gebhart/patrepeval huggingface dataset:
Directed evolution of the site specificity of Cre recombinase (2002)

Cre recombinase from bacteriophage P1 recognizes a 34-bp recombination site, loxP, with exquisite sequence specificity and catalyzes the site-specific insertion, excision, or rearrangement of DNA. To better understand the molecular basis of protein-DNA recognition and generate recombinases with altered specificities, we have developed a directed evolution strategy that can be used to identify recombinases that recognize variant loxP sites. To be selected, members of a library of Cre variants produced by targeted random mutagenesis must rapidly catalyze recombination, in vivo, between two variant loxP sites that are located on a reporter plasmid. Recombination results in an altered pattern of fluorescent protein expression that can be identified by flow cytometry. Fluorescence-activated cell sorting can be used either to screen positively for recombinase variants that recognize a novel loxP site, or negatively for variants that cannot recognize the wild-type loxP site. The use of positive screening alone resulted in a relaxation of recombination site specificity, whereas a combination of positive and negative screening resulted in a switching of specificity. One of the identified recombinases selectively recombines a novel recombination site and operates at a rate identical to that of wild-type Cre. Analysis of the sequences of the resulting Cre variants provides insight into the evolution of these altered specificities. This and other systems should contribute to our understanding of protein-DNA recognition and may eventually be used to evolve custom-tailored recombinases that can be used for gene study and inactivation.
A Map Matching Algorithm for Car Navigation Systems that Predict User Destination (2008)

In this paper, we propose a map matching algorithm for car navigation systems that predict user destination. This car navigation system is a novel system that automatically predicts user purpose and destination to present various information based on predicted purpose without user interaction. It requires the correct road where the car drives in real time, and it also need to know the route from the start point to the current point correctly. The proposal map matching method divides the trajectory into equal intervals and calculates the shortest path score for each one. Testing using GPS data for actual car trips showed that its use results in better destination prediction than with conventional methods in most cases. The results were the best for intervals of 5 minutes.
Context-dependent modeling for acoustic-phonetic recognition of continuous speech (2005)

This paper describes the results of our work in designing a system for phonetic recognition of unrestricted continuous speech. We describe several algorithms used to recognize phonemes using context-dependent Hidden Markov Models of the phonemes. We present results for several variations of the parameters of the algorithms. In addition, we propose a technique that makes it possible to integrate traditional acoustic-phonetic features into a hidden Markov process. The categorical decisions usually associated with heuristic acoustic-phonetic algorithms are replaced by automated training techniques and global search strategies. The combination of general spectral information and specific acoustic-phonetic features is shown to result in more accurate phonetic recognition than either representation by itself.
The Yeast RAD7 and RAD16 Genes Are Required for Postincision Events during Nucleotide Excision Repair (1998)

In eukaryotes, nucleotide excision repair (NER) is a complex reaction requiring multiple proteins. In the yeast Saccharomyces cerevisiae, two of these proteins, Rad7 and Rad16, are specifically involved in the removal of lesions from transcriptionally silent regions of the genome in vivo. Extracts prepared from rad7 or rad16 mutant cells are deficient, but not totally defective, in both oligonucleotide excision and repair synthesis of damaged plasmid DNA. We show that these extracts are, however, fully proficient in the incision step of the NER reaction in vitro. Furthermore, using a cdc9 mutant to trap incision intermediates, we demonstrate that rad7 and rad16 mutants are proficient in NER-dependent DNA incision in vivo. A purified protein complex containing both Rad7 and Rad16 proteins complements the oligonucleotide excision and repair synthesis defects in rad7 and rad16 mutant extracts. We conclude that the products of the RAD7 and RAD16 genes are involved in a postincision event(s) during NER in yeast.
Maize polyamine oxidase: primary structure from protein and cDNA sequencing (1998)

