gebhart/patrepeval huggingface dataset:
Interferon regulatory factor subcellular localization is determined by a bipartite nuclear localization signal in the DNA-binding domain and interaction with cytoplasmic retention factors (2000)

The transduction of type I interferon signals to the nucleus relies on activation of a protein complex, ISGF3, involving two signal transducers and activators of transcription (STAT) proteins, STAT1 and STAT2, and the interferon (IFN) regulatory factor (IRF) protein, p48/ISGF3gamma. The STAT subunits are cytoplasmically localized in unstimulated cells and rapidly translocate to the nucleus of IFN-stimulated cells, but the p48/ISGF3gamma protein is found in both the nucleus and the cytoplasm, regardless of IFN stimulation. Here, we demonstrate that p48 is efficiently and constitutively targeted to the nucleus. Analysis of the subcellular distribution of green fluorescent protein-p48 fragments indicates that p48 contains a bipartite nuclear retention signal within its amino-terminal DNA-binding domain. This signal is preserved in two other IRF proteins involved in immune responses, ICSBP and IRF4. Mutations to clustered basic residues within amino acids 50-100 of p48 or IRF4 disrupt their nuclear accumulation, and DNA-binding ability is not required for nuclear targeting. This is the only example of a nuclear localization signal for any ISGF3 component and assigns a second function to the IRF DNA-binding domain. We also demonstrate that the nuclear distribution of p48 is dramatically altered by coexpression of the STAT2 protein, indicating that STAT2 forms a cytoplasmic complex with p48, overriding the intrinsic p48 nuclear targeting. Retention by STAT2 may serve to regulate the activity of free p48 and/or guarantee that cytoplasmic pools of preassociated STAT2:p48 are available for rapid activation of the IFN response. These findings suggest that analogous mechanisms may exist for regulating the distribution of other IRF proteins.
Effects of the ccd function of the F plasmid on bacterial growth (1985)

The ccd segment of the mini F plasmid containing the ccdA and ccdB genes controls the coordination between plasmid proliferation and cell physiology and fate. When the DNA replication of a thermosensitive-replication plasmid carrying the ccd segment of mini F is blocked, plasmid DNA molecules are progressively diluted through cell division until the copy number reaches 1 per cell. From this time on, there is little increase in the number of viable cells, although cells continue to divide, resulting in a mixed population of viable cells (mostly plasmid containing), nonviable but residually dividing cells, and nonviable nondividing cells. Results are presented suggesting that plasmid-containing cells are viable and continue to divide, whereas plasmid-free segregants are nonviable and form filaments after a few residual divisions, with DNA synthesis reduced or arrested in the filaments. Although the ccd functions are known to induce the SOS response when plasmid replication is blocked, the production of nonviable plasmid-free segregants is independent of the SOS cell division inhibition mechanism determined by the sfiA and sfiC genes.
Incorporation of Nonnatural Amino Acids into Streptavidin through In Vitro Frame-Shift Suppression (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTIncorporation of Nonnatural Amino Acids into Streptavidin through In Vitro Frame-Shift SuppressionTakahiro Hohsaka, Yuki Ashizuka, Hiroshi Murakami, and Masahiko SisidoView Author Information Department of Bioscience and Biotechnology Okayama University 3-1-1 Tsushimanaka, Okayama 700, Japan Cite this: J. Am. Chem. Soc. 1996, 118, 40, 9778–9779Publication Date (Web):October 9, 1996Publication History Received30 April 1996Published online9 October 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja9614225https://doi.org/10.1021/ja9614225rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views1143Altmetric-Citations139LEARN 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:Biopolymers,Fluorescence,Genetics,Monomers,Peptides and proteins Get e-Alerts
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock (2003)

In this study, we modify and extend the bilevel optimization framework OptKnock for identifying gene knockout strategies in the Escherichia coli metabolic network, leading to the overproduction of representative amino acids and key precursors for all five families. These strategies span not only the central metabolic network genes but also the amino acid biosynthetic and degradation pathways. In addition to gene deletions, the transport rates of carbon dioxide, ammonia, and oxygen, as well as the secretion pathways for key metabolites, are introduced as optimization variables in the framework. Computational results demonstrate the importance of manipulating energy-producing/consuming pathways, controlling the uptake of nitrogen and oxygen, and blocking the secretion pathways of key competing metabolites. The identified pathway modifications include not only straightforward elimination of competing reactions but also a number of nonintuitive knockouts quite distant from the amino acid-producing pathways. Specifically, OptKnock suggests three reactions (i.e., pyruvate kinase, phosphotransacetylase, and ATPase) for deletion, in addition to the straightforward elimination of 2-ketoglutarate dehydrogenase, to generate a glutamate-overproducing mutant. Similarly, phosphofructokinase and ATPase are identified as promising knockout targets to complement the removal of pyruvate formate lyase and pyruvate dehydrogenase for enhancing the yield of alanine. Although OptKnock in its present form does not consider regulatory constraints, it does provide useful suggestions largely in agreement with existing practices and, more importantly, introduces a framework for incorporating additional modeling refinements as they become available.
Addition of Rituximab to Chlorambucil Produces Superior Event-Free Survival in the Treatment of Patients With Extranodal Marginal-Zone B-Cell Lymphoma: 5-Year Analysis of the IELSG-19 Randomized Study (2013)

