gebhart/patrepeval huggingface dataset:
Characterization and expression of the Escherichia coli Mrr restriction system (1991)

The mrr gene of Escherichia coli K-12 is involved in the acceptance of foreign DNA which is modified. The introduction of plasmids carrying the HincII, HpaI, and TaqI R and M genes is severely restricted in E. coli strains that are Mrr+. A 2-kb EcoRI fragment from the plasmid pBg3 (B. Sain and N. E. Murray, Mol. Gen. Genet. 180:35-46, 1980) was cloned. The resulting plasmid restores Mrr function to mrr strains of E. coli. The boundaries of the mrr gene were determined from an analysis of subclones, and plasmids with a functional mrr gene produce a polypeptide of 33.5 kDa. The nucleotide sequence of the entire fragment was determined; in addition to mrr, it includes two open reading frames, one of which encodes part of the hsdR. By using Southern blot analysis, E. coli RR1 and HB101 were found to lack the region containing mrr. The acceptance of various cloned methylases in E. coli containing the cloned mrr gene was tested. Plasmid constructs containing the AccI, CviRI, HincII, Hinfl (HhaII), HpaI, NlaIII, PstI, and TaqI N6-adenine methylases and SssI and HhaI C5-cytosine methylases were found to be restricted. Plasmid constructs containing 16 other adenine methylases and 12 cytosine methylases were not restricted. No simple consensus sequence causing restriction has been determined. The Mrr protein has been overproduced, an antibody has been prepared, and the expression of mrr under various conditions has been examined. The use of mrr strains of E. coli is suggested for the cloning of N6-adenine and C5-cytosine methyl-containing DNA.
Angiotensin-converting enzyme and male fertility (1998)

The angiotensin-converting enzyme (ACE; EC 3.4.15.1) gene (Ace) encodes both a somatic isozyme found in blood and several other tissues, including the epididymis, and a testis-specific isozyme (testis ACE) found only in developing spermatids and mature sperm. We recently used gene targeting to disrupt the gene coding for both ACE isozymes in mice and reported that male homozygous mutants mate normally but have reduced fertility; the mutant females are fertile. Here we explore the male fertility defect. We demonstrate that ACE is important for achieving in vivo fertilization and that sperm from mice lacking both ACE isozymes show defects in transport within the oviducts and in binding to zonae pellucidae. Males generated by gene targeting that lack somatic ACE but retain testis ACE are normally fertile, establishing that somatic ACE in males is not essential for their fertility. Furthermore, male and female mice lacking angiotensinogen have normal fertility, indicating that angiotensin I is not a necessary substrate for testis ACE. Males heterozygous for the mutation inactivating both ACE isozymes sire wild-type and heterozygous offspring at an indistinguishable frequency, indicating no selection against sperm carrying the mutation.
Decreased brain stiffness in Alzheimer's disease determined by magnetic resonance elastography (2011)

3D MRE of the brain can be performed reproducibly and demonstrates significantly reduced brain tissue stiffness in patients with AD.
A WW domain protein TAZ is a critical coactivator for TBX5, a transcription factor implicated in Holt–Oram syndrome (2005)

The T-box transcription factor TBX5 plays essential roles in cardiac and limb development. Various mutations in the TBX5 gene have been identified in patients with Holt-Oram syndrome, which is characterized by congenital defects in the heart and upper extremities. In this study, we identified a WW-domain-containing transcriptional regulator TAZ as a potent TBX5 coactivator. TAZ directly associates with TBX5 and markedly stimulates TBX5-dependent promoters by interacting with the histone acetyltransferases p300 and PCAF. YAP, a TAZ-related protein with conserved functional domains, also stimulates TBX5-dependent transcription, possibly by forming a heterodimer with TAZ. TBX5 lacks a PY motif, which mediates the association of other proteins with TAZ, and interacts with TAZ through multiple domains including its carboxyl-terminal structure. Truncation mutants of TBX5 identified in patients with Holt-Oram syndrome were markedly impaired in their ability to associate with and be stimulated by TAZ. These findings reveal key roles for TAZ and YAP in the control of TBX5-dependent transcription and suggest the involvement of these coactivators in cardiac and limb development.
Botnet detection using social graph analysis (2014)

