gebhart/patrepeval huggingface dataset:
Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells (2012)

Data on absolute molecule numbers will empower the modeling, understanding, and comparison of cellular functions and biological systems. We quantified transcriptomes and proteomes in fission yeast during cellular proliferation and quiescence. This rich resource provides the first comprehensive reference for all RNA and most protein concentrations in a eukaryote under two key physiological conditions. The integrated data set supports quantitative biology and affords unique insights into cell regulation. Although mRNAs are typically expressed in a narrow range above 1 copy/cell, most long, noncoding RNAs, except for a distinct subset, are tightly repressed below 1 copy/cell. Cell-cycle-regulated transcription tunes mRNA numbers to phase-specific requirements but can also bring about more switch-like expression. Proteins greatly exceed mRNAs in abundance and dynamic range, and concentrations are regulated to functional demands. Upon transition to quiescence, the proteome changes substantially, but, in stark contrast to mRNAs, proteins do not uniformly decrease but scale with cell volume.
Streptococcal-host interactions. Structural and functional analysis of a Streptococcus sanguis receptor for a human salivary glycoprotein. (1990)

Colonization of oral tissues by Streptococcus sanguis may be influenced by a mucin-like salivary glycoprotein (SAG) through a calcium-dependent interaction with a specific bacterial receptor. We report the nucleotide and deduced amino acid sequence of the S. sanguis receptor (SSP-5) and show that this protein may bind sialic acid residues of SAG. The SSP-5 protein contains three unique structural domains, two of which consist of repetitive amino acid sequences. The N-terminal domain is comprised of four tandem copies of an 82-residue repeat which exhibits homology to M protein of Streptococcus pyogenes. This region is highly charged and predicted to be alpha-helical. A second hydrophilic repetitive domain consists of three copies of a 39-amino acid sequence containing 30% proline flanked by nonrepetitive proline-rich sequence. The third domain consists of 48% proline and resides near the C terminus of the protein. Secondary structure analysis of the SSP-5 sequence also identified four potential helix-turn-helix motifs that resembled E-F hand calcium binding domains. The SSP-5 protein is highly homologous to a surface antigen expressed by the mutans streptococci and the domain structure of SSP-5 is conserved within this family of proteins. The interactions of SSP-5 and of intact S. sanguis with SAG were inhibited by neuraminidase digestion of the salivary glycoprotein and by simple sugars containing sialic acid, suggesting that sialic acid is the primary ligand involved in the binding reaction.
Acene containing polyfluorenes for red, green, and blue emission in organic light-emitting diodes (2001)

We have introduced acene such as anthracene, naphthacene and pentacene into the main chain of polyfluorene to improve stability and to realize color tuning to pure blue, green and red. High molecular weight acene-containing polyfluorenes are successfully synthesized by the Ni[0] mediated Yamamoto-coupling reaction. Average molecular weights of the copolymers are Mw equals 42000 - 96000 (determined by GPC). By the introduction of 10% of acene moiety, the device stability could be significantly improved, indicating the torsion between the acene and fluorene units suppresses interchain aggregation; the copolymers exhibits stable blue, green and red emission in the anthracene-, naphthacene- and pentacene-containing polyfluorenes, respectively. Onset voltage for light emission is 5 - 30 V and the maximum luminance is 240 - 5200 cd/m<SUP>2</SUP>. As a side effect an unique color change on UV irradiation could be observed as well as the reason for its appearance determined.
Hepatitis C virus glycoprotein folding: disulfide bond formation and association with calnexin (1996)

The hepatitis C virus (HCV) glycoproteins (E1 and E2) are released from the polyprotein by signal peptidase-mediated cleavage and interact to form a heterodimer. Since properly folded subunits are usually required for specific recognition and stable oligomer formation, the rate of stable E1E2 complex formation, which is low, may be limited by the rate of HCV E1 and/or E2 folding. In this study, the folding of the HCV E1 and E2 glycoproteins was monitored by observing the kinetics of intramolecular disulfide bond formation. The association/dissociation of E1 and E2 with calnexin was also examined, since this molecular chaperone appears to play a major role in quality control via retention of incompletely folded or misfolded proteins in the endoplasmic reticulum. Our results indicate that the disulfide-dependent folding of E2 occurs rapidly and appears to be complete upon cleavage of the precursor E2-NS2. In contrast, folding of E1 is slow (> 1 h), suggesting that this step may be rate limiting for E1E2 oligomerization. Both HCV glycoproteins associated rapidly with calnexin, but dissociation was slow, consistent with the slow folding and assembly of E1E2 glycoprotein complexes. These results suggest a role for prolonged association with calnexin in the folding and assembly of HCV glycoprotein heterodimer complexes.
Space-Time Wireless Channels (2002)