The first complete amino acid sequence of a flavin-containing polyamine oxidase was solved by a combined approach of nucleotide and peptide sequence analysis. A cDNA of 1737 bp, isolated from maize seedlings by reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends strategies, was cloned and its sequence determined. This cDNA contains information for a polypeptide chain of 500 amino acids. Its amino-terminal sequence shows the typical features of secretion signal peptides. The primary structure of the mature protein was independently confirmed by extensive amino acid sequencing. Structural relationships with flavin-containing monoamine oxidases are also discussed.
NLRP3 inflammasome–mediated neutrophil recruitment and hypernociception depend on leukotriene B4in a murine model of gout (2011)

These results reveal the role of the NLRP3 inflammasome in mediating MSU crystal-induced inflammation and dysfunction of the joints, and highlight a previously unrecognized role of LTB(4) in driving NLRP3 inflammasome activation in response to MSU crystals, both in vitro and in vivo.
Interaction of Hyperthermia and Radiation in CHO Cells: Recovery Kinetics (1976)

The sensitivity to hyperthermic damage (450C + 0.050) and the interaction of hyperthermic damage with radiation damage was determined in Chinese hamster ovary (CHO) fibroblasts in monolayer culture. The survival curve for asynchronous cells heated at 450C was exponential with a shoulder (Do = 3.6 min, D, = 7.5 min, n = 7.3). Fractionation of two equal heat treatments each of 17.5 min indicated that cell survival was maximally enhanced at a fractionation interval of 12 hr to a survival ratio of approximately 400. Of this, a factor of 60 was due to induction of thermotolerance in terms of an increased Do. Recovery of the capacity to accumulate sublethal damage (return of extrapolation number to 7.3) was complete and occurred within the first 4 hr. By 72 hr the Do returned to normal although the D, persisted at 20 min at 45?C. Heating (17.5 min at 450C) followed immediately by radiation (450 rad) or radiation followed immediately by heating did not produce significantly different survival values. Hyperthermia reduced the Do of the radiation-survival curve by a factor of 1.9 and increased the extrapolation number by a factor of 3. The D, remained unchanged. For intervals up to 48 hr, prior hyperthermia increased the extrapolation number and D, of the radiation-survival curve to approximately 1000 and 650 rad, respectively. However, the Do remained unchanged at approximately 83 rad over the entire interval of 0-72 hr. For the sequence of radiation followed by hyperthermia, the D, of the hyperthermiasurvival curve was reduced to 2.9 min at 450C by simultaneous irradiation but returned to near-normal values after a fractionation interval of 2 hr. The Do of the hyperthermiasurvival curve was unaffected by prior irradiation. Hyperthermia decreased the slope and widened the shoulder of the radiation-survival curve while prior irradiation only affected the shoulder of the subsequent hyperthermiasurvival curve. The recovery kinetics and extensive resistance of heated cells to a second heat dose are difficult to explain solely by the rate process theory of protein denaturation. However, denaturation of membrane or chromatin proteins associated with intracellular recovery mechanisms may account for the effects of hyperthermia alone on cell survival and its modification of the radiation response.
Isolation and Characterization of Pre‐rapamycin, the First Macrocyclic Intermediate in the Biosynthesis of the Immunosuppressant Rapamycin by S. hygroscopicus (2004)

It's a rap: A double recombination strategy has been utilized to uncover the biosynthetic route to the key intermediate in the formation of rapamycin. Removal of a section of the rapamycin gene cluster from Streptomyces hygroscopicus produced a strain that generated no rapamycin. Gene complementation proved, surprisingly, that the accumulation of this previously elusive intermediate pre-rapamycin (1) depended on the presence of the gene rapK. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z53764_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Regulation of EphA2 and focal adhesion kinase in breast cancer (1999)