Both treatments were active; the better response rate and EFS obtained with the addition of rituximab did not translate into improved OS.
Microprocessor-Controlled Local Anesthesia Versus the Conventional Syringe Technique in Hair Transplantation (2002)

BACKGROUND Local anesthesia by the traditional injection technique is central to optimizing patient comfort during hair transplant procedures. However, even when carefully and properly performed, some patients still describe their treatment sessions as painful. OBJECTIVE To determine if patients undergoing hair transplantation experience less pain and discomfort when their local anesthesia is performed with the Wand (as of spring 2001, the Wand has been renamed “CompuMed™– Featuring the Wand Handpiece”), a microprocessor pump that precisely controls the infusion rate and pressure of local anesthetic solution. METHODS We used combined retrospective studies and a prospective blinded study of men and women who received hair transplantation treatments between January 1999 and March 2001 at our private outpatient clinics in the United States. A total of 101 patients compared their experiences during their hair transplant sessions performed by us before and after we started using the Wand. Thirty-nine patients compared their experiences during treatments done by 32 other medical groups and when we used the Wand. In addition, 88 patients compared the Wand to injection while blinded to technique. The outcomes were measured with patient pain rating questionnaires using the Wong–Baker Faces Pain Rating Scale (0, no pain–5, severe pain). RESULTS Patients in all three study groups reported that anesthesia with the Wand was less painful. Wand anesthesia was overwhelmingly (68%) described as associated with none (0) or very little (1) pain. Surprisingly, Wand anesthesia was associated with superior comfort not only during the administration of anesthesia (P = .005), but throughout the treatment session and during the first 48 postoperative hours. CONCLUSION Microprocessor-controlled local anesthesia with the Wand is superior to traditional injection in consistently producing comfortable hair transplant treatments.
2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking (2000)

2-Aminopurine (2AP) is a fluorescent analog of guanosine and adenosine and has been used to probe nucleic acid structure and dynamics. Its spectral features in nucleic acids have been interpreted phenomenologically, in the absence of a rigorous electronic description of the context-dependence of 2AP fluorescence. Now, by using time-dependent density functional theory, we describe the excited-state properties of 2AP in a B-form dinucleotide stacked with guanosine, adenosine, cytosine, or thymine. Calculations predict that 2AP fluorescence is quenched statically when stacked with purines, because of mixing of the molecular orbitals in the ground state. In contrast, quenching is predicted to be dynamic when 2AP is stacked with pyrimidines, because of formation of a low-lying dark excited state. The different quenching mechanisms will result in different experimentally measured fluorescence lifetimes and quantum yields.
Sacral nerve stimulation for neuromodulation of the lower urinary tract. (2012)

Sacral neuromodulation (SNM) has become a standard treatment option for patients suffering from urinary urge incontinence, urgency-frequency, and/or nonobstructive urinary retention refractory to conservative and pharmacologic treatment. Since its initial development, the manufacturer of InterStim therapy (Medtronic, Inc., Minneapolis, MN, USA), has introduced technical modifications, while surgeons and researchers have adapted and published various innovations and alterations of the implantation technique. In this article, we feature our SNM technique including patient selection, comprehensive dialogue/evaluation, procedure details, and appropriate follow up. Although there is often great variability in patients with lower urinary tract dysfunction, we maintain that great success can be achieved with a systematic and methodical approach to SNM.
Bayesian networks in neuroscience: a survey (2014)

Bayesian networks are a type of probabilistic graphical models lie at the intersection between statistics and machine learning. They have been shown to be powerful tools to encode dependence relationships among the variables of a domain under uncertainty. Thanks to their generality, Bayesian networks can accommodate continuous and discrete variables, as well as temporal processes. In this paper we review Bayesian networks and how they can be learned automatically from data by means of structure learning algorithms. Also, we examine how a user can take advantage of these networks for reasoning by exact or approximate inference algorithms that propagate the given evidence through the graphical structure. Despite their applicability in many fields, they have been little used in neuroscience, where they have focused on specific problems, like functional connectivity analysis from neuroimaging data. Here we survey key research in neuroscience where Bayesian networks have been used with different aims: discover associations between variables, perform probabilistic reasoning over the model, and classify new observations with and without supervision. The networks are learned from data of any kind-morphological, electrophysiological, -omics and neuroimaging-, thereby broadening the scope-molecular, cellular, structural, functional, cognitive and medical- of the brain aspects to be studied.
Mini-F plasmid genes that couple host cell division to plasmid proliferation. (1983)