Signature-based botnet detection methods identify botnets by recognizing Command and Control (C&C) traffic and can be ineffective for botnets that use new and sophisticate mechanisms for such communications. To address these limitations, we propose a novel botnet detection method that analyzes the social relationships among nodes. The method consists of two stages: (i) anomaly detection in an "interaction" graph among nodes using large deviations results on the degree distribution, and (ii) community detection in a social "correlation" graph whose edges connect nodes with highly correlated communications. The latter stage uses a refined modularity measure and formulates the problem as a non-convex optimization problem for which appropriate relaxation strategies are developed. We apply our method to real-world botnet traffic and compare its performance with other community detection methods. The results show that our approach works effectively and the refined modularity measure improves the detection accuracy.
Evolution of binding affinity in a WW domain probed by phage display (2000)

The WW domain is an approximately 38 residue peptide-binding motif that binds a variety of sequences, including the consensus sequence xPPxY. We have displayed hYAP65 WW on the surface of M13 phage and randomized one-third of its three-stranded antiparallel β-sheet. Improved binding to the hydrophobic peptide, GTPPPPYTVG (WW1), was selected in the presence of three different concentrations of proteinase K to simultaneously drive selection for improved stability as well as high-affinity binding. While some of the selected binders show cooperative unfolding transitions, others show noncooperative thermal unfolding curves. Two novel WW consensus sequences have been identified, which bind to the xPPxY motif with higher affinity than the wild-type hYAP65 WW domain. These WW domain sequences are not precedented in any natural WW domain sequence. Thus, there appear to be a large number of motifs capable of recognizing the target peptide sequence, only a subset of which appear to be used in natural proteins.
Replication of Flaviviruses (1986)

Flaviviruses were classified as members of the togavirus family until 1984, when the International Committee for the Nomenclature of Viruses voted to make Flaviviridae a separate family (Westaway et al., 1986). The togavirus family had originally been defined using morphological criteria. The change in classification was the result of recent research that clearly demonstrated that flaviviruses, although generally similar to alphaviruses in their morphology, differ markedly from the alpha togaviruses in their virion structure, strategy of replication, and morphogenesis.
Separation of Diterpenoid Alkaloid Mixtures Using Vacuum Liquid Chromatography (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSeparation of Diterpenoid Alkaloid Mixtures Using Vacuum Liquid ChromatographyS. William Pelletier, Hitesh P. Chokshi, and Haridutt K. DesaiCite this: J. Nat. Prod. 1986, 49, 5, 892–900Publication Date (Print):September 1, 1986Publication History Published online1 July 2004Published inissue 1 September 1986https://pubs.acs.org/doi/10.1021/np50047a021https://doi.org/10.1021/np50047a021research-articleACS PublicationsRequest reuse permissionsArticle Views1019Altmetric-Citations143LEARN 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
Using bulked extremes and recessive class to map genes for photoperiod-sensitive genic male sterility in rice. (1994)

Photoperiod-sensitive genic male sterile (PS-GMS) rice has a number of desirable characteristics for hybrid rice production. In this study we made use of a published rice genetic linkage map to determine the locations of PSGMS genes and we have characterized the effects of these genes on sterility by using molecular markers. A two-step approach was designed for mapping the genes: (i) identifying possible PSGMS gene-containing chromosome regions with bulked DNA from extreme fertile and extreme sterile plants of a very large F2 population and (ii) determining the map locations of the genes in extreme sterile individuals. We show that this mapping method is much more cost effective and statistically efficient than using a random sample of an F2 population. We identified two chromosomal regions each containing a PSGMS locus, one designated pms1 on chromosome 7 and one designated pms2 on chromosome 3. The existence of these two loci was confirmed by a large sample assay and with data on rationing progenies of the F2 plants. A marker-based analysis shows that the effect of pms1 is 2-3 times larger than that of pms2 and that dominance is almost complete at both loci. Implications in the breeding of PSGMS rice lines are discussed.
Efficient Intracellular Processing of the Endogenous Cystic Fibrosis Transmembrane Conductance Regulator in Epithelial Cell Lines (2004)