Changes in cell adhesion are required for cancer cells to metastasize and sites of cell adhesion are the primary location of tyrosine phosphorylated proteins. Identification and characterization of tyrosine phosphorylated proteins that localize to sites of cell adhesion might reveal new diagnostic and therapeutic targets. Two breast cancer cell line models were used to examine the regulation of EphA2 and the Focal Adhesion Kinase (FAK) by cell adhesion. Using a novel monoclonal antibody screen, EphA2 was identified as an adhesion-regulated, phosphorylated protein. EphA2 expression, tyrosine phosphorylation and localization, but not enyzmatic activity, distinguished cells derived from non-transformed mammary tissue, poorly invasive breast cancer, and metastatic breast cancer. Therefore, EphA2 may be useful as a diagnostic target. EphA2 expression is regulated by three factors known to play a role in breast cancer, as estrogen and Myc repressed EphA2 expression and Ras induced EphA2 expression. EphA2 phosphorylation and localization is regulated by E-cadherin, a cell-cell adhesion protein and known tumor suppressor. In non-transformed epithelial cells, EphA2 co-localized with E-cadherin. While disruption of E-cadherin mediated adhesion inhibited EphA2 tyrosine phosphorylation and cell-cell localization, re-expression of E-cadherin in metastatic breast cancer cells restored this phenotype. Alteration in EphA2 function may directly promote an invasive phenotype, as restoration of EphA2 phosphorylation in metastatic cells inhibited cell proliferation. Therefore, EphA2 may be useful as a therapeutic target. Cell-extracellular matrix (ECM) adhesion is essential for cancer cells to migrate. Characterization of the cell line models used in this study revealed that cells derived from poorly invasive breast cancer had the greatest cell-ECM adhesion and large focal adhesions. These changes in cell adhesion correlated with decreased FAK expression, but increased phosphorylation per FAK molecule. Alteration of cell-ECM adhesion by suspension and matrix binding assays demonstrated FAK expression and phosphorylation was adhesion dependent. Low FAK expression in tumor cells thus reflects the extent of cell adhesion rather than invasiveness directly. This may indicate a susceptibility to FAK directed anti-metastatic therapeutics.
Apolipoprotein B: mRNA Editing, Lipoprotein Assembly, and Presecretory Degradation (2000)

Apolipoprotein (apo)B circulates in two distinct forms, apoB100 and apoB48. Human liver secretes apoB100, the product of a large mRNA encoding 4536 residues. The small intestine of all mammals secretes apoB48, which arises following C-to-U deamination of a single cytidine base in the nuclear apoB transcript, introducing a translational stop codon. This process, referred to as apoB RNA editing, operates through a multicomponent enzyme complex that contains a single catalytic subunit, apobec-1, in addition to other protein factors that have yet to be cloned. ApoB RNA editing also exhibits stringent cis-acting requirements that include both structural and sequence-specific elements-specifically efficiency elements that flank the minimal cassette, an AU-rich RNA context, and an 11-nucleotide mooring sequence-located in proximity to a suitably positioned (usually upstream) cytidine. C-to-U RNA editing may become unconstrained under circumstances where apobec-1 is overexpressed, in which case multiple cytidines in apoB RNA, as well as in other transcripts, undergo C-to-U editing. ApoB RNA editing is eliminated following targeting of apobec-1, establishing that there is no genetic redundancy in this function. Under physiological circumstances, apoB RNA editing exhibits developmental, hormonal, and nutritional regulation, in some cases related to transcriptional regulation of apobec-1 mRNA. ApoB and the microsomal triglyceride transfer protein (MTP) are essential for the assembly and secretion of apoB-containing lipoproteins. MTP functions by transferring lipid to apoB during its translation and by transporting triglycerides into the endoplasmic reticulum to form apoB-free lipid droplets. These droplets fuse with nascent apoB-containing particles to form mature, very low-density lipoproteins or chylomicrons. In cultured hepatic cells, lipid availability dictates the rate of apoB production. Unlipidated or underlipidated forms of apoB are subjected to presecretory degradation, a process mediated by retrograde transport from the lumen of the endoplasmic reticulum to the cytosol, coupled with multiubquitination and proteasomal degradation. Although control of lipid secretion in vivo is primarily achieved at the level of lipoprotein particle size, regulation of apoB production by presecretory degradation may be relevant in some dyslipidemic states.
4-Hydroxyphenylacetate Decarboxylases:  Properties of a Novel Subclass of Glycyl Radical Enzyme Systems (2006)