A practical, approach to space-time wireless channel design. A practical approach to space-time wireless channel design Integrates essential principles from communications, electromagnetics, and random process theory Includes detailed coverage of diversity, multipath applications, and antenna array design Contains extensive examples, illustrations, and problem setsNext-generation broadband radio systems must deliver unprecedented performance and higher data rates, while coping with increased spectral congestion. To achieve these goals, engineers need an in-depth understanding of radio channels that fade in time, frequency, and space. In Space-Time Wireless Channels, leading researcher Gregory D. Durgin presents a pragmatic, first-principles approach that integrates crucial concepts and techniques from communications, electromagnetics, and random process theory.Durgin focuses on comprehension and practicality, offering extensive examples, illustrations, and problem sets, while avoiding gratuitious mathematics and moving most derivations to end-of-chapter appendices. Coverage includes: Fundamentals of space, time, and frequency transmission and random process theory Electromagnetic description of space-time channels and the physics of small-scale fading First- and second-order statistics of fading channels Angle spectrum concepts and applications, including vector/scalar space and multipath shape factors Antenna diversity, temporal diversity, and bit error rates Multipath channels: separation, signaling, block coding, and antenna array design Appendices list special functions, Fourier transform examples, and random process theory concepts, as well as all relevant mathematical symbols, conventions, and acronyms.
The affordances of media spaces for collaboration (1992)

Article The affordances of media spaces for collaboration Share on Author: William W. Gaver Rank Xerox Cambridge EuroPARC, 61 Regent Street, Cambridge CB2 1AB, U.K. Rank Xerox Cambridge EuroPARC, 61 Regent Street, Cambridge CB2 1AB, U.K.View Profile Authors Info & Claims CSCW '92: Proceedings of the 1992 ACM conference on Computer-supported cooperative workDecember 1992 Pages 17–24https://doi.org/10.1145/143457.371596Published:01 December 1992 172citation2,756DownloadsMetricsTotal Citations172Total Downloads2,756Last 12 Months150Last 6 weeks18 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
A paradigm for drug discovery employing encoded combinatorial libraries. (1995)

Very large combinatorial libraries of small molecules on solid supports can now be synthesized and each library element can be identified after synthesis by using chemical tags. These tag-encoded libraries are potentially useful in drug discovery, and, to test this utility directly, we have targeted carbonic anhydrase (carbonate dehydratase; carbonate hydro-lyase, EC 4.2.1.1) as a model. Two libraries consisting of a total of 7870 members were synthesized, and structure-activity relationships based on the structures predicted by the tags were derived. Subsequently, an active representative of each library was resynthesized (2-[N-(4-sulfamoylbenzoyl)-4'-aminocyclohexanespiro]-4-oxo-7 -hydroxy- 2,3-dihydrobenzopyran and [N-(4-sulfamoylbenzoyl)-L-leucyl]piperidine-3-carboxylic acid) and these compounds were shown to have nanomolar dissociation constants (15 and 4 nM, respectively). In addition, a focused sublibrary of 217 sulfamoylbenzamides was synthesized and revealed a clear, testable structure-activity relationship describing isozyme-selective carbonic anhydrase inhibitors.
Reproducible Research in Computational Science (2011)

Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.
Activation of ARK5/miR-1181/HOXA10 axis promotes epithelial-mesenchymal transition in ovarian cancer (2015)

