gebhart/patrepeval huggingface dataset:
Phosphoproteomic analysis reveals an intrinsic pathway for the regulation of histone deacetylase 7 that controls the function of cytotoxic T lymphocytes (2011)

Here we report an unbiased analysis of the cytotoxic T lymphocyte (CTL) serine-threonine phosphoproteome by high-resolution mass spectrometry. We identified approximately 2,000 phosphorylations in CTLs, of which approximately 450 were controlled by T cell antigen receptor (TCR) signaling. A significantly overrepresented group of molecules identified included transcription activators, corepressors and chromatin regulators. A focus on chromatin regulators showed that CTLs had high expression of the histone deacetylase HDAC7 but continually phosphorylated and exported this transcriptional repressor from the nucleus. Dephosphorylation of HDAC7 resulted in its accumulation in the nucleus and suppressed expression of genes encoding key cytokines, cytokine receptors and adhesion molecules that determine CTL function. Screening of the CTL phosphoproteome has thus identified intrinsic pathways of serine-threonine phosphorylation that target chromatin regulators and determine the CTL functional program.
Electronic conduction in aqueous solution (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectronic conduction in aqueous solutionHarald DahmsCite this: J. Phys. Chem. 1968, 72, 1, 362–364Publication Date (Print):January 1, 1968Publication History Published online1 May 2002Published inissue 1 January 1968https://pubs.acs.org/doi/10.1021/j100847a073https://doi.org/10.1021/j100847a073research-articleACS PublicationsRequest reuse permissionsArticle Views652Altmetric-Citations254LEARN 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 options Get e-Alerts
Extracellular cyclic ADP‐ribose increases intracellular free calcium concentration and stimulates proliferation of human hemopoietic progenitors (2000)

Cyclic ADP-ribose (cADPR) is a universal second messenger that regulates many calcium-related cellular events by releasing calcium from intracellular stores. Since these events include enhanced cell proliferation and since the bone marrow harbors both ectoenzymes that generate cADPR from NAD(+) (CD38 and BST-1), we investigated the effects of extracellular cADPR on human hemopoietic progenitors (HP). Exposure of HP to 100 microM cADPR for 24 h induced a significant increase in colony output (P<0.01) and colony size (P<0.003). A horizontal expansion of HP, as demonstrated by a markedly increased replating efficiency in semisolid medium (up to 700 times compared to controls), was also observed, indicating that cADPR priming can affect cell growth for multiple generations over several weeks after exposure. Influx of extracellular cADPR into the cells was demonstrated, and a causal relationship between the functional effects and the increase of intracellular free calcium concentration induced by cADPR on HP was established through the use of specific antagonists. Similar effects on HP were produced by nanomolar concentrations of the nonhydrolyzable cADPR analog 3-deaza-cADPR. These data demonstrate that extracellular cADPR behaves as a cytokine enhancing the proliferation of human HP, a finding that may have biomedical applications for the ex vivo expansion of hemopoietic cells.
Neural networks in Japan (1994)

n pplications of neural networks made their debut in Japan in 1988. Fujitsu used a neural network for robot control [21], and NEC used one to recognize printed characters [4]. Since then, neural networks have been used extensively in Japan, and by 1990, they had been applied to commercial products and industrial systems.
Flux Decline in Nanofiltration Due to Adsorption of Dissolved Organic Compounds:  Model Prediction of Time Dependency (2006)

Flux decline during nanofiltration of aqueous solutions containing dissolved organic compounds is mainly caused by adsorption of these compounds in the membrane pores and on the membrane surface. In this paper, flux decline is modeled by incorporating the loss of permeability due to adsorption in the Spiegler-Kedem equation. This results in a logarithmic relation between normalized flux decline and time until the adsorption equilibrium is reached and the flux reaches a constant value. In this way, the expected flux decline due to adsorption of organic compounds can be estimated. Two different parameters were used in the model: the time delay t(0), which corresponds to the time at which the adsorption process in the membrane pores and on the membrane surface sets in, and the corresponding reduction of free (pore) volume (b). Both parameters depend on the hydrophobicity of the compounds and on the feed concentration.
Plasma Cytokine Fluctuations over Time in Healthy Controls and Patients with Fibromyalgia (2008)