The 4-hydroxyphenylacetate decarboxylases from Clostridium difficile and Clostridium scatologenes, which catalyze the formation of p-cresol, form a distinct group of glycyl radical enzymes (GREs). Cresol formation provides metabolic toxicity, which allows an active suppression of other microbes and may provide growth advantages for the producers in highly competitive environments. The GRE decarboxylases are characterized by a small subunit, which is not similar to any protein of known function in the databases, and provides unique properties that have not been observed in other GREs. Both decarboxylases are functional hetero-octamers (beta(4)gamma(4)), which contain iron-sulfur centers in addition to the glycyl radical prosthetic group. The small subunit is responsible for metal binding and is also involved in the regulation of the enzymes' oligomeric state and activity, which are triggered by reversible serine phosphorylation of the glycyl radical subunits. Biochemical data suggest that the iron-sulfur centers of the decarboxylases could be involved in the radical dissipation of previously activated enzymes in the absence of substrate. The cognate activating enzymes differ from their Pfl and Nrd counterparts in that up to two iron-sulfur centers, in addition to the characteristic SAM cluster, were found. Biochemical data suggested that these [4Fe-4S] centers are involved in the electron transfer to the SAM cluster but do not directly participate in the reductive cleavage of SAM. These data imply a tight regulation of p-cresol formation, which is necessary in order to avoid detrimental effects of the toxic product on the producers.
Inducible Hsp70 as target of anticancer immunotherapy: Identification of HLA‐A*0201‐restricted epitopes (2004)

The design of a broad application tumor vaccine requires the identification of tumor antigens expressed in a majority of tumors of various origins. We questioned whether the major stress-inducible heat shock protein Hsp70 (also known as Hsp72), a protein frequently overexpressed in human tumors of various histological origins, but not in most physiological normal tissues, constitutes a tumor antigen. We selected the p391 and p393 peptides from the sequence of the human inducible Hsp70 that had a high affinity for HLA-A*0201. These peptides were able to trigger a CTL response in vivo in HLA-A*0201-transgenic HHD mice and in vitro in HLA-A*0201+ healthy donors. p391- and p393-specific human and murine CTL recognized human tumor cells overexpressing Hsp70 in a HLA-A*0201-restricted manner. Tetramer analysis of TILs showed that these Hsp70 epitopes are targets of an immune response in many HLA-A*0201+ breast cancer patients. Hsp70 is a tumor antigen and the Hsp70-derived peptides p391 and p393 could be used to raise a cytotoxic response against tumors of various origins.
Pats: Realization And User Evaluation Of An Automatic Playlist Generator. (2002)

[TODO] Add abstract here.
Chaperone-assisted self-assembly of pili independent of cellular energy. (1994)

Assembly of P pili on the surface of pyelonephritic Escherichia coli proceeds from periplasmic chaperone-subunit complexes. The outer membrane protein PapC, which has been termed a molecular usher, is thought to be the site of assembly, where the chaperone dissociates from the subunits as they are incorporated into the pilus across the outer membrane. The kinetics of assembly and the energy requirements of the "secretion" events at the outer membrane were investigated using a pulse-chase analysis in which preformed labeled periplasmic chaperone-subunit complexes were assembled into pili in synchrony by the induction of PapC. Provided that a sufficient amount of PapC was present and functional in the outer membrane, the incorporation of the major PapA subunit into pili was shown to be completed in less than 5 min. Our results also indicated that the targeting of PapC to the outer membrane may be a rate-limiting factor for pilus assembly. Following the arrival of PapC, the formation of pili seemed to proceed spontaneously and was not sensitive to a pH shift or an inhibitor of the electrochemical gradient across the cytoplasmic membrane. We suggest that the secretion of pili across the outer membrane may be independent of cellular energy and thermodynamically driven.
Ridge Estimators in Logistic Regression (1992)