The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-dependent protein kinase A-activated chloride channel that resides on the apical surface of epithelial cells. One unusual feature of this protein is that during biogenesis, approximately 75% of wild type CFTR is degraded by the endoplasmic reticulum (ER)-associated degradative (ERAD) pathway. Examining the biogenesis and structural instability of the molecule has been technically challenging due to the limited amount of CFTR expressed in epithelia. Consequently, investigators have employed heterologous overexpression systems. Based on recent results that epithelial specific factors regulate both CFTR biogenesis and function, we hypothesized that CFTR biogenesis in endogenous CFTR expressing epithelial cells may be more efficient. To test this, we compared CFTR biogenesis in two epithelial cell lines endogenously expressing CFTR (Calu-3 and T84) with two heterologous expression systems (COS-7 and HeLa). Consistent with previous reports, 20 and 35% of the newly synthesized CFTR were converted to maturely glycosylated CFTR in COS-7 and HeLa cells, respectively. In contrast, CFTR maturation was virtually 100% efficient in Calu-3 and T84 cells. Furthermore, inhibition of the proteasome had no effect on CFTR biogenesis in Calu-3 cells, whereas it stabilized the immature form of CFTR in HeLa cells. Quantitative reverse transcriptase-PCR indicated that CFTR message levels are approximately 4-fold lower in Calu-3 than HeLa cells, yet steady-state protein levels are comparable. Our results question the structural instability model of wild type CFTR and indicate that epithelial cells endogenously expressing CFTR efficiently process this protein to post-Golgi compartments.
New insights into the role of extracellular matrix during tumor onset and progression (2002)

Recently, a view of the tumor as a functional tissue interconnected with the microenvironment has recently been described. For many years, the stroma has been studied in the context of the malignant lesion, and only rarely has its role been considered before carcinogenic lesions appear. Recent studies have provided evidence that stromal cells and their products can cause the transformation of adjacent cells through transient signaling that leads to the disruption of homeostatic regulation, including control of tissue architecture, adhesion, cell death, and proliferation. It is now well established that tumor progression requires a continually evolving network of interactions between neoplastic cells and extracellular matrix. A relevant step of this process is the remodeling of microenvironment which surrounds tumors leading to the release of ECM-associated growth factors which can then stimulate tumor and/or endothelial cells. Finally, tumor cells reorganizing the extracellular matrix to facilitate communications and escape the homeostatic control exerted by the microenvironment modify response to cytotoxic treatments.
Structural analysis of complementary DNA and amino acid sequences of human and rat androgen receptors. (1988)

Structural analysis of cDNAs for human and rat androgen receptors (ARs) indicates that the amino-terminal regions of ARs are rich in oligo- and poly(amino acid) motifs as in some homeotic genes. The human AR has a long stretch of repeated glycines, whereas rat AR has a long stretch of glutamines. There is a considerable sequence similarity among ARs and the receptors for glucocorticoids, progestins, and mineralocorticoids within the steroid-binding domains. The cysteine-rich DNA-binding domains are well conserved. Translation of mRNA transcribed from AR cDNAs yielded 94- and 76-kDa proteins and smaller forms that bind to DNA and have high affinity toward androgens. These rat or human ARs were recognized by human autoantibodies to natural ARs. Molecular hybridization studies, using AR cDNAs as probes, indicated that the ventral prostate and other male accessory organs are rich in AR mRNA and that the production of AR mRNA in the target organs may be autoregulated by androgens.
Interferon-Stimulated Gene 15 and the Protein ISGylation System (2010)