A mechanism for stable maintenance of plasmids, besides the replication and partition mechanisms, has been found to be specified by genes of a mini-F plasmid. An oriC plasmid carrying both a mini-F segment necessary for partition [coordinates 46.4-49.4 kilobase pairs (kb) on the F map] and another segment (42.9-43.6 kb), designated ccd (coupled cell division), is more stably maintained than are oriC plasmids carrying only the partition segment; the stability is comparable to that of the parental mini-F plasmid. When replication of a plasmid carrying ccd is prevented and the plasmid copy number decreases, to as few as one per cell, host cell division is inhibited, but not increase of turbidity or chromosome replication. Appearance of plasmid-free segregants is therefore effectively prevented under such conditions. Experimental results suggest that reduction of the copy number of plasmids carrying the ccd region causes an inhibition of cell division and that the ccd region can be dissected into two functional regions; one (ccdB) inhibits cell division and the other (ccdA) releases the inhibition. The interplay of the ccdA and ccdB genes promotes stable plasmid maintenance by coupling host cell division to plasmid proliferation.
Tumor necrosis factor-alpha (TNF-alpha) signal transduction through ceramide. Dissociation of growth inhibitory effects of TNF-alpha from activation of nuclear factor-kappa B. (1993)

Tumor necrosis factor-alpha (TNF-alpha) exerts pleiotropic biologic effects. Although TNF-alpha appears to activate a number of signal transduction pathways, the role of second messengers in mediating the different effects of TNF-alpha are not well defined. In this study, we investigated the role of ceramide as an intracellular mediator of TNF-alpha action. In Jurkat T cells, TNF-alpha caused early activation of the sphingomyelin cycle with peak hydrolysis of sphingomyelin observed at 30 min following addition of TNF-alpha. In this cell line, TNF-alpha caused potent activation of nuclear factor-kappa B (NF-kappa B) and exerted potent cytostatic/cytocidal activity. C2-ceramide mimicked the effects of TNF-alpha on cell growth in a dose-dependent manner, but C2-ceramide was unable to induce activation of NF-kappa B under multiple conditions investigated. C2-ceramide, however, enhanced activation of NF-kappa B in response to TNF-alpha with peak effects observed at a concentration of C2-ceramide of 5 microM. Thus, ceramide functions as a selective mediator of the cytostatic/cytotoxic effects of TNF-alpha and plays a positive feedback role in activation of NF-kappa B. TNF-alpha signaling, therefore, involves multiple second-messenger pathways that function independently or coordinately to transduce distinct functions of TNF-alpha.
Incidence of exotoxin production by Pseudomonas species (1977)

Pseudomonas aeruginosa exotoxin A has been shown to catalyze the transfer of the adenosine 5'-diphosphate (ADP)-ribose moiety of nicotinamide adenine dinucleotide onto elongation factor 2, resulting in the inhibition of mammalian protein synthesis. The enzymatic activity (ADP-ribosyl [ADPR]-transferase) is thought to account for the toxicity of exotoxin A. The distribution of the expression of exotoxin A within Pseudomonas species was examined. Laboratory strains as well as clinical isolates of Pseudomonas aeruginosa were tested. The production of exotoxin A was determined by assaying for ADPR-transferase activity in dialyzed frozen (-20 degrees C) and thawed cell-free supernatants from 22-h cultures or in 10-fold-concentrated supernatants. In addition, toxin production was detected immunologically using a modified Elek test. Exotoxin A production was detected in approximately 90% of the 111 isolates of P. aeruginosa. In contrast, none of the other species of Pseudomonas examined produced exotoxin A detectable by either ADPR-transferase activity or immunological reactivity.
Rac3 induces a molecular pathway triggering breast cancer cell aggressiveness: differences in MDA-MB-231 and MCF-7 breast cancer cell lines (2013)

This discrepancy between the effects of Rac3 knockdown in the two cell lines could be explained as follows: in the MDA-MB-231 line, the Rac3-dependent aggressiveness of the cancer cells is due to the Rac3/ERK-2/NF-κB signaling pathway, which is responsible for MMP-9, interleukin-6, -8 and GRO secretion, as well as the resistance to TNF-induced apoptosis, whereas in the MCF-7 line, this pathway is not functional because of the low expression of NF-κB subunits in these cells. Rac3 may be a potent target for inhibiting aggressive breast cancer.
A SCIENTIFIC PERSPECTIVE (2000)