Epithelial ovarian cancer (EOC) is the sixth most common cancer in females worldwide and, although advances have been made in the detection, diagnosis and therapies for EOC, it remains the most lethal gynecologic malignancy in advanced countries. Nevertheless, relatively little is known concerning the molecular events that lead to the development of this highly aggressive disease. Elucidating the molecular mechanism involved in this disease may prove useful to understand the pathogenesis and progression of the disease, and to identify new targets for effective therapies. In the present study, we examined the role of ARK5 in ovarian cancer and normal matched tissues using western blot analysis and migration and invasion, and wound‑healing assays. The results showed that ARK5 was upregulated in ovarian cancer tissues, compared with adjacent normal tissues. Moreover, it promoted epithelial‑mesenchymal transition (EMT) and inhibited miR-1181 expression in ovarian cancer cells. Subsequent investigations showed that miR-1181 promoted mesenchymal-epithelial transition (MET) in ovarian cancer cells. Downstream target genes of miR-1181 were searched, and it was identified that miR-1181 degraded HOXA10 by targeting its 3' untranslated region (3'UTR) in ovarian cancer cells. The results confirmed that HOXA10 promoted EMT in ovarian cancer cells. Thus, activation of the ARK5/miR-1181/HOXA10 axis may be positively associated with EMT in ovarian cancer.
Characterization of twenty-six new heat shock genes of Escherichia coli (1993)

Most organisms respond to heat by substantial alteration of the pattern of gene expression. This has been particularly well studied with Escherichia coli although the response has by no means been completely characterized. Here we report the characterization of 26 new heat shock genes of E. coli, termed hsl, discovered by global transcription analysis with an overlapping lambda clone bank. We have measured the molecular weights of the corresponding heat shock proteins and mapped each of them to within a few kilobases on the E. coli genome. In vitro, 16 of them can be activated by the E sigma 32 RNA polymerase, which specifically transcribes heat shock genes. In vivo expression kinetics of seven of eight examined new proteins were found to be similar to those of the four most studied heat shock proteins, DnaK, DnaJ, GroEL (MopA), and GroES (MopB). In the course of this work, we confirmed that the catalytic subunit of the ATP-dependent Clp protease (also known as Ti protease), ClpP, is derived from a larger precursor protein. Possible assignments of some of the hsl genes to known proteins are discussed.
Managing power and performance for System-on-Chip designs using Voltage Islands (2002)

This paper discusses Voltage Islands, a system architecture and chip implementation methodology, that can be used to dramatically reduce active and static power consumption for System-on-Chip (SoC) designs. As technology scales for increased circuit density and performance, the need to reduce power consumption increases in significance as designers strive to utilize the advancing silicon capabilities. The consumer product market further drives the need to minimize chip power consumption.Effective use of Voltage Islands for meeting SoC power and performance requirements, while meeting Time to Market (TAT) demands, requires novel approaches throughout the design flow as well as special circuit components and chip powering structures. This paper outlines methods being used today to design Voltage Islands in a rapid-TAT product development environment, and discusses the need for industry EDA advances to create an industry-wide Voltage Island design capability.
Sequential requirements for cell cycle progression of resting human B cells after activation by anti-Ig. (1984)

We have previously demonstrated that in vivo activated normal human B cells reflected differential sensitivity on the basis of cell size to either an activation signal delivered by anti-mu or a proliferative signal delivered by a monoclonal B cell growth factor (BCGF) produced by a human T-T hybridoma. In this manuscript, we have shown that by using an in vitro co-culture system of stimulation with anti-mu and BCGF, purified small (resting) B cells could be induced by anti-mu stimulation to express functionally active BCGF acceptor sites concomitant with RNA synthesis and cell enlargement. We have demonstrated that purified small B cells could be activated to increase both cell size and RNA synthesis within 8 hr of anti-mu stimulation. DNA synthesis by anti-mu-stimulated B cells began at 36 to 44 hr from initial stimulation only when BCGF was added to the culture. In addition, large B cells that had been incubated with anti-mu for 24 to 48 hr manifested significant incorporation of [3H]thymidine if BCGF was added to cultures. These data strongly suggest that anti-mu may induce the G0 phase B cells into the G1 phase and that BCGF may then push at least a subset of these G1 phase-B cells into the S phase. This experimental system may provide a useful model of normal human B cell activation and proliferation and may allow a more precise delineation of each phase of this cascade in the B cell repertoire.
Laparoscopic placement of electrodes for diaphragm pacing using stimulation to locate the phrenic nerve motor points (1998)