Interferon-stimulated gene 15 (ISG15) is one of the most upregulated genes upon Type I interferon treatment or pathogen infection. Its 17 kDa protein product, ISG15, was the first ubiquitin-like modifier identified, and is similar to a ubiquitin linear dimer. As ISG15 modifies proteins in a similar manner to ubiquitylation, protein conjugation by ISG15 is termed ISGylation. Some of the primary enzymes that promote ISGylation are also involved in ubiquitin conjugation. The process to remove ISG15 from its conjugated proteins, termed de-ISGylation, is performed by a cellular ISG15-specific protease, ubiquitin-specific proteases with molecular mass 43 kDa (UBP43)/ubiquitin-specific proteases 18. Relative to ubiquitin, the biological function of ISG15 is still poorly understood, but ISG15 appears to play important roles in various biological and cellular functions. Therefore, there is growing interest in ISG15, as the study of free ISG15 and functional consequences of ISGylation/de-ISGylation may identify useful therapeutic targets. This review highlights recent discoveries and remaining questions important to understanding the biological functions of ISG15.
Congress matters (1991)

It may have its light-hearted moments, but Congress is a serious event and one the media will be watching with interest, as Derek Dean points out
Mechanism of Enhancement of the Antiviral Action of Interferon Against Herpes Simplex Virus-1 by Chloroquine (1996)

Using double immunofluorescence, we have shown previously that interferon (IFN) treatment inhibits the transport of herpes simplex virus-1 (HSV-1) gD from the Golgi complex to the plasma membrane in the virus infected and gD cDNA transfected LMtk-cells. In the present study, we quantitated the gD protein on the cell surface and localized the gD protein in the trans-Golgi network (TGN). The results showed 10-fold less fluorescence for the gD protein on the cell surface in IFN-treated LMtk-cells. Subcellular fractionation studies demonstrated that gD was associated with TGN-enriched membranes. Gold labeling for DAMP distribution using electron microscopy showed that IFN raised the pH of TGN. IFNs induced alkalinization of TGN may be related to the block in the transport of HSV-1 gD. Earlier we reported that a subeffective dose of chloroquine (CHL) or IFN does not change the pHi. However, both CHL and IFN together raise the pHi significantly. To study the biologic significance of the finding, the effect of these subeffective doses of IFN and CHL on the antiviral activity and the transport of the gD protein was studied. Results suggested that CHL enhance the antiviral activity of IFN against HSV-1 and concomitantly increase the inhibition of HSV-1 gD transport. This IFN-induced increase in pHi of the TGN may also explain the inhibitory effect of IFN reported on the terminal steps of some of the enveloped viruses.
Pharmacotherapy for Neuropathic Pain: A Review (2017)

Pfizer, Italy.
LOGAN: Evaluating Privacy Leakage of Generative Models Using Generative Adversarial Networks. (2017)

Generative models estimate the underlying distribution of a dataset to generate realistic samples according to that distribution. In this paper, we present the first membership inference attacks against generative models: given a data point, the adversary determines whether or not it was used to train the model. Our attacks leverage Generative Adversarial Networks (GANs), which combine a discriminative and a generative model, to detect overfitting and recognize inputs that were part of training datasets, using the discriminator's capacity to learn statistical differences in distributions. We present attacks based on both white-box and black-box access to the target model, against several state-of-the-art generative models, over datasets of complex representations of faces (LFW), objects (CIFAR-10), and medical images (Diabetic Retinopathy). We also discuss the sensitivity of the attacks to different training parameters, and their robustness against mitigation strategies, finding that defenses are either ineffective or lead to significantly worse performances of the generative models in terms of training stability and/or sample quality.
Rapid blood clearance of biotinylated IgG after infusion of avidin. (1989)