SUMMARY In this paper it is shown how ridge estimators can be used in logistic regression to improve the parameter estimates and to diminish the error made by further predictions. Different ways to choose the unknown ridge parameter are discussed. The main attention focuses on ridge parameters obtained by cross-validation. Three different ways to define the prediction error are considered: classification error, squared error and minus log-likelihood. The use of ridge regression is illustrated by developing a prognostic index for the two-year survival probability of patients with ovarian cancer as a function of their deoxyribonucleic acid (DNA) histogram. In this example, the number of covariates is large compared with the number of observations and modelling without restrictions on the parameters leads to overfitting. Defining a restriction on the parameters, such that neighbouring intervals in the DNA histogram differ only slightly in their influence on the survival, yields ridge-type parameter estimates with reasonable values which can be clinically interpreted. Furthermore the model can predict new observations more accurately.
Click Chemistry in Mesoporous Materials: Functionalization of Porous Silicon Rugate Filters (2008)

In this paper we report the use of the optical properties of porous silicon photonic crystals, combined with the chemical versatility of acetylene-terminated SAMs, to demonstrate the applicability of "click" chemistry to mesoporous materials. Cu(I)-catalyzed alkyne-azide cycloaddition reactions were employed to modify the internal pore surfaces through a two-step hydrosilylation/cycloaddition procedure. A positive outcome of this catalytic process, here performed in a spatially confined environment, was only observed in the presence of a ligand-stabilized Cu(I) species. Detailed characterization using Fourier transform infrared spectroscopy and optical reflectivity measurements demonstrated that the surface acetylenes had reacted in moderate to high yield to afford surfaces exposing chemical functionalities of interest. The porous silicon photonic crystals modified by the two-step strategy, and exposing oligoether moieties, displayed improved resistance toward the nonspecific adsorption of proteins as determined with fluorescently labeled bovine serum albumin. These results demonstrate that "click" immobilization offers a versatile, experimentally simple, and modular approach to produce functionalized porous silicon surfaces for applications as diverse as porous silicon-based sensing devices and implantable biomaterials.
Interleukin 1 participates in the development of anti-Listeria responses in normal and SCID mice. (1992)

Using T- and B-cell deficient C.B-17 mice with the scid mutation, we have previously documented the existence of a T-cell-independent but interferon gamma-dependent pathway of macrophage activation that confers upon the host partial resistance to the facultative intracellular bacterium Listeria monocytogenes. This pathway is operative in both normal and SCID mice and consists of at least four components: interferon gamma, tumor necrosis factor, macrophages, and natural killer cells. Here we demonstrate that interleukin 1 also participates in this pathway but at a different site of action. Using monoclonal antibodies that neutralize the biologic activities of interleukin 1 alpha and interleukin 1 beta, we document that interleukin 1 participates neither directly in the induction of interferon gamma from isolated SCID natural killer cells nor in the antigen-specific activation of CD4+ T cells derived from Listeria-immune C.B-17 mice. In contrast, injection of a mixture of anti-interleukin 1 alpha, anti-interleukin 1 beta, and a newly derived monoclonal antibody specific for the murine type I interleukin-1 receptor into either SCID or normal C.B-17 mice blocked the in vivo elaboration of class II major histocompatibility complex-positive macrophages after infection of the animals with Listeria. Moreover, SCID mice treated with the anti-interleukin-1 mixture failed to control the growth of Listeria in vivo and eventually succumbed to the infection. These results document that endogenously produced interleukin 1 plays an obligate role in the Listeria-dependent induction of activated macrophages in vivo and demonstrate that the action of interleukin 1 is distinct from the generation of natural killer cell-derived interferon gamma.
The Isolation and Characterization of theEsherichia ColiDNA adenine methylase(dam)gene (1983)

The E. coli dam (DNA adenine methylase) enzyme is known to methylate the sequence GATC. A general method for cloning sequence-specific DNA methylase genes was used to isolate the dam gene on a 1.14 kb fragment, inserted in the plasmid vector pBR322. Subsequent restriction mapping and subcloning experiments established a set of approximate boundaries of the gene. The nucleotide sequence of the dam gene was determined, and analysis of that sequence revealed a unique open reading frame which corresponded in length to that necessary to code for a protein the size of dam. Amino acid composition derived from this sequence corresponds closely to the amino acid composition of the purified dam protein. Enzymatic and DNA:DNA hybridization methods were used to investigate the possible presence of dam genes in a variety of prokaryotic organisms.