We examined the pattern of cytokine secretion across the 24-hr day for women with widespread pain and tenderness having the diagnosis of fibromyalgia (FM) and matched healthy controls. Subjects were given time to habituate to being in a clinical research laboratory environment and then were sampled for cytokines without their being disturbed for a 24-hr period including an 8-hr sleep period. Cytokine levels were uniformly low but characterized by bursts of secretion. Bursting occurred either in singlets or in doublets with a range from 88 to 131 mins between doublet bursts. There was an element of synchronization of these bursts with most occurring at the beginning of sampling. FM patients showed a shift to increased IL-10 in the nighttime compared to controls. The relation between this anti-inflammatory cytokine to the pro-inflammatory cytokines studied also differed between groups: FM patients showed an increased ratio of IL-10 burst amplitude to that of pro-inflammatory cytokines IL-1beta, IL-8, and TNF-alpha. We interpret this to indicate a skew away from the normal balance favoring pro-inflammatory cytokines in controls toward one favoring an anti-inflammatory response in FM. These changes toward anti-inflammatory predominance in FM may explain their common complaint of disturbed sleep because these cytokines are known to disrupt sleep.
Next Generation FEC for High-Capacity Communication in Optical Transport Networks (2009)

Codes on graphs of interest for next generation forward error correction (FEC) in high-speed optical networks, namely turbo codes and low-density parity-check (LDPC) codes, are described in this invited paper. We describe both binary and nonbinary LDPC codes, their design, and decoding. We also discuss an FPGA implementation of decoders for binary LDPC codes. We then explain how to combine multilevel modulation and channel coding optimally by using coded modulation. Also, we describe an LDPC-coded turbo-equalizer as a candidate for dealing simultaneously with fiber nonlinearities, PMD, and residual chromatic dispersion.
Ischemic Neurons in Rat Brains After 6, 8, or 10 Minutes of Transient Hypoxic Ischemia (1997)

The incidence and distribution of ischemic (necrotic) neurons in the brains of rats 72 hr after hypoxic ischemia induced via asphyxiation is described and scored. Anesthetized Sprague-Dawley rats (10/group) were endotracheally intubated and had their airways occluded for 6, 8, or 10 min, which resulted, respectively, in approximately 3, 5, or 7 min of pulselessness (MABP < 10 mm Hg). Survival was 10/10, 9/10, and 6/10 in the 6-, 8-, and 10-min groups: deaths occurred within 1 hr after resuscitation. At 72 hr, rats were reanesthetized and their brains were perfusion-fixed with 3% buffered paraformaldehyde. Paraffin-embedded, 5-micron-thick, H&E-stained sections at 5 coronal levels of the brain had shrunken, hypereosinophilic ischemic neurons in 12 anatomic regions. Ischemic neurons were most consistently found in the lateral reticular thalamic nucleus; lateral caudoputamen; CA1 region of the hippocampus; subiculum; and, with longer asphyxia times, among cerebellar Purkinje neurons. Categorical histologic damage scores were assigned to affected regions on the basis of manual counts of ischemic neurons and summed for the whole brain. Brain histologic damage scores were significantly (p < 0.01) different for the 6-, 8-, and 10-min groups (means of 8 +/- 2; 14 +/- 4; and 22 +/- 4). Brain regions where both the number of rats affected and ranked categorical scores for ischemic neurons increased with asphyxia time were the lateral caudoputamen and cerebellar Purkinje neurons.
Sleep Disturbance in Bipolar Disorder: Therapeutic Implications (2008)

In this review, the authors detail our current understanding of the crucial role that sleep and its disturbances play in bipolar disorder. Multiple lines of evidence suggest that impaired sleep can induce and predict manic episodes. Similarly, treatment of sleep disturbance may serve as both a target of treatment and a measure of response in mania. The depressive phase of bipolar illness is marked by sleep disturbance that may be amenable to somatic therapies that target sleep and circadian rhythms. Residual insomnia in the euthymic period may represent a vulnerability to affective relapse in susceptible patients. Given the importance of sleep in all phases of bipolar disorder, appropriate evaluation and management of sleep disturbance in patients with bipolar illness is further detailed.
Genetic polymorphism of human interleukin‐1α (1993)

Interleukin-1 alpha (IL-1 alpha) has been implicated in the pathogenesis of infectious, autoimmune and inflammatory diseases. There is, however, very little information on the cis-acting sequences involved in IL-1 alpha regulation or whether there is any variation in the structure of the gene. It is known that intron 6 of IL-1 alpha shows a 5 x 46 bp tandem repeat in the genomic sequence. We have studied this region of the gene. Amplification by polymerase chain reaction showed different sized products from different individuals, most being of higher molecular weight than the expected size of 620 bp. Sequencing demonstrated that the polymorphism was due to a variable number of repeats of the 46 bp sequence. This was confirmed by restriction fragment length analysis of genomic DNA. Altogether, 72 unrelated individuals were tested and 6 alleles ranging from 5 to 18 repeats were found, the most frequent allele (62%) containing 9 repeats. This polymorphism may be of interest in gene function, since each repeat contains three potential binding sites for transcriptional factors: an SP1 site, a viral enhancer element and a glucocorticoid-responsive element. The latter, at least, demonstrates site-specific protein binding by electromobility shift assay. The functional significance of the polymorphism and its allelic frequency in inflammatory and autoimmune diseases are currently under investigation.
Fostering a Strong Construction Safety Culture (2010)

