microm in diameter) arose from the medial division and ended in layer Ia, where they ran laterally for long distances; 8) there were three projection patterns: type 1 had its peak in layers III-IV with little input to layer I, and it arose from the ventral division and the dorsal superficial, dorsal, and suprageniculate nuclei of the dorsal division; type 2 had heavy labeling in layer I and less in layers III-IV, arising from the dorsal division nuclei primarily, especially the caudal dorsal and deep dorsal nuclei; and type 3 was a trimodal concentration in layers I, III-IV, and VI that originated chiefly in the medial division and had the lowest density of labeling; and 9) the quantitative profiles with the three methods were very similar. The results suggest that the subdivisions of the auditory thalamus have consistent patterns of laminar distribution to different cortical areas, that an average of five or more layers receive significant input in a specific area, that a given thalamic nucleus can influence areas as far as 20 mm apart, that the first information to arrive at the cortex may reach layer I by virtue of the giant axons, and that several laminar patterns of auditory thalamocortical projection exist. The view that the auditory thalamus (and perhaps other thalamic nuclei) serves mainly a relay function underestimates its many modes for influencing the cortex on a laminar basis.
Hairy brushes (1986)

Paint brushes are modeled as a collection of bristles which evolve over the course of the stroke, leaving a realistic image of a sumi brush stroke. The major representational units are (1) Brush: a compound object composed of bristles, (2) Stroke: a trajectory of position and pressure, (3) Dip: a description of the application of paint to a class of brushes, and (4) Paper: a mapping onto the display device. This modular system allows experimentation with various stochastic models of ink flow and color change. By selecting from a library of brushes, dips, and papers, the stroke can take on a wide variety of expressive textures.
IBM's LVCSR system for transcription of broadcast news used in the 1997 hub4 english evaluation (1998)

This paper describes IBM’s large vocabulary continuous speech recognition (LVCSR) system used in the 1997 Hub4 English evaluation. It focusses on extensions and improvements to the system used in the 1996 evaluation. The recognizer uses an additional 35 hours of training data over the one used in the 1996 Hub4 evaluation [8]. It includes a number of new features: optimal feature space for acoustic modeling (in training and/or testing), filler-word modeling, Bayesian Information Criterion (BIC) based segmentation and segment clustering, an improved implementation of iterative MLLR, variance adaptation, and 4-gram language models. Results using the 1996 and 1997 DARPA Hub4 evaluation data sets are presented.
The influence of ovarian cancer induced peritoneal carcinomatosis on the pharmacokinetics of albendazole in nude mice. (2010)

Angiogenesis in the peritoneal cavity arising from ovarian cancer leads to peritoneal carcinomatosis, malignant ascites formation, morbidity and high mortality. Recent studies in our laboratory have shown albendazole (ABZ) to be a potent inhibitor of angiogenesis and malignant ascites formation. The current study was designed to find the pharmacokinetics of the drug and its major metabolites albendazole sulfoxide (ABZSO) and albendazole sulfone (ABZSO(2)) in an experimental model of ovarian cancer. Additionally, we sought to investigate if the cancer-induced changes in the peritoneal cavity would affect the kinetics of ABZ. On this basis, ABZ was administered 150 mg/kg intraperitoneally to groups of mice bearing peritoneal carcinomatosis and also to groups of healthy mice with no tumor. Blood and peritoneal wash samples were collected for up to 72 h. Concentration of ABZ and its metabolites in the samples were analysed by an established high performance liquid chromatography method. In the healthy mice, drug and metabolite concentrations were found to be low to undetectable. On the contrary, tumor-bearing mice had higher levels of ABZSO in both the plasma and their peritoneal wash. This may at least in part be attributed to the high vascular endothelial growth factor levels present in the peritoneal cavity of the diseased mice. The data obtained in this study suggest that peritoneal carcinomatosis changes ABZ absorption from the peritoneal cavity.
A Fractional-N Divider-Less Phase-Locked Loop With a Subsampling Phase Detector (2014)

A low-noise divider-less PLL, employing a subsampling locked loop, samples the VCO output by a digital pulse-width modulator (DPWM) to perform fractional-N operation. The frequency synthesizer achieves a low in-band phase noise of -112 dBc/Hz at a 2.3 GHz output frequency. The analysis for the frequency synthesizer, especially for the nonlinear characteristics of the circuits, is proposed. Fabricated in a 0.18 μm CMOS technology, the frequency synthesizer consumes 9.6 mA and achieves figure-of-merit of -239.1 dB, corresponding to 266 fs rms jitter.
Development of a novel DDS for site-specific PEGylated proteins (2011)

Because of the shifted focus in life science research from genome analyses to genetic and protein function analyses, we now know functions of numerous proteins. These analyses, including those of newly identified proteins, are expected to contribute to the identification of proteins of therapeutic value in various diseases. Consequently, pharmacoproteomic-based drug discovery and development of protein therapies attracted a great deal of attention in recent years. Clinical applications of most of these proteins are, however, limited because of their unexpectedly low therapeutic effects, resulting from the proteolytic degradation in vivo followed by rapid removal from the circulatory system. Therefore, frequent administration of excessively high dose of a protein is required to observe its therapeutic effect in vivo. This often results in impaired homeostasis in vivo and leads to severe adverse effects. To overcome these problems, we have devised a method for chemical modification of proteins with polyethylene glycol (PEGylation) and other water-soluble polymers. In addition, we have established a method for creating functional mutant proteins (muteins) with desired properties, and developed a site-specific polymer-conjugation method to further improve their therapeutic potency. In this review, we are introducing our original protein-drug innovation system mentioned above.
Dendritic cells pulsed with RNA are potent antigen-presenting cells in vitro and in vivo. (1996)

Immunization with defined tumor antigens is currently limited to a small number of cancers where candidates for tumor rejection antigens have been identified. In this study we investigated whether pulsing dendritic cells (DC) with tumor-derived RNA is an effective way to induce CTL and tumor immunity. DC pulsed with in vitro synthesized chicken ovalbumin (OVA) RNA were more effective than OVA peptide-pulsed DC in stimulating primary, OVA-specific CTL responses in vitro. DC pulsed with unfractionated RNA (total or polyA+) from OVA-expressing tumor cells were as effective as DC pulsed with OVA peptide at stimulating CTL responses. Induction of OVA-specific CTL was abrogated when polyA+ RNA from OVA-expressing cells was treated with an OVA-specific antisense oligodeoxynucleotide and RNase H, showing that sensitization of DC was indeed mediated by OVA RNA. Mice vaccinated with DC pulsed with RNA from OVA-expressing tumor cells were protected against a challenge with OVA-expressing tumor cells. In the poorly immunogenic, highly metastatic, B16/F10.9 tumor model a dramatic reduction in lung metastases was observed in mice vaccinated with DC pulsed with tumor-derived RNA (total or polyA+, but not polyA- RNA). The finding that RNA transcribed in vitro from cDNA cloned in a bacterial plasmid was highly effective in sensitizing DC shows that amplification of the antigenic content from a small number of tumor cells is feasible, thus expanding the potential use of RNA-pulsed DC-based vaccines for patients bearing very small, possibly microscopic, tumors.
The Enduring Hypoxic Response of Mycobacterium tuberculosis (2008)

Our results suggest a reassessment of the role of DosR and the initial hypoxic response in MTB physiology. Instead of a primary role in survival of hypoxia induced bacteriostasis, DosR may regulate a response that is largely optional in vitro and in mouse infections. Analysis of the EHR should help elucidate the key regulatory factors and enzymatic machinery exploited by M. tuberculosis for long-term bacteriostasis in the face of oxygen deprivation.