Laparoscopic mapping of the phrenic nerve motor points using test stimulation was conducted for the implant of epimysial electrodes for diaphragm pacing in dogs. Both visual assessment of muscle activation and measurements of recruitment were useful for identifying an implant location resulting in a mean electrode placement approximately 14 mm from the phrenic nerve motor points in 16 dogs. Postmortem analysis of the stimulus test site locations and corresponding recruitment curves suggested that the phrenic nerve motor points could be predicted during the laparoscopic procedure to within 4.5 mm of the anatomical motor point.
Characterization and Cloning of a DictyosteliumSte20-like Protein Kinase That Phosphorylates the Actin-binding Protein Severin (1998)

After receiving an external stimulus Dictyostelium amoebae are able to rearrange their actin cytoskeleton within seconds, and phosphorylation is a prime candidate for quick modification of cytoskeletal components. We isolated a kinase from cytosolic extracts that specifically phosphorylated severin, a Ca2+-dependent F-actin fragmenting protein. In gel filtration chromatography severin kinase eluted with a molecular mass of about 300 kDa and contained a 62-kDa component whose autophosphorylation caused a mobility shift in SDS-polyacrylamide gel electrophoresis and stimulated phosphorylation of severin. Severin kinase activity could be specifically precipitated with antibodies raised against the 62-kDa polypeptide. Phosphorylation of severin was strongly reduced in the presence of Ca2+, indicating additional regulation at the substrate level. Peptide sequencing and cloning of the cDNA demonstrated that the 62-kDa protein belongs to the Ste20p- or p21-activated protein kinase family. It is most closely related to the germinal center kinase subfamily with its N-terminal positioned catalytic domain followed by a presumptive regulatory domain at the C terminus. The presence of a Ste20-like severin kinase in Dictyostelium suggests a direct signal transduction from the plasma membrane to the cytoskeleton by phosphorylation of actin-binding proteins.
Reducing intercarrier interference in OFDM systems by partial transmit sequence and selected mapping (2002)

Abstract — Orthogonal Frequency Division Multiplexing (OFDM) is sensitive to the carrier frequency offset (CFO). We introduce the Peak Interference-to-Carrier Ratio (PICR) to measure the resulting intercarrier interference (ICI). This paper shows that PICR can be reduced by Partial Transmit Sequence (PTS) and Selected Mapping (SLM) approaches. In PTS, each block of subcarriers is multiplied by a constant phase factor and these phase factors are optimized to minimize the PICR. In SLM, several independent OFDM symbols representing the same information are generated and the OFDM symbol with lowest PICR is selected for transmission. These schemes are analyzed theoretically and their performances are evaluated by simulation.
Clinical benefits in patients with psoriasis after efalizumab therapy: clinical trials versus practice. (2004)

Evaluations of efficacy of the new biologic therapies for psoriasis have used both physician-assessed endpoints and patient-reported outcome measures. The Psoriasis Area and Severity Index (PASI) is commonly used in clinical trials but is too labor intensive for clinical practice, which uses more subjective measures (physician global assessment [PGA] of change and Overall Lesion Severity [OLS] scale). Because psoriasis affects quality of life (QOL), patient-reported assessments of their satisfaction with treatment also are important. The purpose of this study was to evaluate some of the measurement tools used in clinical trials to make them more applicable to the practicing dermatologist. We used results of a placebo-controlled clinical study of efalizumab for the treatment of patients with moderate to severe plaque psoriasis. After treatment, ratings of improvement in psoriasis as measured by the PASI and PGA were closely aligned. It was noted the latter tool could provide a more practical and user-friendly evaluation in clinical practice. After 12 weekly subcutaneous injections of efalizumab, patients who achieved > or = 50% but < 75% improvement in PASI had treatment responses rated as primarily good or excellent using the PGA; additionally, the patients treated with efalizumab had statistically significant improvements (P<.001) in all patient-reported QOL assessments compared with placebo-treated patients, as did patients who achieved a > or = 75% improvement in PASI (PASI 75).
Ingestion of Staphylococcus aureus by bovine endothelial cells results in time- and inoculum-dependent damage to endothelial cell monolayers (1987)