The techniques of immunotherapy and radioimmunoimaging suffer from the problem of background: intravenously injected antibodies remain in the circulation much longer than it is necessary for effective binding to the target. Various approaches, including the postinjection of second antibodies, were explored to overcome the problem with some success. The phenomenon of a 100-fold more rapid blood clearance of biotinylated immunoglobulins after postinjection of an equivalent dose of avidin is described. The concentration of 125I-labeled biotinylated IgG in the circulation of rats slowly decreased to 20% of initial in 24 hr. Avidin injection at any interval during this period induced 90-95% reduction of radioactivity in blood in 15 min. Up to 70% of the radioactivity was recovered in the liver. Avidin-induced blood clearance of biotinylated immunoglobulins may find applications in immunotherapy and radio- or nuclear magnetic resonance immunoimaging.
Pathogenesis of Shigella diarrhea. IX. Simplified high yield purification of Shigella toxin and characterization of subunit composition and function by the use of subunit-specific monoclonal and polyclonal antibodies. (1984)

A simple purification scheme for shigella cytotoxin was devised, resulting in high yields (approximately 50%) and a 1,300-fold increase in specific activity compared with the initial crude bacterial cell lysate. The purified toxin was enterotoxic in ligated rabbit ileal loops and neurotoxic when injected into the peritoneal cavity of mice. Measurement of specific activity of cytotoxin and enterotoxin demonstrated that these two toxicities copurify during the fractionation procedure. On sodium dodecyl sulfate gel electrophoresis, the toxin migrated as two polypeptide subunits, an A subunit of 32,000 mol wt and a B subunit of 6,500 mol wt. Chemical cross-linking experiments demonstrate that the toxin is a complex consisting of one A and five B subunits with a molecular weight of 64,000. Polyclonal rabbit anti-toxin and anti-subunit B antisera were produced as well as subunit-specific mouse monoclonal antibodies. All antibodies preincubated with toxin neutralized cytotoxic effects in HeLa cell monolayers. In contrast, only A subunit-specific antibodies were able to neutralize toxin prebound to the HeLa cell surface. Antibody to the B subunit also inhibited binding of 125I-labeled toxin to these cells by 94% or more. These data demonstrate that the B subunit is involved in shigella toxin binding to the cell surface.
Exogenous stress proteins enhance the immunogenicity of apoptotic tumor cells and stimulate antitumor immunity (2002)

We have previously reported that apoptotic tumor cells can be either immunogenic or nonimmunogenic in vivo, depending on whether or not these cells are heat stressed before induction of apoptosis. Stressed apoptotic cells express heat shock proteins on their plasma membranes and dendritic cells are capable of distinguishing them from nonstressed apoptotic cells. Here we provide evidence that when purified heat shock protein 70 or chaperone-rich cell lysate (CRCL) from syngeneic normal tissue is used as an adjuvant with nonimmunogenic apoptotic tumor cells in vaccination, potent antitumor immunity can be generated. This antitumor immunity is mediated by T cells because antitumor effects are not observed in either severe combined immunodeficiency or T cell-depleted mice. We further demonstrate that vaccination of mice with apoptotic tumor cells mixed with liver-derived CRCL as adjuvant were capable of enhancing the production of T(H)1 cytokines, inducing specific cytotoxic T lymphocytes and eliciting long-lasting antitumor immunity. Stress proteins from autologous normal tissue components therefore can serve as danger signals to enhance the immunogenicity of apoptotic tumor cells and stimulate tumor-specific immunity
Coding of Naturalistic Stimuli by Auditory Midbrain Neurons (1997)

It is known that humans can make finer discriminations between familiar sounds (e.g. syllables) than between unfamiliar ones (e.g. different noise segments). Here we show that a corresponding enhancement is present in early auditory processing stages. Based on previous work which demonstrated that natural sounds had robust statistical properties that could be quantified, we hypothesize that the auditory system exploits those properties to construct efficient neural codes. To test this hypothesis, we measure the information rate carried by auditory spike trains on narrow-band stimuli whose amplitude modulation has naturalistic characteristics, and compare it to the information rate on stimuli with non-naturalistic modulation. We find that naturalistic inputs significantly enhance the rate of transmitted information, indicating that auditiory neural responses are matched to characteristics of natural auditory scenes. 1 Natural Scene Statistics and the Neural Code A primary goal of heari...