AbstractThe following sections are included:IntroductionFinancial Modeling and ComputersEpistemic Uncertainty: Exact and Inexact ModelsExact Models, e.g., Financial StatementsInexact Models, e.g., Behavioral RelationshipsIdentification, Simulation and ExtrapolationPro Forma Financial Statement ProjectionsEnvisioning Information: Unique MappingsExercisesBibliography
'Collision-proof' airspace: Reducing the risk of midair collisions is the goal of an air-traffic control system proposed by the FAA (1980)

Discusses a projected air collision-avoidance system to be put under development shortly in the USA that will make use of airborne computers and ground computers that will warn and command aircraft approaching each other too closely.
Sequence-to-sequence Pre-training with Data Augmentation for Sentence Rewriting (2019)

We study sequence-to-sequence (seq2seq) pre-training with data augmentation for sentence rewriting. Instead of training a seq2seq model with gold training data and augmented data simultaneously, we separate them to train in different phases: pre-training with the augmented data and fine-tuning with the gold data. We also introduce multiple data augmentation methods to help model pre-training for sentence rewriting. We evaluate our approach in two typical well-defined sentence rewriting tasks: Grammatical Error Correction (GEC) and Formality Style Transfer (FST). Experiments demonstrate our approach can better utilize augmented data without hurting the model's trust in gold data and further improve the model's performance with our proposed data augmentation methods. Our approach substantially advances the state-of-the-art results in well-recognized sentence rewriting benchmarks over both GEC and FST. Specifically, it pushes the CoNLL-2014 benchmark's $F_{0.5}$ score and JFLEG Test GLEU score to 62.61 and 63.54 in the restricted training setting, 66.77 and 65.22 respectively in the unrestricted setting, and advances GYAFC benchmark's BLEU to 74.24 (2.23 absolute improvement) in E&amp;M domain and 77.97 (2.64 absolute improvement) in F&amp;R domain.
Proteomic analysis of the acid‐soluble organic matrix of the chicken calcified eggshell layer (2006)

The major difference between inorganic minerals and biominerals is the presence of an organic matrix consisting of proteins, glycoproteins, proteoglycans, and polysaccharides, which is synthesized by specialized cells under genetic control before or during mineralization. The organic matrix is thought to play a major role in the assembly of the biomineral and determination of its mechanical properties. The recent elucidation of the chicken genome provided an opportunity to explore the matrix proteome of a biomineral using up-to-date MS-based technology. We identified 520 proteins in this matrix including the ten matrix proteins already known before. The identified proteins were divided into three abundance groups using the exponentially modified protein abundance index described recently which was roughly calibrated with the few known data on protein yield derived from Edman sequence analysis. A small group of 32 highly abundant proteins contained the presently known eggshell-specific proteins and all of the other known eggshell matrix constituents identified before with much less sensitive conventional methods. The present study, which is the first comprehensive proteomic study of a vertebrate biomineral, is intended as a starting point for the detailed molecular characterization of eggshell matrix proteins, their interactions in the matrix network and functional studies.
Codon preferences in free-living microorganisms. (1990)

A popular interpretation of the major codon preference is that it reflects the operation of a regulatory device that controls the expression of individual proteins. In this popular model, rapidly translated codons are thought to promote the accumulation of the highly expressed proteins and slowly translated codons are thought to retard the expression of poorly expressed proteins. However, this widely accepted model is not supported by kinetic theory or by experimental results. A less fashionable model in which the major codon preference has nothing to do with the expression level of the individual proteins is forwarded. In this model, the major codon preference is viewed as a global strategy to support the efficient function of the translation system and thereby to maximize the growth rates of cells under favorable conditions.
Consequences of the recurrent MYD88L265P somatic mutation for B cell tolerance (2014)

MYD88(L265P) has recently been discovered as an extraordinarily frequent somatic mutation in benign monoclonal IgM gammopathy, Waldenström's macroglobulinemia, and diffuse large B cell lymphoma. In this study, we analyze the consequences for antigen-activated primary B cells of acquiring MYD88(L265P). The mutation induced rapid B cell division in the absence of exogenous TLR ligands and was inhibited by Unc93b1(3d) mutation and chloroquine or TLR9 deficiency, indicating continued dependence on upstream TLR9 activation. Proliferation and NF-κB activation induced by MYD88(L265P) were nevertheless rapidly countered by the induction of TNFAIP3, an NF-κB inhibitor frequently inactivated in MYD88(L265P)-bearing lymphomas, and extinguished by Bim-dependent apoptosis. MYD88(L265P) caused self-reactive B cells to accumulate in vivo only when apoptosis was opposed by Bcl2 overexpression. These results reveal checkpoints that fortify TLR responses against aberrant B cell proliferation in response to ubiquitous TLR and BCR self-ligands and suggest that tolerance failure requires the accumulation of multiple somatic mutations.