The construction industry has a reputation of being one of the most unsafe industries because of its high rates of injuries and fatalities. To improve safety performance, some construction companies have implemented innovative safety management programs. This paper reviews programs implemented by five construction companies in the United States, Australia, and Hong Kong and reviews the objectives, implementation strategies, and lessons learned from each. Seven program elements emerged in all cases: (1) The programs were focused on shaping employees' beliefs, attitudes, and commitment to achieve safe behavior on construction sites; (2) programs were based on the belief that all incidents and injuries are preventable and unacceptable; (3) there was a strong commitment to safety among top management; (4) the programs extended safety management issues to the entire supply chain and involved all stakeholders; (5) safety risk management systems were in place to identify, assess, and respond to on-site hazards, (6) clear authority and accountability for safety were established and safe behavior rewarded; and (7) a safety knowledge database was established to capture lessons learned. The paper suggests that organizations adopt a holistic strategy that focuses not only on improving the physical working environment, safety risk assessments, and employees' safety knowledge, but also on shaping employees' beliefs and attitudes that lead to safe behavior and ultimately to a strong safety culture. In conclusion, a conceptual model for balancing the art and science of managing construction safety is proposed for use by construction enterprises.
Homologous sequences in adenovirus E1A and human papillomavirus E7 proteins mediate interaction with the same set of cellular proteins (1992)

Studies of adenovirus E1A oncoprotein mutants suggest that the association of E1A with the retinoblastoma protein (pRB) is necessary for E1A-mediated transformation. Mutational analysis of E1A indicates that two regions of pRB are required for E1A to form stable complexes with the retinoblastoma protein. In addition to pRB binding, these regions are necessary for E1A association with several other cellular proteins, including p130, p107, cyclin A, and p33cdk2. Here we show that short synthetic peptides containing the pRB-binding sequences of E1A are sufficient for interaction with p107, cyclin A, and p130. The E7 protein of human papillomavirus type 16 contains an element that binds to pRB and appears to be functionally homologous to the E1A sequences. Peptides containing this region of the E7 protein were able to interact with p107, cyclin A, and p130 in addition to pRB. These findings suggest that the common mechanism of transformation used by these viral oncogenes involves their association with a set of polypeptides.
Use of Catalytic Fluoride under Neutral Conditions for Cleaving Silicon–Oxygen Bonds (2011)

This Article describes the development of conditions for cleaving silicon-oxygen bonds using catalytic quantities of fluoride at neutral pH in mixed organic-aqueous solutions that contain buffer. A variety of silicon protecting groups can be removed under these conditions, which show tolerance for acid- and base-sensitive groups. A modified procedure also is presented using catalytic fluoride in anhydrous dimethyl sulfoxide-methanol, which generates primarily volatile silicon byproducts.
Codon usage in bacteria: correlation with gene expressivity (1982)

The nucleic acid sequence bank now contains over 600 protein coding genes of which 107 are from prokaryotic organisms. Codon frequencies in each new prokaryotic gene are given. Analysis of genetic code usage in the 83 sequenced genes of the Escherichia coli genome (chromosome, transposons and plasmids) is presented, taking into account new data on gene expressivity and regulation as well as iso-tRNA specificity and cellular concentration. The codon composition of each gene is summarized using two indexes: one is based on the differential usage of iso-tRNA species during gene translation, the other on choice between Cytosine and Uracil for third base. A strong relationship between codon composition and mRNA expressivity is confirmed, even for genes transcribed in the same operon. The influence of codon use of peptide elongation rate and protein yield is discussed. Finally, the evolutionary aspect of codon selection in mRNA sequences is studied.
The Nrf2-ARE Pathway: A Valuable Therapeutic Target for the Treatment of Neurodegenerative Diseases (2012)

Modulation of NF-E2 related factor 2 (Nrf2) has been shown in several neurodegenerative disorders. The overexpression of Nrf2 has become a potential therapeutic avenue for various neurodegenerative disorders such as Parkinson, Amyotrophic lateral sclerosis, and Alzheimer's disease. The expression of phase II detoxification enzymes is governed by the cis-acting regulatory element known as antioxidant response element (ARE). The transcription factor Nrf2 binds to ARE thereby transcribing multitude of antioxidant genes. Keap1, a culin 3-based E3 ligase that targets Nrf2 for degradation, sequesters Nrf2 in cytoplasm. Disruption of Keap1-Nrf2 interaction or genetic overexpression of Nrf2 can increase the endogenous antioxidant capacity of the brain thereby rendering protection against oxidative stress in neurodegenerative disorders. This review primarily focuses on recent patents that target Nrf2 overexpression as a promising therapeutic strategy for the treatment of neurodegenerative disorders.
Electrorheological-fluid-based microvalves (2005)