Cultured endothelial cells phagocytize Staphylococcus aureus, but the resultant effects are unknown. Monolayers of cultured bovine endothelial cells with or without [3H]adenine label were exposed to 100, 10, or 1 S. aureus organism per endothelial cell for 3.5 h. Lysostaphin was then applied to all cultures to destroy extracellular but not phagocytized S. aureus. In cultures treated for only 20 min with lysostaphin, S. aureus multiplied exponentially after a 9- to 12-h lag period. In cultures treated continuously with lysostaphin, numbers of S. aureus remained constant or decreased. These results indicate that S. aureus became extracellular and multiplied but did not multiply intracellularly. In parallel experiments, the release of 3H-adenine from prelabeled endothelial cell monolayers was assayed to indicate cytotoxicity. Results indicated that the loss of 3H-adenine from endothelial cell monolayers depended on the following: (i) the size of the S. aureus inoculum, (ii) the strain of S. aureus, and (iii) the length of time after exposure to S. aureus. S. aureus endocarditis and persistent septicemia could arise, at least in part, from ingestion of S. aureus by host endothelium. The intracellular location would afford S. aureus protection from host defenses and antibiotics. Eventual damage to endothelial cells could expose collagen, thus resulting in platelet adherence and vegetation formation. Intracellular S. aureus would be continuously released into the circulation, possibly accounting for the persistent bacteremia that is found in S. aureus endovascular infections.
Wax ester fermentation in Euglena gracilis (1982)

Aerobically grown Euglena gracilis , a bleached mutant, shows a prompt synthesis of wax esters with the concomitant fall of the paramylon (a β‐1,3‐glucan) content upon exposure to anaerobiosis. Bringing the anaerobic cells back to aerobiosis causes the reverse conversions. The anaerobic wax ester formation is accompanied by a net synthesis of ATP. The transition between the fermentation and respiration occurs at 10 −5 –10 −7 M of the O 2 concentration.
Diagnostic Performance of Plasma DNA Methylation Profiles in Lung Cancer, Pulmonary Fibrosis and COPD (2015)

Disease-specific alterations of the cell-free DNA methylation status are frequently found in serum samples and are currently considered to be suitable biomarkers. Candidate markers were identified by bisulfite conversion-based genome-wide methylation screening of lung tissue from lung cancer, fibrotic ILD, and COPD. cfDNA from 400 μl serum (n = 204) served to test the diagnostic performance of these markers. Following methylation-sensitive restriction enzyme digestion and enrichment of methylated DNA via targeted amplification (multiplexed MSRE enrichment), a total of 96 markers were addressed by highly parallel qPCR. Lung cancer was efficiently separated from non-cancer and controls with a sensitivity of 87.8%, (95%CI: 0.67-0.97) and specificity 90.2%, (95%CI: 0.65-0.98). Cancer was distinguished from ILD with a specificity of 88%, (95%CI: 0.57-1), and COPD from cancer with a specificity of 88% (95%CI: 0.64-0.97). Separation of ILD from COPD and controls was possible with a sensitivity of 63.1% (95%CI: 0.4-0.78) and a specificity of 70% (95%CI: 0.54-0.81). The results were confirmed using an independent sample set (n = 46) by use of the four top markers discovered in the study (HOXD10, PAX9, PTPRN2, and STAG3) yielding an AUC of 0.85 (95%CI: 0.72-0.95). This technique was capable of distinguishing interrelated complex pulmonary diseases suggesting that multiplexed MSRE enrichment might be useful for simple and reliable diagnosis of diverse multifactorial disease states.
Systematic Inflation of Buckminsterfillerene C 60 : Synthesis of Diphenyl Fulleroids C 61 to C 66 (1991)

The synthesis of a new family of spheroidal carbon molecules derived from the fullerenes is described. The fulleroids are produced by incremental addition of a divalent carbon equivalent that has two phenyl (Ph) rings to fullerene C(60). The fulleroids Ph(2)C(61), Ph(4)C(62), Ph(6)C(63), Ph(8)C(64), Ph(10)C(65), and Ph(12)C(66) have been prepared and characterized.