We present the successful design and fabrication of push-and-pull microvalves that use a giant electrorheological (GER) fluid. Our multilayer microvalves, including the GER fluid control channel, the electrode, the flow channel, and the flexible membrane, are fabricated with polydimethylsioxane-based materials by soft lithography techniques. The GER effect is able to provide high-pressure changes in GER control channel so as to fully close and open an associated flow channel. The fast response time of the GER fluid and the push-and-pull valve design adopted assure fast switching time of the valve less than 10ms and sound reliability. This GER-fluid-based microvalve has other advantages of easy fabrication and biocompatibility and is suitable for most microfluidic applications.
Bloodstream Infections (2016)

Bacteremia and sepsis are conditions associated with high mortality and are of great impact to health care operations. Among the top causes of mortality in the United States, these conditions cause over 600 fatalities each day. Empiric, broad-spectrum treatment is a common but often a costly approach that may fail to effectively target the correct microbe, may inadvertently harm patients via antimicrobial toxicity or downstream antimicrobial resistance. To meet the diagnostic challenges of bacteremia and sepsis, laboratories must understand the complexity of diagnosing and treating septic patients, in order to focus on creating algorithms that can help direct a more targeted approach to antimicrobial therapy and synergize with existing clinical practices defined in new Surviving Sepsis Guidelines. Significant advances have been made in improving blood culture media; as yet no molecular or antigen-based method has proven superior for the detection of bacteremia in terms of limit of detection. Several methods for rapid molecular identification of pathogens from blood cultures bottles are available and many more are on the diagnostic horizon. Ultimately, early intervention by molecular detection of bacteria and fungi directly from whole blood could provide the most patient benefit and contribute to tailored antibiotic coverage of the patient early on in the course of the disease. Although blood cultures remain as the best means of diagnosing bacteremia and candidemia, complementary testing with antigen tests, microbiologic investigations from other body sites, and histopathology can often aid in the diagnosis of disseminated disease, and application of emerging nucleic acid test methods and other new technology may greatly impact our ability to bacteremic and septic patients, particularly those who are immunocompromised.
Normative values for the Beck Anxiety Inventory, Fear Questionnaire, Penn State Worry Questionnaire, and Social Phobia and Anxiety Inventory. (1995)

Community norms are reported for the Beck Anxiety Inventory (BAI ; A. T. Beck, N. Epstein, G. Brown, & R. A. Steer, 1988), Fear Questionnaire (FQ ; I. M. Marks & A. Mathews, 1979), Penn State Worry Questionnaire (PSWQ ; T. J. Meyer, M. L. Miller, R. L. Metzger, & T. D. Borkovec, 1990), and Social Phobia and Anxiety Inventory (SPAI ; S. M. Turner, D. C. Beidel, C. V. Dancu, & M. A. Stanley, 1989). The demographic profile of the samples closely matched the 1990 U.S. national census. On the SPAI, women scored higher than men on the Agoraphobia subscale, and the lowest income group scored higher than higher income participants on the Difference and Social Phobia subscales. Participants under 45 years of age exceeded those aged 45-65 on the BAI, the PSWQ, and FQ Social Phobia, Blood/Injury, and Total Phobia scores. Percentile scores are provided for all measures, as well as discussion oftheir usefulness for assessing clinical significance of therapy outcomes.
SH3: high code density, low power (1995)

Hitachi's SH series microprocessors feature 32-bit RISC architecture with a 16-bit, fixed-length instruction set. We describe SH3, a pipelined implementation of the SH architecture with on-chip cache, MMU, and software-programmable power management. Its higher code density and corresponding improvement in instruction-fetch latency lead to higher performance than typical 32-bit RISC architectures achieve. These features, small die size, and low power consumption make SH3 an ideal microprocessor for portable computing systems or multimedia systems.
Automated speech recognition in medical applications. (1995)

Despite considerable advances in computer technology over the last 20 years, the keyboard and video display are still the principal means of entering and retrieving data. As the use of computers increases, however, the need for alternative ways of interacting with the computer grows as well. This demand was fueled by a need for an intuitive human-machine interface to accommodate increasing numbers of nontechnical users, since limitations in the interface are still obstacles to the widespread acceptance of computer automation . In addition, in some situations the usual methods of interacting with the computer are impractical - for example, when the hands are otherwise occupied, as in microscopy. An approach that addresses both the need for ease of use and the need to keep the hands free is the use of automated speech recognition.